1. health and fitness
2. disease

CIT Rísam PhD Scholarship Programme 2014 Book of Sample Projects Cork Institute of Technology (CIT) invites applications for the Rísam PhD Scholarship Programme 2014. The Irish word Rísam, meaning “to strive or achieve”, underlines the purpose of this scholarship programme which is to promote high-­‐end research directed towards the generation and application of new knowledge. The full application is in three parts, all with the same submission deadline of April 30th, 2014: 1. Part 1: Applicants complete and submit an on-­‐line application containing personal details, academic record and proposal abstract. 2. Part 2: Applicants must submit separately their research proposal to graduate.school@cit.ie, drawn up in conjunction with one of the research clusters and proposed principal supervisor, whose support is confirmed by being named in the on-­‐line application. 3. Part 3: Applicants must arrange to have references submitted by two academic referees to graduate.school@cit.ie, clearly indicating the name of the applicant. Fully developed proposals only are reviewed and ranked by a panel of external experts, for decision and notification by June 20th, 2014. Sample Projects Because the list of projects that follows is not exhaustive, applicants are encouraged to contact research investigators/supervisors directly, especially in areas where specific projects are not included. Thematic Research Area Disciplines x Number Available Projects Biological Sciences x 13 Biomedical Engineering x 2 Bioinformatics Suite Chemistry x 3 Computing x 5 Embedded Systems -­‐ NIMBUS x 8 Electronics x 2 Photonics -­‐ CAPPA Suite Astronomy Page 2 71 76 80 104 124 142 146 148 Health and Exercise Water Treatment x 1 Environmental x 3 Civil & Structural x 3 Architecture x 4 Social Care x 1 Health and Sports Science x 7 149 155 158 165 169 172 Business Entrepeurniship x 1 Agricultural Economics x 1 212 222 Life Sciences and Wellbeing Information and Communications Technology Photonics Maritime, Energy and Sustainable Environment Book of Sample Projects Page 1 CIT Rísam PhD Scholarship Programme 2014 LIFE SCIENCES & WELLBEING Biological Sciences Title of project: Exploitation of bacteriophages and their lytic enzymes for elimination of staphylococci and other food pathogens Name of Principal Supervisor: Aidan Coffey Brief Summary of Research Interests: Characterization and exploitation of bacteriophages and their enzymes for control of pathogenic bacteria CIT Department: Biological Sciences Email: Aidan.coffey@cit.ie Telephone: 021-­‐4335486 Discipline Area by Frascati Classification: 1.6 Microbiology; Virology (3.4 Health-­‐related biotechnology) 1.
Abstract (250 words) Staphylococcus aureus contamination and infection is a major problem in the agri-­‐food sector, particularly in the context of bovine mastitis. The proposed project will focus on a virus (bacteriophage or phage) that kills staphylococci. Bacteriophages, the most numerous biological entities on the planet, can be readily isolated from the environment and have been used in antibacterial therapy since the 1930s in the former Soviet Union. This project will undertake the genome sequencing of phages against problematic bacteria. The study will then focus on the phage gene encoding the bacterial cell-­‐wall-­‐degrading enzyme, which is naturally made during the phage life-­‐cycle to kill bacterial cells. These enzymes, although diverse, are generally peptidase-­‐endolysins that target the amino-­‐acid cross-­‐links specific to staphylococcal peptidoglycan. The endolysin gene will be cloned using an expression-­‐vector (pQE60) in a recombinant E.coli strain (XL1-­‐blue) for overproduction and isolation. Following this, the enzyme will be biochemicall characterized and evaluated for applications. It is noteworthy that while phages themselves frequently have the disadvantage of a limited Book of Sample Projects Page 2 CIT Rísam PhD Scholarship Programme 2014 host-­‐range among epidemiological serotypes of staphylococci, their endolysins have the advantage of targetting a part of the bacterial cell common to the entire genus Staphylococcus. Technologies described above can also be applied to other food pathogens such as E.coli and Salmonella. 2.
Research Context and Contribution to the Research Field Bacteriophage therapy for the treatment of infections has been used for many years in the former Soviet Union. This approach involves exploiting naturally-­‐occurring viruses known as bacteriophages (phages) to kill problematic bacteria. Indeed since 2006, the US-­‐FDA has approved several bacteriophage products, one of which is Listshield. (Fenton et al 2010). Nevertheless, individual phages may have a limited bacterial host-­‐range among epidemiological serotypes of staphylococci from human hospital infections and bovine mastitis. This is largely due to variability in phage receptor molecules on the staphylococcal cell surface. On the other hand, the phage-­‐encoded endolysins have the advantage of targetting a part of the bacterial cell common to the entire genus Staphylococcus, namely the amino-­‐acid cross-­‐bridge (O’Flaherty et al. 2009). This project proposes to focus on the peptidoglycan-­‐degrading endolysin from the staphylococcal bacteriophage DW2. This bacteriophage was previously isolated at Cork Institute of Technology and can be routinely propagated on a laboratory strain of Staphylococcus aureus, designated DPC5246. Bacteriophage Electron Micrograph (left) Diagram (middle). DNA injection into bacterial cell. The first aim of the proposed project is to determine the nucleotide sequence of the bacteriophage DW2 genome, a process which has in recent years become routine and inexpensive (O’Flaherty et al 2004). Following this, bioinformatics software will be exploited to annotate the genome sequence and assign functions to each putative gene using GenBank database information. It is anticipated that the genes for the various bacteriophage structural proteins will be identified, and also genes for exploiting the bacterial DNA replication machinery, which the phage are known to use during infection of a Book of Sample Projects Page 3 CIT Rísam PhD Scholarship Programme 2014 bacterial cell. More significantly though, it is also anticipated to identify the gene encoding the peptidoglycan-­‐degrading endolysin. The nucleotide sequence of several bacteriophage endolysins from several bacterial genera are available in the GenBank genome databases and they are already known to be a diverse range of enzymes such as amidases, peptidases, lysozymes etc., all with one common function, namely degrading the bacterial peptidoglycan to facilitate release of progeny phage at the end of the bacteriophage virulent cycle. It will be possible in this project to perform a comparative analysis of the DW2 endolysin with other bacteriophage endolysin sequences from the databases. It is worth-­‐while to exploit these endolysin as purified antibacterials, given that their molecular targets are prokaryote-­‐specific molecules (cell-­‐wall peptidoglycan). If used exogenously, they can effectively lyse bacterial cells as has previously been demonstrated in pathogenic streptococci and Listeria (Fenton et al., 2010; Henry et al., 2011). Potential targets of the cloned endolysin from staphylococcal phage DW2 could include staphylococci which cause major economic losses in agriculture through mastitis, and also MRSA which frequently cause infections in Irish hospitals. If considered in an industrial context, a cloned endolysin enzyme would be relatively inexpensive to produce, but would be a highly effective approach for eliminating problematic staphylococci. Potential applications could be as a sanitizer for surfaces, or a topical agent for eliminating staphylococci which colonise human and animal skin, where they frequently become a source of infection in humans and animals. Using standard molecular cloning approaches, the gene for the endolysin will be amplified from the bacteriophage DNA by Polymerase Chain Reaction (PCR) with endolysin-­‐specific PCR primers and cloned into the E.coli XL1-­‐blue expression vector pQE60. In this environment, it will be possible to induce over-­‐expression of the endolysin enzyme, which can be achieved using standard IPTG induction of the recombinant E.coli XL1-­‐blue culture. Following this, the enzyme will be purified using ion-­‐exchange chromatography, a purification system which is highly developed at the CIT laboratories (Henry et al., 2011). Following isolation of the endolysin, its host range among the various staphylococcal epidemiological isolates will be defined. This is facilitated by the fact that CIT holds the all representative sequence-­‐types from the National MRSA Reference Laboratory. It is noteworthy that a considerable portion of CIT’s research focusses on molecular typing of hospital and veterinary pathogenic bacteria -­‐ and the institute holds a large collection of potential target bacteria for bacteriophage therapy studies such as this. The cloned DW2 endolysin would also be subjected to a biochemical characterization, leading to definition of its temperature and pH optima and tolerance to various salts and reducing agents, which are routinely included in biochemical studies. Activity of the enzyme will be assessed on the basis of recording the change in optical density (delta-­‐OD) of Book of Sample Projects Page 4 CIT Rísam PhD Scholarship Programme 2014 standardised turbid staphylococcal cultures after addition of purified endolysin to micro-­‐
titre wells. Using the micro-­‐titre approach will facilitate getting a lot of data about the novel DW2 endolysin with relatively small amounts of purified enzyme. Another scientific study which is possible in CIT would be utilising the protein structure software to define an in-­‐
silico 3-­‐dimensional model of the enzyme. This would be achieved by searching the GenBank databases for proteins with greater that 70% similarity in amino-­‐acid sequence to the novel DW2 endolysin. This would be followed by selecting only those proteins for which a crystal structure has been elucidated and published, and then using the best of these (i.e. the protein with the highest amino-­‐acid sequence homology with the DW2 endolysin) as a template for building a predicted 3-­‐D model of the DW2 endolysin. Through a collaborator at the Alimentary Pharmabiotic Centre at UCC, it will be possible to supplement this work with an ex-­‐vivo immune response study using a Human Umbilical Vein Endothelial Cell (HUVEC) assay. In this case, cells will be exposed to the purified endolysin protein and levels of expression of mRNAs from genes encoding different human inflammatory factors (e.g. adhesion molecule, transcriptional activator and cytokines) will be determined by real-­‐time PCR. This will inform on the ability/inability of the endolysin to generate an inflammatory response if used as a therapeutic, which will be ascertained from the in the concentration of specific mRNAs expressed. Investigations such as those described above would result in good scientific publications, which is very important for a PhD project. In addition, it is necessary to accumulate a lot of scientific knowledge about the endolysin to make an informed decision about the best applications. Typical endolysin applications, which would be possible in the CIT laboratory would be surface decontamination assays and staphylococcal biofilm removal assays. References Henry, M., Fenton, M., O'Mahony, J. & Coffey, A. (2011). Purification and applications of bacteriophage lytic enzymes. In: “Protein Purification” Eds Miguel Benitez and Victoria Aguiree. Nova Science Publishers, Inc. NY11788, USA. pp117-­‐ 145. O’Flaherty, S., Ross, R.P., & Coffey, A. (2009). Bacteriophage and their lysins for elimination of infectious bacteria. FEMS Microbiology Reviews 33: 801-­‐819. Fenton, M., Ross, R.P., McAuliffe, O., O’Mahony, J. & Coffey, A. (2010). Recombinant bacteriophage lysins as antibacterials. Bioengineered bugs, 1(1), 9-­‐16. O’Flaherty, S., Coffey, A., Edwards, R, Meaney, W., Fitzgerald, G.F., & Ross, RP. (2004). Genome of staphylococcal phage K: a new lineage of Myoviridae infecting Gram-­‐positive bacteria with a low G-­‐C content. Journal of Bacteriology, 186: 2862-­‐2871. O’Flaherty, S., Ross, R.P., Meaney, W., Fitzgerald, G.F., Elbreki, M.F. & Coffey, A. (2005). Potential of the polyvalent anti-­‐Staphylococcus bacteriophage K for the control of antibiotic-­‐resistant staphylococci from hospitals. Applied and Environmental Microbiology 71 1836-­‐1842. O’Flaherty, S., Ross, R.P., Flynn, J., Meaney, W.J., Fitzgerald, G.F. & Coffey A. (2005). Isolation and characterisation of two anti-­‐staphylococcal bacteriophages specific for pathogenic Staphylococcus aureus associated with bovine infections. Letters in Applied Microbiology. 41: 482-­‐486. Book of Sample Projects Page 5 CIT Rísam PhD Scholarship Programme 2014 3.
Objectives There are seven key objectives in the proposed research: Objective 1. Sequencing of bacteriophage genome Objective 2. Cloning and expression of endolysin gene in E.coli. Objective 3. Purification of endolysin enzyme for other tasks Objective 4. Biochemical characterization of endolysin enzyme Objective 5. Ex-­‐vivo immune response to endolysin using cell-­‐lines Objective 6. Testing of applications of endolysin ncluding (a) use of endolysin for elimination for staphylococci from surfaces (b) use of endolysin to eliminate biofilms Objective 7. Writing publications (four minimum) and PhD thesis 4.
Research Methodology Sequencing and comparison of Phages: Phage DW2 will be propagated in BHI broth on Staphylococus aureus DPC5246. The phage will be plaque purified and propagated in large-­‐scale, after which it will be concentrated using step-­‐gradient ultracentrifugation. The concentrated phage preparation will be used to isolate the phage’s DNA genome. This will be achieved by proteinase K treatment followed by phenol extraction and enthanol precipitation. The genome will be sequenced at the 454 sequencing lab at Moorepark Food Research Centre. Assembly and subsequent analysis of the sequenced phage nucleotides will be done using the appropriate bio-­‐informatic software. Functions for all genes will be assigned using BLAST (Basic Local Alignment Search Tool). Several phage sequences have previously been annotated in the CIT lab and thus there is adequate scope for training on the software. Cloning and expression of endolysin: The genes coding for the peptidoglycan hydrolases or endolysins will will be amplified from the bacteriophage DNA by Polymerase Chain Reaction (PCR) with endolysin-­‐specific PCR primers and and cloned into the E.coli XL1-­‐blue expression vector pQE60. In this environment, it will be possible to induce over-­‐expression of the endolysin enzyme, which can be achieved using standard IPTG induction of the recombinant E.coli XL1-­‐blue culture. Following this, the E. coli cells will be centrifuged and the endolysin recovered from the cell-­‐
pellet by sonication-­‐induced lysis. Following clearing of cell debris, the enzyme will be purified using ion-­‐exchange chromatography, a purification system which is routine in the postgraduate laboratory. The purity and lytic activity of the lysin will be determined by means of sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-­‐PAGE) and by zymogram analysis (SDS-­‐PAGE with staphylococcal cells impregnated in the polyacrylamide). In-­‐vitro analysis of purified endolysin: Micro-­‐titre assays will be used to assess activity of the purified DW2 endolysin. Activity will be defined on the basis of recording the change in optical density (delta-­‐OD) of standardised turbid staphylococcal cultures after addition of purified endolysin to micro-­‐titre wells over specified time periods (e.g. 15 minutes). This assay is workable and simple, although it is possible to purchase commercial peptidoglycan substrate if necessary. These activity assays Book of Sample Projects Page 6 CIT Rísam PhD Scholarship Programme 2014 will be used to define its temperature and pH optima and tolerance to various salts and reducing agents, which are routinely included in biochemical studies. Host range of the DW2 assays will be similarly done using bacterial strains previously collected from hospitals and from the National MRSA reference laboratory and an assay will be designed to determine the efficacy of the lysin on these bacteria. Ex-­‐vivo immune response assay: An assay will be carried out to determine inflammatory response induced by the engineered endolysin. This will be assessed in the level of adhesion molecules, transcriptional activators and cytokines expressed. Endolysin applications: Surface decontamination assays will be performed by taking surface swabs before and after treatment with sprayed endolysin. Biofilm removal assays will be conducted by cultivating staphylococcal biofilms in microtitre plates followed by treatment with endolysin at different concentrations followed by crystal violet staining to define residual biofilm. 5.
Work Plan The DW2 bacteriophage will be propagated during the first six months of the program. Its genomic content will subsequently be sequenced and annotated at the latter half of the academic year. The cloning of the DW2 phage endolysin will be carried out in the second year. Optimising purification of endolysin will be also carried out at the end of the second academic year and into the beginning of the third year. Purification of the endolysin for a range of biochemical assays will be done in the second half of the second year onwards. Assay optimisation for the biochemical method will also be done during this time. Subsequent data collection on environmental parameters like pH and temperature for the endolysin will be carried out during the latter half of the second and early part of the third year. Host range analysis of endolysin across various hospitals MRSA will also be conducted during this time as will the ex-­‐vivo immune response assay which will use cell-­‐lines available in the Alimentary Pharmabiotic Centre at UCC. Applications like the surface decontamination assay and the biofilm removal assay will also be carried out during the final year. For the duration of the PhD degree, at least four publications based on the proposed project will be achieved. And finally, completion of the thesis will be accomplished at the end of the programme. This plan is set out in the Gantt chart overleaf. Book of Sample Projects Page 7 CIT Rísam PhD Scholarship Programme 2014 Gantt Chart of the research tasks Year 1 (3-­‐month stages) Year 2 (3-­‐month stages) Year 3 (3-­‐month stages) Task 1. Sequencing of bacteriophage 1.1 propagation of bacteriophage DW2 1.2 Genome sequencing of bacteriophage 1.3 annotation of sequenced phage 2. cloning and expression of endolysins 2.1 cloning of phage DW2 endolysin 2.2 Optimising purification of endolysin 3 Purification of endolysin for other tasks 4.Biochemical characterization 4.1 Assay optimization 4.2 Data collection on pH temp optima etc 4.3 Host range of endolysin on hospital MRSAs 5 Ex-­‐vivo immune response to endolysin 6 Applications of endolysin -­‐ testing: 6.1 Surface decontamination 6.2 Biofilm removal and/or prevention Task 7 Writing publications and thesis 6.1 Papers for publication 6.2 Completion of thesis Project Management Deliverable: Thesis ® 6.
Ethical issues The proposed research does not involve human or live animal subjects. Book of Sample Projects Page 8 CIT Rísam PhD Scholarship Programme 2014 Title of project: Crystallographic structure determination of bacteriophage-­‐encoded enzymes that specifically target pathogenic bacteria. Name of Principal Supervisor: Aidan Coffey Brief Summary of Research Interests: Characterization and exploitation of bacteriophages and their enzymes for control of pathogenic bacteria CIT Department: Biological Sciences Email: Aidan.coffey@cit.ie Telephone: 021-­‐4335486 Discipline Area by Frascati Classification: 1.6 Microbiology; Virology (3.4 Health-­‐related biotechnology) 1. Abstract (250 words) Bacteriophages express enzymes during their life cycle that target their host bacteria in different ways. Examples are receptor-­‐binding tailspikes that hydrolyse outer cell wall components in the first step of infection, and endolysins to digest the bacterial peptidoglycan layer in order for the bacteriophage progeny to escape from the cell. Here we propose to study the high-­‐resolution structures of these enzymes by X-­‐ray crystallography, in a collaboration between the group of Aidan Coffey of the Cork Institute of Technology and the group of Mark van Raaij at the National Biotechnology Centre in Madrid, Spain. During the last year, we have solved the structure of the CHAPK domain of the staphylococcal lysin LysK produced by bacteriophage K at 1.8 Å resolution. It revealed a papain-­‐like fold with two bound metal ions (calcium and zinc) and a pronounced cleft where the peptidoglycan substrate may bind. Here we propose to co-­‐crystallize this enzyme with substrate analogues and to extend our studies to the other domains of LysK and other phage-­‐encoded enzymes, targeting different pathogens. The LysK amidase and cell wall-­‐binding domains will be cloned, expressed, characterized for activity and crystallized. Other targets for de novo structure solution are an active endolysin of Clostridium difficile, which is a zinc-­‐amidase, an active endolysin from phage me1 of the Gram-­‐negative pathogen Acinetobacter baumannii and a peptidoglycan-­‐targeting peptidase (Enterolysin). The atomic structures of the enzymes will allow detailed understanding of their action and mechanism and may suggest site-­‐directed mutations to alter their activity and host specificity. 2. Research Context and Contribution to the Research Field Bacteriophages are the most numerous biological replicating entities on earth, and second only to bacteria in biomass. Bacteriophages were discovered independently by Frederick Twort (Twort 1915) and Félix d’Herelle (d’Herelle 1917), as entities able to infect and lyse bacteria. Soon after this discovery, d’Herelle realised the potential of bacteriophages to treat human and animal bacterial diseases. In 1919, d’Herelle prepared a phage cocktail to treat a child affected with dysentery, and after trying its safety by administering it to several healthy individuals, it was administered to the child. The boy recovered after a single administration of the phage preparation. Three more patients were treated in the same way, and all of them recovered soon after the administration, but these results were not published (Summers 1999). In 1921, Richard Bruynoghe and Joseph Maisin used Book of Sample Projects Page 9 CIT Rísam PhD Scholarship Programme 2014 bacteriophages to treat staphylococcal skin disease, and the infection regressed within the next 24-­‐
48 hours (Lavigne 2012). Several similar studies were carried out, and phages were used to treat cholera and bubonic plague in several Asian countries. Thanks to these preparations, mortality due to cholera in India dropped to 10% (Kazhal, 1968). Figure 1. Bacteriophage lytic cycle. Tailspikes intervene in step 1, digesting the bacterial capsule if necessary, while endolysins intervene in step 5, lysing the bacterial cell and liberating the phage progeny. (Figure from http://avonapbiology2011-­‐2012.wikispaces.com/Billy+Ju). Phage therapy was soon abandoned by western countries due to the discovery of antibiotics, but in the former Soviet Union bacteriophages were used from 1920 to 1940 for treating open wounds and intestinal Salmonella and Shigella infections. Due to the maintenance of acceptable levels of phages in the organism for 3 to 10 days after their administration, they were used as prophylaxis in regions were infections could spread rapidly (Chanishvili 2012). During recent years, the emergence of antibiotic-­‐resistant bacterial strains due to misuse and abuse of antibiotic is becoming a serious concern, and interest in phage therapy is growing (Golzar 2014). Multiresistant Staphylococcus aureus (MRSA) is one of the most difficult infections to treat. Other emerging antibiotic-­‐resistance strains that cause the most serious complications are Acinetobacter baumanii, Clostridium difficile, Escherichia coli and Enterococcus faecali (Kutateladze 2010). In modern times, bacteriophages are being used for several purposes as sterilizing processed food, treating crops, diagnosing infections, typing bacteria, doing molecular biology assays, but there is still some reticence in using a biological replicating entity for human phage therapy (Lu 2011). If instead of using whole phages, the proteins which bacteriophages employ to debilitate or lyse their host cells are used, this may be less controversial. Here we can think of enzymes that hydrolyse the outer layers of the bacterial cell wall and thus prevent the formation bacterial biofilms or may even dissolve them. Many bacteriophages have tailspikes for initial receptor-­‐binding, these tailspikes often have enzymatic receptor-­‐hydrolysing activity which helps them to penetrate the outside cell wall and get access to the bacterial membrane for infection. Once inside the cell, bacteriophages express endolysins to allow their progeny to escape from the host cell (“lysis from within”). When applied exogenously to Gram-­‐positive pathogens without an external membrane, endolysins causes “lysis from without” or exolysis (Ralston 1964). Gram-­‐positive endolysins are highly specific (Loessner 2005), and no bacterial variants resistant to their phage endolysins have been found yet (Loeffler 2001). Book of Sample Projects Page 10 CIT Rísam PhD Scholarship Programme 2014 Bacteriophage K is a virulent phage that infects staphylococci. It belongs to the Myoviridae family of the Caudovirales order, with a genome of 127,395 bp. Its endolysin, LysK, a peptidoglycan hydrolase (Loessner 2005), kills a range of cocci, including multi-­‐resistant Staphylococcus aureus (MRSA; O'Flaherty 2005). LysK contains three domains: an N-­‐terminal cysteine-­‐histidine dependent amido-­‐hydrolase/peptidase (CHAP) domain, a central amidase domain and a C-­‐terminal SH3b cell wall-­‐binding domain. The LysK amidase domain cleaves peptidoglycan between N-­‐acetylmuramic acid and L-­‐alanine of the stem peptide, while the CHAP domain is thought to cleave it between the D-­‐alanine and the first glycine of the penta-­‐glycine cross-­‐bridge. A truncated enzyme called CHAPK, containing only the first 165 amino acids of LysK corresponding to the CHAP domain, showed an exolysis activity twofold higher than the native protein (Horgan 2009). The SH3b domain may be inhibitory, regulating the LysK activity. CHAPK is able to lyse several staphyloccocal species, independently from their origin, their antibiotic resistance profile or their ability to produce exopolysaccharides (EPS), which in turn is associated with biofilm formation. It is also effective against other related genera, such as Micrococcus or Streptococcus (Fenton 2011). Figure 2. High-­‐resolution crystallographic structure of CHAPK solved pby the proposers in 2013 (Sanz-­‐
Gaitero et al., 2013; Sanz-­‐Gaitero et al., manuscript in preparation). Left: Cartoon representation of the structure with secondary structure elements and the calcium ion (black ball) high-­‐lighted. Bound organic solvent molecules are also shown. Right: Transparent surface representation with a peptidoglycan fragment modelled into the proposed substrate-­‐binding groove. The group of Aidan Coffey has worked on the characterization and exploitation of bacterial viruses (bacteriophages) for several years and has published over 100 peer-­‐reviewed research papers. Several phage genomes have been fully sequenced and many genes of interest have been cloned and characterised by the group. He actively collaborates with leading researchers throughout Europe resulting in significant advances in the topic and increased opportunities at CIT for PhD students. The research group of Mark van Raaij at the Centro Nacional de Biotecnologia (CNB, National Centre of Biotechnology) specializes in resolving the structure and function of proteins involved in virus-­‐host cell interactions. One group of proteins are viral fibres, which certain viruses use to recognize their host cells and initiate infection. Fibres generally recognize their host cells in a reversible way and once this process has occurred, a second, irreversible step commits the virus to Book of Sample Projects Page 11 CIT Rísam PhD Scholarship Programme 2014 infection. Another important group of proteins are those that bacteriophages use to lyse their host cells, as described above. We also collaborate with other research groups in crystallization and structure solutions of proteins and the peptides they produce, and have determined structures of cyclic antibiotic peptides and bacterial dehydroquinases complexed with inhibitors. Currently, our research group is composed of three PhD students, a postdoc and the PI, with the necessary expertise in construction of expression vectors, protein expression and purification, plus protein crystallography and structure solution. References Chanishvili N (2012) Phage therapy-­‐history from Twort and d'Herelle through Soviet experience to current approaches. Adv Virus Res 83, 3–40. Fenton M, Cooney JC, Ross RP, Sleator RD, McAuliffe O, O’Mahony J, Coffey A (2011) In silico modeling of the staphylococcal bacteriophage-­‐derived peptidase CHAP(K). Bacteriophage 1, 198-­‐206. Golkar Z, Bagasra O, Pace DG (2014) Bacteriophage therapy: a potential solution for the antibiotic resistance crisis. J Infect Dev Ctries 8, 129-­‐136. d’Herelle F (1917) Sur un microbe invisible antagoniste des bacilles dysenteriques. Comptes rendus Acad Sciences 165, 373-­‐
375. Horgan M, O’Flynn G, Garry J, Cooney J, Coffey A, Fitzgerald GF, Ross RP, McAuliffe O (2009) Phage lysin LysK can be truncated to its CHAP domain and retain lytic activity against live antibiotic-­‐resistant staphylococci. Appl Environ Microbiol 75, 872-­‐874. Kazhal N, Iftimovich R (1968) From the History of Fight Against Bacteria and Viruses. Nauchnoe Izdatelstvo. Bucharest, Rumania. Kutateladze M, Adamia R (2010) Bacteriophages as potential new therapeutics to replace or supplement antibiotics. Trends Biotechnol 28, 591-­‐595. Lavigne R, Robben J (2012) Professor Dr. Richard Bruynoghe: A 1951 overview of his bacteriophage research spanning three decades. Bacteriophage 2, 1-­‐4. Loeffler JM, Nelson D, Fischetti VA (2001) Rapid killing of Streptococcus pneumonia with a bacteriophage cell wall hydrolase. Science 294, 2170-­‐2172. Loessner MJ (2005) Bacteriophage endolysins -­‐ current state of research and applications. Curr Opin Microbiol 8, 480-­‐487. Lu TK, Koeris MS (2011) The next generation of bacteriophage therapy. Curr Opin Microbiol 14, 524-­‐531. Ralston DJ, McIvor M (1964) Lysis-­‐from-­‐without of Staphylococcus aureus strains by combinations of specific phages and phage induced lytic enzymes. J Bacteriol, 88:676–681, Sep 1964. Sanz-­‐Gaitero M, Keary R, Garcia-­‐Doval C, Coffey A, van Raaij MJ (2013) Crystallization of the CHAP domain of the endolysin from Staphylococcus aureus bacteriophage K. Acta Cryst F69, 1393-­‐1396. Summers WC. Felix d’Herelle and the Origins of Molecular Biology. Yale University Press, 1999. Twort FW (1915) An investigation on the nature of ultra-­‐microscopic viruses. Lancet 2, 1241-­‐1243. 3. Objectives The goals of the research proposal presented here are the following: 1. Co-­‐crystallize the CHAPK domain of the staphylococcal endolysin LysK produced by bacteriophage K with peptidoglycan substrate analogues and solve the structures of the complexes by X-­‐ray crystallography. 2. Express, purify and crystallize the LysK amidase and cell wall-­‐binding domains and if suitable crystals can be obtained, solve their structures. 3. Pursue the following additional targets for crystallization and structure solution: an active zinc amidase endolysin of Clostridium difficile; an endolysin from phage me1 of the Gram-­‐negative pathogen Acinetobacter baumannii and a peptidoglycan-­‐targeting peptidase (Enterolysin), all already cloned at the Cork Institute of Technology. Note: It may not be possible to successfully express, purify and crystallize all the mentioned Book of Sample Projects Page 12 CIT Rísam PhD Scholarship Programme 2014 enzymes, as is common for any crystallographic project. However, our experience in expression, purification, crystallization and crystallography of bacteriophage proteins should lead to several novel, interesting protein structures relevant for potential medical applications. 4. Research Methodology Expression vectors for the proteins will be constructed for expression in Escherichia coli (I). Thereafter, they will be purified (II), characterized (III) and crystallised (IV). X-­‐ray crystallographic data will be collected from the crystals (V) and their structures will be determined (VI), analysed and published (VII). I. Protein Expression The recombinant proteins will be expressed in first instance with His-­‐tags: inclusion of His-­‐tags usually facilitates purification from cell extracts, but can sometimes hinder crystallisation. In this case, His-­‐tags may be removed by proteolysis or the protein may be cloned in an expression vector so it is expressed without a His-­‐tag. N-­‐terminal and C-­‐terminal His-­‐tags will be tried. If necessary for structure solution (MAD phasing), seleno-­‐methionine may be introduced into the proteins using previously described protocols. Different strains of Escherichia coli (XL1Blue, JM109, JM109(DE3), BL21(DE3) or BL21(DE3)/pLysS) will be used for expression, to optimise the amount of soluble protein obtained. Once suitable expression conditions for a protein are established, 1 to 5 litre scale expression experiments will be performed, to allow the purification of between 2-­‐50 mg of protein per experiment. To lyse large quantities of cells, a French press will be used. In some cases, where the whole protein does not crystallise, it will be necessary to perform new cloning experiments to optimise subsequent purification, to express a stable domain identified by proteolysis experiments or to express other rationally designed deletion mutants. Vectors of the Qiagen pQE and Novagen pET and DUET families, which we have used with success in the past, will preferentially be used. Expression clones will be sequenced to confirm they are correct. II. Purification Purification protocols will be designed for the proteins. Common techniques that will be used are: i) fractionation using ammonium sulphate; ii) specific precipitation of impurities (for example of DNA with streptomycin sulphate); and iii) column chromatography. His-­‐tagged proteins will be purified using a Ni-­‐NTA column as a first step. Proteins without His-­‐tags will be purified by ion exchange chromatography (Biorad UnoQ6, UnoS6, Macro-­‐Prep HighQ, HighS, CM y DEAE), hydrophobic interaction chromatography (Pharmacia Phenylsepharose, Butylsepharose, Octylsepharose; Biorad Macro-­‐Prep tButyl y Methyl), hydroxy-­‐apatite chromatography (Biorad Macro-­‐Prep CHT-­‐II) and size exclusion chromatography (Pharmacia S100, S200, S300). To be able to crystallise some of the proteins, it may be necessary to first identify a stable domain by limited proteolysis using trypsin, chymotrypsin or other proteases. Proteins will be concentrated using Centricon membrane filters (Millipore) with the suitable molecular weight cutoff in a refrigerated table centrifuge. Their purity will be analysed using different techniques: SDS-­‐PAGE electrophoresis, spectrophotometric measurements (especially the absorbance at 280 and 260 nm). The protein folding degree may be analysed by NMR spectroscopy, the N-­‐terminal sequence by Edman degradation and the overall shape of the protein may be analysed by transmission electron microscopy (available in the department). III. Characterization Enzyme assays to look at levels of activity of endolysins will be performed. Activity will be defined on the basis of recording the change in optical density of standardised turbid bacterial cultures after Book of Sample Projects Page 13 CIT Rísam PhD Scholarship Programme 2014 addition of purified endolysin to micro-­‐titre wells over specified time periods (e.g. 15 minutes). This assay is workable and simple, although it is possible to purchase commercial peptidoglycan substrate if necessary. These activity assays will be used to define the precise role of possible coordination atoms (like the calcium and zinc ions identified in CHAPK), which are likely to be associated with the different peptidoglycan hydrolases (lysins). IV. Crystallization Purified proteins will be crystallised at 4 or 21 ºC, using the available crystallisation rooms. The technique we will preferentially use is vapour diffusion in sitting drops. If necessary, microbatch or microdialysis techniques can also be employed. In first instance, standard crystallisation screens will be used. The principal precipitants (ammonium sulphate and poly-­‐ethylene glycols) will be investigated more extensively, at different concentrations and pH. Fine-­‐tuning of the crystallisation conditions will be done, and additives like detergents, salts, organic compounds and divalent cations will also be tried. V. Data collection Once obtained, the crystals will be analysed using rotating anode diffractometers. First diffraction quality at room temperature will be determined of crystals mounted in loops protected by plastic sleeves containing crystallisation solution (Mitegen). Thereafter, cryo-­‐conditions will be sought to be able to measure complete datasets at 100 K of crystals mounted in cryo-­‐loops. Collection of complete datasets will be done using rotating anode diffractometers or at the synchrotron, for instance at the protein crystallography beamline XALOC of the ALBA synchrotron at Barcelona, Spain. VI. Structure solution To facilitate structure solution, heavy atom derivatives will be prepared introducing heavy metals like mercury into the crystals. This should allow the use of phasing techniques like MIR (multiple isomorphous replacement) or SIRAS (single isomorphous replacement with anomalous signal) for protein structure solution. MAD (multi-­‐wavelength anomalous dispersion) or SAD (single-­‐wavelength anomalous dispersion) may also be used, especially if the derivatised crystals turn out not to be sufficiently isomorphous to the native, or where selenomethionine has been incorporated into the crystals. Crystallographic data processing will be performed using free-­‐for-­‐academic software like MOSFLM, Scala, CCP4i, Arp-­‐Warp, PHENIX and SHARP. VII. Structure analysis, presentation and publication The results of the current project will be published as scientific papers in international journals, doctoral theses and communications to international and national scientific meetings. 5. Work Plan A three-­‐year work plan is presented with the aim to determine several high-­‐resolution crystal structures of enzymes that may be used to target pathogenic bacteria: In Year 1 (2014-­‐2015), co-­‐crystallization of CHAPK with substrate and/or product analogues (oligo-­‐glycine) and structure solution will be performed. Construction of expression vectors for other the LysK domains and purification trials will also be performed. In Year 2 (2015-­‐2016), the student will perform crystallization of LysK amidase domain and cell-­‐
binding domains and structure solution attempts. Crystallization of the zinc-­‐amidase endolysin of Clostridium difficile, the endolysin from phage me1 of the Gram-­‐negative pathogen Acinetobacter Book of Sample Projects Page 14 CIT Rísam PhD Scholarship Programme 2014 baumannii and the peptidoglycan-­‐targeting peptidase Enterolysin, will also be attempted. Structure solution and refinement of the successfully crystallized proteins will be performed. In Year 3 (2016-­‐2017), structure solution and refinement of the successfully crystallized proteins will be continued. Finally, the writing and defence of the PhD thesis will also take place in this year. Gantt Chart of the research tasks Tasks Year 1 (3-­‐month stages) Year 2 (3-­‐month stages) Year 3 (3-­‐month stages) 1.1. Crystallization of CHAPK in presence of substrate and product analogues 1.2. Crystallographic data collection, structure solution and refinement 2. Crystallization of other phage proteins 2.1. Cloning and expression of LysK amidase and cell wall-­‐binding domains 2.2. Purification, characterization and crystallization of LysK amidase and cell wall-­‐
binding domains 2.3. Characterization and crystallization of the zinc-­‐amidase endolysin of Clostridium difficile, the endolysin from phage me1 of the Gram-­‐
negative pathogen Acinetobacter baumannii and the peptidoglycan-­‐targeting peptidase Enterolysin 2.4. Crystallographic data collection, structure solution and refinement of the successfully crystallized proteins 3. Writing publications and thesis 1. Co-­‐crystallization studies with CHAPK 3.1. Papers for publication 3.2. Completion of thesis 4. Project Management Deliverable: Thesis Tasks deliberately overlap, in order to combine labwork with in silico work. On the basis of past experience, we estimate that the PhD student will solve at least two new protein structures plus several structures of complexes of the staphylococcal lysin CHAPK with ligands, sufficient for several (at least four) publications in international journals and for writing a high-­‐quality doctoral thesis. 6.
Ethical issues The proposed research does not involve human or live animal subjects. 7. External Collaboration/Other Institutions Book of Sample Projects Page 15 CIT Rísam PhD Scholarship Programme 2014 The proposal described here will be carried out in a close collaboration between the groups of Aidan Coffey at CIT and Mark van Raaij at CNB (Madrid). We envisage that the construction of expression vectors will mainly take place at CIT, while protein expression and purification will be performed at both institutes. Enzymatic activity assays will take place at CIT, while protein crystallization and crystallography will be performed at CNB. The student performing the work will be based at CNB, but will visit CIT regularly to perform experiments and discuss progress. Book of Sample Projects Page 16 CIT Rísam PhD Scholarship Programme 2014 Title of project: Identification of novel dietary bioactive compounds that positively affect metabolic health Name of Principal Supervisor: Dr. Fiona O Halloran Brief Summary of Research Interests: Development of molecular and cell-­‐based bioassays to identify and characterise food bioactives that modulate human and animal health. CIT Department: Email: Biological Sciences fiona.ohalloran@cit.ie Discipline Area by Frascati Classification: Telephone: 021 4335916 1.6 Biological Sciences 1. Abstract (250 words) It is well recognised that obesity has reached epidemic levels. In 2008 it was estimated that approximately 1.46 billion adults worldwide were overweight. In the Republic of Ireland alone surveys indicate that the prevalence of obesity in adults has increased, with reports that 26% of Irish men and 21% of Irish women are obese. Obesity is a major risk factor for cardiovascular disease and type 2 diabetes mellitus (T2DM). Adipose tissue is a metabolically active endocrine organ. Studies have shown that modulation of the metabolic pathways of adipocytes using dietary bioactive compounds has the potential to improve obesity-­‐associated metabolic disorders. Satiety hormones, such as Glucagon-­‐like peptide 1 and Cholecystokinin are appetite regulators secreted by several body organs, including the gastrointestinal tract. The identification of food-­‐derived bioactives that increase secretion of these gut hormones is an attractive therapeutic to controlling appetite. This project, in collaboration with colleagues in the Chemistry department of Cork Institute of Technology and Scientists in the Teagasc Food Research Centres, aims to establish in-­‐vitro cell based bioassays for the purpose of identifying novel food-­‐derived bioactive compounds that modulate the release of adipokines and /or satiety hormones and positively affect metabolic health. Real-­‐Time PCR assays will be applied to investigate gene expression and immunoassay technologies will serve to quantify levels of secreted products. In addition, a major consideration for any bioactive is confirmation that it will be bioavailable at effective concentrations. Using co-­‐culture transwell in vitro cell models the bioavailability of all potential bioactive fractions will be investigated. Book of Sample Projects Page 17 CIT Rísam PhD Scholarship Programme 2014 Title of project: Molecular serotyping and pathogenic profiling of Group B Streptococci of human and bovine origin. Name of Principal Supervisor: Dr Lesley Cotter & Dr. Fiona O Halloran Brief Summary of Research Interests: Microbial identification and epidemiological typing. Assessment of antimicrobial resistance and potential control strategies. CIT Department: Email: Biological Sciences lesley.cotter@cit.ie Discipline Area by Frascati Classification: Telephone: 00353-­‐21-­‐4335294 1.6 Biological Sciences 1. Abstract (250 words) Group B streptococci (GBS) are important clinical and bovine pathogens. In humans, GBS infection is a major concern for neonates, the elderly and the immunocompromised, often with fatal outcomes. Bovine GBS isolates are a major cause of mastitis with implications for milk production and resultant economic losses. Epidemiological studies evaluating strain serotype distribution reveals important data that identifies the prevalent and emerging serotypes in a population, and importantly aids in the production of appropriate vaccines. Currently GBS serotype determination is achieved by latex agglutination which is expensive and often results in non-­‐typeable isolates. A preliminary study conducted in the Biological Sciences department, CIT has shown that molecular serotyping by multiplex PCR offers an efficient, reproducible and cheaper alternative. This project, in conjunction with the Department of Microbiology in CUH, proposes to apply this assay to evaluate the local serotype prevalence in Munster and to use the surveillance data to aid in control and prevention of this organism. Many virulence markers are associated with GBS. Our preliminary data, where PCR assays were used to screen for some of these genetic determinants, suggests varying pathogenic profiles among isolates. This work will be expanded to screen a large collection of clinical and bovine isolates for virulence markers and, using in vitro cell culture models, determine if certain pathogenic profiles are more associated with cell invasion and therefore more pathogenic. Finally, in collaboration with Teagasc, Moorepark, the potential of specific bioactive molecules to act as alternative control agents to conventional antibiotics will be investigated. Book of Sample Projects Page 18 CIT Rísam PhD Scholarship Programme 2014 Title of project: Investigation of natural antimicrobial agents for the prevention and control of biofilms on medical devices. Name of Principal Supervisor: Dr. Máire Begley, Department of Biological Sciences, CIT (maire.begley@cit.ie) Dr. Jim O’ Mahony, Department of Biological Sciences, CIT (Jim.OMahony@cit.ie) Dr. Aoife Burke, Department of Mechanical, Biomedical and Manufacturing Engineering, CIT (Aoife.Burke@cit.ie) Dr. Hugh O’Donnell, Department of Mechanical, Biomedical and Manufacturing Engineering, CIT (Hugh.ODonnell@cit.ie) 1. Abstract (250 words) Microbial biofilms play a pivotal role in healthcare-­‐associated infections, particularly those related to the implantation of medical devices such as urinary and intravascular catheters, and orthopaedic devices such as hip and knee implants. As biofilms are inherently refractory to treatment with antibiotics, implant-­‐associated infections are recalcitrant to typical antimicrobial therapy and host defences. Consequently these bacterial infections are difficult to eradicate and relapses frequently occur. Medical device removal and replacement is often required which, in many cases, is both impractical and costly. The possibility of coating or impregnating medical devices with antimicrobial agents has been explored as a prophylactic approach to medical device-­‐related infections. To date, most research has focused on coating the devices with antibiotics. While the results of such studies are promising, the concern has been raised that the use of antibiotic-­‐coated devices may lead to the proliferation of microbial antibiotic resistance. The aim of our proposed study is to investigate the potential of selected natural antimicrobial agents to prevent and control microbial biofilm development on a range of medical device materials. Initial work will focus on an examination of the development of biofilms on a range of materials used in the manufacture of medical devices. Experiments will employ a selection of relevant microbial species and any resultant biofilms will be examined using a combination of Lux technology, dye binding assays and microscopy. These biofilm models will subsequently be employed to investigate the effects of natural agents (e.g. phage lysins and bacteriocins) on biofilm formation and progression. External collaborator: Gerard Flynn, National Clinical Head of Medical Devices, HSE. Book of Sample Projects Page 19 CIT Rísam PhD Scholarship Programme 2014 Title of project: Use of cell engineering strategies to improve biotechnology production capacity Name of Principal Supervisor: Dr. Jim O’ Mahony, Department of Biological Sciences, CIT Dr. Máire Begley, Department of Biological Sciences, CIT Dr. Rosemary Rea, Department of Biological Sciences, CIT 1. Abstract (250 words) Biological cells are now seen as modern factories for producing both native and engineered biomolecules. Many bio-­‐pharmaceutical and biotechnology companies now employ both procaryotic and eukaryotic cells to produce modern medicines such as antibodies, hormones, vaccines etc. Given the central role of these cells, it is imperative to create and maintain the most stable and efficacious host cell possible. Using sophisticated and well established cell engineering strategies this project will use a number of industry specific biological cells to investigate how to improve cellular production. Specifically, the use of lux labelled cells, promoter fusions, peptide engineering strategies and high throughput screening techniques will be employed to develop a new bank of cells with improved functionality. Additionally, the student will partner with Merck (Brinny) to refine and improve a suite of bio-­‐assays that are currently in operational use. This will involve assessing various types and methods of bioassays such as measurement of cell protection using Cell titre glo, MTS assay, reporter gene fusions, etc. These assays will be optimized, developed and assessed for their suitable inclusion into pre-­‐existing and standardised QC laboratory procedures. External collaborators: Matt Maher, and Fionnula Flannagan, Technical Operations Division, Merck, Brinny. Book of Sample Projects Page 20 CIT Rísam PhD Scholarship Programme 2014 Title of project: porcines in Malaysia Analysis and characterisation of acute gastroenteritis viruses in Name of Principal Supervisor: Dr Helen O’Shea (second supervisor Dr Hugh McGlynn), External supervisor; Professor Ammu K Radhakrishnan Brief Summary of Research Interests: Research in my group is mainly in the areas of virology and epidemiology, in particular gastroenteritis viruses, but I also have an interest in the area of antibiotic resistance, biofilms and the antibacterial/antiviral effects of bioactive glass. CIT Department: Email: Biological Sciences helen.oshea@cit.ie Discipline Area by Frascati Classification: • Virology and molecular biology; Telephone: +353214335401 A 1. Natural sciences, 1.6 Biological sciences, 1. Abstract (250 words) Summarise the objectives, the main expected originality and the research methodology to be used. Viral agents (e.g. rotavirus (RV), caliciviruses) are an important cause of gastroenteritis in terms of mortality and morbidity in human and veterinary medicine. Worldwide, RV is responsible for the death of 520,000 children per year. Like influenza viruses, RVs can exchange genes during co-­‐
infections (reassortment), resulting in novel virus strains, capable of infecting both humans and animals. Current understanding of the zoonotic risk of these viruses worldwide is hampered by a paucity of information concerning the strain types implicated in disease in various species. Detailed analysis of the molecular epidemiology of these pathogens would permit meaningful investigation of the potential magnitude of interspecies transmission. While there is some limited information regarding human rotavirus in Malaysia, very little information currently exists describing the strains of RV and caliciviruses circulating in animals. This project will build on an existing multidisciplinary research team with expertise in virology, cell culture, molecular biology, phylogenetic analysis, epidemiology, human and veterinary medicine. This team, together with our new collaborator (Prof Ammu K Radhakrishnan, IMU), will compile detailed molecular and phylogenetic data on RNA viruses, (with an emphasis on Rotaviruses A & C) implicated in disease in porcines in Malaysia. This project will provide a huge potential utility for the development and improvement of diagnostic tests for veterinary medicine. This study will provide important data with regard to the rotavirus vaccination programme in children in Malaysia, as the RV strains circulating in swine also circulate in Book of Sample Projects Page 21 CIT Rísam PhD Scholarship Programme 2014 humans and this may pose a risk to vaccine efficacy in humans. 2.
Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. Globally, factors affecting pig production include nutrition, genetics and animal health and welfare. Viral gastroenteritis (GE), in particular RV, poses a major threat for both pig and human health as these viruses may have a significant economic impact both on human healthcare and on the pig industry. RVs are one of the most frequently detected viral agents associated with diarrhoea affecting piglets between 1 and 8 weeks of age (Saif et al., 1994). RV infection of pigs has been recognised in both enzootic and epizootic forms of diarrhoea resulting in economic losses in commercial piggeries (Saif and Fernandez, 1996). Antigenic and molecular characterization of RVs in pigs has revealed a broad heterogeneity in the circulating strains, thereby complicating vaccination programmes. In humans, RV is responsible for over 100 million cases of gastroenteritis worldwide, with over 520,000 deaths occurring annually. The CIT research team in collaboration with UCC, UCD and DCU has developed expertise in the area of rotavirus detection in humans and porcines (O’ Halloran et al., 2000, Reidy et al., 2005, Lennon et al., 2008, Cashman et al., 2011, Gunn et al., 2012, Collins et al., 2008, 2009, 2010 a,b ). Our group has already set up RT-­‐PCR for detection of rotavirus and other major viral agents of GE in both humans and porcines and have the capability to expand this project. More recently, a large scale collaboration between CIT, DCU, UCC and University of Leuven, Belgium are involved in a large scale genomic project, sequencing the genomes of selected archived and recent human and porcine rotavirus isolates in Ireland (Mining And Modelling ; Animal Rotavirus Epidemiology, Project Ref No: 11/SF/327). In Malaysia, the pig population numbers approximately 1.5 million animals. Forty percent of the Malaysian population consumes pork and the swine industry is worth US $500 million. However, very little data exists with regard to viral gastroenteritis organisms in the Malaysian swine herd. This project will focus on developing and applying molecular assays for these viral pathogens in pigs in Malaysia, with a view towards establishing the prevalence rate of these pathogens. The project will Book of Sample Projects Page 22 CIT Rísam PhD Scholarship Programme 2014 form a baseline for future surveillance studies to assess the importance of these viruses with regard to best practice in animal husbandry and vaccination programs. These measures will result in benefits for the swine industry through reduced losses. Pigs are anatomically and physiologically similar to humans in terms of dentition, ocular, dermal, cardiovascular, renal and digestive systems. Swine are considered to be a potential reservoir for emerging RVs affecting humans as a consequence of interspecies-­‐transmission, accumulation of point mutations, recombination and reassortment (Iturriza-­‐Gòmara et al., 2001; Maunula and von Bonsdorff, 2002; Nakagomi and Nakagomi, 2002; Phan et al., 2007). Currently, two RV vaccines are available for the prevention of RV gastroenteritis in children in Malaysia. However, a large number of RV strains circulating in the swine population also co-­‐circulate in the human population. Therefore, the characterization of RV strains in pigs in Malaysia will ensure effective vaccine coverage of the RV vaccine in humans and in addition will highlight the appearance of new strains which may emerge from swine and pose a threat to RV prevention in children. This project will help focus on developing and applying standardised diagnostic skills for these pathogens in pigs in Malaysia, with a view towards establishing the prevalence of these pathogens. In addition, this project will contribute to the growing body of information of viral gastroenteritis in swine and will ensure efficient and effective pig production. This study will also add to the emerging molecular techniques that are being developed to detect novel pathogenic viral micro-­‐organisms. References Saif LJ, Jiang B. Nongroup A rotaviruses of humans and animals. Curr Top Microbiol Immunol. 1994;185:339-­‐71. Saif LJ, Fernandez FM. Group A rotavirus veterinary vaccines. J Infect Dis. 1996 Sep;174 Suppl 1:S98-­‐
106 Iturriza-­‐Gómara M, Isherwood B, Desselberger U, Gray J. Reassortment in vivo: driving force for diversity of human rotavirus strains isolated in the United Kingdom between 1995 and 1999. J Virol. 2001 Apr;75(8):3696-­‐705. Maunula L, Von Bonsdorff CH. Norovirus genotypes causing gastroenteritis outbreaks in Finland 1998-­‐2002. J Clin Virol. 2005 Nov;34(3):186-­‐94. Nakagomi O, Nakagomi T. Genomic relationships among rotaviruses recovered from various animal species as revealed by RNA-­‐RNA hybridization assays. Res Vet Sci. 2002 Dec;73(3):207-­‐14 Phan TG, Okitsu S, Maneekarn N, Ushijima H. Genetic heterogeneity, evolution and recombination in emerging G9 rotaviruses. Infect Genet Evol. 2007 Sep;7(5):656-­‐63 Selected host researcher references Book of Sample Projects Page 23 CIT Rísam PhD Scholarship Programme 2014 •
Helen O’Shea, Emily Mulherin, Jelle Matthijnssens, Matthew P McCusker, PJ Collins, Olivia Cashman, Lynda Gunn, Marijke E Beltman, Séamus Fanning . Complete genomic sequence analyses of the first group A giraffe rotavirus reveals close evolutionary relationship with rotaviruses infecting other members of the Artiodactyla Veterinary Microbiology (2014) •
Gunn L., Feeney S.A., Cashman O., Collins P.J., Coyle P.V. and O’Shea H. Molecular Characterization of Group A Rotavirus Found in Elderly Patients in Ireland; Predominance of G1P[8], Continued Presence of G9P[8], and Emergence of G2P[4]. J Med Virol 24 May 2012 Volume 84, Issue 12, pages 2008–2017. DOI: 10.1002/jmv.23416 •
Matthijnssens J, Miño S, Papp H, Potgieter C, Novo L, Heylen E, Zeller M, Garaicoechea L, Badaracco A, Lengyel G, Kisfali P, Cullinane A, Collins PJ, Ciarlet M, O'Shea H, Parreño V, Bányai K, Barrandeguy M, Van Ranst M. Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several new genotypes and a largely conserved genotype constellation.J Gen Virol. (2011); 93(Pt 4):866-­‐75 [Epub ahead of print]PMID:22190012 •
Cashman O, O'Shea H. Detection of human bocaviruses 1, 2 and 3 in Irish children presenting with gastroenteritis. Arch Virol. 2012 Sep;157(9):1767-­‐73. Epub 2012 May 22. PMID: 22614812 •
O. Cashman, P J. Collins, G. Lennon, B. Cryan, V. Martella, S. Fanning, A. Staines, H. O’ Shea. Molecular characterisation of group A rotaviruses detected in children with gastroenteritis in Ireland in the years 2006-­‐2009. Epid & Infect (2011) 14:1 •
Susan McElligott, P.J. Collins, R.D. Sleator, V. Martella, N. Decaro, C. Buonavoglia, and H. O’Shea Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland Archives of Virology (2011);156(3):495-­‐503. •
Collins, P.J., Martella, V., Buonavoglia, C. O’Shea H. Identification of a G2-­‐like porcine rotavirus bearing a novel VP4 type, P[32] Vet Res (2010) 41(5): 73. •
Collins PJ, Martella V, Sleator RD, Fanning S, O'Shea H. Detection and characterisation of group A rotavirus in asymptomatic piglets in southern Ireland. Arch Virol 2010 ;155:1247. •
Cashman, O., Lennon, G., Sleator, R.D., Power, E., Fanning, S., O’Shea, H. Changing profile of the bovine rotavirus G6 population in the south of Ireland from 2002 to 2009 Vet Micro (2010) 146:238. •
Collins, P.J., Martella, V., Buonavoglia C O’Shea, H. Detection and characterization of porcine sapoviruses from asymptomatic animals in Irish farms. Veterinary Microbiology.(2009); 139(1-­‐
2):176-­‐82. •
Collins, P.J. Cullinane, A. Martella, V. O’Shea, H. Molecular characterisation of equine rotavirus in Ireland. J Clin Micro (2008).46:10 3346. •
Collins, P.J., Martella, V. O’Shea, H. (2008). Detection and characterisation of group C rotavirus in asymptomatic piglets in Ireland. J Clin Micro 46:9 2973. •
Mulherin, E., Bryan, J., Beltman, M., O’ Grady, L., Pidgeon, E., Garon, L., Lloyd, A., Bainbridge, J., O’ Shea, H., Whtye, P. and Fanning, S. Molecular Characterisation of a Bovine-­‐Like Rotavirus Isolated from a Giraffe. BMC Veterinary Research (2008), 4:46. •
G. Lennon, N. Reidy, B. Cryan, S. Fanning, H. O'Shea Changing profile of rotavirus in Ireland: Predominance of P[8] and emergence of P[6] and P[9] in mixed infections. J Med Virol (2008). 80: 524. •
G. Lennon, O. Cashman, K. Lane, B. Cryan and H. O’Shea. Prevalence and Characterization of Enteric Adenoviruses in the South of Ireland. J. Med. Virol. (2007) 79:1518–1526. Book of Sample Projects Page 24 CIT Rísam PhD Scholarship Programme 2014 •
N. Reidy, G. Lennon, S. Fanning, E. Power and H. O'Shea Molecular characterisation and analysis of bovine rotavirus strains circulating in Ireland 2002–2004.Vet. Microbiol. (2006) 117, 242-­‐247. •
Reidy, N.. O’Halloran, F. Fanning, S Cryan, B. and O’Shea, H. Emergence of G3 and G9 Rotavirus and Increased Incidence of Mixed Infections in the Southern Region of Ireland 2001-­‐
2004. J Med Virol (2005). 77; 571. •
O’Halloran, F., Lynch, M., Cryan, B., O’Shea, H. & Fanning, S. (2000).Molecular characterization of Rotavirus in Ireland: Detection of Novel Strains Circulating in the Population. J Clin Microbiol. 2000 Sep;38(9):3370-­‐4. •
Yap KL, Yasmin Malik, Wong YH, Ooi YE, Tan SC, Jegathesan M, Khor CM, Low MCK, 1992: A one-­‐year community-­‐based study on the incidence of diarrhoea and rotavirus infection in urban and suburban Malaysian children. Medical Journal of Malaysia •
Yap Kok Leong, Yasmin A Malik, 1989 : Epidemiologic Study on Rotaviral and Enteropathogenic Bacterial Infections in Children. First IRPA/UKM Research Workshop. Air Keroh, Malacca. 2 -­‐ 3 September 1989 •
O'Mahony J, Foley B, Morgan S, Morgan JG, Hill C. VP4 and VP7 genotyping of rotavirus samples recovered from infected children in Ireland over a 3-­‐year period.J Clin Microbiol. 1999 Jun;37(6):1699-­‐703. •
Identification and genetic characterisation of a novel picornavirus from chickens. (2014). Bullman, S., Kearney, K., O' Mahony, M., Kelly, L., Whyte, P., Fanning, S. & Morgan, J.G. J Gen Virol. 2014 Feb 4. doi: 10.1099/vir.0.061085-­‐0. [Epub ahead of print]. 3.
Objectives The overall objectives of this project are: 1. To create and catalogue a sample bank of swine faecal samples with known viral gastroenteritis association in Malaysia. 2. To employ the use of established molecular assays to determine the prevalence of known emerging viruses in swine. 3. To carry out molecular characterisation on known and newly discovered viruses. 4. To employ selected bioinformatics tools to investigate the phylogeny of these viruses. 5. To utilize Deep Genome Sequencing on newly discovered viruses to establish their potential pathogenic threat. 6. To link in with other European Rotavirus Networks of Excellence, particularly EuroRotaNet. 7. To provide information pertinent to the porcine strains circulating in Malaysia to inform vaccine producers. Book of Sample Projects Page 25 CIT Rísam PhD Scholarship Programme 2014 8. To generation information via publications, conferences and media organisations regarding the epidemiological situation regarding RV circulating in porcines in Malaysia. 4.
Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. This project will use a number of different methodologies in order to achieve its objectives: 1. On farm testing for selected viruses In order to determine the prevalence of gastrointestinal viruses in Malaysian swine farms, these viruses will be assessed by collection of faecal samples from symptomatic and asymptomatic pigs between 1-­‐8 weeks of age at selected swine farms. 2. To establish prevalence of selected RNA viruses in Malaysia The molecular techniques employed in this project will include methods such as DNA/RNA extraction methods, RT-­‐PCR/PCR and real-­‐time PCR assays, DNA sequencing, and bioinformatics among others. This project will use highly sensitive molecular assays such as PCR and RT-­‐PCR for the detection of gastrointestinal viruses in swine. Such methods facilitate detection of low numbers of viruses and will minimise the number of false negatives when compared to other comparable methods. 3. Molecular characterisation on RV isolates Positive samples will be commercially sequenced in Germany. Various on-­‐line phylogenetic tools such as bioedit and MEGA will be used to determine the phylogenetic relationship between the isolates in this study and those in the Genbank database. 4. Use of Next Generation Sequencing (NGS) on selected isolates NGS technologies have revolutionised the study of genomics and molecular biology. NGS has allowed scientists to extract genetic information from biological systems revealing limitless insight about genomes. We propose utilising NGS in this project and sequencing the genomes of selected isolates from this study. This data on RV genomics projects will provide insight into how RVs evolve during their spread through the porcine and human population and are of huge potential utility for development and improvement of both diagnostic tests and vaccines in veterinary medicine. Book of Sample Projects Page 26 CIT Rísam PhD Scholarship Programme 2014 5. Dissemination of information A broad spectrum of dissemination tools will be used for general dissemination, and specific customised dissemination will take place where there is a need to communicate to sub-­‐groups or end-­‐users. The pre-­‐selection of the following targeted end users reflects the dissemination strategy of the overall project. The detailed interested parties and will include: • The global research community via conferences, workshops, international symposia and via peer-­‐reviewed scientific journals • Veterinary practitioners • The Malaysian pig farming industry and associated industries 5. Work Plan Present the research work plan, outlining the main research tasks and timing. Summary Table of Project Tasks Task No. Title Task 1: The establishment of a sample bank [months 1-­‐34] Task 2: Harmonisation of tools and procedures [months 1-­‐12] Task 3: Detection, characterisation and association with disease of RNA viruses found in samples from Malaysian pigs [months 3-­‐30] Task 4 Virus discovery [months 6-­‐30] Task 5: Task 6: Sequence analysis and bioinformatics [months 1-­‐24] Dissemination (to include publication of peer reviewed papers and thesis preparation) and Technology Transfer Book of Sample Projects Page 27 CIT Rísam PhD Scholarship Programme 2014 GANNT charts and flow diagrams of the research tasks Figure 1 Gant chart illustrating timeframe for completion of the proposed Tasks, with associated milestones and deliverables. Timeframe for completion of the proposed Tasks Year 1 Quarter 1 2 3 4 Month 1-­‐3 4-­‐6 7-­‐9 M1.1 2 1 3 2 3 4 1 2 3 4 10-­‐12 13-­‐
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M1.2 M1.3 M1.4 D1.1 M2.1 M2.2 D2.1 M3.1
D3.1 M3.2 D3.2 M4.1
D4.1 M5.1 M5.2 D5.1 M6.1 D6.1 M1.1 Selection of swine farms for sampling M1.2 Year 1 sample collection completed and archived M1.3 Year 1 sample collection completed and archived M1.4 Year 1 sample collection completed and archived D1.1 Complete sample bank established M2.1 Techniques transferred to Post-­‐graduate student M2.2 Transfer completed and independent group established D 2.1 Harmonisation of tools and procedures achieved M3.1 Detection and characterisation of RNA viruses found in samples from Malaysian pigs M3.2 Analysis of association with disease of RNA viruses found in Malaysian pigs D3.1 Detection, characterisation and association with disease of RNA viruses found in samples from Malaysian pigs completed Book of Sample Projects Page 28 CIT Rísam PhD Scholarship Programme 2014 M4.1 Virus discovery D4.1 Analysis and molecular characterisation of selected viruses, selection for sequence analysis M5.1 Selected samples subjected to sequence analysis and bioinformatics M5.2 Selected samples subjected to whole genome sequence analysis and bioinformatics D5.1 Sequence analysis completed M6.1 Dissemination appropriate platforms selected and targeted D6.1 Dissemination completed Deliverables Literature reviews complete for selected viruses PCR and RT-­‐PCR screening for selected viruses in selected Malaysian farms completed Updated sequence alignments of selected viruses Sequencing and phylogenetic analysis of selected viruses from Malaysia Application of NGS to selected samples, where applicable Submitted manuscripts on RT-­‐PCR and phylogenetic analysis of selected viruses Submitted manuscript(s) on prevalence of selected viruses in Malaysia Dissemination of final results of project to relevant stakeholders 6. Ethical issues If the proposed research directly involves human or live animal subjects, discuss the ethical issues involved and the actions that will be taken to ensure compliance with CIT ethics guidelines and with the CIT Child Protection Policy (if children are involved). The proposed project does not involve human or live animal subjects. 7. External Collaboration/Other Institutions Indicate any external collaboration envisaged. On-­‐going projects between CIT, UCC and DCU and the University of Leuven, Belgium have drawn together a formidable, synergistic, inter-­‐institutional, interdisciplinary research team, with National and International collaborators. The Molecular Virology Unit at CIT has established expertise in all aspects of modern molecular biology and epidemiology, in collaboration with Professor Anthony Staines at DCU. Researchers in this team have contributed Book of Sample Projects Page 29 CIT Rísam PhD Scholarship Programme 2014 substantially to the current understanding of molecular epidemiology of rotavirus and other gastrointestinal viruses in humans and animals in Ireland. Our partner in UCC (Dr John Morgan) also has wide experience in the area of gastrointestinal viruses. Our collaborator in Belgium, Dr J. Matthijnssens, is a leading expert in rotavirus genetic analysis, particularly in the area of deep genome sequencing. Our team has recently been awarded DAFM funding to undertake a large scale genomic project. This novel project involves a new collaboration with IMU and UKM, Malaysia, which adds another dimension, as there is enormous potential to expand our research into Malaysia. This project will therefore build on the experience in the areas of molecular and epidemiological analysis of gastroenteritis viruses in the CIT/UCC/DCU teams to address the important area of novel viruses and will fill a significant knowledge gap, one that has the potential for benefits to the pig industry. The project will particularly build on the work that has been carried out on RV infection in pigs, as this is now known to have an important role in enteric disease in swine in terms of morbidity, mortality and economic costs. Institution/ Company Lead Scientist/ Collaborator Detail of Collaboration (e.g. knowledge exchange, networking, co-­‐
funding, resource-­‐sharing) DCU Anthony Staines Provision of expert advice. Prof Staines is an epidemiologist and a collaborator in several successful grants with CIT. UCC John Morgan Dr Morgan is a virologist and a collaborator in several successful grants with CIT. U Leuven Jelle Matthijnssens Dr Matthijnssens is an expert in NGS and bioinformatics and a collaborator in several successful grants and publications with CIT. IMU, Malaysia Ammu K Radhakrishnan Prof Krishnan is an immunologist who will co-­‐supervise the post-­‐
graduate student UKM, Malaysia Yasmin A Malik Prof Malik is a virologist with experience and several publications on rotavirus in Malaysia. Book of Sample Projects Page 30 CIT Rísam PhD Scholarship Programme 2014 Title of project: A genomic and serological study into hepatitis viruses in Irish farm animals, wildlife and food chain critical control points Name of Principal Supervisor: Dr Helen O’Shea (external supervisor Dr John McKillen) Brief Summary of Research Interests: Research in my group is mainly in the areas of virology and epidemiology, in particular gastroenteritis viruses, but I also have an interest in the area of antibiotic resistance, biofilms and the antibacterial/antiviral effects of bioactive glass. CIT Department: Email: Biological Sciences helen.oshea@cit.ie Discipline Area by Frascati Classification: • Virology and molecular biology; Telephone: +353214335401 A 1. Natural sciences, 1.6 Biological sciences, 1. Abstract (250 words) Summarise the objectives, the main expected originality and the research methodology to be used. Hepatitis E virus (HEV) is the largest cause of acute hepatitis in humans. It is spread by the faecal-­‐
oral route and was once considered to be a virus of developing countries. Now, however, while the incidence is lower than in developing countries, there is increasing awareness of the potential risks to public health associated with zoonotic transmission of the virus. In several European countries HEV has been detected in a number of animal species, also at critical control points within the pork supply chain, raising questions for human health and food safety and security. Yet there is a paucity of information regarding HEV in Ireland, particularly regarding HEV in pigs and the pork production chain. Thus, this project intends to implement a panel of tools for the detection and genotyping of HEV and use these to address important unanswered questions regarding this increasingly important virus. In particular it is intended to; •
•
Develop molecular and non-­‐molecular tools for the detection HEV viruses and antibodies; Apply these tools to investigate the prevalence of HEV viruses in livestock and wildlife, to detect novel variants and phylogenetically analyse detected strains; •
Determine the presence of HEV at critical control points in the pork production chain; In this way, baseline information will be provided on HEV in Ireland which could lead to larger future studies and will allow an initial evaluation of the risk of HEV infection in humans from a variety of sources. This project proposal is in collaboration with Dr John McKillen, AFBI. Book of Sample Projects Page 31 CIT Rísam PhD Scholarship Programme 2014 2.
Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. Hepatitis E virus is the largest cause of acute hepatitis in humans and the World Health Organisation estimates that around two billion people are at significant risk of infection due to living in endemic regions. It is spread by the faecal-­‐oral route and large outbreaks can occur in areas of poor sanitation or in the aftermath of flooding or natural disasters. HEV was once considered to be a virus of developing countries and in developed countries was mainly associated with international travel. Now, however, while the incidence is lower than in developing countries, there is increasing awareness of the potential risks to public health associated with zoonotic transmission of the virus. In several European countries HEV has been detected in pigs and a host of other animals as well as at a number of critical control points within the pork food supply chain, such as abattoirs and point-­‐
of-­‐sale, raising questions for human health and food safety and security in a complex processing chain. Infection with HEV can present as acute hepatitis and pregnant women are particularly at risk. The causative agent of hepatitis E, hepatitis E virus (HEV), is a member of the genus Hepevirus, family Hepeviridae. It is a non-­‐enveloped, positive-­‐sense, ssRNA virus with a 7.2-­‐kb-­‐long genome. Four genotypes of HEV have been recognised to date. Genotypes 1 and 2 have been detected only in humans, whereas genotypes 3 and 4 are zoonotic nature. Diagnosis is by antibody ELISA or RT-­‐PCR and sequence analysis of RT-­‐PCR amplicons allows genotyping and has demonstrated cross-­‐species infection of the zoonotic strains. Pigs are considered to be one of the main animal reservoirs for HEV but RT-­‐PCR has been used to detect the virus in a range of species and this has led to increased awareness of the potential threat this virus poses to our food safety and security. Little research has been undertaken into the presence of HEV in animal reservoirs in Ireland. The purpose of this project is to develop a set of tools that will us to gather baseline data on the seroprevalence, virus prevalence and genetic characteristics of HEV circulating in Irish swine herds. In addition, other farm animals and wildlife will be examined. These data will be compared to sequences from global strains of HEV to allow a better understanding of the molecular epidemiology, disease transmission and evolution of the virus. This work will allow us a basic understanding of impact of HEV in Irish livestock and wildlife both as a pathogen and as a potential reservoir for interspecies transmission. The project could be followed up by epidemiologically stratified virus or seroprevalence studies and the development of tools here would greatly facilitate this. Finally, as HEV has important implications for food security and safety as well as animal and human health, the critical control points in the production chain such as abattoirs and point of sale whereby exposure to HEV may occur should be examined. Again, no current knowledge exists regarding these issues and the generation of baseline data is important to establish potential risk and evaluate mitigating activities. Book of Sample Projects Page 32 CIT Rísam PhD Scholarship Programme 2014 This project proposal is part of a larger funded research programme, in collaboration with Dr John McKillen, AFBI, Belfast (DARD DIRECTED AGRI-­‐FOOD AND BIOSCIENCES INSTITUTE (AFBI) RESEARCH WORK PROGRAMME 2014/15 Proposal number 14/3/01; Molecular diagnostics of novel/emerging/exotic viral threats to Northern Ireland livestock and assessment of emerging threats from wildlife). References • Pérez-­‐Gracia MT, Suay B, Mateos-­‐Lindemann ML. Hepatitis E: An emerging disease. Infect Genet Evol. 2014 Mar;22C:40-­‐59. Review. • Pérez-­‐Gracia MT, Suay B, Mateos-­‐Lindemann ML. Hepatitis E: An emerging disease. Infect Genet Evol. 2014 Mar;22C:40-­‐59. Review. • Gerber PF, Xiao CT, Cao D, Meng XJ, Opriessnig T. Comparison of real-­‐time reverse transcriptase (RT)-­‐PCR assays for detection of swine hepatitis E virus in fecal samples. J Clin Microbiol. 2014 Jan 15. • Song YJ, Park WJ, Park BJ, Lee JB, Park SY, Song CS, Lee NH, Seo KH, Kang YS, Choi IS. Hepatitis E virus infections in humans and animals. Clin Exp Vaccine Res. 2014 Jan;3(1):29-­‐36. Epub 2013 Dec 18. Review. • Lee WJ, Shin MK, Cha SB, Yoo HS. Development of a novel enzyme-­‐linked immunosorbent assay to detect anti-­‐IgG against swine hepatitis E virus. J Vet Sci. 2013;14(4):467-­‐72. • García M, Fernández-­‐Barredo S, Pérez-­‐Gracia MT. Detection of hepatitis E virus (HEV) through the different stages of pig manure composting plants. Microb Biotechnol. 2014 Jan;7(1):26-­‐31. • Ruggeri FM, Di Bartolo I, Ponterio E, Angeloni G, Trevisani M, Ostanello F. Zoonotic transmission of hepatitis E virus in industrialized countries. New Microbiol. 2013 Oct;36(4):331-­‐44. Epub 2013 Oct 1. Review. • Andraud M, Dumarest M, Cariolet R, Aylaj B, Barnaud E, Eono F, Pavio N, Rose N. Direct contact and environmental contaminations are responsible for HEV transmission in pigs. Vet Res. 2013 Oct 28;44:102. doi: 10.1186/1297-­‐9716-­‐44-­‐102. • Yugo DM, Meng XJ. Hepatitis E virus: foodborne, waterborne and zoonotic transmission. Int J Environ Res Public Health. 2013 Sep 25;10(10):4507-­‐33. • Christou L, Kosmidou M. Hepatitis E virus in the Western world-­‐-­‐a pork-­‐related zoonosis. Clin Microbiol Infect. 2013 Jul;19(7):600-­‐4. Review. • Meng XJ. Zoonotic and foodborne transmission of hepatitis E virus. Semin Liver Dis. 2013 Feb;33(1):41-­‐9. doi: 10.1055/s-­‐0033-­‐1338113. Epub 2013 Apr 5. Review. • Smith DB, Purdy MA, Simmonds P. Genetic variability and the classification of hepatitis E virus. J Virol. 2013 Apr;87(8):4161-­‐9. Erratum in: J Virol. 2013 Jul;87(13):7787. • Kaba M, Moal V, Gérolami R, Colson P. Epidemiology of mammalian hepatitis E virus infection. Intervirology. 2013;56(2):67-­‐83. doi: 10.1159/000342301. Epub 2013 Jan 22. Review. Book of Sample Projects Page 33 CIT Rísam PhD Scholarship Programme 2014 • Kumar S, Subhadra S, Singh B, Panda BK. Hepatitis E virus: the current scenario. Int J Infect Dis. 2013 Apr;17(4):e228-­‐33. Review. Selected host researcher references • Helen O’Shea, Emily Mulherin, Jelle Matthijnssens, Matthew P McCusker, PJ Collins, Olivia Cashman, Lynda Gunn, Marijke E Beltman, Séamus Fanning . Complete genomic sequence analyses of the first group A giraffe rotavirus reveals close evolutionary relationship with rotaviruses infecting other members of the Artiodactyla Veterinary Microbiology (2014) • Gunn L., Feeney S.A., Cashman O., Collins P.J., Coyle P.V. and O’Shea H. Molecular Characterization of Group A Rotavirus Found in Elderly Patients in Ireland; Predominance of G1P[8], Continued Presence of G9P[8], and Emergence of G2P[4]. J Med Virol 24 May 2012 Volume 84, Issue 12, pages 2008–2017. DOI: 10.1002/jmv.23416. • Matthijnssens J, Miño S, Papp H, Potgieter C, Novo L, Heylen E, Zeller M, Garaicoechea L, Badaracco A, Lengyel G, Kisfali P, Cullinane A, Collins PJ, Ciarlet M, O'Shea H, Parreño V, Bányai K, Barrandeguy M, Van Ranst M. Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several new genotypes and a largely conserved genotype constellation.J Gen Virol. (2011); 93(Pt 4):866-­‐75 [Epub ahead of print]PMID:22190012 • Cashman O, O'Shea H. Detection of human bocaviruses 1, 2 and 3 in Irish children presenting with gastroenteritis. Arch Virol. 2012 Sep;157(9):1767-­‐73. Epub 2012 May 22. PMID: 22614812 • O. Cashman, P J. Collins, G. Lennon, B. Cryan, V. Martella, S. Fanning, A. Staines, H. O’ Shea. Molecular characterisation of group A rotaviruses detected in children with gastroenteritis in Ireland in the years 2006-­‐2009. Epid & Infect (2011) 14:1 • Susan McElligott, P.J. Collins, R.D. Sleator, V. Martella, N. Decaro, C. Buonavoglia, and H. O’Shea Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland Archives of Virology (2011);156(3):495-­‐503. • Collins, P.J., Martella, V., Buonavoglia, C. O’Shea H. Identification of a G2-­‐like porcine rotavirus bearing a novel VP4 type, P[32] Vet Res (2010) 41(5): 73. • Collins PJ, Martella V, Sleator RD, Fanning S, O'Shea H. Detection and characterisation of group A rotavirus in asymptomatic piglets in southern Ireland. Arch Virol 2010 ;155:1247. • Cashman, O., Lennon, G., Sleator, R.D., Power, E., Fanning, S., O’Shea, H. Changing profile of the bovine rotavirus G6 population in the south of Ireland from 2002 to 2009 Vet Micro (2010) 146:238. • Collins, P.J., Martella, V., Buonavoglia C O’Shea, H. Detection and characterization of porcine sapoviruses from asymptomatic animals in Irish farms. Veterinary Microbiology.(2009); 139(1-­‐
2):176-­‐82. • Collins, P.J. Cullinane, A. Martella, V. O’Shea, H. Molecular characterisation of equine rotavirus in Ireland. J Clin Micro (2008).46:10 3346. Book of Sample Projects Page 34 CIT Rísam PhD Scholarship Programme 2014 • Collins, P.J., Martella, V. O’Shea, H. (2008). Detection and characterisation of group C rotavirus in asymptomatic piglets in Ireland. J Clin Micro 46:9 2973. • Mulherin, E., Bryan, J., Beltman, M., O’ Grady, L., Pidgeon, E., Garon, L., Lloyd, A., Bainbridge, J., O’ Shea, H., Whtye, P. and Fanning, S. Molecular Characterisation of a Bovine-­‐Like Rotavirus Isolated from a Giraffe. BMC Veterinary Research (2008), 4:46. • G. Lennon, N. Reidy, B. Cryan, S. Fanning, H. O'Shea Changing profile of rotavirus in Ireland: Predominance of P[8] and emergence of P[6] and P[9] in mixed infections. J Med Virol (2008). 80: 524. • G. Lennon, O. Cashman, K. Lane, B. Cryan and H. O’Shea. Prevalence and Characterization of Enteric Adenoviruses in the South of Ireland. J. Med. Virol. (2007) 79:1518–1526. • N. Reidy, G. Lennon, S. Fanning, E. Power and H. O'Shea Molecular characterisation and analysis of bovine rotavirus strains circulating in Ireland 2002–2004.Vet. Microbiol. (2006) 117, 242-­‐247. • Reidy, N.. O’Halloran, F. Fanning, S Cryan, B. and O’Shea, H. Emergence of G3 and G9 Rotavirus and Increased Incidence of Mixed Infections in the Southern Region of Ireland 2001-­‐2004. J Med Virol (2005). 77; 571. • O’Halloran, F., Lynch, M., Cryan, B., O’Shea, H. & Fanning, S. (2000).Molecular characterization of Rotavirus in Ireland: Detection of Novel Strains Circulating in the Population. J Clin Microbiol. 2000 Sep;38(9):3370-­‐4. • Identification and genetic characterisation of a novel picornavirus from chickens. (2014). Bullman, S., Kearney, K., O' Mahony, M., Kelly, L., Whyte, P., Fanning, S. & Morgan, J.G. J Gen Virol. 2014 Feb 4. doi: 10.1099/vir.0.061085-­‐0. [Epub ahead of print]. • McMenamy MJ, McKillen J, McNair I, Duffy C, Blomström AL, Charreyre C, Welsh M, Allan G. Detection of a porcine boca-­‐like virus in combination with porcine circovirus type 2 genotypes and Torque teno sus virus in pigs from postweaning multisystemic wasting syndrome (PMWS)-­‐
affected and non-­‐PMWS-­‐affected farms in archival samples from Great Britain. Vet Microbiol. 2013 Jun 28;164(3-­‐4):293-­‐8. • McNair I, McNeilly F, Duffy C, McKillen J, McMenamy M, Welsh M, Allan G. Production, characterisation and applications of monoclonal antibodies to two novel porcine bocaviruses from swine in Northern Ireland. Arch Virol. 2011 Dec;156(12):2157-­‐62. • McKillen J, McNeilly F, Duffy C, McMenamy M, McNair I, Hjertner B, Millar A, McKay K, Lagan P, Adair B, Allan G. Isolation in cell cultures and initial characterisation of two novel bocavirus species from swine in Northern Ireland. Vet Microbiol. 2011 Aug 26;152(1-­‐2):39-­‐45. • Welsh MD, Baird PM, Guelbenzu-­‐Gonzalo MP, Hanna A, Reid SM, Essen S, Russell C, Thomas S, Barrass L, McNeilly F, McKillen J, Todd D, Harkin V, McDowell S, Choudhury B, Irvine RM, Borobia J, Grant J, Brown IH. Initial incursion of pandemic (H1N1) 2009 influenza A virus into European pigs. Vet Rec. 2010 May 22;166(21):642-­‐5. Book of Sample Projects Page 35 CIT Rísam PhD Scholarship Programme 2014 • Willoughby K, Gilray J, Maley M, Dastjerdi A, Steinbach F, Banks M, Scholes S, Howie F, Holliman A, Baird P, McKillen J. Lack of evidence for circovirus involvement in bovine neonatal pancytopenia. Vet Rec. 2010 Apr 3;166(14):436-­‐7. • Blomström AL, Belák S, Fossum C, McKillen J, Allan G, Wallgren P, Berg M. Detection of a novel porcine boca-­‐like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome. Virus Res. 2009 Dec;146(1-­‐2):125-­‐9. • Rodriguez-­‐Sanchez B, Sanchez-­‐Vizcaino JM, Uttenthal A, Rasmussen TB, Hakhverdyan M, King DP, Ferris NP, Ebert K, Reid SM, Kiss I, Brocchi E, Cordioli P, Hjerner B, McMenamy M, McKillen J, Ahmed JS, Belak S. Improved diagnosis for nine viral diseases considered as notifiable by the world organization for animal health. Transbound Emerg Dis. 2008 Aug;55(5-­‐6):215-­‐25. • Allan GM, Caprioli A, McNair I, Lagan-­‐Tregaskis P, Ellis J, Krakowka S, McKillen J, Ostanello F, McNeilly F. Porcine circovirus 2 replication in colostrum-­‐deprived piglets following experimental infection and immune stimulation using a modified live vaccine against porcine respiratory and reproductive syndrome virus. Zoonoses Public Health. 2007;54(5):214-­‐22. • Caprioli A, McNeilly F, McNair I, Lagan-­‐Tregaskis P, Ellis J, Krakowka S, McKillen J, Ostanello F, Allan G. PCR detection of porcine circovirus type 2 (PCV2) DNA in blood, tonsillar and faecal swabs from experimentally infected pigs. Res Vet Sci. 2006 Oct;81(2):287-­‐92. 3.
Objectives To •
•
•
Develop molecular and non-­‐molecular tools for the detection HEV viruses and antibodies; Use these tools to investigate the prevalence of these viruses in livestock and wildlife; Use these tools to determine the genetics of these viruses and phylogenetically analyse their relationship to known strains from other countries, including whole genome analysis; •
Carry out horizon scanning for variants and new potential pathogens using a degenerate PCR approach; •
Determine the presence of HEV at critical control points in the pork production chain; 4.
Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. This project focuses on developing and applying standardised diagnostic skills for novel pathogens in pigs on an all-­‐island basis, with a view towards establishing the prevalence of these pathogens. This will form the foundation for future studies to assess the importance of novel viruses in complex porcine disease syndromes, to focus surveillance programs and allow accurate targeting of vaccination programs/husbandry etc. The focus is on producing benefits for the swine industry through reduced losses. Book of Sample Projects Page 36 CIT Rísam PhD Scholarship Programme 2014 1. Establishment of a sample bank: A wide range of samples will be collected to include: • Archival samples, including blood, stored at CIT and AFBI from a range of livestock and wildlife species • Faeces samples collected on farm with assistance from veterinary practices and industry contacts • Samples collected at abattoirs and other critical control points • Wildlife samples collected by Prof. Jaimie Dick at QUB • Pork products taken at point of sale 2. Implementation of a range of tools for HEV detection: • Antibody ELISA for porcine HEV • Specific RT-­‐PCR for detection of HEV nucleic acid in pigs, poultry, sheep, cattle and wildlife in faeces • Degenerate RT-­‐PCR for detection of novel HEV variants • Establish adenovirus assays for detection of faecal contamination • Establish a protocol for sample preparation for the analysis of HEV by NGS 3. Determination of the prevalence of HEV in Irish pig populations: The prevalence of HEV and antibodies will be determined using the tools in (2) and the samples in (1). These data will be statistically evaluated where possible. 4. Evaluation of the presence of HEV at critical control points in the pork production process: RT-­‐PCR assays implemented in (2) will be applied to samples from (1) taken at critical control points in the food supply chain in order to identify areas where there is a risk of human infection. These will include: • Swabs from abattoirs will be tested for HEV to determine if the virus in maintained on key abattoir surfaces • The same swabs will be tested for porcine adenoviruses as an indicator of porcine faecal contamination as well as human adenoviruses as an indicator of human faecal contamination. These analyses will determine potential routes of HEV transmission in the food chain, even in the absence of HEV virus. • Testing pork products at point of sale • Slurry samples from pig farms 5. Evaluation of livestock and wildlife pools as reservoirs of emerging HEV infections: Potentially under-­‐considered species will be evaluated by RT-­‐PCR for the presence of hepatitis viruses, including by the use of degenerate PCR approaches. This will help to establish potential risk of infection from other HEV reservoirs as well as identify the potential for new emerging strains of the virus. 1. RT-­‐PCR testing will be carried out deer species in Ireland provided by Professor Jaimie Dick at QUB. 2. RT-­‐PCR will be carried out on a range of livestock and wildlife species. 6. Sequence analysis of HEV strains: Standard sequencing as well as state-­‐of-­‐the-­‐art Next Generation Sequencing methodologies will be applied to genetically characterise HEV strains from Ireland and compare these to known sequences in order to understand the position of Ireland in a global context as well as determining the role of pigs as a transmission reservoir via comparison to human isolates. 1. RT_PCR amplicons from (3) and (4) will sequenced using standard dideoxy chain termination methods Book of Sample Projects Page 37 CIT Rísam PhD Scholarship Programme 2014 2. A sub-­‐sample of porcine viruses will be subjected to full genome sequence analysis using Next Generation Sequencing 3. be used to construct phylogenetic trees and maps of Irish strains from all species 5.
Work Plan Present the research work plan, outlining the main research tasks and timing. Summary Table of Project Tasks Task No. Task 1: Task 2: Title The establishment of a sample bank [months 1-­‐30]. Implementation of a range of tools for HEV detection [months 1-­‐12] Task 3: Determination of the prevalence of HEV in Irish pig populations [months 3-­‐30] Task 4 Evaluation of the presence of HEV at critical control points in the pork production process: [months 3-­‐30]. Task 5: Evaluation of livestock and wildlife pools as reservoirs of emerging HEV infections: [months 12-­‐30]. Task 6: Task 7: Sequence analysis of HEV strains [months 12-­‐30]. Dissemination (to include publication of peer reviewed papers and thesis preparation) and Technology Transfer [months 12-­‐36]. Figure 1 Gant chart illustrating timeframe for completion of the proposed Tasks, with associated milestones and deliverables. Timeframe for completion of the proposed Tasks Year 1 Quarter 1 2 3 4 1 2 3 4 1 2 3 4 Month 1-­‐3 4-­‐6 7-­‐9 10-­‐12 13-­‐
15 16-­‐
18 19-­‐
21 22-­‐
24 25-­‐
27 28-­‐
30 31-­‐
33 34-­‐36 M1.1 M1.2 M1.3
D1.1 M2.1 M2.2 D2.1 M3.1 M3.2 D3.1 M4.1 D4.1 M5.1 D5.1 Task 1 Task 2 Task 3 Task 4 Task 5 2 Book of Sample Projects 3 Page 38 CIT Rísam PhD Scholarship Programme 2014 M6.1
M6.2 D6.1 M7.1 D7.1 Task 6 Task 7 Milestones and deliverables: Task 1 M1.1 Year 1 sample collection completed and archived (month 12) M1.2 Year 2 sample collection completed and archived (month 24) M1.3 Year 3 sample collection completed and archived (month 30) D1.1 Complete sample bank established (month 30) Task 2 M2.1 Techniques transferred to post-­‐graduate student (month 6) M2.2 Implementation of tools achieved (month 12) D 2.1 Protocols established for HEV detection and genotyping tools (month 12) Task 3 M3.1 Evaluation of HEV prevalence in pigs complete (month 24) M3.2 Evaluation of antibody prevalence in Irish pigs complete (month 24) D3.1 Report on HEV prevalence in Ireland complete (month 30) Task 4 M4.1 Virus testing at pork production critical control points complete (month 30) D4.1 Report on HEV prevalence at critical control points complete (month 30) Task 5 M5.1 Virus testing on livestock and wildlife samples complete (month 30) D5.1 Report on the prevalence of HEV in livestock and wildlife complete (month 30) Task 6 M6.1 Sequencing of HEV PCR amplicons complete (month 30) M6.2 Whole genome sequencing of PCR complete (month 30) D6.1 Phylogenetic analysis of Irish HEV complete (month 30) Book of Sample Projects Page 39 CIT Rísam PhD Scholarship Programme 2014 Task M7.1 Dissemination appropriate platforms selected and targeted (month 36) D7.1 Dissemination completed (month 36) 6.
7.
Ethical issues If the proposed research directly involves human or live animal subjects, discuss the ethical issues involved and the actions that will be taken to ensure compliance with CIT ethics guidelines and with the CIT Child Protection Policy (if children are involved). The proposed project does not involve human or live animal subjects. External Collaboration/Other Institutions Indicate any external collaboration envisaged. On-­‐going projects between CIT, UCC and DCU have drawn together a formidable, synergistic, inter-­‐institutional, interdisciplinary research team, with National and International collaborators. The Molecular Virology Unit at CIT has established expertise in all aspects of modern molecular biology and epidemiology, in collaboration with Professor Anthony Staines at DCU. Researchers in this team have contributed substantially to the current understanding of molecular epidemiology of rotavirus and other gastrointestinal viruses in humans and animals in Ireland. Our partner in UCC (Dr John Morgan) also has wide experience in the area of gastrointestinal viruses. Our collaborator in Belgium, Dr Jelle Matthijnssens, is a leading expert in rotavirus genetic analysis, particularly in the area of deep genome sequencing. Our team has recently been awarded DAFM funding to undertake a large scale genomic project. This novel project involves a new collaboration with AFBI, which adds another dimension, as many research projects into the pathogenicity and diagnosis of economically important pathogens of swine have been successfully carried out at AFBI, and AFBI is recognised internationally as one of the key laboratories researching the emergence of porcine circovirus type 2 (PCV2). This project proposal is part of a larger funded research programme, in collaboration with Dr John McKillen, AFBI, Belfast (DARD DIRECTED AGRI-­‐FOOD AND BIOSCIENCES INSTITUTE (AFBI) RESEARCH WORK PROGRAMME 2014/15 Proposal number 14/3/01; Molecular diagnostics of novel/emerging/exotic viral threats to Northern Ireland livestock and assessment of emerging threats from wildlife). This project will therefore build on the experience in the areas of molecular and epidemiological analysis of gastroenteritis viruses in the CIT/UCC/DCU teams and in porcine veterinary medicine at AFBI to address the important area of novel viruses and will fill a significant knowledge gap, one that has the potential for benefits to the pig industry. The project will also build on the work that has been carried out at AFBI on a range of porcine diseases such as PCV2, as this is now known to have an important role in respiratory disease, and not just in post-­‐weaning multisystemic wasting syndrome as well as on the experience gained following their role in the Book of Sample Projects Page 40 CIT Rísam PhD Scholarship Programme 2014 first identification of pandemic H1N1 influenza in European pigs. Currently AFBI are involved in the European Surveillance Network for Influenza (ESNI) in pigs and have a range of other appropriate international contacts including in industry, allowing access to a great range of resources including, validated diagnostic assays, control materials, next generation sequencing and advice on a wide range of issues from epidemiology to phylogenetics. Institution/ Company Lead Scientist/ Collaborator Detail of Collaboration (e.g. knowledge exchange, networking, co-­‐
funding, resource-­‐sharing) AFBI Dr John McKillen Provision of samples and expert advice. AFBI have extensive expertise in the area of small DNA viruses. DCU Anthony Staines Provision of expert advice. Prof Staines is an epidemiologist and a collaborator in several successful grants with CIT. UCC John Morgan Dr Morgan is a virologist and a collaborator in several successful grants with CIT. U Leuven Jelle Matthijnssens Dr Matthijnssens is an expert in NGS and bioinformatics and a collaborator in several successful grants and publications with CIT. Book of Sample Projects Page 41 CIT Rísam PhD Scholarship Programme 2014 Title of project: Irish Swine Industry Molecular diagnostics of novel and emerging viral threats to the Name of Principal Supervisor: Dr Helen O’Shea (external supervisor Dr John McKillen) Brief Summary of Research Interests: Research in my group is mainly in the areas of virology and epidemiology, in particular gastroenteritis viruses, but I also have an interest in the area of antibiotic resistance, biofilms and the antibacterial/antiviral effects of bioactive glass. CIT Department: Email: Biological Sciences helen.oshea@cit.ie Telephone: +353214335401 Research Proposal Discipline Area by Frascati Classification: • Virology and molecular biology; A 1. Natural sciences, 1.6 Biological sciences, Bocavirus Parvovirus 1. Abstract (250 words) Summarise the objectives, the main expected originality and the research methodology to be used. Virus infections pose severe threats to pig health and can cause enormous economic burdens for the pig industry. Recently, a number of small novel DNA viruses have emerged globally. These novel parvoviruses (porcine bocavirus, porcine hokovirus and porcine parvoviruses 2 & 4) are understudied and little is known about their biology and potential pathogenicity. Investigations of possible pathogenicity are complicated as these viruses are frequently widespread in pig populations worldwide and difficult to isolate. The etiology of many diseases is believed to be multifactorial, with concurrent infections of multiple viruses being crucial for development of the complete clinical picture and the newly emerging DNA viruses have been suggested to have a possible role in these multifactorial diseases. Also, investigations of other endemic viruses that do not cause clinical disease have shown that infection may still result in significant agricultural losses as a result of subclinical effects. Therefore, in this project we will provide the tools needed to study the prevalence, biology and pathogenicity of these emerging viruses. We will also generate data that will provide much-­‐needed, information on the complexity of concurrent infections of multiple viruses and isolates that facilitate controlled functional studies. This project proposal is in collaboration with Dr John McKillen, AFBI. Book of Sample Projects Page 42 CIT Rísam PhD Scholarship Programme 2014 2.
Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. The emergence of novel viruses poses a major threat for pig health as these viruses may have a significant economic impact on the pig industry. A number of small DNA viruses have emerged during the past two decades in pig populations worldwide. These include novel circoviruses (e.g. porcine circovirus 2, PCV2) and porcine parvoviruses (PPVs). Studies have shown that many porcine diseases may be multifactorial and that co-­‐infections often play a crucial role in disease development. Much is known about PCV2 as it has been associated with several severe diseases, however, in the last 10 years a number of additional porcine DNA viruses whose epidemiology and pathogenicity are less well understood have been discovered worldwide. Among these are different novel PPVs (such as porcine bocavirus, PPV 2 & 4, porcine hokovirus etc.). Research carried out by our collaborators in AFBI on PCV2 epidemiology and pathogenicity has demonstrated the need to monitor emerging viruses that may at first seem innocuous and may already be endemic in pig populations but can rapidly become a global problem. In addition, it has been demonstrated that porcine diseases can be multifactorial and that co-­‐factors in infection can be critical in the development of disease. As such, it is crucial to monitor the prevalence of these novel parvoviruses and to assess their pathogenicity either alone or in combination with other pathogens. Previous work at AFBI into chicken anaemia virus has demonstrated that endemic viruses which do not cause clinical disease may result in significant agricultural losses as a result of sub-­‐clinical effects. Chicken anaemia virus (CAV) has been shown to result in a 13% drop in net income per 1000 birds, reduce feed conversion rates (FCR) by 2% and result in a 2.5% depression in the average weight of birds at slaughter (McNulty, 1991). It is possible that recently discovered viruses prevalent in global pig populations may have the potential to affect pig farming in a similar way to CAV in the poultry industry. As such, these viruses should be fully investigated, beginning with an assessment of their prevalence. Therefore, in this project we will provide the tools needed to study the prevalence, biology and pathogenicity of these emerging viruses. We will also generate data/project results that will provide a much-­‐needed knowledge of their disease association, provide information on the complexity of concurrent infections of multiple viruses and provide isolates/infectious clones that enable controlled functional studies. This project proposal is part of a larger funded research programme, in collaboration with Dr John McKillen, AFBI, Belfast (DARD DIRECTED AGRI-­‐FOOD AND BIOSCIENCES INSTITUTE (AFBI) RESEARCH WORK PROGRAMME 2014/15 Proposal number 14/3/01; Molecular diagnostics of novel/emerging/exotic viral threats to Northern Ireland livestock and assessment of emerging threats from wildlife). Book of Sample Projects Page 43 CIT Rísam PhD Scholarship Programme 2014 References •
Anderson, L. J.(2007). Human bocavirus: a new viral pathogen. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 44, 911-­‐912. •
Ge, F. F., Yang, D. Q., Ju, H. B., Wang, J., Liu, J., Liu, P. H. & Zhou, J. P. (2013). Epidemiological survey of porcine epidemic diarrhea virus in swine farms in Shanghai, China. Archives of virology. •
Kekarainen, T. & Segales, J. (2012). Torque Teno Sus Virus in Pigs: an Emerging Pathogen? Transboundary and emerging diseases. •
Khamrin P, Maneekarn N, Kongkaew A, Kongkaew S, Okitsu S, Ushijima H. Porcine kobuvirus in piglets, Thailand. Emerg Infect Dis. 2009 Dec. •
Li, L., Kapoor, A., Slikas, B., Bamidele, O. S., Wang, C., Shaukat, S., Masroor, M. A., Wilson, M. L., Ndjango, J. B., Peeters, M., Gross-­‐Camp, N. D., Muller, M. N., Hahn, B. H., Wolfe, N. D., Triki, H., Bartkus, J., Zaidi, S. Z. & Delwart, E. (2010). Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. Journal of virology 84, 1674-­‐1682. •
Marthaler, D., Jiang, Y., Otterson, T., Goyal, S., Rossow, K. & Collins, J. (2013). Complete Genome Sequence of Porcine Epidemic Diarrhea Virus Strain USA/Colorado/2013 from the United States. Genome announcements 1. •
McKillen, J., McNeilly, F., Duffy, C., McMenamy, M., McNair, I., Hjertner, B., Millar, A., McKay, K., Lagan, P., Adair, B. & Allan, G. (2011). Isolation in cell cultures and initial characterisation of two novel bocavirus species from swine in Northern Ireland. Veterinary microbiology 152, 39-­‐45. •
Nieto, D., Kekarainen, T., Aramouni, M. & Segales, J. (2013). Torque teno sus virus 1 and 2 distribution in tissues of porcine circovirus type 2-­‐systemic disease affected and age-­‐matched healthy pigs. Veterinary microbiology 163, 364-­‐367. •
Opriessnig T, Xiao CT, Gerber PF, Halbur PG. Emergence of a novel mutant PCV2b variant associated with clinical PCVAD in two vaccinated pig farms in the U.S. concurrently infected with PPV2. Vet Microbiol. 2013 Apr 12;163(1-­‐2):177-­‐83. •
Segalés J., Allan G.M. & Domingo M. (2006), Porcine circovirus diseases, In: Straw B.E., Zimmerman J.J., D'Allaire S., Taylor D.J. (eds) Diseases of swine, 9th edition. Blackwell Publishing, Ames, Iowa, USA, p 299-­‐307. •
Sikorski, A., Arguello-­‐Astorga, G. R., Dayaram, A., Dobson, R. C. & Varsani, A. (2013). Discovery of a novel circular single-­‐stranded DNA virus from porcine faeces. Archives of virology 158, 283-­‐289. •
Xiao, C. T., Halbur, P. G. & Opriessnig, T. (2013). Molecular evolutionary genetic analysis of emerging parvoviruses identified in pigs. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 16, 369-­‐376. Book of Sample Projects Page 44 CIT Rísam PhD Scholarship Programme 2014 Selected host researcher references •
Gunn L., Feeney S.A., Cashman O., Collins P.J., Coyle P.V. and O’Shea H. Molecular Characterization of Group A Rotavirus Found in Elderly Patients in Ireland; Predominance of G1P[8], Continued Presence of G9P[8], and Emergence of G2P[4]. J Med Virol 24 May 2012 Volume 84, Issue 12, pages 2008–2017. DOI: 10.1002/jmv.23416 [In print] •
Matthijnssens J, Miño S, Papp H, Potgieter C, Novo L, Heylen E, Zeller M, Garaicoechea L, Badaracco A, Lengyel G, Kisfali P, Cullinane A, Collins PJ, Ciarlet M, O'Shea H, Parreño V, Bányai K, Barrandeguy M, Van Ranst M. Complete molecular genome analyses of equine rotavirus A strains from different continents reveal several new genotypes and a largely conserved genotype constellation.J Gen Virol. (2011); 93(Pt 4):866-­‐75 [Epub ahead of print]PMID:22190012 •
Cashman O, O'Shea H. Detection of human bocaviruses 1, 2 and 3 in Irish children presenting with gastroenteritis. Arch Virol. 2012 Sep;157(9):1767-­‐73. Epub 2012 May 22. PMID: 22614812 •
O. Cashman, P J. Collins, G. Lennon, B. Cryan, V. Martella, S. Fanning, A. Staines, H. O’ Shea. Molecular characterisation of group A rotaviruses detected in children with gastroenteritis in Ireland in the years 2006-­‐2009. Epid & Infect (2011) 14:1 •
Susan McElligott, P.J. Collins, R.D. Sleator, V. Martella, N. Decaro, C. Buonavoglia, and H. O’Shea Detection and genetic characterization of canine parvoviruses and coronaviruses in southern Ireland Archives of Virology (2011);156(3):495-­‐503. •
Collins, P.J., Martella, V., Buonavoglia, C. O’Shea H. Identification of a G2-­‐like porcine rotavirus bearing a novel VP4 type, P[32] Vet Res (2010) 41(5): 73. •
Collins PJ, Martella V, Sleator RD, Fanning S, O'Shea H. Detection and characterisation of group A rotavirus in asymptomatic piglets in southern Ireland. Arch Virol 2010 ;155:1247. •
Cashman, O., Lennon, G., Sleator, R.D., Power, E., Fanning, S., O’Shea, H. Changing profile of the bovine rotavirus G6 population in the south of Ireland from 2002 to 2009 Vet Micro (2010) 146:238. •
Collins, P.J., Martella, V., Buonavoglia C O’Shea, H. Detection and characterization of porcine sapoviruses from asymptomatic animals in Irish farms. Veterinary Microbiology.(2009); 139(1-­‐
2):176-­‐82. •
Collins, P.J. Cullinane, A. Martella, V. O’Shea, H. Molecular characterisation of equine rotavirus in Ireland. J Clin Micro (2008).46:10 3346. •
Collins, P.J., Martella, V. O’Shea, H. (2008). Detection and characterisation of group C rotavirus in asymptomatic piglets in Ireland. J Clin Micro 46:9 2973. •
Mulherin, E., Bryan, J., Beltman, M., O’ Grady, L., Pidgeon, E., Garon, L., Lloyd, A., Bainbridge, J., O’ Shea, H., Whtye, P. and Fanning, S. Molecular Characterisation of a Bovine-­‐Like Rotavirus Isolated from a Giraffe. BMC Veterinary Research (2008), 4:46. •
G. Lennon, N. Reidy, B. Cryan, S. Fanning, H. O'Shea Changing profile of rotavirus in Ireland: Predominance of P[8] and emergence of P[6] and P[9] in mixed infections. J Med Virol (2008). 80: 524. •
G. Lennon, O. Cashman, K. Lane, B. Cryan and H. O’Shea. Prevalence and Characterization of Enteric Adenoviruses in the South of Ireland. J. Med. Virol. (2007) 79:1518–1526. •
N. Reidy, G. Lennon, S. Fanning, E. Power and H. O'Shea Molecular characterisation and analysis of bovine rotavirus strains circulating in Ireland 2002–2004.Vet. Microbiol. (2006) 117, 242-­‐247. Book of Sample Projects Page 45 CIT Rísam PhD Scholarship Programme 2014 •
Reidy, N.. O’Halloran, F. Fanning, S Cryan, B. and O’Shea, H. Emergence of G3 and G9 Rotavirus and Increased Incidence of Mixed Infections in the Southern Region of Ireland 2001-­‐
2004. J Med Virol (2005). 77; 571. •
O’Halloran, F., Lynch, M., Cryan, B., O’Shea, H. & Fanning, S. (2000).Molecular characterization of Rotavirus in Ireland: Detection of Novel Strains Circulating in the Population. J Clin Microbiol. 2000 Sep;38(9):3370-­‐4. •
Identification and genetic characterisation of a novel picornavirus from chickens. (2014). Bullman, S., Kearney, K., O' Mahony, M., Kelly, L., Whyte, P., Fanning, S. & Morgan, J.G. J Gen Virol. 2014 Feb 4. doi: 10.1099/vir.0.061085-­‐0. [Epub ahead of print]. •
McMenamy MJ, McKillen J, McNair I, Duffy C, Blomström AL, Charreyre C, Welsh M, Allan G. Detection of a porcine boca-­‐like virus in combination with porcine circovirus type 2 genotypes and Torque teno sus virus in pigs from postweaning multisystemic wasting syndrome (PMWS)-­‐affected and non-­‐PMWS-­‐affected farms in archival samples from Great Britain. Vet Microbiol. 2013 Jun 28;164(3-­‐4):293-­‐8. •
McNair I, McNeilly F, Duffy C, McKillen J, McMenamy M, Welsh M, Allan G. Production, characterisation and applications of monoclonal antibodies to two novel porcine bocaviruses from swine in Northern Ireland. Arch Virol. 2011 Dec;156(12):2157-­‐62. •
McKillen J, McNeilly F, Duffy C, McMenamy M, McNair I, Hjertner B, Millar A, McKay K, Lagan P, Adair B, Allan G. Isolation in cell cultures and initial characterisation of two novel bocavirus species from swine in Northern Ireland. Vet Microbiol. 2011 Aug 26;152(1-­‐2):39-­‐45. •
Welsh MD, Baird PM, Guelbenzu-­‐Gonzalo MP, Hanna A, Reid SM, Essen S, Russell C, Thomas S, Barrass L, McNeilly F, McKillen J, Todd D, Harkin V, McDowell S, Choudhury B, Irvine RM, Borobia J, Grant J, Brown IH. Initial incursion of pandemic (H1N1) 2009 influenza A virus into European pigs. Vet Rec. 2010 May 22;166(21):642-­‐5. •
Willoughby K, Gilray J, Maley M, Dastjerdi A, Steinbach F, Banks M, Scholes S, Howie F, Holliman A, Baird P, McKillen J. Lack of evidence for circovirus involvement in bovine neonatal pancytopenia. Vet Rec. 2010 Apr 3;166(14):436-­‐7. •
Blomström AL, Belák S, Fossum C, McKillen J, Allan G, Wallgren P, Berg M. Detection of a novel porcine boca-­‐like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome. Virus Res. 2009 Dec;146(1-­‐2):125-­‐9. •
Rodriguez-­‐Sanchez B, Sanchez-­‐Vizcaino JM, Uttenthal A, Rasmussen TB, Hakhverdyan M, King DP, Ferris NP, Ebert K, Reid SM, Kiss I, Brocchi E, Cordioli P, Hjerner B, McMenamy M, McKillen J, Ahmed JS, Belak S. Improved diagnosis for nine viral diseases considered as notifiable by the world organization for animal health. Transbound Emerg Dis. 2008 Aug;55(5-­‐6):215-­‐25. •
Allan GM, Caprioli A, McNair I, Lagan-­‐Tregaskis P, Ellis J, Krakowka S, McKillen J, Ostanello F, McNeilly F. Porcine circovirus 2 replication in colostrum-­‐deprived piglets following experimental infection and immune stimulation using a modified live vaccine against porcine respiratory and reproductive syndrome virus. Zoonoses Public Health. 2007;54(5):214-­‐22. •
Caprioli A, McNeilly F, McNair I, Lagan-­‐Tregaskis P, Ellis J, Krakowka S, McKillen J, Ostanello F, Allan G. PCR detection of porcine circovirus type 2 (PCV2) DNA in blood, tonsillar and faecal swabs from experimentally infected pigs. Res Vet Sci. 2006 Oct;81(2):287-­‐92. Book of Sample Projects Page 46 CIT Rísam PhD Scholarship Programme 2014 3.
Objectives To •
Develop molecular and non-­‐molecular tools for the detection of these viruses and antibodies to them; •
Use these tools to investigate the phylogeny of these viruses; •
Use these tools to determine the prevalence of these viruses and their antibodies in swine in the Republic of Ireland and elsewhere, also in products of swine origin (including human vaccines) and relate this information to animal health status; •
Carry out horizon scanning for variants and new potential pathogens using novel molecular methods, including viral metagenomics by next-­‐generation sequencing and use of degenerate PCR approaches; •
Develop cell culture systems to replicate and further analyse these viruses; 4.
Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. This project focuses on developing and applying standardised diagnostic skills for novel pathogens in pigs on an all-­‐island basis, with a view towards establishing the prevalence of these pathogens. This will form the foundation for future studies to assess the importance of novel viruses in complex porcine disease syndromes, to focus surveillance programs and allow accurate targeting of vaccination programs/husbandry etc. The focus is on producing benefits for the swine industry through reduced losses. To establish prevalence of novel DNA viruses in the Republic of Ireland Pig samples will collected and tested for the selected viruses and antibodies. All testing will be performed according to standardised Integrated Monitoring and Control of Foodborne Viruses in European Food Supply Chains protocols or similar state-­‐of-­‐the-­‐art methods. This work will involve collaboration with the AFBI, Stormont. Stakeholders will be provided with a report on the findings to include a summary of current knowledge and details of the all-­‐island surveillance. Book of Sample Projects Page 47 CIT Rísam PhD Scholarship Programme 2014 On farm testing for selected viruses (porcine bocavirus, porcine hokovirus and porcine parvoviruses 2 & 4) Animals will be tested from selected herds in Southern Ireland. This will be carried out in consultation with the AFBI epidemiologist and DARD Policy and Economics Division statistician, as part of the larger research project. Industry contacts (partners with Dr John Mc Killen AFBI) will help to facilitate collection of a range of samples. Thus, this novel project will form part of an all-­‐island approach to animal health. Molecular diagnostics will include PCR, RT-­‐PCR, ELISA. A Report on the prevalence of these novel viruses in NI and ROI will be generated. 5. Work Plan Present the research work plan, outlining the main research tasks and timing. Summary Table of Project Tasks Task No. Title Task 1: The establishment of a sample bank [months 1-­‐34]. Task 2: Harmonisation of tools and procedures [months 1-­‐12] Task 3: Detection, characterisation and association with disease of small DNA viruses found in samples from Irish pigs [months 3-­‐30] Task 4 Virus discovery [months 6-­‐30]. Task 5: Assessment of permissive cell lines which may support the replication of these viruses [months 1-­‐24]. Dissemination (to include publication of peer reviewed papers and thesis preparation) and Technology Transfer Task 6: Figure 1 Gant chart illustrating timeframe for completion of the proposed Tasks, with associated milestones and deliverables. Timeframe for completion of the proposed Tasks Year 1 Quarter 1 2 3 4 Month 1-­‐3 4-­‐6 7-­‐9 10-­‐12 13-­‐
2 Book of Sample Projects 1 3 2 3 4 1 2 3 4 16-­‐
19-­‐
22-­‐
25-­‐
28-­‐
31-­‐
34-­‐36 Page 48 CIT Rísam PhD Scholarship Programme 2014 15 18 21 24 27 30 33 Task 1 M1.1 M1.2 M1.3 M1.4 D1.1 Task 2 M2.1 M2.2 D2.1 M3.1
D3.1 M3.2 D3.2 M4.1
D4.1 Task 5 M5.1 M5.2 D5.1 Task 6 M6.1 D6.1 4. M1.1 Selection of swine farms for sampling M1.2 Year 1 sample collection completed and archived M1.3 Year 1 sample collection completed and archived M1.4 Year 1 sample collection completed and archived D1.1 Complete sample bank established M2.1 Techniques transferred to Post-­‐graduate student M2.2 Transfer completed and independent group established D 2.1 Harmonisation of tools and procedures achieved M3.1 Detection and characterisation of novel DNA viruses found in samples from Irish pigs M3.2 Analysis of association with disease of novel DNA viruses found in Irish pigs D3.1 Detection, characterisation and association with disease of novel DNA viruses found in samples from Irish pigs completed M4.1 Virus discovery D4.1 Analysis and molecular characterisation of selected viruses, selection for sequence analysis M5.1 Selected samples subjected to sequence analysis and bioinformatics Book of Sample Projects Page 49 CIT Rísam PhD Scholarship Programme 2014 D5.1 Sequence analysis completed M6.1 Dissemination appropriate platforms selected and targeted D6.1 Dissemination completed Deliverables Literature reviews complete for selected viruses Completed accreditation ready protocols for selected viruses Completed RT-­‐PCR and phylogenetic analysis of selected viruses Updated sequence alignments of selected viruses Submitted manuscript on RT-­‐PCR and phylogenetic analysis of selected viruses PCR and RT-­‐PCR screening for selected viruses in Southern Ireland farms complete Complete sequencing and phylogenetic analysis of selected viruses from NI and RoI Submitted manuscript(s) on prevalence of selected viruses in RoI Further development of NGS techniques Application of NGS to clinical samples Training of staff in NGS benchwork Training of staff in basic bioinformatics Submitted manuscript on NGS applications in veterinary virology Dissemination of final results of project e.g. on AFBINI external website 6. Ethical issues If the proposed research directly involves human or live animal subjects, discuss the ethical issues involved and the actions that will be taken to ensure compliance with CIT ethics guidelines and with the CIT Child Protection Policy (if children are involved). The proposed project does not involve human or live animal subjects. 7. External Collaboration/Other Institutions Indicate any external collaboration envisaged. On-­‐going projects between CIT, UCC and DCU have drawn together a formidable, synergistic, inter-­‐institutional, interdisciplinary research team, with National and International collaborators. The Molecular Virology Unit at CIT has established expertise in all aspects of modern molecular biology and epidemiology, in collaboration with Professor Anthony Staines at DCU. Researchers in this team have contributed substantially to the current understanding of molecular epidemiology of rotavirus and other gastrointestinal viruses in humans and animals in Ireland. Our partner in UCC (Dr John Morgan) also has wide experience in the area of gastrointestinal viruses. Our collaborator in Belgium, Dr Jelle Matthijnssens, is a leading expert in rotavirus genetic analysis, particularly in the area of deep genome sequencing. Our team has recently been awarded DAFM funding to undertake a large scale genomic project. Book of Sample Projects Page 50 CIT Rísam PhD Scholarship Programme 2014 This novel project involves a new collaboration with AFBI, which adds another dimension, as many research projects into the pathogenicity and diagnosis of economically important pathogens of swine have been successfully carried out at AFBI, and AFBI is recognised internationally as one of the key laboratories researching the emergence of porcine circovirus type 2 (PCV2). However, the focus of these projects has been on PCV-­‐associated disease and on diagnostics for exotic threats. Despite the fact that novel viruses have recently been detected in pigs, little is known about the economic impact of these viruses. This project will therefore build on the experience in the areas of molecular and epidemiological analysis of gastroenteritis viruses in the CIT/UCC/DCU teams and in porcine veterinary medicine at AFBI to address the important area of novel viruses and will fill a significant knowledge gap, one that has the potential for benefits to the pig industry. The project will particularly build on the work that has been carried out PCV2, as this is now known to have an important role in respiratory disease, and not just in post-­‐weaning multisystemic wasting syndrome. The work will also build on the experience gained by AFBI following their role in the first identification of pandemic H1N1 influenza in European pigs. Currently AFBI are involved in the European Surveillance Network for Influenza (ESNI) in pigs, allowing access to a great range of resources including, validated diagnostic assays, control materials, next generation sequencing and advice on a wide range of issues from epidemiology to phylogenetics. Institution/ Company Lead Scientist/ Collaborator Detail of Collaboration (e.g. knowledge exchange, networking, co-­‐
funding, resource-­‐sharing) AFBI Dr John McKillen Provision of samples and expert advice. AFBI have extensive expertise in the area of small DNA viruses. Pig Regen Howard Tonks Assistance with collection of samples and expert advice Moss Vet Dermot Sparrow/ Jesus Borobia Assistance with collection of samples and expert advice DCU Anthony Staines Provision of expert advice. Prof Staines is an epidemiologist and a collaborator in several successful grants with CIT. UCC John Morgan Dr Morgan is a virologist and a collaborator in several successful grants with CIT. U Leuven Jelle Matthijnssens Dr Matthijnssens is an expert in NGS and bioinformatics and a collaborator in several successful grants and publications with CIT. Book of Sample Projects Page 51 CIT Rísam PhD Scholarship Programme 2014 Title of project: Lactococcus lactis Development of a live oral vaccine delivery system using Name of Principal Supervisor: Dr Roy Sleator Brief Summary of Research Interests: My research is focused on convergent technologies; specifically the application of bioinformatics and biotechnology for improved clinical outcomes. These are core objectives of BioExplore; a central pillar of CIT’s research infrastructure. CIT Department: Email: Biological Sciences roy.sleator@cit.ie Discipline Area by Frascati Classification: Telephone: 021 4335405 3.4 Medical Biotechnology 1. Abstract (250 words) According to the World Health Organisation infectious diseases are responsible for approximately 25% of all mortalities worldwide with infectious diarrhoea accounting for over 2 million deaths globally per annum. Vaccines are an effective solution to the problem of infectious disease but further research is needed to develop effective vaccine vectors that are easy to administer. Dr. Sleator’s research group has recently shown that the Gram positive food-­‐grade organism Lactococcus lactis can be easily engineered to provide an effective vaccine platform for delivering selected antigens to the immune system. His group has also shown that survival of the bacterium in the gastrointestinal tract can be enhanced through simple engineering approaches. In this proposed PhD project we wish to combine these different strands of research to develop a Lactococcus lactis-­‐
based live vaccine vector that has an enhanced capacity to survive and deliver antigen in the intestine. The aim is to develop a commercially viable platform with which to deliver multivalent vaccines to the host gastro intestinal (GI) tract in an easy-­‐to-­‐administer preparation. 2.
Research Context and Contribution to the Research Field Oral multivalent vaccines that protect against a variety of pathogens remain a desirable and realistic goal. A live bacterial vector would be easy to produce using existing biotechnological capacities (batch growth of bacteria) and is easily administered without the need for medical personnel. Unlike the use of attenuated pathogens as delivery agents, L. lactis is extremely safe and can be readily manipulated at the genetic level. We propose to build upon existing research to examine the hypothesis that enhancing survival of L. lactis in the gut will enhance its capacity to act as a vaccine delivery vector. Clearly Dr. Sleator’s group has the capacity and knowledge to bring this work forward (see Pubmed for relevant publications in Vaccine, Human Vaccines & Immunotherapy and J Med Microbiology). Not only will this make a new contribution to knowledge but we believe that this will lead to patentable technology for further exploitation. Objectives Book of Sample Projects Page 52 CIT Rísam PhD Scholarship Programme 2014 Aims: Research by the Sleator lab has shown that L. lactis can be engineered to express the bile resistance locus bilE with a resultant enhancement of ability to survive in the murine GI tract (Watson et al., 2008). Here we will further engineer L. lactis to express both bilE and common vaccine antigens (tetanus toxoid fragment, ovalbumin, listeriolysin O fragment, cholera toxin fragment). Objectives: The objective of the work is to enhance the survival of the live vaccine vector in the host in order to improve vaccine delivery to the mucosal immune system. We will test the ability of the engineered strain to survive in mice and will determine the outcome of local and systemic immunity by performing evaluations of T cell (ELISPOT, flow cytometry, cytokine profiling) and B cell (mucosal sIgA, IgG, IgM) mediated responses. We will also perform oral challenge assays (with Listeria in the case of LLO vaccination or V. cholerae (in the case of cholera toxin fragment vaccination). Research questions: We will test the hypothesis that enhancing L. lactis survival in the host GI tract will improve the ability of this vector to deliver vaccine antigens. 3. Research Methodology Genetic manipulation of L. lactis: We will utilise cloning of genes into the shuttle plasmids pNZ44 and pNZ8048. The bilE gene has already been cloned into pNZ8048 (Watson et al, 2008). We will utilise high-­‐fidelity Taq polymerase to amplify DNA encoding specific antigenic epitopes (tetanus toxoid fragment, ovalbumin, listeriolysin O fragment, cholera toxin fragment) for subsequent cloning. Vaccination studies: Balb/C mice or C57Bl/6j mice will be used for vaccination studies. Mice will be orally dosed with BilE positive or negative vaccine strains using defined vaccination protocols. Sensitive quantitative real-­‐time PCR will be used for estimating numbers of live L. lactis in mouse faeces during vaccination. Immunity assays: Levels of immunity generated by vaccination will be determined by ELISPOT, ELISA (for levels of specific antibody) and flow cytometry (for measures of cell proliferation, induction of MHC and intracellular cytokine). Challenge studies: Mice vaccinated with L. lactis strains expressing listeriolysin O will be orally challenged with murinized virulent L. monocytogenes. Pregnant mice will be vaccinated with L. lactis expressing cholera toxin fragment and pups will be challenged by wild-­‐type V. cholerae (see Price et al., PLoS One. 2013). 4.
Work Plan Chapter 1: Influence of bile tolerance upon the efficacy of live L. lactis vaccine vectors. Sep 2014 to September 2015 Creation of plasmids expressing BilE in combination with tetanus toxoid (TTD) and ovalbumin (Ova) epitopes and analysis in murine oral vaccination model. Chapter 2: Design of a L. lactis-­‐based live cholera vaccine. June 2015 to September 2016 Creation of plasmids expressing BilE with portions of the cholera toxin B subunit (CTB). Oral vaccination of pregnant mice. Challenge studies with wild-­‐type V. cholerae in neonates (Price et al., 2013). Book of Sample Projects Page 53 CIT Rísam PhD Scholarship Programme 2014 Chapter 3: Design of a L. lactis-­‐based live Listeria vaccine. June 2016 to September 2017. Creation of plasmids expressing BilE with portions of the Listeriolysin O toxin (LLO). We will use the enhanced bile tolerant strain of L. lactis to orally vaccinate mice and challenge with murinized L. monocytogenes (Monk et al., 2010). Chapter 4: Insertional inactivation of thyA with bilE in L. lactis to provide a biologically-­‐contained safe vaccine vector. June 2017 to August 2018. To overcome concerns about using transferrable plasmids we will create a ‘biologically contained’ vaccine strain through double homologous recombination with the bilE gene. 5. Ethical issues All animal experimentation will be conducted using the APC’s preclinical trial platform. Ethical approval for which has been obtained from UCC’s ethical review panel. 6. External Collaboration/Other Institutions The project will carried out in collaboration with Dr Cormac Gahan of the Alimentary Pharmabiotic Centre at UCC. Given that CIT is a partner instutue of the APC and that Sleator is an APC Funded Investigator, all of the physical and intellectual infrastructure of the APC are available to the student, including the many platform technologies and associated expertise. This will be a significant advantage to the student and the project. References: (Price et al., 2013, Watson et al., 2008) PRICE, J. V., JARRELL, J. A., FURMAN, D., KATTAH, N. H., NEWELL, E., DEKKER, C. L., DAVIS, M. M. & UTZ, P. J. (2013) Characterization of influenza vaccine immunogenicity using influenza antigen microarrays. PLoS One, 8, e64555. WATSON, D., SLEATOR, R. D., HILL, C. & GAHAN, C. G. (2008) Enhancing bile tolerance improves survival and persistence of Bifidobacterium and Lactococcus in the murine gastrointestinal tract. BMC Microbiol, 8, 176. Book of Sample Projects Page 54 CIT Rísam PhD Scholarship Programme 2014 Title of project: Understanding bacterial growth in tumours – towards an effective tumour-­‐targeting therapeutic delivery system Name of Principal Supervisor: Dr Roy Sleator Brief Summary of Research Interests: My research is focused on convergent technologies; specifically the application of bioinformatics and biotechnology for improved clinical outcomes. These are core objectives of BioExplore; a central pillar of CIT’s research infrastructure. CIT Department: Email: Biological Sciences roy.sleator@cit.ie Discipline Area by Frascati Classification: Telephone: 021 4335405 3.4 Medical Biotechnology 1. Abstract (250 words) Cancer is the most common cause of death in developed countries. Anti-­‐cancer therapy faces major challenges, particularly in terms of the specificity of treatment. The ideal anti-­‐
cancer therapy would selectively eradicate tumours whilst minimizing the side effects to normal tissue. Bacteria represent attractive therapeutic delivery vectors, since they are naturally capable of homing to tumours when systemically administered, resulting in high levels of replication locally. The Sleator lab has shown that Listeria monocytogenes represents a highly effective tumour targeting vector that is capable of therapeutic gene delivery to tumours resulting in a reduction in tumour size. Other groups have demonstrated the safety and efficacy of L. monocytogenes in human clinical trials in patients with cancer indicating that this bacterium has significant potential for translation into the clinic. However, to improve safety and efficacy it is necessary to engineer L. monocytogenes strains to ensure effective growth in tumours whilst restricting replication in normal tissues. To address this issue we will analyse a signature-­‐tagged mutagenesis bank of L. monocytogenes for mutants which grow in the relatively nutrient-­‐rich tumour micro-­‐
environment but demonstrate limited systemic growth. We will also analyse a number of auxotrophic mutants generated in a parallel study for the same attributes. The work will be the first to systematically analyse the nature of bacterial growth in the unique tumour environment and is expected to lead to the development of novel engineered strains with tumour-­‐targeting potential. 2.
Research Context and Contribution to the Research Field Oral multivalent vaccines that protect against a variety of pathogens remain a desirable and realistic goal. A live bacterial vector would be easy to produce using existing biotechnological capacities (batch growth of bacteria) and is easily administered without the need for medical personnel. Unlike the use of attenuated pathogens as delivery agents, L. lactis is extremely safe and can be readily manipulated at the genetic level. Book of Sample Projects Page 55 CIT Rísam PhD Scholarship Programme 2014 We propose to build upon existing research to examine the hypothesis that enhancing survival of L. lactis in the gut will enhance its capacity to act as a vaccine delivery vector. Clearly Dr. Sleator’s group has the capacity and knowledge to bring this work forward (see Pubmed for relevant publications in Vaccine, Human Vaccines & Immunotherapy and J Med Microbiology). Not only will this make a new contribution to knowledge but we believe that this will lead to patentable technology for further exploitation. Objectives Aims: The aim of this work is to understand the molecular basis of bacterial growth in tumours and to identify tumour-­‐specific mutants of L. monocytogenes with potential for future therapeutic use in patients with cancer. Objectives: We will screen a signature-­‐tagged mutagenesis (STM) bank of L. monocytogenes using a tumour-­‐bearing mouse model. The STM approach allows the detection of 96 individually tagged mutants in a complex environment and will permit the detection of mutants which grow in the tumour but fail to replicate in the spleen and liver. This will yield important and novel information on the tumour microenvironment and how the bacterium grows in this environment. Research Question: Many bacterial species are capable of growth in tumours. This has led to significant research to determine whether bacteria can act to specifically target tumours for therapeutic use (drug or DNA delivery). Very little is known about why bacteria grow so well in the tumour environment but it is likely that hypoxia, localised immune-­‐suppression and nutrient release (through necrosis) may all play a role. We aim to determine which L. monocytogenes gene systems are important for bacterial growth in the tumour environment. We will utilise this information to develop a potential gene/medicine delivery vector based upon engineered L. monocytogenes which preferentially grows within the tumour microenvironment. 3.
Research Methodology Task 1 Screening of a Signature Tagged Mutagenesis (STM) bank in tumour-­‐bearing mice. A STM bank has already been created in a murinized L. monocytogenes background, this system allows the individual tagging of mutants so that they can be followed in groups of 96 during murine infection. We will inoculate each pool of 96 mutants into immunocompetent Balb/c mice bearing CT26 solid tumours on the flank of the animal. After a period of 4 days we will harvest internal organs and tumours and identify mutants that are missing from spleens and livers but present in tumours (using a PCR approach). Using this approach we predict that it will be possible to screen 30 pools of mutants (2880 mutants in total). The site of transposon insertion and thus gene identification is achieved by PCR and sequencing. Task 2 Parallel analysis of known auxotrophic mutants. The host lab has a number of auxotrophic mutants that are compromised in nutrient acquisition (purine, pyrimidine and Book of Sample Projects Page 56 CIT Rísam PhD Scholarship Programme 2014 amino acid auxotrophy). We predict that some of these mutants may be compromised in systemic growth but may still survive in the tumour environment (given the high levels of nutrient availability in solid tumours). We will therefore test these mutants for their ability to colonise CT26 tumours and relative ability to survive in spleens and livers of tumor bearing mice. Task 3 Recreation of clean deletion mutants in L. monocytogenes. We will make defined deletion mutants in wild-­‐type L. monocytogenes (both wild-­‐type and murinised (murine optimised) backgrounds). This will be done using standard techniques available in Dr. Sleator’s lab (using double-­‐crossover of pKSV7 carrying the truncated version of the gene). Task 4 Analysis of deletion mutants in tumour bearing mouse models. We will create bioluminescent variants of our deletion mutants (using plasmid pHELP-­‐Lux) and analyse growth of our potential tumour-­‐targeting vectors in a variety of tumour models (incl CT26 and 4T1 tumours and human xenografts in nu/nu mice). Book of Sample Projects Page 57 CIT Rísam PhD Scholarship Programme 2014 4.
Work Plan Task 1 Screening of a Signature Tagged Mutagenesis (STM) bank in tumour-­‐bearing mice. This is a key task in the project and we predict that this will take approximately one year to complete. Initial experiments will investigate dose and infection time in CT26 Balb/c mice in order to optimise parameters for the subsequent screening of the STM banks. Task 2 Parallel analysis of known auxotrophic mutants. We predict that this will take 9 months and will be run in parallel with Task 1 (see Gantt chart). Task 3 Recreation of clean deletion mutants in L. monocytogenes. This will be necessary in Book of Sample Projects Page 58 CIT Rísam PhD Scholarship Programme 2014 order to prove a link between mutation site and the in vivo effect and to prevent false positives due to downstream effects of the transposon. We will start to create clean deletion mutants as soon as information starts to emerge from the STM screen. It is estimated that this task will take approximately 9 months. Task 4 Analysis of deletion mutants in tumour bearing mouse models. It is relatively straightforward to create lux-­‐tagged varieties of our clean mutants using the plasmid pHELP-­‐
Lux. These will be used to study colonisation dynamics in mouse models with solid tumours using available bioluminescence imaging platforms (Caliper IVIS 100 and IVIS Lumina). Indeed, luc-­‐labelled tumour cell lines (CT26, 4T1) are available and will permit dual labelling of bacteria and tumour cells in order to provide precise localisation of bacteria within the tumour microenvironment. 5. Ethical issues All animal experimentation will be conducted using the APC’s preclinical trial platform. Ethical approval for which has been obtained from UCC’s ethical review panel. 6. External Collaboration/Other Institutions The project will carried out in collaboration with Dr Cormac Gahan of the Alimentary Pharmabiotic Centre at UCC. Given that CIT is a partner instutue of the APC and that Sleator is an APC Funded Investigator, all of the physical and intellectual infrastructure of the APC are available to the student, including the many platform technologies and associated expertise. This will be a significant advantage to the student and the project. Book of Sample Projects Page 59 CIT Rísam PhD Scholarship Programme 2014 Title of project: Tuberculosis and other mycobacterial identification using MALDI tof Mass Spectrometry: revolutionising identification, treatment and epidemiology of this major group of pathogens Name of Principal Supervisor: Drs Brigid Lucey & Jim O’Mahony Brief Summary of Research Interests: Diagnostic microbiology and new technologies for the identification and epidemiological characterisation of Mycobacterium spp., including M. tuberculosis: contribution to human health. CIT Department: Email: Biological Sciences Brigid.lucey@cit.ie; Jim.omahony@cit.ie Telephone: 021 433 5484 Discipline Area by Frascati Classification: Biological Sciences 1.6 (Microbiology) 1. Abstract (250 words) Between four and five hundred new cases of TB are diagnosed in Ireland every year; some are drug resistant. However, there are many other mycobacterial species that cause human infections also. The proposed project will include a comparison of the current gold-­‐standard method used for Mycobacterium identification in the Cork University Hospital, (namely the HAIN method), with the novel Matrix-­‐Assisted Laser Desorption Ionisation-­‐Time of Flight Mass Spectrometry (MALDI-­‐TOF). The first objective is to assess the feasibility of replacing the currently-­‐used method with a faster and more efficient system in terms of sensitivity, specificity, cost, and turn-­‐around time. This will be facilitated by examining a bank of >100 Mycobacterium strains of diverse species, (comprising Mycobacterium tuberculosis complex (MTC) and also comprising Mycobacterium Other Than Tuberculosis (MOTT)), all previously isolated from clinically ill patients. Furthermore however, the mass-­‐spectra of certain Mycobacterium species will be studied to ascertain the potential of the MALDI-­‐TOF as a predictor of antimicrobial therapy resistance; thereby allowing the potential for an efficacious drug regime to be employed to improve the outcome for the patient, along with a reduction in hospital stay. We also propose to develop this component of the project into a more substantial research aim which will determine whether the optimised MALDI-­‐tof system will provide accurate and efficient epidemiological data to help ascertain when outbreaks and sporadic infections are occurring. Finally, the efficacy of the MALDI tof for the detection of mycobacteria from liquid culture without the need for traditionally lengthy culturing times will be determined. Research Context and Contribution to the Research Field Currently a number of testing methodologies are employed in the screening and identification of TB; the frontline test is usually the Tuberculin skin test (otherwise known as Mantoux testing), which if the individual has been exposed to or has an active TB infection will result in a positive result, characterised by subcutaneous oedema or swelling, (CDC, 2013). The primary screening test used routinely in the laboratory is acid fast staining; Ziehl-­‐Neelsen staining, which allows the medical scientist/researcher to observe dark red/purple staining under a light microscope where acid fast Book of Sample Projects Page 60 CIT Rísam PhD Scholarship Programme 2014 bacteria are present such as Mycobacterium species. This is a useful screening test but is not as sensitive as the molecular methods described below or the immune based blood test available. The latter, namely interferon-­‐gamma release assays are also carried out which test the individual’s reactivity against TB bacteria (CDC, 2013), of which one such test is the QuantiFeron-­‐TB Gold IN-­‐tube test. A disadvantage of this testing is that it does not distinguish between latent infection and active infection; another is high cost. The current gold standard identification of Mycobacterium species is the Genotype CM (HAIN system) in CUH. St. James’s hospital in Dublin (the reference laboratory for TB in Ireland) also utilises the same system as that in CUH. The advantages of the HAIN system over previous systems such as Speed-­‐Oligo identification, with respect to sensitivity, specificity, along with faster turn-­‐around times have been published (World Health Organisation, 2012; O'Donnell, et al., 2012)The disadvantages include high cost, labour intensity of method, and the still relatively slow turn-­‐around times (approximately 7-­‐10 days for molecular identification in St. James’ hospital following culture positivity). Mycobacterium species can only be tested on these systems after proving to be positive on a culture based instrument known as the BacT alert, which by the utilisation of a culture bottle with a base that changes colour in the presence of respiration, the instrument then alerts the scientist to the presence of a microorganism. This liquid-­‐based continuous monitoring system is used both in St. James’s Hospital and in CUH for culturing clinical samples suspected of being infected with Mycobacterium spp. The microorganism must then be subcultured on a solid medium (typically on Löwenstein-­‐Jensen media for Mycobacterium species) before it can then be analysed using the HAIN system. Culturing on the solid-­‐phase medium is likely to take a number of weeks before there is enough growth for the HAIN system to be used for identification. Other systems that have been published that may have efficacy include PCR based techniques including a nano-­‐gold assay in conjunction with spectrophotometry (Hussain, et al., 2013), and the combination of a novel mycobacterial growth indicator tube with conventional PCR (Perez-­‐Porcana, et al., 2012). The downside of nucleic acid amplification techniques is that they are expensive and time consuming, and usually require batching of tests due to financial limitations, reducing the perceived time savings that should occur. The current study should result in significant reduction in the time to confirm a case of TB as per the guidelines as per S.I. No. 452/2011 infectious diseases (amendment) regulations of 2011. This study should result in increased confirmed cases versus probable cases and ergo more detailed confirmed cases being reported to the HSPC annually, enabling better epidemiological data. Studies surrounding MTC and MOTT in Ireland have been stunted in recent years due to a number of factors, including the lack of Category 3 containment facilities in the state, many of which are confined to medical laboratory settings. The problem associated with this is that in recent years, primarily due to the economic crisis; the embargo on employment and reduced staff and supplies budgets in the public sector it has been very difficult for medical scientists to complete research with in the facilities because of their diagnostic workload. This has resulted in a dearth of epidemiological studies The most recent epidemiological typing (spogliotyping) study was completed by Prof. Michael Prentice et al. between 2004 and 2006 for the South-­‐west of the country for a subset of mycobacterial species only (Ojo, et al., 2010). The current study is well placed, having the advantage of the use of the containment facilities of the Cork University Hospital Microbiology Department along with the close collaborative relationship that already exists between the Microbiology Book of Sample Projects Page 61 CIT Rísam PhD Scholarship Programme 2014 Department with the Biological Sciences Department at CIT, as evidenced by the already strong biomedical science research link and strong publication record. The rates of Multi-­‐Drug Resistant TB (MDR-­‐TB) and Extensively-­‐Drug Resistant TB (XDR-­‐TB) are on the increase worldwide and are of great concern to the international and national public health authorities. Currently where MDR-­‐TB cases are identified, the samples must be sent to reference laboratories abroad for further sensitivities, the MALDI-­‐tof may offer the opportunity to tailor an antibiotic therapy, thereby eliminating the need for improper antibiotic therapy and thus result in the cessation of sending MDR-­‐TB samples abroad for further sensitivities. The epidemiological aspect of the study will also explore the association between certain strains of various subspecies of MOTT/MTC and certain conditions. For example the link between cystic fibrosis patients and Mycobacterium abscessus has been well documented. M.abscessus has been identified in sputum samples in cystic fibrosis patients in 2-­‐4% of patients (Olivier, et al., 2003), and may be associated with poorer prognosis. The study will investigate epidemiological relationships that may exist between strains of this species among a group of patients. The MALDI-­‐Tof analyser has been used in research since the 1980s following its earliest description by Karas et al., in 1985 (Karas, et al., 1985)but it has been only recently been hailed as a reliable, efficient and promising instrument with regard to identification of clinically significant infectious microorganisms, and in some cases the resistance/sensitivity patterns of these organisms. Furthermore, its potential use as a rapid detection method for MTC has not been widely explored, as exemplified in Ireland. The prospect of being able to identify the Mycobacterium species following positive detection on the BacT system directly, will allow for more rapid diagnosis which will be significantly more advantageous than having to wait for growth on solid medium (the use of liquid media is recommended by the WHO for culture and drug sensitivities (WHO, 2007)). The proposed research will attempt to provide the rapid identification of an index case in any community-­‐based outbreak, and also in the case of in-­‐patients, to reduce hospital in-­‐patient stay (including reduction of costs associated with isolation of the patient). This will be expected to result in the provision of therapy that is more rapidly prescribed and administered The MALDI-­‐tof has also proven to be efficacious in the identification of other microorganisms and has begun to be used in the clinical laboratory as a diagnostic tool in some centres. Due to the restrictions aforementioned, the clinical laboratories have not utilised the instrument to its full potential as the staff only have the time to validate the instrument according to the conditions that are required by various accreditation bodies and to date have not have the opportunity to fully investigate the diagnostic robustness of the MALDI-­‐tof with regard to diagnostic research. Objectives •
•
To compare the MALDI-­‐Tof method of MTC and MOTT identification against the current gold standard method in use in the CUH, namely the HAIN method, and using no fewer than 100 Mycobacterium species and no fewer than 100 non-­‐Mycobacterium species To validate the MALDI-­‐tof method for identification of clinical Mycobacterium species Book of Sample Projects Page 62 CIT Rísam PhD Scholarship Programme 2014 2.
•
To test the efficacy of the MALDI-­‐tof system for the identification of antimicrobial resistance mechanisms among mycobacteria •
To ascertain the validity of using mass spectra for epidemiological analysis in the case of detecting and monitoring outbreaks •
To ascertain the efficacy of the MALDI-­‐tof at typing MTC and MOTT versus established methods Research Methodology Matrix-­‐assisted laser desorption ionization–time of flight mass spectrometry (MALDI-­‐tof) is a very effective method of measuring the mass of a protein. All bacteria have different proteins on the surface of their cells. These proteins each have their own specific mass which corresponds to a spectral fingerprint. This spectral fingerprint can be traced back to the specific organism with which the protein is associated. The method is relatively simple, rapid, and associated with significantly lower consumable costs than traditional microbiological or molecular identification methods (van Belkum et al., 2012). Many studies have shown how the use of a MALDI-­‐tof for routine diagnosis in a clinical setting has reduced the time to identification (TTI) and reduced consumable costs (Lotz, et al., 2010).As this is a novel method of diagnosis with a very high initial capital investment cost, there have been very few studies looking at the use of the MALDI-­‐tof to identify Mycobacterium spp. There have however been very positive results on the reduction of costs and speed of identification elsewhere (Lotz, et al., 2010).The opportunity now exists to apply this technology in a very practical and applied setting to a clinically significant bacterial pathogen: The genus Mycobacterium consists of approximately 150 species, many of which are clinically significant both to humans and animals. Multi Drug Resistance is increasing for many of these species, and treatment regimens also vary between species; for these reasons that it is extremely important to make the correct diagnosis quickly and correctly. Inappropriate treatments increase morbidity and mortality among patients and can increase the risk of drug resistance developing. Traditionally, mycobacteria are notoriously difficult to detect and characterise. Current approaches mostly focus on using the HAIN method of identification which although more useful than previous methods (O'Donnell, et al., 2012) is relatively labour intensive and requires expensive reagents. The incorporation of a new, cheaper more discriminatory identification method for mycobacteria will be hugely advantageous for this high throughput clinical diagnostic laboratory. To summarise, the research methodology will allow the following to be undertaken: •
Comparison of the current system in use in the CUH for Mycobacterium identification: the HAIN system with the generation of mass spectra by the MALDI-­‐tof instrument. •
Validation of the MALDI-­‐tof instrument for the identification of clinical isolates of Mycobacterium species. Book of Sample Projects Page 63 CIT Rísam PhD Scholarship Programme 2014 3.
•
Novel studies including the efficacy of the instrument for detecting Mycobacterium that have flagged as positive on the BacT alert system without solid culture (major time reduction) and the effectiveness of the instrument at detecting resistance mechanisms with the comparison of mass spectra against known resistant organisms. •
Epidemiological studies of MTC and MOTT in the region, to determine the efficacy of the MALDI-­‐Tof for determining strain diversity within a given species. •
To determine the potential wider clinical application of the instrument. Work Plan Description of Tasks: Time Frame (Yearly) Year 1 Validation of mycobacterial inactivation methods for infection control Cultivation of Mycobacterium tuberculosis complex (MTB) and Mycobacteria Other Than Tuberculosis (MOTT) (n=>100) Validation of MALDI-­‐ tof including: Comparison between HAIN (gold standard identification system) and the MALDI-­‐Tof system at Cork University Hospital (CUH) Analysis of microbiological and mass spectra findings in relation to clinical findings Antibiotic resistance profiling comparison with MALDI-­‐Tof mass spectra Molecular typing for epidemiological Book of Sample Projects Year 2 Year 3 Year 4 Page 64 CIT Rísam PhD Scholarship Programme 2014 analysis (M.absessus) Determining Efficacy of Inula helenium as an antibiotic agent against MDR/XDR-­‐
TB Ed4Life Structured PhD coursework Dissemination Project Management Interim and final report Present the research work plan, outlining the main research tasks and timing. 4. Ethical issues Ethical approval has been sought and granted in advance at Cork University Hospital for this research proposal. 5. External Collaboration/Other Institutions Dr GD Corcoran, Consultant Microbiologist & and Mr Brendan O’Reilly, FAMLS, MBA, Chief Medical Scientist, Department of Medical Microbiology, Cork University Hospital. References: CDC, 2013. Testing for TB infection. [Online] Available at: www.cdc.gov/tb/topic.testing Hussain, M., Samir, T. & Azzay, H., 2013. Unmodified gold nanoparticles for direct and rapid detection of Mycobacterium tuberculosis complex. Clinical Biochemistry, 46(7-­‐8), pp. 633-­‐637. Karas, M., Bachmann, D. & Hillenkamp, F., 1985. Influence of the wavelength in high-­‐irradiance ultraviolet desorption mass spectrometry of organic molecules. Annals of Chemistry, 57(14). Lotz, A. et al., 2010. Rapid Identification of Mycobacterial Whole Cells in Solid and Liquid Culture Media by Matrix-­‐Assisted Laser Desorption Ionization-­‐Time of Flight Mass Spectrometry. Journal of Clinical Microbiology, 48(12). O'Donnell, N., Corcoran, D., Lucey, B. & Barrett, A., 2012. Molecular-­‐based mycobacterial identification in a clinical laboratory setting: a comparison of two methods. British Journal of Biomedical Science, 69(4). Book of Sample Projects Page 65 CIT Rísam PhD Scholarship Programme 2014 Ojo, O. et al., 2010. Molecular epidemiology of Mycobacterium tuberculosis clinical isolates in Southwest Ireland. Infection, genetics and evolution: Journal of molecular epidemiology and evolutionary genetics in infectious diseases, 10(7), pp. 1110-­‐1116. Olivier, K. et al., 2003. Nontuberculosis Mycobacteria. Repiratory and Critical Care Medicine, 167(8), pp. 828-­‐834. Perez-­‐Porcana, T. et al., 2012. Evaluation of New Strategies for the Diagnosis of Tuberlosis Among Pediatric Contacts of Tuberculosis Patients. The Pediatric Infectious Disease Journal, 31(9), pp. e141-­‐
e146. Van Belkum, A., Welker, M., Erhard, M. & Chatellier, S., 2012. Biomedical Mass Spectrometry in Today's and Tomorrow's Clinical Laboratories. Journal of Clinical Microbiology, 50(5). WHO, 2007. TB diagnostics and laboratory strengthening-­‐ WHO polocy. [Online] Available at: www.who.int/tb/laboratory/policy_liquid_medium_for_culture_dst/en/ World Health Organisation, 2012. Tuberculosis: Frequently asked questions XDR-­‐TB. [Online] Available at: www.who.int/tb/challenges/xdr/faqs/en Book of Sample Projects Page 66 CIT Rísam PhD Scholarship Programme 2014 Working Title of project: Determination of the prevalence of Yersinia spp. among patients presenting with acute gastroenteritis in a hospital setting Name of Principal Supervisors: Drs Brigid Lucey & Roy Sleator Brief Summary of Research Interests: Molecular diagnostics: towards advanced, novel identification of bacterial causes of gastroenteritis CIT Department: Email: Biological Sciences Brigid.lucey@cit.ie; Roy.sleator@cit.ie; Telephone: Discipline Area by Frascati Classification: 021 433 5484 Biological Sciences 1.6 (Microbiology) 1. Abstract (250 words) The true burden of gastroenteritis in Ireland is unknown, and in >80% of cases where a faeces sample is tested from an acutely ill patient, the causative agent remains unknown, because detection methods have been designed only for the detection of the organisms perceived to be the most common causes of infection. This has a negative impact on infection control and appropriate patient treatment. However, the advent of novel molecular methods of detection provides a means to expand our knowledge in this field. Foodborne Yersinia enterocolitica, and Y. pseudotuberculosis have been associated with gastroenteritis, pseudoappendicitis and extraintestinal diseases, and this is a notifiable disease in Ireland. Traditional culture methods have very limited sensitivity, are rarely used at all, and there are no reports of molecular detection in Ireland, currently. Yersinia enteritis outbreaks have been detected in many European countries, however, and these organisms are in the top four listed by the CDC. This project will screen 3,000 faeces samples at Cork University Hospital for the presence of Yersinia, in conjunction with Serosep (an Irish molecular diagnostics company) which is currently developing a novel commercial molecular detection system based on its EntericBio® platform. Prospective screening will be conducted in parallel using the commercial system, an in-­‐house molecular detection method, and, concentrated retrospective culture in the case where molecular detection of Yersinia is first indicated. The expected outcomes from this project are anticipated to include previously unavailable data on the detection, characterisation and epidemiology on Yersinia spp. from patients with acute gastroenteritis. 2. Research Context and Contribution to the Research Field • Central questions: • What is the prevalence of Yersinia gastroenteritis in Ireland among acutely ill patients? • What is the spectrum of clinical gastroenteritis that is caused by this group of organisms? • Should Yersinia be tested for routinely in patients with gastroenteritis? • Do some strains cause more severe disease than others? Book of Sample Projects Page 67 CIT Rísam PhD Scholarship Programme 2014 The difficulties with determining the prevalence of enteric pathogens other than the few that have been already well-­‐characterised is that all conventional systems for their detection have tended to be relatively insensitive. However, the advent of molecular technology for in vitro diagnostics revolutionises the sensitive detection of genes specific for the target of interest. This has allowed our group to conduct retrospective culture for the pathogen of interest, whereby sole focus may be made on the subset of samples that is flagged to be positive. In some cases, this retrospective culturing after the molecular detection of the pathogen has necessitated the development of novel culture media, as exemplified by this research group, after its discovery of the presence and relevance of the novel campylobacter C. ureolyticus in cases of acute gastroenteritis. This research will help to pave the way further for the elucidation of the causes of acute gastroenteritis in Ireland and elsewhere. Yersinia has been shown to be capable of causing severe infection, where it has been detected successfully, previously. 3. Objectives • The aims of this research are to: • Validate a novel EntericBio real time PCR method for the molecular detection of multiple bacterial enteric pathogens including Yersinia spp. from acutely ill patients, by comparison with an expanded gold standard method to include a combination of culture and alternative molecular-­‐based detection. • Speciate detected Yersinia strains, along with determination of antibiotic resistance, virulence characteristics and strain relatedness. • Link microbiological and molecular findings to clinical disease severity. • Provide information that will help to inform patient healthcare in Ireland and elsewhere. • Disseminate these findings in peer-­‐reviewed publications. 4. Research Methodology • Conduct a prospective study of the presence of Y. enterocolitica and Y. pseudotuberculosis in samples of patient faeces using a combination of real time PCR methods and enrichment culture at Cork University Hospital. • Testing will be conducted on all faeces samples received by Microbiology, CUH on a sequential basis to number not fewer than 3,000 samples from the start date of the project. • Microbiological techniques to be used will include real time PCR methods, which will combine a commercial system (Serosep Ltd.), and an in-­‐house method which will be developed from available sequence data. A culture method will be validated to maximise culture sensitivity, and that will include broth enrichment and subculture to selective agar. • A bioinformatics-­‐based approach to identify molecular bio-­‐markers which will definitively identify whether the pathogen, if present, is the primary cause of the infection. This will be achieved following genome sequence analysis of the most prevalent Yersinia strains linked with infection. Book of Sample Projects Page 68 CIT Rísam PhD Scholarship Programme 2014 5.
6.
7.
Work Plan Ethical issues This CIT-­‐based research will be conducted on anonymised patient samples, and subjected to the same ethical rigour as other collaborative research undertaken by this research group with the Department of Microbiology at Cork University Hospital. External Collaboration/Other Institutions Medical and Scientific personnel at the Department of Medical Microbiology, Cork University Hospital. References Comparison of the EntericBio multiplex PCR system with routine culture for detection of bacterial enteric pathogens. O’Leary J, Corcoran D, Lucey B. J Clin Microbiol. 2009; 47(11):3449-­‐53. Emerging dynamics of human campylobacteriosis in Southern Ireland Bullman S, Corcoran D, O’Leary J, O’Hare D, Lucey B Sleator RD FEMS Immunol Med Microbiol. 2011; 63:248-­‐253 Book of Sample Projects Page 69 CIT Rísam PhD Scholarship Programme 2014 Molecular diagnostics: the changing culture of medical microbiology. Bullman S, Lucey B, Sleator RD. Bioeng Bugs. 2012; 3 :1-­‐7. Molecular-­‐based detection of non-­‐culturable and emerging campylobacteria in patients presenting with gastroenteritis. Bullman S, O'Leary J, Corcoran D, Sleator RD, Lucey B. Epidemiol Infect. 2012; 140: 684-­‐688. Koziel M, Lucey B, Bullman S, Corcoran GD, Sleator RD. Cow’s milk: A potential reservoir for the emerging gastrointestinal pathogen Campylobacter ureolyticus. Gut Pathogens 2012; 4:4-­‐14. Koziel M., Corcoran GD, O’Callaghan I., Sleator RD, Lucey B. Validation of the EntericBio Panel II multiplex polymerase chain reaction system for detection of Campylobacter spp., Salmonella spp., Shigella spp., and verotoxigenic E. coli for use in a clinical diagnostic setting. Diagn Microbiol Infect Dis. 2013; 75:46-­‐9. Bullman S, Lucid A, Corcoran D, Sleator RD, Lucey B. Genomic Investigation into Strain Heterogeneity and Pathogenic Potential of the Emerging Gastrointestinal Pathogen Campylobacter ureolyticus. PLoS One. 2013;8(8):e71515. O’Doherty A, Koziel M, de Barra L, Corcoran GD, Bullman S, Lucey B, Sleator R. Development of Nalidixic acid Amphotericin B Vancomycin (NAV) Medium for the isolation of Campylobacter ureolyticus from the stools of patients presenting with acute gastroenteritis. Br J Biomed Sc. 2014; 71 (1): 6-­‐12. Book of Sample Projects Page 70 CIT Rísam PhD Scholarship Programme 2014 Biomedical Engineering Title of project: VI sports training aid Name of Principal Supervisor: Keith Bryan Brief Summary of Research Interests: Biomedical Devices, Sports Equipment and Mechanics of Humans motion. CIT Department: Email: Mechanical, Biomedical & Manufacturing Engineering keith.bryan@cit.ie Discipline Area by Frascati Classification: Telephone: 021 4335423 2.6 Medical engineering 1. Abstract (250 words) The following research proposal is for the development of a system to allow Visually Impaired (VI) athletes train independently on an outdoor running track. Currently, any VI athlete requires the assistance of a third party to guide the VI athlete around a track or other surface, which is done by joining both users via an elasticated wrist strap. Communication to the VI athlete is done orally by the assistant which poses numerous safety risks to both parties, including uneven terrain, oncoming vehicles or pedestrians. The proposed system would allow tracking of the VI athlete on the running track. The system would position the athlete correctly in one of the eight running lanes and alert the user if they are moving out of the correct position. Research into tracking systems, communication systems, collision prevention and other safety mechanisms to position the VI athlete whilst running around the track would form the core of the research undertaken. The resultant device produced would allow the VI athlete train independently on an outdoor track, whilst optimising their safety. The implications for VI persons would be increased safety when performing aerobic exercise. Cardiovascular fitness of VI persons would also be increased significantly as a result of the device due to improved independence with decreased reliance on other non-­‐visually impaired people. 2. Research Context and Contribution to the Research Field Currently, options for VI athletes in regards to cardiovascular training are very limited. Many sports equipment in gyms utilize braille communication systems, however, in regards to outdoor aerobic exercise, all VI athletes rely on the help of an assistant attached to their wrist who acts as their “eyes” in determining the appropriate path to run on and alerts the VI athlete of any dangers. Paralympians who would be regarded as the elite of disabled athletes, also require an assistant if they are visually impaired. The problem with this is that it can be quite difficult to find an Book of Sample Projects Page 71 CIT Rísam PhD Scholarship Programme 2014 assistant who is capable of exercising at the VI athletes level, and who is willing to dedicate their time and resources to helping them do so. The research undertaken will involve three main areas. Firstly, the method used to track the VI athletes position around the running track and how to signal them that they need to move their position to keep in the correct position. This research will involve a detailed understanding of various tracking systems such as GPS, proximity sensors and other methods to track position. Research into obstacle detection for other track users and other hazards will also be required. A full understanding of the different methods to enable obstacle detection, and a critical evaluation of these methods will also be required. Finally, research into communication methods for the VI athlete must also be completed. Currently, cardiovascular fitness amongst visually impaired people is significantly poorer than comparable people with full vision. Lieberman and McHugh (2001) [1], studied the fitness of children who are visually impaired in comparison to children who have full vision, and found that “fewer than 20% of the children with visual impairments passed at least four items on the Fitness gram, compared to 48%-­‐70% of the sighted children”. The tests carried out on the children covered four main areas; cardiovascular endurance, flexibility, muscular strength and body composition. The minimum standards for this test were determined by the Cooper Institute of Aerobics Research, CIAR, 1994 [2]. James H. Rimmer (2005) [3], issued a report that examined the absence of people with disabilities from public fitness and recreational facilities. Rimmer found that, “most manufacturers of exercise equipment do not consider in their design specifications how to make their equipment accessible for people with physical, cognitive, and sensory disabilities”. In terms of the health implication of this Rimmer also noted that, “inaccessible equipment is a major problem in terms of participation in fitness-­‐enhancing activities for people with disabilities”. 3.
Objectives •
•
•
•
4.
Research the current methods and systems (if any) in place to allow VI athletes perform cardiovascular exercise. Research into current systems in use in other sports for VI athletes which could be further developed for use in athletics. Develop a safe, reliable and novel method of tracking the VI athlete as the move around the running track, preventing him/her from impact from other athletes or from moving out of their running lane. Develop a communication system to alert the VI athlete of hazards in their vicinity. The communication system should also be able to alert the user when they are approaching the bends on a running track. Research Methodology Book of Sample Projects Page 72 CIT Rísam PhD Scholarship Programme 2014 It is envisaged that the initial period of the PhD would involve research into existing models and systems used to track and aid visually impaired athletes during exercise. An extensive knowledge of current systems in use will be required. Liaising with visually impaired athletes and determining their requirements from such a device would also take place. The conceptual part of the PhD will involve an extensive Literature Review on existing technologies in use and how aspects of such technologies could be applied to the project. After an insight into control systems, current technologies, and on completion of the literature review, a full understanding of what will be required in designing and developing the tracking and communication system for a visually impaired athlete will be established. Following on from this research, the research could then progress to the systems research stage. This research stage would initially involve research into current tracking systems such as GPS, Local Tracking and Sensors Equipment. Communication Methods with the Visually Impaired athlete would also need to be investigated. Programming of a system to allow tracking of the athlete whilst on a running track would also need to be developed and optimised. The later part of the PhD will involve the development and optimisation of the prototype produced. 5.
Work Plan Months Title WP 1 0 – 6 Literature Review WP 2 6 -­‐ 12 Increase Knowledge of Communication Systems and Tracking Systems WP 3 6 – 12 Research of Communication Methods and Systems required WP 4 9 – 12 Increase Knowledge of Programming Required to Develop System. WP 5 12 – 15 Production of System and Development of Prototype. Design of Experiments to show systems operates and analysis of its limitations. WP 6 15 – 18 Data Acquisition WP 7 21 – 24 Analysis of Data WP 8 24 – 30 Optimisation of System WP 9 30 – 36 Thesis Writing and Editing 6. Ethical issues An Ethical Framework has been implemented in MEDIC and this will also be applied to this project for all work carried out in the gait lab and running track. In addition, full consideration has been given to the ethical implications of this research proposal. On confirmation of the awarding of the scholarship, a full ethical report and approval will be sought from a research ethical review committee, and will be submitted prior to the commencement of the Scholarship or within three months of the start date. Book of Sample Projects Page 73 CIT Rísam PhD Scholarship Programme 2014 7.
External Collaboration/Other Institutions None at present. 8.
References 1
Lieberman and McHugh (2001) Health Related Fitness of Children who are Visually Impaired 2
Fitness Standards, Cooper Institute of Aerobic Research. 2012 [ONLINE] 3
Available at: http://www.tri-­‐
c.edu/workforce/publicsafety/Documents/Website%20CooperStandard%20BAS%203.22.11.pdf. James Rimmer (2005), The Conspicuous Absence of People with Disabilities in Public Fitness and Recreational Facilities. 2012 [ONLINE] Available at: http://www.uic-­‐chp.org/ARTICLES/Rimmer/Rimmer.AJHP%20Article.2005.pdf. Book of Sample Projects Page 74 CIT Rísam PhD Scholarship Programme 2014 Title of project: agents and sensory agents. Investigation of mesoporous silica materials as drug delivery Name of Principal Investigator: Dr. Aoife Burke, Department of Mechanical, Biomedical and Manufacturing Engineering, CIT (Aoife.Burke@cit.ie) Dr. Hugh O’Donnell, Department of Mechanical, Biomedical and Manufacturing Engineering, CIT (Hugh.ODonnell@cit.ie) Dr. Máire Begley, Department of Biological Sciences, CIT (maire.begley@cit.ie) Dr. Jim O’ Mahony, Department of Biological Sciences, CIT (Jim.OMahony@cit.ie) 1. Abstract (250 words) Mesoporous materials are defined as porous substances with pore diameters between 2 and 50 nm. Since the discovery mesoporous silica materials by the Mobil Corporation in 1992 they have been the centre of a lot of interest within the material science community. This interest is fostered to some extent by their 2-­‐dimensional structures but also due to their expected applications in catalysis, sensing, molecular sieving, templating of nanostructures and in separation and adsorption processes. Mesoporous silica materials also have great potential as drug delivery agents and sensory agents. The advantages of using mesoporous materials for these applications include the ease of synthesis from commercially available reagents, high specific surface areas, controllable pore dimensions and high hydrothermal stability. Mesoporous silica can also be readily functionalised with many ligands to focus on particular drug delivery or extraction of contaminants as required. Further to this magnetic nanoparticles can be embedded into the porous structure for application as sensory materials. Mesoporous silica materials have also been awarded with GRAS (Generally Regarded As Safe) status from the FDA as when these silica materials are ingested they can be broken down by the metabolic system into their natural form of salicylic acid. These characteristics allow mesoporous silica to be employed in a number of commercial areas that include controlled drug delivery and biosensors. The aim of our proposed study is to investigate suitable mesoporous silica materials for drug delivery applications and sensory applications. Mesoporous silica materials will be synthesised and functionalised with further experiments focusing on the drug molecule attachment. The synthesis of magnetic nanoparticles will be subsequently investigated for the potential of attachment within the porous structure. Book of Sample Projects Page 75 CIT Rísam PhD Scholarship Programme 2014 Bioinformatics Title of project: Advancing bioinformatics to meet Biomedical Needs Name of Principal Supervisor: Dr Paul Walsh Brief Summary of Research Interests: Bioinformatics, Machine Learning High Performance Computation CIT Department: Email: Computing paul.walsh@cit.ie Discipline Area by Frascati Classification: Telephone: 021-­‐4335572 1.2 Computer and information sciences 1. Abstract (250 words) The project(s) is driven by the need to urgently address the rapid growth of biomedical data generation for personalised medicine. This is exemplified by the exponential drop in sequencing costs and advances in data capture from biomedical devices, with a single researcher capable of generating Terabytes of data within hoursi. So while the generation of massive biomedical data is continuously becoming easier for researchers, their ability to retrieve information and derive decisions becomes more and more difficult. With the foregoing in mind, the objective of this project(s) is to create a secure, scalable and user-­‐
friendly high performance bioinformatics platform for rapidly executing computationally challenging statistical and bioinformatics methods that address current and future clinical needs in personalized medicine. In essence this will be a fully deployed integrated bioinformatics analysis software platform that provides cloud scalability in a compact in situ hardware architecture providing researchers in clinical settings the tools to enable personalised medicine. The platform will strike a critical balance between statistical power, maximum performance, compute density, energy efficiency, data management, usability and patient privacy. 2.
Research Context and Contribution to the Research Field It is recognised that there currently is a lack of computational infrastructure that is needed to generate, maintain, transfer and analyze large-­‐scale information securely in biomedicine and to integrate ’omics data with other data sets, such as clinical data from patientsii. On data access level, information integration of classic data types with arrays, up to ISO standardization, will be pursued; this addresses the Variety in Big Data. Volume and Veracity on array data will be addressed through high-­‐level querying utilizing parallel, distributed query. 3 .Objectives Summarise the key objectives of the research. The platform will strike a critical balance between statistical power, maximum performance, compute density, energy efficiency, data management, Book of Sample Projects Page 76 CIT Rísam PhD Scholarship Programme 2014 usability and patient privacy. This will be achieved by: 1) Developing operating procedures for the application of these new bioinformatics tools in compliance with standardization guidelines ensuring the safety of products without sacrificing scientific merit or interfering with innovative processes. 2) Engaging with the numerous clinical end users from the beginning of the project to elucidate comprehensive clinical needs so as to improve accessibility and user-­‐friendliness of bioinformatics research. 3) Establishing workflows for integrating data from heterogeneous sources into a common information model suitable for homogeneous retrieval and combination of all data. 4) Deploying an innovative distributed data storage platform offering integrated retrieval on data and metadata through an ISO candidate standard. Parallelization, distributed processing, and integrated external tools will enable this data store to comprehensively query Terabyte-­‐sized objects in < 1 sec. 5) Applying innovative statistical methods for fusion of data from disparate high-­‐throughput sources (sequencing, transcription arrays, clinical data) ensuring a statistical bottleneck in integrated analysis is addressed. 6) Using high performance computing to address computational bottlenecks in the application of complex analyses to large data sets, verified by quantitative metrics (speedup, throughput, power, cost of ownership, ROI) 7) Developing pioneering user interfaces for enabling bioinformatics research among non-­‐specialist users thereby maximising accessibility and utility. 8) Creating data protection, privacy and holistic security mechanisms that inherit and respect the strict directives of the European Commission (including the EU Data Protection Directive 95/46/ECiii and the upcoming General Data Protection Regulation – GDPRiv), ensuring non-­‐repudiation of end-­‐
users, fostering data access control though sophisticated context-­‐aware access policy models, and fortifying data protection against cyber and physical security breaches through the adoption of scalable encrypted database technologies. In meeting the above objectives these projects will make bioinformatics more clinically relevant by facilitating access and use of key high performance tools by non-­‐specialists. Such a platform will represent a step-­‐change in the analysis of big biomedical data and will generate significant opportunities for CIT in the areas of biomedical research, software, cloud computing and big data. In turn this will build upon CITs capabilities and reputation in the area of advanced bioinformatics. THE PROPOSED SUPERVISOR DR PAUL WALSH COMPLETED HETAC RESEARCH M ETHODS MODULE 3. Research Methodology Describe the methodology to be used in the proposed research WHERE HE ACHIEVED DISTINCTION IN BOTH and why it is appropriate to the research objectives. QUALITATIVE AND QUANTIATIVE RESEARCH M ETHODS. Book of Sample Projects Page 77 CIT Rísam PhD Scholarship Programme 2014 A range of research methodologies will be considered and the most appropriate will be considered for each objective. The field of computing can be seen as an interdisciplinary endeavour as it encompasses subjects such as logic, mathematics, physics, psychology and in the case of this proposal life science. Since this research encompasses elements of computer science and life science both qualitative and quantitative research techniques will be judiciously selected as necessary in consultation with the PhD supervisor. Such decisions will be taken as guided by publications such as Scientific Methods in computer Science1. 4.
Work Plan Present the research work plan, outlining the main research tasks and timing. Stu Dent. PhD Year 1 GANTT Chart Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Literature Review Conduct Initial Stakeholder Survey/focus groups Refine project Scope Submit Review Paper Implement initial prototype/model Study 1 Study 1 Data collection Study 1 analysis / report Implement initial prototype/model Study 2 Stage 1 Research training Present Paper Annual monitoring Nov Dec Jan Feb Mar Apr May Jun Jul Aug Stu Dent. PhD Year 2 GANTT Chart Task Sept Oct 1
Scientific Methods in Computer Science, Gordana DODIG-CRNKOVIC, Department of Computer Science
Mälardalen University, Västerås, Sweden, http://www.mrtc.mdh.se/publications/0446.pdf
Book of Sample Projects Page 78 CIT Rísam PhD Scholarship Programme 2014 Implement system/model Study 2 Study 2 Data collection Study 2 Analysis Study 2 Report Stage 1 Research training Annual monitoring Present Paper Stu Dent. PhD Year 3 GANTT Chart Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Refine model Stabalise Final valuation data collection Write up Thesis Stage 1 Research training Annual monitoring Final paper/viva voce 5.
6.
Ethical issues If the proposed research directly involves human or live animal subjects, discuss the ethical issues involved and the actions that will be taken to ensure compliance with CIT ethics guidelines and with the CIT Child Protection Policy (if children are involved). External Collaboration/Other Institutions None 1
W. Wang and E. Krishnan, "Big Data and Clinicians: A Review on the State of the Science". JMIR Med Inform 2014;2(1):e1, doi:10.2196/medinform.2913. 1
Costa FF ,"Big Data In Biomedicine". Drug Discovery Today. In press (2013). doi: http://dx.doi.org/10.1016/j.bbr.2011.03.031. 1
http://ec.europa.eu/justice/data-­‐protection/document/review2012/com_2012_11_en.pdf 1
http://eur-­‐lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:31995L0046:en:HTML Book of Sample Projects Page 79 CIT Rísam PhD Scholarship Programme 2014 Chemistry General Discipline Area:
Title of project:
Analytical Chemistry
Orthopaedic Research - The application of High Resolution
Inductively Coupled Plasma Mass Spectrometry (ICP-HRMS) to
clinical samples for the determination of element contamination from
orthopaedic implants.
Name of Principal Supervisor: Dr Ambrose Furey / Dr Mary Lehane
Email:
ambrose.furey@cit.ie
Discipline Area by Frascati Classification: Chemistry Telephone: 0214335875
Natural Sciences, Chemical Sciences, Analytical 1. Abstract (250 words)
Following the recent success from the Science Foundation Ireland Research Infrastructure
Call 2012 [Proposal #12/RI/2335 (2)], an instrument called an Inductively Coupled Plasma
High Resolution Mass Spectrometer (ICP-HR MS) will be purchased in 2013 (e-tender
submitted 18th February 2013). Dr Furey is applying for funding to support a researcher who
will be involved in:
1. Installation, assessment and operation on-site the ICP-HR MS.
2. Development of validated methods for the detection of trace metals (Cobalt and
Chromium) in clinical samples.
3. Setting up of an accredited laboratory for clinical metal analysis in the Department of
Chemistry (Laboratory C145).
4. Liaising with project collaborators, consultant biochemist at Cork University Hospital
(Dr John O’Mullane) and with a number of Orthopaedic surgical teams.
5. Performing screening campaigns on clinical samples and contextualising metal levels
found to medical conditions suffered by patients.
The originality of this research stems from the fact that:
1. In 2012, the Medicines and Health Care Products Regulatory Agency (MRHA), in the
UK issued an alert and recall campaign on De Puy ASR XL Acetabular metal-onmetal hip replacement systems. 12% of patients who received an ASR device needed
“revision surgery.” In Ireland it is estimated that 15,000 patients are affected and
require annual metal exposure assessment.
http://en.wikipedia.org/wiki/2010_DePuy_Hip_Recall
2. a limited number of medical samples have been tested to-date for Irish patients (UK
labs) and no published data is available.
3. this is the only available ICP-HR MS available on the island of Ireland for clinical
analysis (routine and research purposes).
Book of Sample Projects Page 80 CIT Rísam PhD Scholarship Programme 2014 2.
Research Context and Contribution to the Research Field
During the last few years, interest in the role of trace elements in biological systems has
increased. Recent publications [Begerow, J., Turfeld, M., and Dunemann, L., 2000. New horizons in
human biomonitoring of environmentally and occupationally relevant metals – sector-field ICP-MS versus
electrothermal AAS. J. Anal. At. Spectrom., 15, 347-352; Rodushkin, I., Ödman, F., Olofsson, R., and
Axelsson, M.D., 2000. Determination of 60 elements in whole blood by sector-field inductively coupled plasma
mass spectrometry. J. Anal. At. Spectrom., 15, 937-944; Taylor, A., Branch, S., Halls, D.J., Owen, L.M.W., and
White, M., 2000. Clinical and biological materials, foods, and beverages. J. Anal. At. Spectrom., 2000, 15, 451-
stress the growing importance of ICP-MS for trace element quantification in biological
and clinical samples and describe approaches to avoid the many analytical problems
associated with these sample types. Additional complications include non-spectroscopic
interferences from the complex salt- and protein-rich matrix [Harrington C.F., Fairman B., Ellis L.,
487.]
Roberts D.J., and P. Case, 1999. The analysis of whole blood for trace metals using a double focusing magnetic
sector ICP-MS instrument. in: Plasma Source Mass Spectrometry New Developments and Applications. Eds.:
G. Holland and S.D. Tanner. Royal Soc. Chem. Spec. Publ. 241, 95-107; Barany, E., Bergdahl., I.A., Schütz, A.,
Skerfving, S., and Oskarsson, A., 1997. Inductively coupled plasma mass spectrometry for direct multi-element
analysis of diluted human blood and serum. J. Anal. At. Spectrom., 1997, 12, 1005-1009].
The goal of the
research described in this proposal is to provide a fast, sensitive, and reliable method for trace
element analyses in a range of clinical matrices, i.e., blood, serum and urine, using high
resolution ICP-HR MS. To assess this, a suite of clinically important trace elements (Al, As,
Bi, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sb, Se, Tl, V, and Zn) will be quantified using
external calibration with aqueous solutions. The calibration used will be valid for all matrices
and sample preparation will be confined to a simple dilution step (if possible).
Quality control (QC) samples will be used to assess the accuracy and precision of the applied
analytical method. As part of inter-laboratory comparison, additional series of human and
bovine samples will be obtained for analysis that have been spiked with a combination of
trace elements and matrix components (including Ca2+, K+, Mg2+, Na+, Cl-, PO43-, SO42-,
creatinine, glucose, and urea). Urine samples, based on a commercial human urine QC
sample (Sigma Aldrich), will be spiked to simulate different matrix concentrations. The
matrix of the bovine blood samples will be unaltered. The samples will be spiked with
elements Al, As, Bi, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sb, Se, Tl, V, and Zn at
concentrations designed to replicate the wide range found in clinical practice. Cobalt (Co)
and Chromium (Cr) are the principle target metals for this project. However in ICP-MS,
sample-specific matrix elements (e.g. Na, K, Ca, Cl, S and C) may combine with
‘background’ plasma ions (e.g. Ar, O, N and H) to form interfering polyatomic species that
has the potential to interfere with all target metals. For Cobalt and Chromium analysis, high
resolution ICP-MS is required because using low resolution ICP-MS Cobalt (Co) analysis
suffers from interfering polyatomic species 43Ca16O+, 42Ca16OH+, 118Sn2+ while Chromium
(Cr) analysis suffers from interfering polyatomic species 40Ar12C+, 40Ca12C+, 38Ar14N+,
36
Ar16O+, 35Cl16OH+, 37Cl15N+, 36S16O+, leading to overestimate of Co and Cr levels. High
resolution ICP-MS ensure ‘accurate’ analyte quantitation devoid of interference from
polyatomic species.
Book of Sample Projects Page 81 CIT Rísam PhD Scholarship Programme 2014 The unequivocal separation of analyte ions from spectral interferences is a prerequisite of
accurate and precise elemental analysis. High mass resolution is the universal means for this
separation. The capability of high mass resolution is a feature unique to the Thermo
ELEMENT 2 (sole supplier of this high resolution ICP-MS technology): it is the only high
performance, double focusing magnetic sector field ICP-MS. In 2011, Dr Furey visited a
Thermo Scientific instrumentation demonstration laboratory in Paris and spent three day
assessing the ICP-HR MS technology. ICPHR-MS is the accepted and most powerful
technique for the analysis and quantification of trace elements. Its applications range from the
semiconductor industry to geological and environmental analyses, from biological research to
material sciences. The most severe limitation of ICP-MS are polyatomic interferences on the
elemental signals, originating from Argon and/or the sample matrix. High Mass resolution is
the Gold Standard for the identification and elimination of interferences. Elimination of
interferences enables accurate and reliable quantitative multi-element analyses at trace levels,
even without sample preparation. The ELEMENT 2 ICP-HR MS redefines high resolution
ICP-MS by setting a new standard for productivity at the highest level of analytical
performance, ease-of-use, stability and productivity. Auto-tuning of all parameters, including
lenses, gas flows and the torch position ensures a reproducible and reliable system setup.
Refined ion optics deliver high transmission at high resolution. Features include:
• Multi-element analysis across the periodic table covering a mg/L to sub pg/L
concentration range.
o Compatible with inorganic and organic solution matrices and solids.
• High mass resolution to access spectrally interfered isotopes.
o Produces unambiguous elemental spectra.
• A multi-elemental detector for transient signals.
o For example, CE, HPLC, GC, FFF and laser ablation.
• High precision isotope ratios.
o On non-interfered or interfered isotopes.
• Fully automated tuning and analysis.
o In conjunction with a comprehensive, customizable quality control system.
• Reliability and robustness to serve as a 24/7 production control tool.
o Highest sample throughput.
• Highest flexibility and accessibility to serve as an advanced research tool.
The Thermo ELEMENT 2 can be used as element-specific detectors for speciation analysis
when coupled to a chromatographic separation technique like HPLC, IC, CE or GC. Not only
metals, but also elements like P, S, F, Cl, Br and I can be detected quasi-simultaneously
within each scan. Due to the high accelerating voltage of 8000V and excellent focusing
properties, the Thermo ELEMENT 2 possess sensitivities of > 106 cps/ppb 115In, leading to
extremely low limits of detection. Therefore, even low abundant elemental species can be
detected. By using Medium (R=4000) or High Mass Resolution (R=10000), the analyte ions
can be completely resolved from polyatomic interferences caused by the mobile phase and/or
Book of Sample Projects Page 82 CIT Rísam PhD Scholarship Programme 2014 the sample matrix. This leads to high specificity, low backgrounds and avoids possible
misidentification of species not containing the elements of interest.
Fast magnetic scanning and even faster scanning of the electrical field lead to duty cycles
(measurement times / measurement times + settling times) of > 90% for full mass range
analysis (multi-element speciation with many elements) or > 99.9 % when the elements of
interest are within a mass range of 30%. This fast scanning is important for chromatography
with many data points per time interval.
The linear dynamic range of > 109 (Thermo ELEMENT2) enables accurate detection of low
and high abundant elemental species.
Following the recent success from the Science Foundation Ireland Research Infrastructure
Call 2012 [Proposal #12/RI/2335 (2)], an instrument called an Inductively Coupled Plasma
High Resolution Mass Spectrometer (ICP-HR MS) will be purchased in 2013
http://www.sfi.ie/news-events/press-releases/sfi-sets-ambition-of-becoming-world-leadingscience-funding-agency-by-2020-minister-bruton/
This is a significant investment [Gross Cost pre-discount = €584,578; CIT 10% contribution
= €58,458 and SFI contribution, following discount of €141,582 is €384,537] and
achievement for Dr Ambrose Furey and for the research office (Dr Niall Smith, HOD) in
CIT. This investment cements the collaboration between CIT, CUH (Dr John O’Mullane Consultant Biochemist and his colleagues Prof. John Higgins Head of the College of
Medicine and Health UCC; Mr Mark Dolan Chair of the Division of Orthopaedics CUH
/UCC; Mr Rehan Gul, Orthopaedic Surgeon, CUH; Dr Orla Healy, Public Health Specialist,
CUH) and Tyndall, UCC (Dr Alan O’Riordan; metal sensor development and validation).
This RISAM proposal (2013) will concentrate specifically on the collaboration between
CIT and CUH and in 2014 a separate RISAM proposal may be submitted on the
collaboration between CIT and Tyndall.
The overall contribution that this application will make to CIT and to the general field of
research is a follows:
• This technology (ICP-HRMS) and supporting infrastructure will ensure that
MBRS/PROTEOBIO can accomplish its clinical research goals (currently focused on
small molecule biomarkers) and diversify into the area of elemental analyse
determination, supporting the strategy outlined in the document “Reconfiguration of
Acute Hospital Services, Cork and Kerry – a roadmap to develop an integrated university
hospital network”.
• This technology will develop CIT as an Analytical Centre (a reference point for medical
elemental assessment. Further, through its collaboration with a number of research
groups in CUH (listed below), this centre can participative in National and International
Clinical Trials (following ethical approval):
• assess clinical samples for pertinent metals following the installation of Orthopaedic
medical devices,
Book of Sample Projects Page 83 CIT Rísam PhD Scholarship Programme 2014 •
•
•
•
•
•
- assess clinical samples following the discovery of medical issues associated with
medical devices,
- assess short term and long term persistence of free and bound metals levels in clinical
samples with patient with medical devices.
- Assess clinical samples of patients with element nutritional requirements, e.g.
prescribed Co, Cr, Zinc, Molibnium.
- assess Point of Care (PoC) elemental methods (assessment of pertinent issues such as:
Accuracy, Precision, Reproducibility, Sensitivity of PoC methods, etc.).
- determine element levels in epidemiological population studies so that realistic
background levels are available for comparison with orthopaedic patients.
- study the biological release of for example the metals (Co, Cr) over time following
surgery.
- evaluate the efficacy of different implant designs, and other aspects of patient
management protocols. Evaluate and develop diagnostic techniques for the diagnosis
and/or monitoring of element levels following joint replacement.
This technology (ICP-HRMS) will complement the current suite of LC-MS technologies
(QIT MS, QqQ MS, FT-MS [Orbitrap]) currently available in MRSC/PROTEOBIO
funded under the PRTLI IV funding call. The ICP-HR MS will give the laboratory the
scope to carry out detailed and forensic investigations of pertinent metals in clinical
samples, food, water and environmental matrices.
This ICP-HRMS technology will address the urgent requirement for the measurement of
Co and Cr in Orthopaedic patients with hip implants related to failure and revision.
Established best future practice will require the routine measurement of Co and Cr in
blood samples of all patients with hip implants to meet the clinical research, evaluation
and audit needs of these patients. This capacity does not exist in Ireland and all samples
are currently being transported to a medical hospital in London for analysis using this
exact technology. The purchase of this technology will correct this issue and ensure the
speedily assessment of patients.
The clinical scientific research, audit and evaluation of all trace metals in hip implant
patients in conjunction with Orthopaedic Surgeons would be greatly facilitated by the
location of this technology within the Academic Medical Health Centre Consortium
located in Cork / Kerry.
Metrology capability in terms of traceability of calibration of trace metals from field
methods through reference methods to definitive methods in laboratory medicine would
also be possible.
This technology will eventually develop to support a National Service that is capable of
Accreditation to ISO 15189, to meet the demands being placed on diagnostic services
currently and thus replace expensive outsourcing to the UK.
This infrastructure and RISAM scholarship will be the first stepping stone to facilitate the
advancement of Orthopaedic research (listed above) for the next 3 years to solve many
pertinent questions associated with patient care.
3. Objectives
Book of Sample Projects Page 84 CIT Rísam PhD Scholarship Programme 2014 The RISAM PhD researcher will be trained on ICP- HR MS (instrumentation, software,
extraction SOPs and validation steps) and will (under the supervision of Dr A. Furey):
1.
Installation, assessment and operation on-site the ICP-HR MS.
2.
Development of validated methods for the detection of trace metals (Cobalt and
Chromium) in clinical samples.
3.
Set up an accredited laboratory for clinical metal analysis in the Department of
Chemistry (Laboratory C145).
Liaising with project collaborators, consultant biochemist at Cork University Hospital
(Dr John O’Mullane) and with a number of Orthopaedic surgical teams [Prof. John
Higgins, Mr Mark Dolan, Mr Rehan Gul and Dr Orla Healy].
4.
5.
Performing screening campaigns on clinical samples and contextualising metal levels
found to medical conditions suffered by patients.
6.
Develop an analytical blueprint for the analysis of metals in a range of clinical
samples in compliance with accreditation standards
7.
Prepare peer reviewed publications and a PhD thesis.
8.
Participate in the Ed4Life modules.
4. Research Methodology
The instruments to be used as part of this project include the state-of-the-art Inductively
Coupled Plasma High Resolution Mass Spectrometer (ICP-HR MS) funded under the Science
Foundation Ireland Research Infrastructure Call 2012 [Proposal #12/RI/2335 (2)]. This
instrumentation will be located in laboratory C145 funded under the Higher Education
Authority of Ireland-The Programme for Research in Third Level Institutions (HEA-PRTLI),
Cycle II. All clinical samples will be delivered to a specialised chemistry laboratory located
in the CREATE building funded under HEA-PRTLI V. In this laboratory only clinical
samples will be used. Clinical samples (blood, urine, tissue) will be extracted (digestion),
diluted, stored (short and long-term) and only aliquots of extraction will be transferred for
analysis in laboratory C145. A fully documentation trail will be implements to ensure chain
of custody. Also all clinical samples will follow ethical approval and protocols with
submission for ethical approval from the Clinical Ethics Research Committee of the Cork
Teaching Hospital.
In MRSC/PROTEOBIO, this instruments available to post-graduate researchers cost over
€2.5 million and instrument time schedules will be organised by Dr Furey to ensure that
adequate time is available for each researcher to become fully competent with each
technology. Dr Furey has a strategy of team work in his group where researchers work
Book of Sample Projects Page 85 CIT Rísam PhD Scholarship Programme 2014 together and share their knowledge and experience with each instrument. Each researcher
once competent, with a technology, writes a detailed instrument SOP that is compiled with all
other SOPs for general use by all. Samples for each project, once extracted, are run as
campaigns on agreed instruments. This ensures that all results are obtained in the shortest
possible window and during a period when the instruments are fully operational and working
within supplier specifications. Daily calibration (<20 mins) are run on each instrument by
each post-graduate and all readings are recorded in instrument log-books and post-graduate
note books.
5.
Work Plan
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1 Training of postgraduate student. Installation, assessment and
operation on-site the ICP-HR MS.
2 Literature review of elements, orthopaedic devices and clinical
reasons for routine assessment and patient care following
orthopaedic surgery.
3 Task #1: Development of validated methods for the detection of
trace metals (Cobalt and Chromium) in clinical samples
4 Task #2: Set up and maintain an accredited laboratory for clinical
metal analysis in the Department of Chemistry (Laboratory C145).
5 Task #3: Liaising with project collaborators, consultant biochemist
at Cork University Hospital (Dr John O’Mullane) and with a
number of Orthopaedic surgical teams [Prof. John Higgins, Mr
Mark Dolan, Mr Rehan Gul and Dr Orla Healy].
6 Task #4: Performing screening campaigns on clinical samples and
contextualising metal levels found to medical conditions suffered by
patients.
7 Task #5: Develop an analytical blueprint for the analysis of metals
in a range of clinical samples in compliance with accreditation
standards
8 TASK #6: Preparation of Scientific Output (Peer reviewed
publications)
9 Dissemination and reporting; PhD Thesis write-up
Task #1:
Development of validated methods for the detection of trace metals
(Cobalt and Chromium) in clinical samples.
Following training from competent Thermo Scientific engineer, the RISAM post-graduate
researcher will undertake to develop and validate a method for the detection of trace metals
(Cobalt and Chromium) in a range of clinical matrices, i.e., blood, serum and urine, using
high resolution ICP-HR MS. To assess this, a suite of clinically important trace elements (Al,
Book of Sample Projects Page 86 CIT Rísam PhD Scholarship Programme 2014 As, Bi, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sb, Se, Tl, V, and Zn) will be quantified using
external calibration with aqueous solutions. The calibration used will be valid for all matrices
and sample preparation will be confined to a simple dilution step (if possible). However if
sound statistical data cannot achieved for some clinical matrices applying the simple dilution
step, samples will be subjected to acid digestion and clean-up protocols.
Quality control (QC) samples will be used to assess the accuracy and precision of the applied
analytical method. Human and bovine samples will be obtained for analysis that have been
spiked with a combination of trace elements and matrix components (including Ca2+, K+,
Mg2+, Na+, Cl-, PO43-, SO42-, creatinine, glucose, and urea). Urine samples, based on a
commercial human urine QC sample (Sigma Aldrich), will be spiked to simulate different
matrix concentrations. The matrix of the bovine blood samples will be unaltered. The
samples will be spiked with elements Al, As, Bi, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sb, Se,
Tl, V, and Zn at concentrations designed to replicate the wide range found in clinical practice.
Cobalt (Co) and Chromium (Cr) are the principle target metals for this project. Interfering
polyatomic species generated in the ICP-MS plasma will also be quantified so that all
potential interferes are known and dealt with correctly. For example, for Cobalt and
Chromium analysis, high resolution ICP-MS is required because using low resolution ICPMS Cobalt (Co) analysis suffers from interfering polyatomic species 43Ca16O+, 42Ca16OH+,
118
Sn2+ while Chromium (Cr) analysis suffers from interfering polyatomic species 40Ar12C+,
40
Ca12C+, 38Ar14N+, 36Ar16O+, 35Cl16OH+, 37Cl15N+, 36S16O+, leading to overestimate of Co and
Cr levels. High resolution ICP-MS therefore ensures ‘accurate’ analyte quantitation devoid of
interference from polyatomic species.
Clinical validation procedures will be followed (www.intechopen.com; Procedures for Validation of
Diagnostic Methods in Clinical Laboratory Accredited by ISO 15189 written by Silvia Izquierdo Álvarez and
Francisco A. Bernabeu Andreu) to ensure method accreditation.
Task #2:
Set up and maintain an accredited laboratory for clinical metal analysis
in the Department of Chemistry (Laboratory C145).
Clinical validation procedures will be followed (www.intechopen.com; Procedures for Validation of
Diagnostic Methods in Clinical Laboratory Accredited by ISO 15189 written by Silvia Izquierdo Álvarez and
Francisco A. Bernabeu Andreu)
to ensure method accreditation. The RISAM post-graduate
researcher will be guide and trained through this process by Dr A. Furey and Dr J.
O’Mullane. Processes will be implemented to ensure sustainability of accreditation protocols.
Task #3:
Liaising with project collaborators, consultant biochemist at Cork
University Hospital (Dr John O’Mullane) and with a number of
Orthopaedic surgical teams [Prof. John Higgins, Mr Mark Dolan, Mr
Rehan Gul and Dr Orla Healy].
The RISAM post-graduate researcher will be actively involved in meetings with the
Book of Sample Projects Page 87 CIT Rísam PhD Scholarship Programme 2014 consortium to ensure he/she has all available information so that he/she understands the
complete project area (sample extraction, method validation, laboratory accreditation,
orthopaedic device design, orthopaedic procedures, etc.).
Task #4:
Performing screening campaigns on clinical samples and contextualising
metal levels found to medical conditions suffered by patients.
The RISAM post-graduate researcher will have to be trained in sample management so that
samples are extracted, analysed, quantified and reported in a timely fashion. The RISAM
post-graduate researcher should in time understand the significant of quantified results
(levels detected) from a medical perspective so that he/she can make correlations with
specific medical conditions. There will be a period where the RISAM post-graduate
researcher will have to study the area of Orthopaedic medicine so that he/she can
contextualise the analytical results.
Task #5:
Develop an analytical blueprint for the analysis of metals in a range of
clinical samples in compliance with accreditation standards.
On completion of Tasks 1-4, an analytical blueprint for the analysis of metals in a range of
clinical samples in compliance with accreditation standards will be written. This document
will be a major output in Year 3 of the PhD research and form a main part of the PhD thesis.
TASK #6:
Preparation of Scientific Output (Peer reviewed publications)
A detailed literature review will be prepared by the RISAM post-graduate and it will be
submitted to an appropriate journal for publication. Regular 6 monthly reports will be
supplied to the CITs Registrar’s Office and the RISAM post-graduate will be expected to
give 3 monthly PowerPoint publications to Dr Furey and other Department of Chemistry
research staff. Drafts of scientific papers will be written as the work progresses and goals will
be set. Scientific papers generated during this study will be co-authored by researchers
present at CIT and Teagasc. Journals considered for publication will be Rapid
Communication in Mass Spectrometry, Analytical and Bioanalytical Chemistry, Analytical
Chemistry and appropriate Clinical journals.
6.
Ethical issues
In consultation with Dr John O’Mullane all clinical samples for this project will follow
ethical approval and protocols with submission for ethical approval from the Clinical Ethics
Research Committee of the Cork Teaching Hospitals. Dr Furey has experience with these
Book of Sample Projects Page 88 CIT Rísam PhD Scholarship Programme 2014 application following recent research success in the determination of a potential ADHD
biomarker with clinician Dr Helen Keeley (Consultant Child and Adolescent Psychiatrist,
Child and Adolescent Mental Health Services, Health Service Executive, South, North Cork
Area and the National Suicide Research Foundation, Cork) [Moriarty, M., Lee, A., O’Connell, B.,
Keeley H. and Furey, A. Development of an LC-MS/MS method for the analysis of serotonin and related
compounds in urine and the identification of a potential biomarker for attention deficit
hyperactivity/hyperkinetic disorder. Anal. Bioanal. Chem. 401 (2011) 24810].
For security of clinical samples it is proposed that the chemistry laboratory in the new
CREATE building (PRTLI V) will be used solely for clinical research. Samples will be
delivered to, processed, extracted and archived (long term storage) in this laboratory and a
fully documentation trail will be implements to ensure chain of custody. Only samples
aliquots will be delivered to C145 for element analysis following strict delivery procedures
from the CREATE building laboratory to C145.
Book of Sample Projects Page 89 CIT Rísam PhD Scholarship Programme 2014 General Discipline Area:
Title of project:
Analytical Chemistry
Food and Animal Feed Safety - The development of LC-MS/MS
methods for the detection of Pyrrolizidine Alkaloids and other
cereal/plant toxins in food and animal feed.
Name of Principal Supervisor: Dr Ambrose Furey / Dr Mary Lehane
Email:
ambrose.furey@cit.ie
Discipline Area by Frascati Classification: Chemistry Telephone: 021-4335875
Natural Sciences, Chemical Sciences, Analytical 1. Abstract (250 words)
Pyrrolizidine Alkaloids (PAs) are known secondary plant metabolites which can cause
hepatotoxicity in both humans and livestock. PAs can be consumed through the use of plants
for food, medicinal purposes and as contaminants of agricultural crops and food.
Internationally, PA-contaminated grain has posed the largest health risk, although any PA
contamination in our food chain should be recognised as a potential health threat. A
completed PhD project funded by the Irish Department of Agriculture, Food and the Marine;
titled “Safe and Healthy Foods” identified PA contamination in both indigenous and imported
honey (n= 350 samples).
In this health conscious era where sugar is regarded as the primary agent responsible for
diabetes, honey is not being used as a ‘natural sweetener’. There is now a necessity to profile
food products (cereals, cereal bars, health foods etc.) which have honey as an ingredient and
as a substitute to sugar.
Animal feed (e.g. grain, pellet feeds) will also be assessed for PA content as feed has the
potential to allow PA’s enter the food chain through milk and meat products.
This project will profile foods and feed products using a range of mass spectrometry
technologies (MS) including i. liquid chromatography (LC) coupled to a quadrupole MS; ii.
LC coupled to an ion-trap MS and iii. LC coupled to a high mass accuracy ion-trap fouriertransform MS. These techniques will quantify known PA’s and elucidate new metabolites.
This proposal represents a novel proactive, rather than reactive approach to the protection of
food and feed quality.
2.
Research Context and Contribution to the Research Field
Pyrrolizidine alkaloids (PAs) are naturally occurring plant toxins which have gained attention
due to their hepatotoxic effects on both humans and livestock. PA-containing plants originate
from the families Asteraceae, Boraginaceae and Fabaceae and are widespread in their
distribution, being present in 3% of all flowering plants (Smith and Culvenor, 1981). PAs are
proven hepatotoxic, carcinogenic, genotoxic, and pneumotoxic compounds (Culvenor et al.,
1976; Mattocks 1986; Schoental 1968). Those which cause toxicity consist of a 1, 2unsaturated necine ring and a necic acid from which carboxylic esters form a macrocyclic
Book of Sample Projects Page 90 CIT Rísam PhD Scholarship Programme 2014 structure (Prakash, Pereira, Reilly and Seawright, 1999). The structure of retronecine and
otonecine type PAs are given in Figure 1.
Figure 1 Representative chemical structures for Retronecine-type and Otonecine-type PA
toxins used within this study.
This project is a continuation of a successfully completed PhD project (2008-2012) funding under the Food for Health Research Initiative (FHRI) administered by the Irish Department
of Agriculture, Food and the Marine; and the Health Research Board (Contract#:
07FHRITAFRC5). This project was titled “Safe and Healthy Foods” and a main collaborator
was Dr Martin Danaher (Ashtown Food Research Centre, Teagasc). This project identified
PA contamination in both indigenous and imported honey (n= 350 samples).
In this health conscious era where sugar is regarded as the primary agent responsible for
diabetes, honey is not being used as a ‘natural sweetener’. There is now a necessity to profile
food products (cereals, cereal bars, health foods etc.) which have honey as an ingredient and
in products where honey is the substitute ingredient to sugar.
Animal feed will also be assessed for PA content as numerous feed products (e.g. Silage, hay,
grain, pellet feeds) have to potential for contamination allowing PA to enter the food chain
through milk and meat products.
Livestock losses (acute doses) have been firmly established due to the presence of toxic PAs.
These losses can occur from foraging on PA-containing plants but are predominately from
Book of Sample Projects Page 91 CIT Rísam PhD Scholarship Programme 2014 contaminated feed, hay or silage, as PAs in their dried state become more palatable (Candrian
et al., 1984; Stegelmeier et al., 1999; Stegelmeier 2011) however to-date very little
information is available on chronic exposure levels in livestock and their subsequent
assimilation into the food chain. No information is available from on PA levels in feed
(indigenous and imported) and the resultant Irish meat and dairy products.
Cases of PA exposure in humans have occurred worldwide, although developing countries
have been more susceptible. The reasons behind this are two-fold; firstly PA-containing
plants are particularly hardy surviving long periods of drought and secondly poor crop
management. Mass intoxications have arisen from the use of contaminated grain. The
earliest case termed 'bread poisoning' dates from 1920 (Willmot and Robertson, 1920) and
more recent cases have occurred in both Afghanistan and Ethiopia in 2008 (IRIN Asia 2008a
and 2008b; Molyneux, Gardner, Colegate and Edgar, 2011). PA-toxicity also arises from the
direct consumption of PA-containing plants used as food, in salads, cooking spices, herbal
teas and medicines. Wiedenfeld (2011) provides a comprehensive list of cases where the
source of human intoxication was unequivocally identified as PAs.
Food products from animal origin such as milk, eggs and honey are prone to contain PAs.
Although there are no recorded cases of human PA poisoning from these foodstuffs they
should not be overlooked. Studies have shown that PAs can be carried-over into milk
(Deinzer, Arbogast and Buhler, 1982; Dickinson, Cooke, King and Mohamed, 1976;
Hoogenboom et al., 2011) from inadvertent grazing on ragwort (Senecio jacobaea) and into
eggs from hens feeding on unfettered grain infiltrated with Heliotropium and Echium spp.
seeds (Edgar and Smith, 2000) however this information is quite limited and only represent
PA profiles and levels from the study country. Honey and pollen products also have been
shown to contain toxic PAs. Earlier reports document the occurrence of PAs in honey from
Senecio jacobaea (Deinzer, Thomson, Burgett and Isaacson, 1977; Crews, Startin and Clarke,
1997) and Echium plantagineum (Culvenor, Edgar and Smith, 1981) with PA levels of up to
3,900 and 950 µg kg-1 of honey detected, respectively. Crews et al. (1997) stated that the
higher PA content honey samples were recognised by beekeepers as being unpalatable due to
the presence of Senecio jacobaea. A study conducted (Beales, Betteridge, Colegate and
Edgar, 2004) on 63 pre-processed honey samples included a small number of retail samples
(n = 5) which were shown to contain up to 250 µg kg-1 of honey. A later study on 9
commercial floral honeys detected PA levels in seven samples between 170 and 2,850 µg kg-1
of honey (Betteridge, Cao and Colegate, 2005). However, the most recent studies of retail
honey found upper PA concentrations of 120 µg kg-1 (Kempf et al., 2008) and 267 µg kg-1 in
honey (Dübecke, Beckh and Lüllmann, 2011). This honey data correlates with the recently
generated PhD data however much large sample numbers were tested (n = 350) outlining
exact PA toxin profiles and concentrations in indigenous honey, imported EU honey,
imported EU blended honey, imported Asia honey, imported South American honey,
imported Australia honey and imported EU /Asia/Australia blended honey.
There are no set maximum residue limits (MRLs) for PAs in food or feed. Guidelines or
tolerable daily intakes (TDIs) have been established through several independent studies
(Edgar, Colegate, Boppré and Molyneux, 2011) but since the detection methods are not
standardised the TDIs for toxic PAs range from 0.1 to 1.0 µg kg-1 body weight per day or 0.1
to 1.0 µg/day over a 6 week period. It is for this reason that we now need to undertake a
concise study of food and feed products affected by PA, so that PA exposure levels can be
determined, based on the Irish population (eg. children, adult, elderly) honey and ‘PA
contaminated foods’ consumption rates. This data will contribution to the general field of
research and through contacts with Teagasc (Ashtown [Dr Martin Danaher] and Morepark
Book of Sample Projects Page 92 CIT Rísam PhD Scholarship Programme 2014 [Dr Kieran Jordan]) and Food safety Authority of Ireland (FSAI), Dr Furey (CIT Dept. of
Chemistry Research Principal Investigator / Director: Mass Spectrometry Research Centre
(MSRC) / Lecturer in Chemistry) will submit published data for inclusion in any national
study which will eventually be used for the establishment of EU and national Maximum
Residue Levels (MRL) in food and animal feed.
3. Objectives
Applying LC-MS methodologies (LC-ion trap MS and LC-QqQ MS/MS) already developed
and validated for honey in CIT (MSRC) as part of the previous “Safe and Healthy Foods”
project, the RISAM PhD researcher will be trained on these methodologies (instrumentation,
software, extraction SOP, solid phase extraction clean-up SOP and validation steps) and will:
1.
Screen a number of honey samples (n=50) each year of the project supplied by Irish
producers to ensure they contain minimal levels of PA’s.
2.
Develop and validate a high mass accuracy ion-trap fourier-transform MS (Orbitrap
XL: LC-IT-FTMS) method for the simultaneous determination of Pyrrozlidine
alkaloids (PA), which will be applied to food products (cereals, cereal bars, health
foods etc.) and animal feed (e.g. grain, pellet feeds, silage) samples.
3.
Isolate known and unknown PA’s for use as standards and in mass spectrometry
fragmentation studies from real samples using the recently purchased Agilent 971-FP
Flash Purification System (2012). This is an automated flash chromatography
instrument for natural product chemistry isolation offering very fast, easy, safe and
secure purification of known and unknown compounds.
4.
Apply multiple tandem mass spectrometric methodologies to identify fragment ions,
which relate to characteristic structural features of the PA class of compounds, to
enable recognition of new toxin congeners, metabolites and degradation products in
food and feed samples.
5.
Develop a high mass accuracy nanomate electrospray-MSn-FTMS protocol (no LC) to
enable the rapid profiling (< 2.5 mins) of food and feed extracts to allow unequivocal
identification of PA toxins. Use this methodology to look for other potential food/feed
toxins such as ergot alkaloids and mycotoxins.
6.
Carry out an extensive PA survey on food and feed samples purchased from
supermarkets and supplied by Teagasc respectively and correlate PA levels with
food/feed consumption rates documented by Teagasc for the Irish human and animal
population over the past decade.
7.
To develop an analytical blueprint for the analysis of PA toxins in a range of Irish
Food and feed products so as to ensure the protection of food quality against PA
toxins for regulatory agencies in Ireland.
8.
To preparation peer reviewed publications and a PhD thesis.
9.
To ensure the applicants participates in the Ed4Life modules.
Book of Sample Projects Page 93 CIT Rísam PhD Scholarship Programme 2014 7. Research Methodology
The instruments to be used as part of this project include the state-of-the-art chromatographic
and mass spectrometry instrumentation purchased using funds received from the projects:
• Higher Education Authority of Ireland-The Programme for Research in Third Level
Institutions (HEA-PRTLI), Cycle 4. ‘Environment and Climate Change: Impacts and
Responses’.
• Council of Directors, Technological Sector Research - Strand III 2006 Scheme,
‘Investigation of medicinal herbal products supplied to the Irish market to determine
pharmacological efficacy and safety and to study native Irish herbs to determine whether
they contain chemical constituents at pharmacologically significant levels for use in
herbal and volatile oil preparations’ 06/CR05.
• Higher Education Authority of Ireland-The Programme for Research in Third Level
Institutions (HEA-PRTLI), Cycle 2. ASTOX, ZEBRATOX and AZP projects; 2002.
This equipment includes:
1. LC-MS/MS: Agilent 6340 – ion-trap mass spectrometer with multiple ionisation probes
and MSn capability linked to an Agilent 1200 HPLC.
2. LC-MS/MS: Applied Bio systems API 3000 – triple stage quadruple mass spectrometer
with multiple ionisation probes (ESI, APCI) for accurate quantitative data analysis.
4. LC-MS/MS: Thermo Quantum DiscoveryMAX – triple stage quadrupole mass
spectrometer with multiple ionisation probes (ESI, APCI) for accurate quantitative data
analysis.
5. Orbitrap Discovery: LC-IT-FTMS: Thermo, high mass accuracy linear ion trap – fourier
transform mass spectrometer with Rs = 30,000.
7. NanoMATE ESI source (Advion) – NanoESI source to allow the analysis of trace
fractions (<10 µl) for mass spectrometry fragmentation studies coupled to an Orbitrap
XL: LC-IT-FTMS: Thermo, high mass accuracy linear ion trap – fourier transform mass
spectrometer) with Rs = 100,000.
8. ROXY Electrochemical cell (Antec) – coupled to the Orbitrap XL FT-MS, the
electrochemistry cell can be applied for the investigation of analyte metabolism using
standards.
9. Agilent 971-FP Flash Purification System (2012): a personal flash chromatography
instrument for marine biotoxin isolation offering very fast, easy and secure purification
of known and unknown biotoxins.
This instrument cost over €2.5 million and will ensure the RISAM PhD researcher is ideally
suited for employment in the pharmaceutical, food and environmental industries. Time
schedules will be organised by Dr Furey to ensure that adequate time is available for each
researcher to become fully competent with each technology. Dr Furey has a strategy of team
work in his group where researcher work together and share their knowledge and experience
with each instrument. Each researcher once competent, on a technology writes a detailed
instrument SOP that is compiled with all other SOPs for general use by all. Samples for each
project, once extracted, are run as campaigns on agreed instruments. This ensures that all
results are obtained in the shortest possible window and during a period when the instruments
are fully operational and working within supplier specifications. Daily calibration (<20 mins)
are run on each instrument by each post-graduate.
Book of Sample Projects Page 94 CIT Rísam PhD Scholarship Programme 2014 8.
Work Plan
Samples will be sourced from known honey suppliers (Boyne Valley, etc.), supermarkets
(known brands that have been shown previously to have PAs present), processed foods
containing honey (cereals, cereal bars, health foods etc.) sourced from various processors,
suppliers and supermarkets and from animal feed suppliers (co-ordinated by Teagasc).
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1 Training of postgraduate student
2 Literature review of PA residues in milk, eggs, LCMS/MS and LC-FTMS training and method
development.
3 Task #1: Develop and implement a LC-MS/MS and LCFT-MS screening programme (specific period over the
three years) for food and animal feed.
4 Task #2: Isolate known and unknown PA’s for use as
standards using the Agilent 971-FP Flash Purification
System.
5 Task #3: Conduct mass spectrometric studies of the
fragmentation processes of isolated PA toxins, ergot
alkaloids and metabolites (ROXY system).
6 Task #4: Development of a high mass accuracy
nanoMate electrospray MSn-FTMS protocol.
7 TASK #5: Preparation of Scientific Output (Peer
reviewed publications)
8 Dissemination and reporting; PhD Thesis write-up
Book of Sample Projects Page 95 CIT Rísam PhD Scholarship Programme 2014 TASK #1:
Develop and implement a LC-MS/MS and LC-FT-MS screening program
for the detection of PA for food and animal feed.
This task will involve examining published methodologies, in-house developed
methodologies and applying other LC-MS/MS technologies (equipment list 1-7) for the
determination of PA alkaloids and develop the best approach for use in a monitoring
programme. Methods to-date principally screens alkaloid toxin groups individually but with
the LC-MS technology in CIT we are now able to combine various toxin groups (PAs, ergot
alkaloids and mycotoxins) under one single method. This approach will ensure a complete
toxin screen can be carried out as one chromatographic run therefore reducing
instrumentation use, providing a novel application and ensuring the timely reporting of
results. When using a triple quadrupole, the use of selective precursor product ion pairs
obviates the need for chromatographic resolution that is required during spectroscopic
detection methodologies. The most difficult aspect of this task will be selecting the most
appropriate HPLC column chemistry to analyse these toxins simultaneously. The approach to
be taken will be to trial a variety of different columns, mobile phases and buffers. In addition,
investigations will be made to determine whether sufficient quantitative limits of detection
can be obtained with direct analysis or whether online or offline sample preparation is
required. MSRC (formerly PROTEOBIO) has recently purchased an on-line preconcentration enhancement liquid chromatography quadrupole mass spectrometer (on-line PE
LC-MS/MS) which has the capabilities to pre-concentrate sample extracts (5-20 ml) on line
during sequence runs. This technology coupling a CTC Combi PAL (CTC Analytics AG,
Zwingen, CH) autosampler with LC-MS/MS has revolutionised the testing of food extracts
for trace levels of chemical contaminants. Samples taken from any region of the world can be
filtering into a crimped vial at source, stored and transported at 4 °C and immediately
sequenced for analysis once delivered to CIT. Over the first 6-12 months, this method will be
developed and validated by the RISAM post-graduate for the specific toxins outlined in this
proposal.
Dr Furey and co-workers have just published an extremely sensitive LC-MS/MS methods
for PA detection in honey, published in the Journal of Food Chemistry (Impact factor:
3.655) in 2013. This method was highly acclaimed by the FSAI in Ireland and has been
integrated into national monitoring programs for honey quality in collaboration with
Teagasc and the Public Analyse Laboratory, Dublin [Griffin, C., Danaher, M., Elliott, C.,
Kennedy, D. G. and Furey, A. (2011) Detection of Pyrrolizidine Alkaloids in Commercial
Honey using Liquid Chromatography-Ion Trap Mass Spectrometry. Journal of Food
Chemistry (2013) 136 1577–1583]. The RISAM post-graduate will be fully trained on this
methodology and validate it got the detection of PA’s in other food and animal feed.
Following this the methodology will be transferred to the LC-IT-FTMS, Thermo Orbitrap
Discovery mass spectrometer where both high resolution and high mass accuracy data will
be generated for the detection of previously known and unknown PA’s in similar samples.
TASK #2:
Isolate known and unknown PA’s for use as standards using the Agilent
971-FP Flash Purification System.
Dr Furey has a strong research collaboration with Dr Martin Danaher of Teagasc Ashtown
Food research centre and to-date they have completed two CIT PhD programmes following
funding under the Walsh Fellowship 2006 (Ref#: 06/RDTA/AFRC/479; Dr Brian Kinsella)
and 2007 (Ref #: 2007085; Dr Michelle Whelan). This collaboration on veterinary drug
Book of Sample Projects Page 96 CIT Rísam PhD Scholarship Programme 2014 residues and the expertise gained on tracing target analytes and their metabolites as they
make their way throughout the food chain, has resulted in over 10 high impact peer-reviewed
publication (see supporting CV). Dr Furey is an expert in the isolation of biotoxins, bioactive
compounds, proteins and chemical residues from complex matrices. Dr Furey has coauthored over 60 peer-reviewed research publications, 15 invited contributions to major
reference works (peer-reviewed), 8 Editorials, 17 peer-reviewed publications in International
Books, 26 Irish conference papers and 90 International Conference papers and has an h-index
of 29 (Google Scholar).
Combining both skills the RISAM post-graduate will be taught on the correct statistical
procedures to collect representative food/feed samples for both the quantitation/profiling and
isolation of PA toxins, ergot alkaloids and mycotoxins from food and feed samples.
Presently there are only 14 PA standards commercially available from a potent list of 250+
known PA compounds. Therefore the isolation of PA standards is essential for food and feed
safety but also there is a significant commercial potential from this project, especially if an
isolation blueprint for the isolation of PA toxins from food and feed can be developed.
Further project funding by Enterprise Ireland on the isolation and supply of PA toxins as
standard material is a commercial idea that Dr Furey has been working upon. To this end, Dr
Furey invested (2012) in an automated flash chromatographic instrument (Agilent 971-FP
Flash Purification system) for use in the isolation of purified standards (toxins and non-toxic
compounds). This automated technology can subject chosen fractions to specific chemistry
phases (Polar silica phase, Non-polar C8 and C18 phases, Weak/Strong Cation Exchange,
Weak/Strong Anion Exchange, Size-exclusion chromatography) so as to ensure the optimised
purification of compounds based on their individual chemistries. Previously Dr Furey’s team
would fill long glass columns with specific phase however reproducible and robust protocols
could not be developed for reproducible and sustainable quantities of isolated product. This
isolation technology will be focused on producing validated blueprints for targets compounds
isolation, therefore the training given to the RISAM post-graduate will be of pharmaceutical
standard both in understanding all the phase chemistry theory and the art of isolation (e.g.
compound stability, pH influences, buffer influences, recrystallation, etc.). This task will also
ensure the sufficient supply of PA toxins as analytical standards for the project.
TASK #3. Conduct mass spectrometric studies of the fragmentation processes of
isolated PA toxins, ergot alkaloids and metabolites.
Isolated and purified PA toxins, ergot alkaloids and any isolated unknown analogues will be
studied using mass spectrometry. Nano-electrospray ionisation allows detailed studies to be
undertaken with relatively small amounts of material, and MRSC has a high mass accuracy
linear ion trap – fourier transform mass spectrometer (Orbitrap XL: NanoMate-IT-FTMS;
awarded under PRTLI IV funding) fitted with this source. The NanoMate-IT-FTMS will be
used to produce high mass accuracy collision induced dissociation spectra. The product ion
observed in these spectra will be assigned molecular formula and structure based upon the
chemistry of the parent molecule. While the internal IT-MS of the NanoMate-IT-FTMS
produces low resolution data, the trapping process can often remove ambiguity when more
than one assignment is possible, i.e. fragmentation of that ion (producing a new product
spectrum) can often produce ion assignments that can prove or disprove the precursor ion
assignment. The complementarily of data generated by IT-MS and FT-MS in one instrument
has been observed on numerous occasions by Dr Furey and has the potential to develop the
research topic area substantially ensuring CIT is recognised as a key global food/feed toxin
Book of Sample Projects Page 97 CIT Rísam PhD Scholarship Programme 2014 identification research centre. The goal of this part of the project is to train the student in the
use and application of IT-MS and FT-MS and to confirm the structures of isolated known and
unknown alkaloids.
The research group has a new Roxy Electrochemical cell (Antec, UK; 2012) which can
induce molecules (purified standards from Task #2) to undergo chemical changes which
mimic Phase I and Phase II metabolites formed by cytochromes in vivo and allows for the
investigation of the likely products of metabolism. This is invaluable when searching for the
pertinent compounds in clinical samples following an intoxication incident.
Additionally the assigned fragments will be investigated with respect to developing a
predictive methodology for the identification of food/feed toxin analogues, metabolites and
degradation products. This task has the potential to produce very significant publications for
the RISAM post-graduate and his supervisor Dr Furey.
TASK #4:
Develop a high mass accuracy nanoMate electrospray-MSn-FTMS
protocol (no LC) to enable the rapid profiling (< 2.5 mins) of food and
feed extracts to allow unequivocal identification of PA toxins. Use this
methodology to look for other potential food/feed toxins such as ergot
alkaloids and mycotoxins.
Given the scarcity of some purified toxins, mass spectrometric studies will be carried out
using a nano-electrospray ionisation source coupled to a high resolution, high mass accuracy
mass spectrometer (Orbitrap XL: LC-IT-FTMS). This source allows detailed
experimentations to be undertaken using very small amount of toxin (< 1 µg) and mass
spectral (MSn and high mass accuracy) libraries will be produced for each toxin. This
technology will be applied to all samples (food / animal feed) sourced from Irish and from
prepared cultured from both countries.
A recent development with mass spectrometry has been the solvent-less nano electrospray
sources developed for mass spectrometers. Advion Inc. from the USA has developed a
solvent-less nano electrospray sources called the NanoMate, this use very small volumes (5
µl which can be infused continuously in the mass spectrometer for 30 minutes rather than a
60 second LC chromatography peak. The advantages of NanoMate coupled to a MS
instrument are that the low samples volumes used allow for easier interfacing with the high
vacuum present in a mass spectrometer and the longer spray time and data acquisition
presents an effective concentration increase. Essentially the sensitivity is increased
significantly, to the point where small concentrations typical of a small number of cells, can
be detected. Thus it is possible to obtain toxin profiles from as few as 5 µls of extract,
depending upon the toxicity of the isolation sample extracts themselves. The aim of the task
is to develop a nanoMate ESI-MS protocol, using a high mass accuracy linear ion trap –
fourier transform mass spectrometer (Orbitrap XL: LC-IT-FTMS), which can unequivocally
confirm the presence of alkaloid toxins through the production of high mass accuracy MSn
spectra. This protocol will be used to assess small volumes of extracts (n = 5 – 20 µl) that are
collected from isolated steps. This approach will allow for the unequivocal linking of suspect
food or animal feed samples with PA toxins without the need to run long chromatographic
LC-MS/MS sequences.
Book of Sample Projects Page 98 CIT Rísam PhD Scholarship Programme 2014 Previously, plant alkaloid toxins had to be bulk extracted from kilograms of dried material,
isolated, matrix cleaned and analysed. These previous protocols were both time consuming
and labour intensive. LC-IT-FTMS has revolutionised the speed and accuracy of mass
spectral target analyte identification. Recently Dr Furey with PhD graduate, Dr Merisa
Moriarty applied this NanoMate ESI technology, for the first time, to clinical samples and
successfully quantified a key biomarker in ADHD patient urine samples [Moriarty, M.,
Lehane, M., O’Connell, B., Keeley, H. and Furey, A. Development of a Nano-Electrospray
MSn Method for the Analysis of Serotonin and Related Compounds in Urine using a LTQOrbitrap Mass Spectrometer. Talanta 90 (2012) 1– 11 (5-Year Impact Factor: 3.487)].
TASK #5:
Preparation of Scientific Output (Peer reviewed publications)
A detailed literature review will be prepared by the RISAM post-graduate and it will be
submitted to an appropriate journal for publication. Regular 6 monthly reports will be
supplied to the CITs Registrar’s Office and the RISAM post-graduate will be expected to
give 3 monthly PowerPoint publications to Dr Furey and other Department of Chemistry
research staff. Drafts of scientific papers will be written as the work progresses and goals will
be set. Scientific papers generated during this study will be co-authored by researchers
present at CIT and Teagasc. Journals considered for publication will be Environmental
Science and Technology, Rapid Communication in Mass Spectrometry, Analytical and
Bioanalytical Chemistry, Analytical Chemistry, Chromatographia, Journal of Separation
Science and Toxicon.
9.
Ethical issues
Not applicable to this application References
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Extraction and LC-MS analysis of pyrrolizidine alkaloids in honeys. Journal of Agriculture
and Food Chemistry, 52, 6664-6672.
Betteridge, K., Cao, Y., and Colegate, S. M. (2005). Improved method for extraction and
LC-MS analysis of pyrrolizidine alkaloids and their N-oxides in honey: application to Echium
vulgare honeys. Journal of Agriculture and Food Chemistry, 53, 1894-1902.
Candrian, U., Luthy, J., Schmid, P., Schlatter, Ch., & Gallasz, E. (1984). Stability of
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935-937.
Crews, C., Startin, J. R., & Clarke, P. A. (1997). Determination of pyrrolizidine alkaloids in
honey from selected sites by solid phase extraction and HPLC-MS. Food Additives and
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Book of Sample Projects Page 99 CIT Rísam PhD Scholarship Programme 2014 Culvenor, C. C. J., Edgar, J. A., Jago, M. V., Qutteridge, A., Peterson, J. E., & Smith, L. W.
(1976). Hepato- and pneumotoxicity of pyrrolizidine alkaloids and derivatives in relation to
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Deinzer, M. L., Thomson, P. A., Burgett, D. M., & Isaacson, D. L. (1977). Pyrrolizidine
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of pyrrolizidine alkaloids in goat's milk. Analytical Chemistry, 54, 1811-1814.
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V. B. R., and Schreier, P. (2008). Pyrrolizidine alkaloids in honey: risk analysis by gas
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Academic Press.
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alkaloid toxicity in livestock: a paradigm for human poisoning? Food Additives and
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Mroczek, T., Glowniak, K., and Wlaszczyk, A. (2002). Simultaneous determination of Noxides and free bases of pyrrolizidine alkaloids by cation-exchange solid-phase extraction
and ion-pair high-performance liquid chromatography. Journal of Chromatography A, 949,
249-262.
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alkaloids. Journal of Natural Products, 44, 129-152.
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R. A., & Molyneux, R. J. (1999). Pyrrolizidine alkaloid plants, metabolism and toxicity.
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Pyrrolizidine alkaloid-containing toxic plants (Senecio,
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North America: Food Animal Practice, 27, 419-428.
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Willmot, F. C., & Robertson, G. W. (1920). Senecio disease, or cirrhosis of the liver due to
Senecio poisoning. Lancet, ii, 848-849.
Book of Sample Projects Page 101 CIT Rísam PhD Scholarship Programme 2014 Title of project: Optical sensing of chemical species General Discipline Area: Chemical Sensing Name of Principal Supervisor: Dr William Doherty Email: William.doherty@cit.ie Telephone: 021 4335865 1.
2.
3.
4.
Abstract (250 words) Detection of chemical species can be achieved used varied analytical methodologies. Electrochemical methods based on ISEs are designed to allow the ion of interest through the membrane or interact with the membrane resulting in a potential that can be accurately measured. Deployment of ISE’s is problematic as they need to be conditioned and suffer from electromagnetic interference. Optical detection does not suffer from electromagnetic interference and can deployed easily at long distances (fibre optics). Detection of ions using novel fluorophores engineered to selectively couple with the ion of interest is of considerable interest worldwide. Detection of nitrate ion as a precursor in the ammonia cycle in aquaculture is of huge economic importance. Current optical methods involve UV detection of the nitrate ion but this is susceptible to many chemical interferents and is unsuitable to fibre deployment. Research Context and Contribution to the Research Field Detection of chemical species can be achieved in many different ways: from traditional “wet chemical” techniques to electrochemical to optical detection. Although traditional methods and electrochemical detection in particular can have high resolution the ability to deploy such systems and remotely operate over long periods of time experience many difficulties. Electromagnetic interference is a major concern due to the long electric cabling required to transmit the potentials measured over long distances, subsequent deterioration in signal unless digitised at source and the possibility of consumable usage. Optical probes based on absorbance or luminescence measurements can easily be deployed over long distances and can be multiplexed. Research into novel fluorophores and ionophores that can selectively reversibly bind to ions is ongoing worldwide. Taking advantage of existing knowledge and techniques, manipulation of existing materials will be undertaken to enhance the selectivity and detection of nitrate ion. In aquaculture for example ammonia is the end product of respiration. In confined areas this quickly reaches toxic levels. Part of the nitrogen cycle involves nitrite ions, nitrate ions and ammonium ions which all contribute to the total nitrogen in solution. As ammonia can be formed by reduction of nitrate, it is important to have the ability to monitor the levels of nitrate in aquaculture, environmental systems and other such aqueous systems. Objectives The key objectives of this proposal are the identification and development of ionophores and ion-­‐selective chromogenic (fluorogenic/phophogenic) material that can be used to selectively identify dissolved ions such as nitrate, nitrite and other ionic species. These materials will then be incorporated into a matrix to allow easy sampling by optical methods. These methodologies depend on the characteristics of the sampling matrix, either by ATR within coated fibres, fluorescence/quenching detection of embedded substrates etc. Research Methodology Book of Sample Projects Page 102 CIT Rísam PhD Scholarship Programme 2014 Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. Work Plan Literature review – 3 months. Identification of suitable existing systems(ionophores/fluorpohores etc) for nitrate ion selectivity – 3 months Identification of probable systems for nitrate ion selectivity – 3 months (overlap with previous WP) Synthesis and characterisation of (2 or 3) preferred systems – 12 months Synthesis and characterisation of (2 or 3) probable systems – 12 months (overlap with previous WP) Development of suitable embedded matrix for fluorescent or absorbent measurements for best system and its characterisation – 12 months Ethical issues NA 5.
6.
Book of Sample Projects Page 103 CIT Rísam PhD Scholarship Programme 2014 INFORMATION & COMMUNICATIONS TECHNOLOGY Computing Title of project: Parallelised Classification of Large Scale Distributed Technical Support Data in the Cloud using Deep Learning -­‐ in conjunction with VMware General Discipline Area: Cloud Computing Name of Principal Investigators: Aisling O’Driscoll Email: aisling.odriscoll@cit.ie Telephone: 4335506 1. Abstract (250 words) Technical Support call centres frequently receive several thousand customer queries on a daily basis. Traditionally, such organisations discard data related to customer enquiries within a relatively short period of time due to limited storage capacity. However, in recent years, the value of retaining and analysing this information has become clear, enabling call centres to identify customer patterns, improve first call resolution and maximise daily closure rates. This research proposes the development and evaluation of an analytics platform for the processing and categorisation of similar technical support calls based on open source big data technologies. The Hadoop programming model, extended ecosystem and the Mahout Big Data Analytics library will be utilised for categorising similar support calls in order to expedite case resolution and accuracy to maximise daily closure rates and improve staff performance. The first phase of the research projects involves a comprehensive comparative analysis of the performance of existing classification algorithms. The second phase will develop and analyse the performance of a deep learning algorithm for deployment on a cloud-­‐based system. Deep learning algorithms are a new category of machine learning that have proven to be highly effective for a range of complex classification techniques. The performance of this algorithm will be comprehensively evaluated with the algorithm results obtained from phase 1. Such an approach should reduce query resolution time and will also ultimately aid technical support teams to increase customer satisfaction and prevent customer churn. Furthermore the proposed research can be used to identify the most problematic product features and can highlight staff knowledge gaps leading to more directed staff training programmes. It is envisaged that the proposed research will be conducted in close collaboration with VMware with the performance of the devised clustering algorithm and software platform evaluated using VMware technical support data. Particular emphasis will be placed on the timeliness and accuracy of the algorithm to optimise search techniques. While research associated with machine learning and data mining algorithms is well established, research on big data analytics and large scale distributed machine learning is very much in its infancy with libraries such as Mahout and Jubatus still undergoing considerable development. Some initial experimentation has been undertaken in this area however clean small data sets have largely been considered and limited clustering algorithms have been evaluated [1-­‐3]. The proposed research will facilitate the streamlining of call centre operations and evaluating multiple clustering algorithms in terms of performance and accuracy. Book of Sample Projects Page 104 CIT Rísam PhD Scholarship Programme 2014 For further details, contact Dr. Aisling O’ Driscoll (aisling.odriscoll@cit.ie, +353 21 4335506) or Dr. Ted Scully (ted.scully@cit.ie, +353 21 4335116. Esteves RM, Pais R, Rong C (2011) K-­‐means Clustering in the Cloud – A Mahout Test. In : IEEE International Conference on Advanced Information Networking and Applications (WAINA ‘11), 2011, pp. 514-­‐519. [2] Esteves RM, Rong C (2011) Using Mahout for Clustering Wikipedia’s Latest Articles: A Comparison between K-­‐means and Fuzzy C-­‐means in the Cloud. In: IEEE Third International Conference on Cloud Computing Technology and Science (CloudCom ‘11), 2011, pp. 565-­‐569. [3] Ericson K, Palliekara S (2011) On the Performance of Distributed Data Clustering Algorithms in File and Streaming Processing Systems. In: IEEE Fourth International Conference on Utility and Cloud Computing, 2011. [1]
Book of Sample Projects Page 105 CIT Rísam PhD Scholarship Programme 2014 Title of project: Performance Modelling, Monitoring and Analysis of Virtualised Big Data Workloads -­‐ in conjunction with VMware General Discipline Area: Cloud Computing Name of Principal Investigators: Aisling O’Driscoll Email: aisling.odriscoll@cit.ie Telephone: 4335506 1. Abstract (250 words) Given the large increase in the proliferation of data sources such as sensors, medical images, financial data, retail, radio frequency identification and social media, commonly referred to as ‘big data’, the need to quickly and accurately process and analyse massive data sets is becoming increasingly challenging. One of the technologies most often associated with Big Data is Apache Hadoop which is based on the MapReduce Java framework and distributed file system originally proposed by Google [v]. While Hadoop is widely recognised as the leading technology for quickly processing massive, often unstructured data sets (the total Hadoop market is expected to reach $13.95 Billion by 2017), it was designed for “bare metal” commodity machines with locally attached storage and processing and rack awareness. However many enterprises have already made considerable investment in their existing infrastructure and cloud environments, often making widespread use of virtualisation to enable elastic computing, allowing systems and service to scale on demand. A virtualised Hadoop solution would allow rapid deployment of clusters (currently a technically challenging process), elasticity, high availability, optimal use of resources and multi-­‐tenancy of workloads. However deploying virtualised Hadoop clusters is extremely challenging, because while Hadoop will function in the cloud, many of its design benefits are negated as data processing may not be localised, resulting in high network communications, and with the benefit of rack awareness not considered in many cloud deployments. To address these challenges, an open source project, Serengeti [vi] was devised and was first debuted at the “HadoopWorld” conference in June 2012. A commercial equivalent of this known as VMware vSphere Big Data Extensions (BDE) was released in late 2013. As a further challenge, data centres are often now expanding beyond their walls, with larger distributed data centres established with Metropolitan Area Networks (MANs). This research thus proposes a comprehensive performance analysis of a virtualised Hadoop environment using Project Serengeti and VMware vSphere Big Data Extensions (BDE) on a MAN. A variety of elastic cluster topologies will be analysed using the Virtual Hadoop Manager (VHM) mechanism with a performance analysis studying the effects of static versus elastic clusters over different workloads and topologies. The objective is to determine a correlation between workload type, cluster type and cluster topology with respect to Hadoop performance in a MAN. Workloads will include artificial workloads as well as real-­‐world applications and a comprehensive simulation analysis will also be used for a scalability evaluation. It is further Book of Sample Projects Page 106 CIT Rísam PhD Scholarship Programme 2014 envisaged that research will be conducted into delivering Map-­‐Reducable machine learning libraries to deliver Big Data as a Service (BDaaS) in a virtualised environment with this research contributing towards the open source Serengeti project. It is envisaged that the proposed research will be conducted in close collaboration with VMware and the BDE developers. For further details, contact Dr. Aisling O’ Driscoll (aisling.odriscoll@cit.ie, +353 21 4335506). 1
[ ] 1
[ ] Dean, J.a.G., S.,, “MapReduce: Simplified Data Processing on Large Clusters”. 6th Symposium on Operating Systems Design and Implementation in cooperation with ACM SIGOPS (OSDI), 2004. http://www.projectserengeti.org/ Book of Sample Projects Page 107 CIT Rísam PhD Scholarship Programme 2014 Title of project: Predictive Big Data Analytics for Anomaly Detected in Cloud Platforms Name of Principal Supervisor: Dr. Ted Scully, Dr. Aisling O’Driscoll Brief Summary of Research Interests: Research interests of Dr. Scully include machine learning, optimization, and big data analytics. Research interests of Dr. O’Driscoll include cloud computing, PaaS and big data processing. CIT Department: Email: 4335506 Computing Ted.Scully@cit.ie, Aisling.ODriscoll@cit.ie Telephone: Discipline Area by Frascati Classification: +353 21 4335116, +353 21 Computer and information sciences 1. Abstract (250 words) The migration of global IT organizations to new technologies such as cloud computing and virtualization has dramatically changed the operational environment faced by IT management. There has been a substantial increase in the amount of data collected – such as log, transaction data, events, and machine data. This has been accentuated by user and application mobility as well as smart devices. This data represents critical information sources for both the prediction and resolution of IT system problems such as outages, sub-­‐optimal system performance or lack of compliance with customer Service Level Agreements (SLAs). Consequently, there has been a concerted move to develop smart and scalable solutions to assist IT management through the use of advanced analytical techniques. It is estimated that by 2016, 20% of Global 2000 enterprises will have an IT operations analytics architecture in place, up from less than 1% in 2011 [1]. The proposed research addresses this through the development of a predictive analytics platform for cloud based systems, focusing on the area of anomaly and fraud detection. The proposed platform will utilise deep learning algorithms, a recent advancement in the area of machine learning. Such algorithms are proving to be highly successful in tackling core problems such as image recognition, speech recognition and have demonstrated an exceptional ability to identify patterns in large amounts of data. The proposed data analytics platform will identify and predict anomalous system behaviour in cloud-­‐based systems thus equipping IT management professionals with the ability to prevent or mitigate the negative impact of such undesirable events. This proposal is supported by the data analytics group of a large multi-­‐national company. 2. Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. Book of Sample Projects Page 108 CIT Rísam PhD Scholarship Programme 2014 Global IT organizations have been quick to adopt Cloud computing which utilises virtualization, enabling a more flexible model for delivering IT service and thus delivering substantial cost benefits. Forbes has reported that 77% of CIOs and Senior IT leaders state that cloud-­‐based infrastructure is in use today in their enterprises [2]. This change, augmented by the widespread adoption of mobile applications and the requirement to support connectivity for a broad range of devices, has resulted in an explosion of data. Such data contains information pertinent to the state of system components, thus representing critical information sources for problem resolution. Adding this data to the events received daily from deterministic performance monitoring tools quickly generates a big data problem for IT management. An IT organisation that does not collate all available sources of information may not be able to adequately solve or, even more importantly, pre-­‐empt a problem at any point in time. The inability to do so can result in costly downtime, potentially impacting profit and market share and reducing customer satisfaction. Legacy techniques traditionally relied upon by IT Management are no longer proving effective, given the increase in the variety and volume of data sources. As such leading multi-­‐nationals such as IBM and HP have recognised this opportunity and have invested in the development of technologies to help address these issues. Substantial growth in the area of data analytical tools for IT Management is anticipated over the coming years with Gartner supporting this viewpoint [1]. Efficiently and effectively mining such large and diverse datasets represents a significant challenge. Over the past number of years many industries have aggressively pursued pattern-­‐based strategies to do this and to enable competitive advantage. The objective of this approach is to exploit the vast amounts of data available in order to identify patterns that can have a positive or negative impact on an organisation's strategy or operations. The realization of such strategies requires the development of new technologies that can identify patterns of change in large amounts of data in order to indicate opportunity or risk. The objective of the research described in this proposal is the development of a predictive data analytics platform that will facilitate pattern based recognition and prediction of anomalous behaviour such as potential outage, service degradation or other unexpected changes. The core underlying technology will be based on innovative deep learning algorithms (a category of machine learning). Machine learning has, over the last two decades, become one of the mainstays of information technology, solving a broad range of problems such as facial recognition, natural language processing, spam detection, computer vision, sentiment analysis, etc. The advent of big data and cloud computing has opened an array of new research challenges and opportunities in areas of machine learning such as classification, pattern recognition etc. Deep learning, a new category of machine learning algorithm, has had a remarkable impact and can be used to train hierarchical machine learning models, such as neural networks. Over the last 24 months alone deep learning has recorded a number of breakthrough results in different application areas including speech recognition, image understanding and drug design, significantly outperforming previous algorithms. The results have been so impressive that even mainstream media has taken note; the New York Times devoted a front page article to the topic [3]. Deep Book of Sample Projects Page 109 CIT Rísam PhD Scholarship Programme 2014 learning is already the core technology used in speech recognition on Android phones and automatic tagging of pictures on Facebook. Deep learning has proven itself to be very effective tool for identifying patterns in big data environments. While deep learning models are computationally demanding, it has become increasingly inexpensive due to powerful resources available via elastic cloud computing architectures. The Cork Institute of Technology currently maintains its own private cloud infrastructure for dedicated research work. This architecture as well as cost effective public cloud architecture will be used for developing and testing the proposed platform. 3.
Objectives Summarise the key objectives of the research. The primary research objectives include: 1. Establishing the current the current state-­‐of-­‐the-­‐art in the area of anomaly detection, with specific focus on the use of machine learning algorithms for anomaly detection in cloud-­‐
based systems. 2. Construction of an appropriate cloud-­‐based deployment and testing environment coupled with the establishment of an appropriate test to use for performance benchmarking and comparative analysis. 3. Research current state of the art in deep learning algorithms. 4. Research and develop novel deep learning algorithm for pattern based anomaly detection n cloud-­‐based environment. 5. Evaluation and refinement of deep learning algorithm on a cloud test environment. Comparative analysis to with previous anomaly detection techniques. 6. Analysis of the scalability and performance limitations of this technique and trial of the devised solution as a Proof of Concept (PoC) with the analytics platform of multi-­‐national partner. 4. Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. •
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An extensive review into the area of machine learning and deep learning algorithms, focusing on the current state of the art in pattern-­‐based anomaly detection. Research and development of novel deep learning algorithms for predication and identification of anomalous system patterns in big data cloud environments Book of Sample Projects Page 110 CIT Rísam PhD Scholarship Programme 2014 •
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Setup and configuration of a distributed Hadoop cluster and “big data” analytics platform using the CIT private cloud infrastructure and Amazons Elastic Map Reduce (EMR) PaaS (Platform as a Service) technology. Empirical evaluation and refinement of deep learning using in-­‐house or test data (provided by multi-­‐national partner company) with the afore-­‐mentioned Hadoop cluster. Validation of scalability and performance against state of the art algorithms for anomaly detection over public and private cloud PaaS technologies. Development of analytical tool that couples the deep learning algorithm with an intelligible interface providing early warning of abnormal behaviour such as potential outage, service degradation or unexpected changes. It is envisaged use of big data MapReduce open source machine learning libraries such as Mahout and Jubatus will be used. Work Plan Present the research work plan, outlining the main research tasks and timing. The proposed research is divided into nine work packages that will guide the research and development activities: •
Work Package 1 – Comprehensive state-­‐of-­‐the-­‐art review of anomaly detection, focusing on the technologies current used for anomaly detection in standard environments and cloud-­‐
based platforms. •
Work Package 2 – Review of deep learning and the application of this technology to identifying patterns in big-­‐data environments. Work Package 3 – Setup and configuration of a distributed Hadoop cluster as a deployment environment. Work Package 4 – Research and construction of an appropriate cloud-­‐based testing environment that will facilitate performance benchmarking and comparative analysis. Work Package 5 – Research and development of deep learning algorithm to produce an initial deep learning prototype for anomaly detection Work Package 6 – Evaluation and comparative analysis of algorithm performance coupled with iterative refinement of the algorithm. Work Package 7 – Development of front end analytical tool that provides an intelligible interface providing early warning of abnormal behaviour Work Package 8 – Periodic meeting with industry collaborators to validate and drive real-­‐
world relevantly of research work. Work Package 9 – Dissemination in the form of conference contribution, high impact peer reviewed publications. Thesis submission and viva. •
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Ph.D. Year 1 Book of Sample Projects Page 111 CIT Rísam PhD Scholarship Programme 2014 Ph.D. Year 2 Book of Sample Projects Page 112 CIT Rísam PhD Scholarship Programme 2014 Ph.D. Year 3 6.
Ethical issues Not Applicable 7.
External Collaboration/Other Institutions The data analytics group of a large multi-­‐national company have expressed their support for the project proposal. It is anticipated that the Ph.D. student will work closely with this company. 8.
References [1] Gartner Group IT Operations Analytics: Pattern-­‐Based Strategies in the Data Center, Published: 23 December 2011. [2] Columbus, I (07 January 2013). CIOs On Cloud Computing Adoption: Conquer Complexity And Help Help Us Grow. Retrieved from http://www.forbes.com/sites/louiscolumbus/2013/07/01/cios-­‐on-­‐cloud-­‐adoption-­‐conquer-­‐
complexity-­‐and-­‐help-­‐us-­‐grow/ [3] Markoff, J, (23 November 2012), Scientists See Promise in Deep-­‐Learning Programs. Retreived from http://www.nytimes.com/2012/11/24/science/scientists-­‐see-­‐advances-­‐in-­‐deep-­‐
learning-­‐a-­‐part-­‐of-­‐artificial-­‐intelligence.html?smid=pl-­‐share&_r=1& Book of Sample Projects Page 113 CIT Rísam PhD Scholarship Programme 2014 Title of project: The Application of Large Scale Optimisation Techniques to Multiple Sequence Alignment using Distributed “Big Data” Analytics Name of Principal Supervisor: Email: ted.scully@cit.ie General Discipline Area: Dr Ted Scully (second Aisling O’ Driscoll) Telephone: Click here to enter text. Computing/Biology (Big Data, Cloud Computing, BioInformatics, Optimization, Machine Learning) This project is suitable for a student with a degree in computer science (or a cognate discipline) and a strong interest in applying computational techniques to solve biological problems. *Detailed research methodologies and contributions have been redacted due to IP sensitivities. 1. Abstract (250 words) In this post-­‐genomics era, an unprecedented proliferation of sequence data is being generated. This data is so vast that since 2008, it is outpacing Moore’s Law, a trend that has remained true for approximately 40 years. A consequence of this is that the medical discoveries of the future will largely depend on the ability to analyse these large genomic data sets. It is necessary that the field of bioinformatics, where computing algorithms are applied to solve life science problems, now adopts cloud computing and “big data” technologies with the benefit to mankind of deciphering such big biological data sets making it the ultimate use case. Multiple sequence alignment (MSA) is a fundamental biological analysis method involving the mass comparison of DNA or protein sequences (computationally a genome sequence is a string with 3 billion characters) to identify similarities, thereby facilitating evolutionary tracking of individuals as well as the identification of protein structure which can be used to design new drug therapies and improve patient diagnostics. The proposed research presents a dual approach. Firstly multi-­‐objective evolutionary algorithms (MOEAs), a machine learning computing technique which incidentally is based on modelling biological processes, will be employed to improve the quality and scalability of MSA algorithms. Secondly, as these machine learning algorithms are inherently parallel, they will be coupled with the distributed high-­‐performance capabilities of cloud computing and parallelised ‘big data’ frameworks to develop a distributed MOEA for the rapid optimisation of mass multiple sequence alignments. 2. Research Context and Contribution to the Research Field This proposed research will be conducted in close collaboration with research underway by existing postgraduate and postdoctoral researchers funded via EU FP7 and nationally funded research projects. The student will be an integral part of this vibrant team and will be contributing to the research in this space. Modern biology now presents new challenges in terms of data management, processing and analysis with biological sequence data being generated at a rate that exceeds Moore’s Law by a factor of 4. This is driven by the dropping cost of sequencing with a decrease in cost from $1 million in 2007 to $1 thousand in 2012. Currently, a much bigger issue than simply storing big data is processing it in a Book of Sample Projects Page 114 CIT Rísam PhD Scholarship Programme 2014 timely manner, and subsequently analysing the data for meaningful deductions. The Multiple Sequence Alignment (MSA) process is integral as it allows scientists to evaluate the impact that mutation in sequences may have on individuals in one particular species or the variation it introduces across many different species. Also in the biopharmaceutical and biomedical fields, multiple sequence alignments have an important role in the preparation of certain vaccines which may be produced from a modified protein strand, which without sequence alignment, would be impossible to complete. However MSA algorithms are currently limited to in their scalability often restricted to <= 50 sequences at one time with more requiring very significant high performance computing. Thus optimisation of these techniques is required to advance their scalability while ensuring the quality of the alignments. Evolutionary algorithms have been successfully applied to the problem of multiple sequence alignment for proteins for this purpose. Furthermore multi-­‐objective evolutionary algorithms have exhibited promising performance and have been identified as a sequence alignment technique that warrants further investigation. It should be further noted that even with the advent of cloud computing techniques and “elastic” computing” i.e. scale up or down compute power on demand, mass MSA presents scalability challenges. A local change scalability optimisation will have huge implication when scaled. The importance of mass MSA is that it can be applied across whole populations to derive complete environmental and regional evaluations with this emergent field known as “meta-­‐genomics”. This research makes two contributions that advances the state of the art in this space which is still very much in its infancy: • The use of machine learning techniques such as MOEAs to optimise the scalability and performance of MSA algorithms. • The application of parallelised NoSQL PaaS (Platform as a Service) technologies to exploit the inherent distributed nature of these MOEAs to provide large scale MSA computation and integration with existing big data machine learning libraries. Machine learning is a scientific discipline that is concerned with the design and development of algorithms that allow computers to learn from data, with evolutionary algorithms forming a category of algorithms. Evolutionary algorithms are population-­‐based meta-­‐heuristic optimization algorithms based on an analogy to biological evolution and have been successfully applied to a broad range of real-­‐world problems such as scheduling, load-­‐balancing and data-­‐mining. Standard evolutionary algorithms generate a relatively large population of candidate solutions (there may be several hundred) and iteratively evolve these solutions over time. In a symbiotic coincidence with the proposed research, this process of evolution involves the use of methods inspired by biological evolution, such as reproduction, mutation, recombination, and selection. Multi-­‐objective evolutionary algorithms are a class of evolutionary algorithm designed to deal with such problems. MOEAs are regarded as effective and robust multi-­‐objective optimizers and consequently have rapidly increased in popularity. Specifically within the field of Bioinformatics, MOEAs have been successfully applied to problems such as molecular docking, DNA sequence design, oligo-­‐nucleotide probe design, gene networks and multiple sequence alignment for proteins. Importantly, further investigation and analysis of such an evolutionary approach to the challenges of scalable, high Book of Sample Projects Page 115 CIT Rísam PhD Scholarship Programme 2014 quality multiple sequence alignments has been identified as an area that would benefit from further research and evaluation Also importantly, the afore-­‐mentioned MOEA algorithms have all been centralised implementations. However MOEAs are naturally distributed with multiple populations evolving independently over time. Therefore not only would MSA greatly benefit in terms of the scalability and quality of alignments using MOEAs but the second objective of this research is to couple the distributed high-­‐
performance capabilities of cloud computing and parallelised natured of emerging NoSQL programming frameworks to develop a distributed multi-­‐objective evolutionary algorithm for the rapid optimization of the multi-­‐sequence alignment problem. This will involve the development of an MOEA based algorithm based NoSQL technologies as well as utilisation of a distributed machine learning library. In the last 18 months, the huge benefits associated with utilising the MapReduce coding framework as the basis for scalable bioinformatics algorithm development. This includes cloud based distributed and parallelised MapReduce pipelines for alignment, mapping, assembly, gene expression, SnP analysis and optimisation. Ultimately by combining the aforementioned NoSQL big data technology and distributed machine learning platforms, facilitated by cloud computing infrastructure and using an MOEA optimised algorithm, mass MSA on a PB level or beyond will be possible thereby facilitating large scale meta genomics projects. 3. Objectives The primary research questions include: 1. What is the current state-­‐of-­‐the-­‐art for optimising multiple sequence alignment algorithms for scalability while not compromising the quality of alignments when using machine learning algorithms? 2. What is the current state of the art in distributed machine learning cloud platforms? 3. Which platform’s underlying architecture is the most appropriate for developing a cloud based multi-­‐objective evolutionary algorithm. 4. Does such a cloud-­‐based multi-­‐objective evolutionary algorithm represent a performance improvement over the current centralised multi-­‐objective approach to multiple sequence alignment for proteins? 5. What are the upper scalability and performance limitations of this technique? The proposed research will answer the above questions and has the following goals/objectives: 1. Perform an extensive analysis of machine learning techniques used for enhancing scalability and quality in the bioinformatics space, current optimization solutions in the multiple-­‐
sequence alignment of sequences and parallelised cloud based versions of same. 2. Evaluate and select the most appropriate parallelised and distributed platform for algorithm development. Book of Sample Projects Page 116 CIT Rísam PhD Scholarship Programme 2014 3. Design and develop an MOEA that is parallelised in nature, which can avail of the large scale cloud computing processing capabilities and evaluate the performance of the MOEA with current techniques. 4. Identification of optimal configuration setting for cloud-­‐based MOEA e.g. the impact on performance of the number of slave populations, number of individuals per population, mutation, crossover operators needs to assess. 5. Identification of a generic framework for such cloud-­‐based MOEAs so that this approach can then be applied to other problems within the Bio-­‐Informatics space. 4.
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An extensive review into in the area of advanced bioinformatics concepts (with a particular focus on multiple sequence alignment), high performance computing and NoSQL solution, machine learning (specifically genetic algorithms) and cloud computing will need to be conducted. Setup and configuration of a distributed Hadoop cluster and “big data” analytics platform using the CIT private cloud infrastructure and Amazons Elastic Map Reduce (EMR) PaaS (Platform as a Service) technology. Evaluation and extension of parallelised machine learning frameworks such as Mahout for MOEAs and implementation of a distributed MOEA MSA algorithm using parallelised programming. Validation of scalability and performance enhancements against state of the art MSA algorithms over public and private cloud PaaS technologies. Work Plan The proposed research is divided into five work packages that will guide the research and development activities: Work Package 1 – Overview of the role of machine learning (particularly evolutionary algorithms) in Bioinformatics (specifically MSA) and the application of distributed and parallelised cloud enabled technologies for same. Work Package 2 – Develop and build a distributed PaaS platform with associated large scale machine learning platform. Work Package 3 -­‐ Implement a localised MOEA optimised MSA and evaluate the scalability and quality of the resulting multiple sequence alignment. Work Package 4 – Extend the cloud based machine learning platform for MOEA support and implement the developed parallelised MOEA MSA algorithm by extending this platform. Work Package 5 – Dissemination in the form of conference contribution, high impact peer reviewed publications. Thesis submission and viva. Book of Sample Projects Page 117 CIT Rísam PhD Scholarship Programme 2014 Ph.D. Year 1 Ph.D. Year 2 Ph.D. Year 3 Book of Sample Projects Page 118 CIT Rísam PhD Scholarship Programme 2014 Working Title of project: Clinical Meta-­‐Analysis of the human gut microbiome using Distributed Cloud Computing Processing and Analytics Frameworks Name of Principal Supervisor: Dr. Aisling O’ Driscoll, Dr. Roy Sleator Brief Summary of Research Interests: Research interests of Dr. O’Driscoll include cloud computing, Platform/Data as a Service (PaaS, DaaS) and big data processing. Dr. Sleator’s research interests include the application of Bioinformatics and molecular based approaches to improving gastrointestinal health; Both of these are central pillars of CIT’s Bio-­‐EXPLORE and ICT research strategies. Dr. O’ Driscoll and Dr. Sleator co-­‐coordinate the CIT MSc in Computational Biology and are funded investigators in this space. In recognition of the timeliness and relevance of their joint research, an article published in the Journal of Biomedical informatics in July 2013, has been viewed ~5000 times and is the fourth most downloaded article in this journal in the last 90 days [1]. CIT Department: Email: 4335405 COMPUTING aisling.odriscoll@cit.ie, roy.sleator@cit.ie Telephone: +35321 4335506, +35321 1. Abstract (250 words) Infectious gastroenteritis is a leading cause of mortality worldwide and incurs significant economic costs for both patient diagnosis and hospitalisation, largely associated with identifying the causative agent. It is increasingly recognised, that computing based (in silico) molecular detection techniques identify these more quickly (~3 hours vs ~3 days in a lab) and more specifically. However, this is only the tip of the iceberg and begs the question – what else is being missed? More importantly, with the rise of large publicly available open data sets and the understanding that future discoveries will largely be made by those who have advanced computer science skills, the ability to efficiently process and analyse vast genomic data sets, both in terms of cost and timely processing but also with respect to the availability of parallelised analytical applications that are suitable to utilise such compute capabilities, is vital. This project proposes to undertake a large scale comparative genomics meta-­‐analysis of the human gut microbiome with a specific focus on microbes of clinical importance, using parallelised frameworks and cloud computing technology. Utilising this platform, the algorithms underpinning key biological processes will be parallelized using the powerful Map Reduce computing paradigm with new algorithms devised by scanning and comparing the genomes of major gastrointestinal pathogens for unique molecular identifiers using large scale distributed machine learning libraries. 2. Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. Advances in next-­‐generation sequencing technologies have resulted in the generation of unprecedented levels of sequence data. Therefore, modern biology now presents new challenges in terms of data management, query and analysis. Human DNA is comprised of approximately 3 billion base pairs with a personal genome representing approximately 100 gigabytes (GB) of data, the equivalent of 102,400 photos. Book of Sample Projects Page 119 CIT Rísam PhD Scholarship Programme 2014 Moore’s Law describes a trend coined by Intel co-­‐founder Gordon Moore which states that “the number of transistors that can be placed on an integrated circuit board is increasing exponentially, with a doubling time of roughly 18 months”. Put more simply: computers double in speed and half in size every 18 months. This trend has remained true for approximately 40 years, until the completion of the Human Genome project in 2003. Since then, a deluge of biological sequence data has been generated; a phenomenon largely spurred by the falling cost of next generation sequencing (sequencing a human genome has decreased in cost from ~$1 million in 2007 to ~$1 thousand in 2012). With mobile sequencing thumb drives on the horizon, it shows no sign of slowing. Over the coming years, the U.S. National Cancer Institute will sequence a million genomes to understand biological pathways and genomic variation. Given that the whole genome of a tumour and a matching normal tissue sample consumes 1TB uncompressed data (this could be reduced by a factor of 10 if compressed); one million genomes will require ~1 million TB, equivalent to 1,000 petabyte (PB) or 1 Exabyte (EB). Until recent years, Moore’s law managed to keep ahead of the genomic curve, slightly outpacing the generation of biological sequence data by its growth in storage and processing capacity. However, since 2008, genomics data is outpacing Moore’s Law by a factor of 4. Biology’s big data sets are now more expensive to store, process and analyse than they are to generate. This challenge is ongoing and is still not adequately addressed. The proposed research will focus on the development of improved algorithms to analyse the human microbiome, a computational challenge of a much greater magnitude, both in terms of timely processing and accurate analysis. 2Kg of bacteria exists in the average human gut which is 10 times more bacterial cells than human cells. Furthermore, there is 100 times more bacterial DNA than human DNA. Thus, while the human genome project at the turn of the century resulted in a huge growth in biotechnology, massively exceeding Moore’s law, now 10 years later, processing and analysing the human microbiome is 100 times more complex. The proposed research involves using elastic cloud computing and big data technologies such as the Apache Hadoop project (including extended eco system and new distributed machine learning libraries), which provide distributed parallelised data processing and analysis of petabyte (PB) scale data sets, to develop parallelised algorithms to address this challenge. Developing such algorithms as well as collecting and compiling the data to perform the correlation of niche specific factors such as pH, awand bile within the gut to determine unique biomarkers is likely to represent a larger ‘big data’ problem than computing the correlations themselves. While the powerful MapReduce paradigm is maturing within the field of technology, its potential is largely unexplored in the area of bioinformatics. Combining this with a processing and analysis challenge of a much greater magnitude (the human microbiome) and proposing the use of parallelised machine learning classification algorithms using this paradigm (research in this space is rapidly accelerating), will result in cutting edge and high impact research, not only from a computer science perspective but also in the area of gut health. 3.
Objectives Summarise the key objectives of the research. Book of Sample Projects Page 120 CIT Rísam PhD Scholarship Programme 2014 Overarching research questions include: 1. What are the current approaches in big data frameworks and cloud computing techniques and how can these be applied to in silico analysis & SnP detection to achieve benefits of computational speed, efficiency, scalability and cost? 2. What are the most appropriate distributed machine learning algorithms to best enable the process of sensitive and specific pathogen identification and phylogenetic analysis? 3. Can a definitive ‘bank’ of gastrointestinal specific virulence markers be constructed as biomarkers of bacterial associated gastroenteritis ? Goals/objectives: 1. Development of a bio-­‐cloud platform providing large scale distributed sequence alignment and assembly. 2. Development and analysis of a biomarker detection algorithm (parallelised in nature) to scan and compare genomes of major bacterial gastrointestinal pathogens for unique biomarkers. 3. Develop and analysis of an iterative parallelised molecular evolution genetic algorithm to categorise virulent and avirulent gastrointestinal pathogens. 4.
Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. •
Setup and configuration of a distributed Hadoop cluster using the private and public cloud infrastructure and services. It is proposed to use distributed and parallelized cloud processing and analytics, based on the Apache Hadoop project (based on a CDH4 distribution and using Python streaming), as well as subprojects such as HIVE, Twister, Mahout (or Jubatus), to devise the proposed algorithms. Furthermore, project Serengeti will be explored to enable easy management of the Hadoop cluster in a virtualised environment on the private cloud rather than via “bare metal” commodity servers to facilitate elastic scaling of the cluster. •
Identification and utilization of open data sets including the AWS human microbiome project and emerging Application program Interfaces (APIs) such as Google Genomics. Design, implementation and evaluation of current distributed algorithms for large scale sequencing, especially assembly and alignment. Many of these algorithms comprise iterative components. Given the iterative nature of such algorithms the Twister iterative MapReduce project will be investigated. •
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Design, implementation and evaluation of parallelised algorithms to identify unique biomarkers (SnPs and indels) indicative of particular gastrointestinal symptoms. Such an approach will allow billions of bases of sequences to be compared and genotyped accurately in under a few hours. Sequence data will be obtained from the public databases in combination with proprietary patient sequence data which is exclusively available to this project. •
Design, implementation and evaluation of a molecular evolution genetic algorithm to categorise existing and newly identified gastrointestinal strains and classify virulent versus Book of Sample Projects Page 121 CIT Rísam PhD Scholarship Programme 2014 avirulent groups using supervised and unsupervised machine learning techniques, such as classification and clustering algorithms. 5.
Work Plan Present the research work plan, outlining the main research tasks and timing. This project will use a five stage process. The identified work packages have been briefly described below: WP1: Overview of the state of the art in Cloud Computing, Distributed and Parallelised Programming and Analytical Frameworks and Advanced Bioinformatics -­‐ 6 months An extensive overview of key cloud computing concepts, technologies as well distributed and parallelised frameworks will be undertaken. A further review of the application of machine learning for bioinformatics applications will be undertaken along with a state of the art review in the area of advanced molecular diagnostics and phylogenetics algorithms. WP2: Testbed Development -­‐ 10 months A distributed and parallelised cloud processing and analytics virtualised test-­‐bed will be set up comprised of an Apache Hadoop cluster, as well as subprojects HIVE, Twister and Mahout. APIs such as Google Genomics [2] and publicly available data sets such as the AWS Human Microbiome project data set (5TB) [3]. WP3: Parallelised MapReduce Assembly and Alignment Algorithms – 15 months Using the test-­‐bed from WP2, Map Reduce algorithms for parallelised assembly and alignment will be designed and evaluated for construction of a full genomic sequences and alignment of multiple sequences. WP4: Parallelised MapReduce BioMarker Identification – 11 months Proprietary patient sequence data exclusive to this project, together with AWS public datasets will be investigated using a custom developed MapReduce biomarker (SnP) identification algorithm to scan and compare the genomes of major bacterial gastrointestinal pathogens for unique molecular identifiers. Existing and newly identified pathogenic bacterial strains will be categorised using parallelised classification algorithms via the Mahout/Jubatus libraries and virulent/a-­‐virulent strains grouped using distributed clustering. WP5: Dissemination and Dissertation -­‐ Ongoing (Thesis: 6 months) This work package is on-­‐going for the duration of the research including dissemination of literature review and research results via seminars, conferences, journal publications, articles, postgraduate fairs, undergraduate demo sessions and finally via a formal thesis. 6.
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Ethical issues Not Applicable – use of publicly available anonymised datasets available on public cloud computing platforms as well as existing ethically approved genomic data. External Collaboration/Other Institutions Book of Sample Projects Page 122 CIT Rísam PhD Scholarship Programme 2014 8.
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Dr O’ Driscoll and Dr. Sleator are both funded investigators with Teagasc Moorepark and the Alimentary Pharmabiotic Centre (leading centre in gut health). Dr. O’ Driscoll is also currently collaborating with leading Cloud Computing and Virtualisation multinationals and academic research groups in this research space. It is further anticipated that the student will partake in open source online communities such as BioPython, Google Genomics developers etc. Dissemination and Impact Dr. O’ Driscoll and Dr. Sleator have an established and active publication record with a joint H index of 28 and total citations exceeding 5000. As noted in the abstract, their published research in this specific research area has been widely downloaded and referenced. Its significance was also recognised by their recent funding through the Alimentary Pharmabiotic Centre (APC) SFI funded Innovation Platform which funded a small number of leading edge research projects in gut health. References [1] O'Driscoll A, Daugelaite J, Sleator RD: "Big data", Hadoop and cloud computing in genomics. Journal of biomedical informatics 2013, 46(5):774-­‐81 [2] https://developers.google.com/genomics/ [3] http://aws.amazon.com/datasets/1903160021374413 Book of Sample Projects Page 123 CIT Rísam PhD Scholarship Programme 2014 Nimbus Centre for Embedded Systems Research Overview Embedded systems are the hidden sensors, computers and controllers underpin our entire technological world – without them, much of the technology we take for granted in our daily lives would simply stop working. The next phase of embedded systems technology is networked embedded systems (NES) where embedded systems communicate to form networks of distributed intelligence from the local scale such as smart buildings, to massively networked systems, e.g. energy management on a national scale and the Internet of Things. Research on this topic in CIT is carried in the Nimbus Centre for Embedded Systems Research. The NIMBUS Centre is Ireland’s only research centre devoted to the field of networked embedded electronic systems and is housed in a custom-­‐built facility on the CIT campus. Nimbus was originally funded in 2007 under the Higher Education Authority’s Programme for Research in Third Level Institutions (PRTLI) and co-­‐funded under the European Regional Development Fund (ERDF). The Centre is equipped with state-­‐of-­‐the-­‐art facilities and equipment for embedded systems research, development and application. NIMBUS, and its sixty five researchers and engineers, is managed by CIT staff with extensive international research, industry collaboration and education experience. The core ethos of Nimbus is “Research that leads to Innovation” and the Centre’s structure, shown in the figure below, reflects this ethos. linked to CIT Energy and Sustainable Environment (ESE) Cluster Nimbus: “Research that leads to Innovation” Book of Sample Projects Page 124 CIT Rísam PhD Scholarship Programme 2014 Research Rather than focus in-­‐depth on specific, narrow aspects of embedded systems, Nimbus research addresses research on methodologies for knitting together the disparate strands of embedded systems technology to efficiently address different application domains. These methodologies for systems integration – bringing together hardware, networking, software and network management – are key to NES innovation. Applications Nimbus has identified two emerging application areas where embedded systems will have global impact: “Energy and Water” and the “Smart Objects and Environments” that will make up the “Internet of Things”. While Nimbus also works in other application areas, these two areas have been selected as drivers of research since the solutions to the challenges they present can also be applied in many other domains. Innovation Nimbus has an internal group, TEC-­‐Centre, which is the Nimbus industry interface and which is engaged in research and application development with a large number of Irish companies and start-­‐ups. The TEC-­‐Centre also manages the Centre’s intellectual property, licensing and spin-­‐off activities. The “whole system design” ethos and the diversity of applications addressed by Nimbus mean that multidiscplinarity is key to the Centre’s strategy. Nimbus staff reflect the different sub-­‐disciplines of embedded systems and, across CIT, Nimbus collaborates with researchers in areas such as computing, energy, water, manufacturing and architecture. At national level, CIT has close collaborations with Tyndall National Institute, the Environmental Research Institute and the Cork Centre for Constraint Computing at UCC, with the School of Computer Science and Statistics in TCD and with UCD and NUIG, among others. Internationally, Nimbus is active in EU research programmes with partners from across Europe and is project coordinator of a number of major EU-­‐funded projects. Within the CIT academic structure, Nimbus is a Centre in the School of Mechanical, Electrical, and Process Engineering within the Faculty of Engineering and Science, with particularly close associations with the Department of Electronic and Electrical Engineering where Nimbus contributes to both undergraduate and postgraduate teaching. Postgraduate Study at Nimbus Nimbus offers postgraduate research opportunities up to PhD (Level 10) for full-­‐time, part-­‐time and workplace students from a range of disciplines including electronics, telecommunications, computing, software, networking, energy, mechanical engineering and mechatronics. In Nimbus, students have the opportunity to carry out full-­‐time or part-­‐time research towards a masters or PhD degree in embedded systems hardware, software, networking and applications. Nimbus application areas include energy, water, smart cities, location and tracking, the built environment, health and related areas. Opportunities also exist for postgraduate study in collaboration with Nimbus up to doctoral level in the workplace. Nimbus postgraduate students carry out their research with supervisors with international reputations in their fields and with extensive experience in postgraduate supervision. These students came from a wide range of backgrounds With state of the art facilities, highly experienced Book of Sample Projects Page 125 CIT Rísam PhD Scholarship Programme 2014 supervisors, strong national and international research collaborations and deep engagement with industry, Nimbus provides a first-­‐class environment for postgraduate study. Please visit www.nimbus.cit.ie/education for further information and details of currently available opportunities. NIMBUS RISAM Scholarship Project Abstracts 2014 If you wish to apply for any of the six projects listed below please contact the supervisor by email (with a copy to john.barrett@cit.ie) enclosing a detailed CV, copies of your examination transcripts, English language certification (if relevant), and any further information you think may support your application. If your application is accepted, you will then be supported through the RISAM application process. An overview of the Nimbus Centre is included after the project abstracts and more detailed information can be found at www.nimbus.cit.ie . Book of Sample Projects Page 126 CIT Rísam PhD Scholarship Programme 2014 1. Design for Reliability of Embedded Systems in High Vibration Environments Embedded sensing systems are increasingly being deployed in environments where they are exposed to high levels of vibration in applications such as transport, engine and machinery monitoring, robotics, and wearable systems. These vibrations, with high g-­‐forces and wide frequency spectra, place significant reliability stresses on the embedded systems but the vibrations also provide mechanical energy that can be converted using mechanical-­‐to-­‐
electrical energy-­‐harvesting transducers and used to power the embedded system. This, however, presents a considerable challenge in system design of the embedded system as the harvester must necessarily be exposed to the vibrations while, at the same time, the embedded system needs to be isolated from the vibrations. This research project will investigate the design for reliability of embedded sensing systems in such high vibration environments, studying materials and electronic packaging designs for maximising the reliability of the embedded systems. A combination of simulations and measurements will be used in the investigation. Student profile The project will suit a mechanical or mechatronics engineering graduate but it may also be suitable for a materials science or physics graduate with interest and experience in mechanics of materials. Project supervisor will be Dr. John Barrett http://nimbus.cit.ie/author/johnb/ john.barrett@cit.ie Frascati: 2.2, 2.3, 2.5 Book of Sample Projects Page 127 CIT Rísam PhD Scholarship Programme 2014 2. Smart City Wireless Sensor Networks: Software Architecture Design Sensing infrastructures are gradually evolving with wireless sensor networks (WSNs) being a part of a global sensing infrastructure. Expectations for next generation infrastructures, like that of Smart Cities where by 2030 60% of the of the world’s population is expected to live in cites will place increasing strain on urban resources and services, presents an opportunity to drive a more sustainable economic development and where the virtual world of mobile services, Internet of Things and Social Networks can be merged with the physical infrastructures of smart homes, smart buildings and smart utilities etc. to give rise to a unified communication and collaboration sensing infrastructure. Smart cities is a view to the future for cities where novel services will be offered based on the digital integration of city infrastructures through computing systems that enable on-­‐demand service delivery. Smart cities will revolutionise the way in which organisations will communicate in future urban environments, which will be based on the paradigm of integration and on-­‐demand service delivery. While WSNs are seen as an enabling technology for next generation networks a shift away from the single application serving a single end user is needed. The fit for purpose WSN design and deployment common nowadays will not be sustainable in next generation WSNs networks, where multiple applications and end users are expected to act on a single infrastructure harmoniously. To serve the needs for smart cities this proposal will target the development of a software architecture to support infrastructure virtualisation and management in Smart City WSNs that can be dynamically provisioned to support multiple end user organisations concurrently. Student profile The project will suit a graduate with an electronic engineering or computing/informatics background. Project supervisors will be Dr. Susan Rea http://nimbus.cit.ie/author/susan-­‐rea/ susan.rea@cit.ie and Dr. Alan McGibney http://nimbus.cit.ie/author/alanm/ alan.mcgibney@cit.ie Frascati: 1.2, 2.2 Book of Sample Projects Page 128 CIT Rísam PhD Scholarship Programme 2014 3. Aware, Intelligent and Responsive System for Smart Habitat Over the last decades, the continuous advancements in ubiquitous and pervasive computing paradigm have encouraged researchers to realise more smartness residential settings. In spite of fairly long history of smart home technology, they are still seen through analogies to science fiction stories or movies and are failed to move far in the direction of mainstream diffusion in market. However, recent rapid-­‐paced developments in technology including wearable sensors, intelligence appliances, robotics, communication protocols and so on, have created a new wave of interest in smart living concept that is illustrated as a residence equipped with computing and information technology which is resident aware and intelligent enough to anticipates their needs, and responsive to raise their comfort, convenience and security through the management of the technology. The goal of the current project is to offer intelligent support to the inhabitants by investigating and developing solutions imbued with the awareness of the resident context(location , preferences, activities), physical context (lighting, temperature, house design), and time context (hour of the day, day of week, season, year). As a result, novel framework will be proposed for knowledge based recommender system that will curtail the complexity associated with autonomous management of smart home services by offering smart choice based on contextual information to autonomous agents. The research will focus on following critical aspects, but are not limited to; 1. Interoperable knowledge representation format of home domain which covers context-­‐related information. 2. Identifying activities of home occupants or current states of the home devices/environments by reasoning over knowledge structure populated with stream of measurements and data from diverse set of sensors attached with objects. 3. Recommendation algorithm that will take into account the detailed contextual knowledge to identify appropriate services and dispose them to autonomous agents for execution. Student profile The project will suit a graduate with an informatics and programming background. Project supervisor will be Dr. Jasvinder Singh http://nimbus.cit.ie/author/jasvinder/ jasvinder.singh@cit.ie Frascati: 1.2, 2.2 Book of Sample Projects Page 129 CIT Rísam PhD Scholarship Programme 2014 4. Tracking for Security Tracking of people and asset is an essential part of any security system when positions and past trajectories can support seamless authentication. High proliferation of smart phones, Wi-­‐Fi networks and camera surveillance systems in corporate environments allows the introduction of mobile access credentials, which brings the user’s continuous position into the security system as an essential part of the decision process of unobtrusive seamless access authorisation. Research on the seamless authentication covers: •
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smart phone and RFID based indoor/outdoor tracking systems, surveillance camera based tracking systems, occupancy detection and inference event-­‐driven software platform development for time-­‐critical elastic processing of large amount of data in the cloud/edge Student profile The project will suit a graduate with an interest in complex system development leading to the implementation of working prototypes and integrated systems and a background from one of the following areas: computing, electronics, and physics. Basic understanding of stochastic data processing is an advantage. Project supervisor will be Dr. Martin Klepal http://nimbus.cit.ie/author/mklepal/ martin.klepal@cit.ie Frascati: 1.2, 2.2 Book of Sample Projects Page 130 CIT Rísam PhD Scholarship Programme 2014 5. Building occupancy monitoring based on CCTV camera networks and sensor fusion Continuous monitoring of building occupancy is relevant for a variety of applications ranging from safety and security to energy management and building usage optimisation. Different applications require different levels of granularity, have to be based on a variety of sensor deployments, and have varying accuracy requirements. At present no single solution is available and many challenges prevail. Currently we are particularly interested in how CCTV camera networks can be integrated with other occupancy monitoring equipment and how this data can be efficiently processed and fused. Other areas of interest include how inference of typical behaviour patterns might be learned, how this information can be fed back into the fusion algorithms, and how behaviour might be influenced to achieve and optimise application goals. There are also research opportunities in optimal deployment planning and calibration of CCTV camera networks, and developing a scalable system architecture that allows coping with the very high processing and data volume requirements posed by video processing in large real world deployments. Student profile The project will suit a graduate with a computing/informatics background. Project supervisor will be Dr. Christian Beder http://nimbus.cit.ie/author/christianb/ christian.beder@cit.ie Frascati: 1.2, 2.2 Book of Sample Projects Page 131 CIT Rísam PhD Scholarship Programme 2014 6. Sound Source Separation using Kernel Additive Models Sound Source Separation (SSS) attempts to extract individual instruments or sound sources from recordings of mixtures of sound sources, such as a pop song, or a live recording of an ensemble. It has applications in music education, remixing and up-­‐mixing of recordings, noise reduction, and audio forensics. Many different approaches have been proposed to tackle this problem, including factorisation-­‐based methods such as non-­‐negative matrix factorisation and Bayesian/statistical techniques. Recently, a new framework for performing source separation, termed Kernel Additive Modelling (KAM), has been proposed. This framework generalises a number of recent and efficient techniques for SSS, and allows for easy development of new separation algorithms. KAM assumes that a source at some location can be estimated using its values at other nearby locations, where nearness is defined through a source-­‐specific proximity kernel. These kernels provide an efficient way to account for features such as periodicity, continuity, smoothness, stability in time and frequency, as well as other features, in ways that are not easily achieved using Bayesian and factorisation-­‐based source separation methods. It is proposed to investigate the use of the KAM framework to develop new and novel algorithms for SSS. Student profile The project will best suit a graduate with a signal processing or mathematical modelling background. Project supervisor will be Dr. Derry Fitzgerald who is a senior Post-­‐Doctoral Researcher in NIMBUS. He was a Stokes Lecturer in Sound Source Separation algorithms at the Audio Research Group in DIT from 2008-­‐2013. Previous to this he worked as a post-­‐doctoral researcher in the Dept. of Electronic Engineering at Cork Institute of Technology, having previously completed a Ph.D. and an M.A. at Dublin Institute of Technology. He has also worked as a Chemical Engineer in the pharmaceutical industry for some years. In the field of music and audio, he has also worked as a sound engineer and has written scores for theatre. He has recently utilised his sound source separation technologies to create the first ever officially released stereo mixes of several songs for the Beach Boys, including Good Vibrations, Help me Rhonda and I Get Around. His research interests are in the areas of sound source separation, upmixing from mono to stereo, tensor factorizations, automatic music transcription and music information retrieval systems. derry.fitzgerald@cit.ie Frascati: 1.1, 1.2, 1.3, 2.2 Book of Sample Projects Page 132 CIT Rísam PhD Scholarship Programme 2014 Working Title of project: gestural and locational data Password-­‐free Authentication by associating behavioural, Name of Principal Supervisor: Dr Alex Vakaloudis Brief Summary of Research Interests: Independent Living, e-­‐learning, security CIT Department: Email: Nimbus/TEC alex.vakaloudis@cit.ie Discipline Area by Frascati Classification: Telephone: 021 4335163 Information science (social aspects) 1. Abstract (250 words) The textual username/password paradigm for authentication has always had its critiques. With technological advances and especially with the wide-­‐spread commercialisation of smartphones and touch-­‐screen tablet devices other methods for authentication are coming to the foreground. Due to the availability of tools (camera, microphone, speaker) and sensors (accelerometer) biometric techniques such as facial or fingerprint recognition as well as gesture-­‐based ones have been adopted by tablet/smartphone manufacturers. The main research objective of this proposal is to make the authentication procedure password-­‐
free and produce a unified authentication technique based on three factors namely, biometric (who are you), gestural (what do you know) and positional (where are you) data. Towards achieving this, the dependencies between the three factors will be specified in a formal level. Secondly to evaluate implementations (e.g. iris, fingerprint for biometric) of each factor against use cases of general and specialised applications. Although biometric or gestural or even location based authentication techniques exist for years there is no approach to unify them adding value from their dependencies. The final outcome therefore will be a formalised framework defining a text-­‐free unified approach to authentication. 2. Research Context and Contribution to the Research Field Breaking the link between passwords and authentication has been researched for years but it is in our days that it is becoming mainstream because of the capabilities of smartphones and tablets. Apple have introduced fingerprint authentication. The FIDO alliance (Google, Microsoft, Blackberry etc.) is an industry-­‐led group aiming to specify password-­‐less techniques. It is fair to claim that the password-­‐free authentication is an active, on-­‐going research area. There are a number of published works on biometric, gestural and locational authentication. Although there is no specific focus on the capabilities of everyday devices (e.g. limited resolution on a phone’s camera) we intend to use previous works at least on the individual factor authentication. The distinctions between the traditional username/password way will be highlighted; for instance while there exist a unique matching for a textual password this cannot be applied to a gestural factor. Book of Sample Projects Page 133 CIT Rísam PhD Scholarship Programme 2014 3.
Our contribution would be on unifying these three factors to provide a single authentication profile. We intend to show that the three factor authentication is more than simply a three-­‐step security measure and to our knowledge the dependency between them has not been investigated and can have added value from a security perspective. Objectives 1. Specify the ontologies of the biometric, gestural and locational elements of authentication, their dependencies and the relationships to the traditional notions of username and password. 2. Develop a formal model for the authentication process and formalise the factors that have an impact of it, for example determine the “strength” of a gesture (in a similar manner to a strong password) 3. Develop the algorithms that manage the unified authentication decision 4. Develop the techniques that drive the behavioural characteristics of the gestural element 5. Work on a case study either on general population or on people with special needs. 4.
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Research Methodology As mentioned above, there are methods to achieve biometric and gestural authentication. Where applicable we are going to be based on previous work that tackles individual factor authentication (e.g. biometric). Although the core of this project belongs to computer science, input will be needed by occupational therapists and user experience experts. The modelling of the authentication engine will be driven by the user requirements (generic or specialised use) that will highlight peculiarities on non-­‐textual authentication. For example if drawing a line is used for gestural authentication, is gradual drifting from the stored pattern an expected intolerable or to be monitored occurrence and how should it be treated? Specification and formalisation of parameters relative to the authentication process will also be fulfilled. Of interest is incorporating a device’s technical limitations into the modelling. For example the sensitivity of the gesture could be related to the resolution of the biometric. Work Plan WP1: Specify the conceptual definition of entities in the unified authentication process. WP2: Define the User experience for general and specialised (e.g. deaf people) and particular devices. WP3: Develop and implement algorithms for the authentication engine and define test-­‐driven scenaria. WP4: Perform a pilot study to verify model and implementation work . WP5: Writing up and dissemination. Book of Sample Projects Page 134 CIT Rísam PhD Scholarship Programme 2014 As we intend to satisfy both generic and specialised usages we need to adopt an agile-­‐based approach with iterations as illustrated in the following table 6.
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Year 1 Year 2 Year 3 WP1 WP2 WP3 WP4 WP5 Ethical issues Pilot studies will involve volunteers testing the end product and since the area of concern is authentication we have an issue of privacy. Every action involving individuals will be subject to approval by the CIT authorities and abide with the Data Protection Act. Any personal data (e.g. photos) will be kept in CIT servers and will be destroyed when not needed. External Collaboration/Other Institutions Sensipass is a company with patents on the biometric/gesture domain and with which Nimbus/CIT are working with. Researching this domain is within their interests and they can also provide links to specialised groups like the National Association of the Blind in Ireland and abroad Book of Sample Projects Page 135 CIT Rísam PhD Scholarship Programme 2014 Title of project: Distributed Predictive Control with Self-­‐modelling capabilities: Application to building energy management Name of Principal Supervisor: Dr. Samira Roshany-­‐Yamchi & co-­‐supervisor: Juan Manuel Escano Brief Summary of Research Interests: Modelling, Control and Automation, Distributed Control, Distributed Estimation, Model Predictive Control, Energy Optimization, Embedded Systems CIT Department: Embedded Research Email: Electrical and Electronics Engineering – NIMBUS Centre for samira.roshany@cit.ie Discipline Area by Frascati Classification: Telephone: 0877875423 Engineering and Technology 1. Abstract (250 words) The monitoring of real energy use in energy-­‐efficient buildings frequently shows major differences with respect to the predicted performance. This is even worse if a set of interacting buildings is considered. It is therefore important to capture the real complexities of the energy performance of the actual buildings and districts. In addition, effective methodologies for the correct understanding of user behaviour need to be addressed. At building level, the research focus is on developing methodologies and tools to monitor and assess actual building energy performance, considering relevant factors such as user behaviour, complex energy systems performance and weather forecast, and to be able to predict accurately building energy loads and consumption along the whole lifecycle. The effective monitoring and management of energy flows to reduce energy consumption and to ensure that the building is operated in a way that meets design intent should also be addressed. Common indicators, measuring technologies and data analysis methods should be developed to monitor building performance during operation. A building (or set of building) is a system with varying parameters. This implies that any model is changing over time. The complexity associated with it can be handled by a distributed modeling paradigm. Considering a distributed control scheme based on self-­‐adjusting model can reach a feasible solution of the problem. The new methods and tools could include energy performance diagnostics for predictive maintenance, to provide the accuracy required to properly value retrofit technologies and support decision making during the different stages in the life of the buildings. 2. Research Context and Contribution to the Research Field The proposed research project addresses the problems of i. Mathematical modeling of the control problem. ii. Stability analysis toward better performance of the system and also preventing costly outages through better failure detection. iii. Exploitation of distributed computing with the aim of decreasing the computational complexity and consequently minimizing the costs. iv. Analysis of dynamic re-­‐configurability for the distributed control system. Book of Sample Projects Page 136 CIT Rísam PhD Scholarship Programme 2014 v. Design of a self-­‐learning system to adapt dynamically the model of the system performance. 3.
Objectives Most of the new solutions proposed for energy generation and consumption, are intrinsically distributed [1], e.g. this represents a significant change in the design paradigm of power systems that has been traditionally based on large concentrated power plants. Furthermore, in the case of renewable generation, the primary source is partly unpredictable. In the case of micro systems, often owned by end users, the direct control, from the distribution point of view, is generally impossible. One of the major trends in the generation and consumption is the effects on the control of the generation trends [1]. More unpredictable generation requires more power reserve, more energy storage, and more controllable load control to achieve load-­‐generation balance. Furthermore, for best exploitation of the resources and operation of the power system, this should be achieved dynamically, thus implying demanding requirements on monitoring, control and communications. The major challenges that one facing the successful application of distributed control are as follows: !
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Complexity (many subsystems/agents): When the number of control agents involved in the distributed control structure gets numerous, suitable negotiation strategies among the control agents are needed to achieve reasonable performance and behavior. This issue will be more challenging when the agents in a networked large-­‐scale system are supposed to be smart. Constraints: In building, large numbers of constraints including demand response constraints and regulation service constraints (described below) should be taken into account. Demand response constraints are as follows: 1. Limited communication: communication protocols need to be established for the demand response so that less communication is required between the control agent and the demand response agent to avoid complexity. 2. Mechanical wear-­‐and-­‐tear of appliances: Excessive wear and tear on appliances should be avoided. This means that the controller cannot send signals to the consumers (homes and businesses) too frequently. 3. Uncertainty of response: one of the essential components of the demand response is the ability for a customer to override the controller’s signal at any time. As the population of demand response participants increases, so does the variance of this uncertainty. The objectives of the research are to address the following issues: Book of Sample Projects Page 137 CIT Rísam PhD Scholarship Programme 2014 Investigate critical problems in the area of controlling the building energy performance as large-­‐scale networked systems. -­‐ Develop a reconfigurable control algorithm applicable to the building(s) energy performance. -­‐ To define distributed control strategy in order to reduce the computational complexity and increase the algorithm efficiency. Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. -­‐
4. Research Methodology A natural choice for the control design framework is Model Predictive Control (MPC). MPC is an advanced control strategy that uses dynamical model of the system to predict the future output of the system. The main reasons for its success can be numerated as follows: 1. It handles multivariable control problems naturally. 2. It can take account of actuator limitations. 3. It allows operation closer to constraints (compared with conventional control), which frequently leads to more profitable operation. The distributed MPC control algorithm for the building must provide the appropriate power reference signal for each asset and load. The energy control algorithm is considered fixed and known. To pursue the above objectives, the project aims to develop models for distributed model predictive control (DMPC) of the energy building system and the relation to the power set-­‐points and resulting loads. In DMPC algorithm the overall system is decomposed into smaller, more manageable subsystems with interacting parts and then instead of having one centralized MPC controller we will have several interacting local MPC controllers. Since in DMPC the local controllers have less number of inputs and outputs, the computational complexity will be reduced in compare with centralized MPC. In the distributed structure the assets and loads essentially only communicate with their neighbours and the effect of each one on its neighbour and also the effect of communication failure will be studied in this work. Book of Sample Projects Page 138 CIT Rísam PhD Scholarship Programme 2014 Fig.1 Distributed model predictive control for a building [11] Fig.2 Centralized model predictive control for a building [11] The distributed algorithms will be assessed in simulation study on Nimbus testbed (C.I.T.). We will identify information theoretic capacities that will characterize the value of information for prediction and control. We will use these analyses to determine communication requirements for effective control, and to identify thresholds at which additional information is of little value. Book of Sample Projects Page 139 CIT Rísam PhD Scholarship Programme 2014 Control algorithm properties such as stability, convergence, robustness and computational complexity will also be studied. In order to test the algorithm a simulation environment will be developed through MATLAB and Simulink. 5.
Work Plan Seven milestones are defined (see Gantt chart) which guide the project: M1 – completing the literature review, (6 months) M2 – developing the mathematical distributed model of the building energy performance, (4 months) M3 – developing the implementable control strategy on the building by using real data/model, (8 months) M4 – simulation models and analysis the simulation results, (4 months) M5 – methodology validation (stability, convergence, robustness…), (5 months) M6 – final analysis complete, (3 months) M7 – writing PhD thesis, (6 months) Deliverables include as: D1-­‐ comprehensive state of the art review on distributed control structures, D2-­‐ presenting modular distributed building energy control, D3-­‐ simulated proposed controller based on real data from Nimbus testbed (CIT). D4-­‐ simulation results & analysis, D5-­‐ evaluation and comparison of the method through graphics and tables, D6-­‐ final report on efficient distributed control structure for building(s). D7-­‐ PhD thesis and peer reviewed Journal and conference papers 6. Ethical issues No ethical issues are involved. 7. External Collaboration/Other Institutions For this project we will collaborate with control centre in Delft University of Technology and also Seville University in Spain Book of Sample Projects Page 140 CIT Rísam PhD Scholarship Programme 2014 References [1] A. Monti, F. Ponci, A Benigni and J. Liu, “Distributed intelligence for Smart Grid Control”, International School on Non-­‐sinusoidal Currents and Compensation, June 15-­‐
18, 2010, Lagow, Poland. [2] H. Li, L. Lai, and W. Zhang, “Communication Requirement for Reliable and Secure State Estimation and Control in Smart Grid”, IEEE Transaction on smart Grid, vol. 2, No. 3, September 2011. [3] H. Hindi, D. Greene and C. Laventall, “Coordinating Regulation and Demand Response in Electric Power Grids using Multi-­‐rate Model Predictive Control”, Proceeding of the IEEE Conference on Innovative Smart Grid Technologies, January 2011. [4] S. Roshany–Yamchi, R. R. Negenborn, M. Cychowski, B. de Schutter, J. Connell and K. Delaney, Distributed Model Predictive Control and Estimation of Large-­‐Scale Multi-­‐
Rate Systems, 18th International Federation of Automatic Control, IFAC, world congress, Invited paper, Milan, Italy, pp. 416–422, 28 Aug – 2 Sep, 2011. [5] S. Roshany–Yamchi, R. R. Negenborn, M. Cychowski, K. Delaney and J. Connell, A Game Theory Approach to Distributed Multi-­‐Rate Model Predictive Control, 22nd IET Irish Signals and Systems Conference, Dublin, Ireland, pp. 225–230, June, 2011. [6] S. Roshany–Yamchi, R. R. Negenborn, M. Cychowski, B. de Schutter, K. Delaney and J. Connell, Kalman Filter-­‐Based Distributed Predictive Control of Large-­‐Scale Multi-­‐
Rate Systems: Application to Power Networks, IEEE Transaction on Control Systems Technology, Issue 99, pp. 1-­‐13, 2011. [7] J. Liu, A. Monti, D. Obradovic, “Decentralized LQG Control Based on Local Model with Online Set-­‐point Adaptation for Distributed Power Generation”, IEEE ECC, September 2010, Atlanta, GA (USA). [8] A. Molderink, V. Bakker, M. G. C. Bosman, J. L. Hurink and G. J. M. Smit, “On the effects of MPC on a domestic energy efficiency optimization methodology”, IEEE International Energy Conference, pp. 120-­‐125, 2010. [9] J. Ma, S. J. Qin, B. Li and T. Salsbur, “Economic Model Predictive Control for Building Energy Systems”, IEEE PES Innovative Smart Grid Technologies (ISGT), pp. 1-­‐6, 17-­‐19 January, 2011. [10] J. Bendtsen, K. Trangbaek and J. Stoustru, “Hierarchical Model Predictive Control for Resource Distribution”, 49th IEEE Conference on Decision and Control, pp. 2468-­‐
2473, Hilton Atlanta Hotel, Atlanta, GA, US, December 15-­‐17, 2010. [11] http://dmpc.eu/archives/tag/distributed-­‐mpc Book of Sample Projects Page 141 CIT Rísam PhD Scholarship Programme 2014 Electronics Title of project: Silicon Oscillator Name of Principal Supervisor: John Horan Brief Summary of Research Interests: IC design, In particular Silicon Clocks/ high speed serial communications CIT Department: Email: Electronics John.horan@cit.ie Discipline Area by Frascati Classification: Telephone: 5983 2.2 1. Abstract (250 words) The objective of the project would be to produce an optimised silicon oscillator which will compete with crystal oscillators in a wide range of applications. This would demand that the frequency of the oscillator is temperature and stress independent, and at the same time its phase noise must be acceptable in a wide range of applications. The student will examine a range of circuit topologies in use, along with details of the available CMOS processing options and design an optimised oscillator in line with the above goals. Having designed the Oscillator the student will couple it with specialised dividers which will allow digital ppm tuning of frequencies. The resulting IC should represent a significant step forward in the price/performance of oscillators available to the market. 2. Research Context and Contribution to the Research Field The world has $2billion/year market for clock sources in electronics. Up to recently these sources were primarily driven crystal oscillators. In the last few years silicon oscilators have arrived in the market. Early version had poor accuracy and as a result didn’t impact the market significantly. More recently a company (www.SiTIME.com) has introduced resonators which are embedded in silicon which have caused crystal oscillators to be replace in many markets. This is a superb technology but it is a little costly. The goal of the proposed project is to produce a pore CMOS silicon solution to rival siTime ‘s solution in performance and cost half the price. 3. Objectives Produce a silicon Oscillator design which has (a) a stable frequency over temperature , stress and supply voltage variation (b) phase noise specifications compatible with major market applications (c) integration with a soon to be patented high resolution frequency divider system 4. Research Methodology Literature research Sample oscillators design / make silicon samples Characterisation of test structures Modelling of parameter Book of Sample Projects Page 142 CIT Rísam PhD Scholarship Programme 2014 5.
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Optimisation of design / make another test circuit Measure and refine design Integrate final design with specialised dividers for final silicon. Work Plan 1st 6 months Literature research 2nd 6 Design test chip 3rd 6 months make measurements/models moise/effects 4th 6 months make new optimised structre 5th 6 months intergrate with high speed specialized dividers 6th 6 months test chip and write up results. Ethical issues None External Collaboration/Other Institutions Will couple with some of Tyndall’s high speed silicon designers. Book of Sample Projects Page 143 CIT Rísam PhD Scholarship Programme 2014 Title of project: Dynamics of Spin Coating General Discipline Area: Applied Mathematics Name of Principal Supervisor: Dr Seán Lacey Email: sean.lacey@cit.ie Telephone: 021-­‐4335917 1. Abstract (250 words) Spin coating is a widely used procedure in industrial applications. It is used in the production of certain types of semiconductors, magnetic disk coating, CDs, DVDs, antireflection coatings, television tube phosphor coatings. Consequently, there has been a significant amount of research directed at understanding and so controlling the process. This project will investigate axisymmetric spin coating of Newtonian, power law and Ellis models. The project will focus on shear-­‐thinning and shear-­‐thickening fluids. The derived mathematical model will involve the effects of surface tension, gravity, centrifugal and Coriolis forces, and disjoining pressure. 2. Research Context and Contribution to the Research Field Coating is used in numerous industrial applications. For example, the electronic industry is continuously trying to produce smaller components. Current production methods are reaching their limits. New techniques are now being developed where nano scale components are formed by self assembly. In a typical process using this approach, channels in which the self assembling materials are confined, are created by lithography. A uniform layer of non-­‐
Newtonian fluid is applied uniformly over the geometry. It contains solvent and the monomers which will self assemble. The excess solution is removed by the technique of spin coating and solvent evaporation. A coated layer should be very regular but also as thin as possible. However, finger instabilities are likely to form at the edge of the liquid and compromise the quality of coating. 3. Objectives The aim of this project is to determine under what conditions and in what type of environment can the finger instabilities be controlled. 4. Research Methodology a. Derive an equation to describe the film thickness of a fluid, with a view to performing a stability analysis. The stability of the film is affected by the higher-­‐
order effects of surface tension, gravity, centrifugal and Coriolis forces, and disjoining pressure. b. Assuming that these effects are weak, an asymptotic equation will be derived which takes into account these effects as perturbations. Book of Sample Projects Page 144 CIT Rísam PhD Scholarship Programme 2014 5.
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c. The resulting equations will be used to examine the stability of the steady-­‐state distribution of the film for small normal mode numbers. Work Plan a. Lubrication approximation to the Navier-­‐Stokes equations. b. Asymptotic perturbation techniques. c. Stability will be investigated using an eigen value method. Ethical issues N/A Book of Sample Projects Page 145 CIT Rísam PhD Scholarship Programme 2014 PHOTONICS General Discipline Area: Photonics Name of Contact: Dr Bryan Kelleher Email: bryan.kelleher@cit.ie Summary: Research in the Centre for Advanced Photonics and Process Analysis (CAPPA) CAPPA conducts research in a range of areas, all of which involve the investigation or application of photonics, i.e. light. Major research strands include non-­‐linear dynamics of lasers and ultrafast laser physics, and the understanding of the dynamics of novel semiconductor materials and devices. CAPPA researchers collaborate with prominent international universities as well as both multi-­‐
national and SME industry partners. The main research areas are described below. CAPPA would welcome discussions for RISAM project proposals in any of these areas. Please contact Dr. Bryan Kelleher for further details or expressions of interest. Laser Dynamics •
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Experimental and theoretical studies of a range of dynamical laser systems. Laser dynamics is a rich source of fundamental science and real-­‐world applications Dynamics of continuous wave and mode-­‐locked semiconductor lasers: optical injection & feedback – fundamental science and real-­‐world applications Novel semiconductor devices including quantum dots and nanopillars Swept source lasers including Fourier Domain Mode Locked Lasers (FDMLs) and used in biomedical imaging Optical Coherence Tomography (OCT) and also provide a fertile source of non-­‐linear dynamics Time-­‐Resolved Photoluminescence Spectroscopy •
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Explore ultrafast dynamics of optical devices at speeds much faster than conventional spectrum analysers Streak camera and helium cryostat (4K) allow simultaneous temporal and spatial profile (streak image) of light pulse Can reveal invaluable information on recombination processes, including transition lifetimes Has been used to study Coulomb-­‐induced emission dynamics in Sb-­‐based QDs, for mid-­‐
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Study ultrafast processes in semiconductor structures Provides direct, time domain measurements of gain and refractive index non-­‐linearities in optical waveguides Sub-­‐picosecond resolution Book of Sample Projects Page 146 CIT Rísam PhD Scholarship Programme 2014 •
Has been used to determine dependence of capture time of InAs/GaAs quantum dots on bias current, used in semiconductor optical amplifiers for telecommunications applications Chemical Analysis & Imaging •
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A powerful extension of spectroscopy, including Fourier Transform Infrared (FTIR), Raman & UV-­‐Vis spectroscopy and microscopy Provides both chemical composition and distribution of components, using the unique spectral peaks of the different compounds Can be used to monitor processes, detect counterfeit products, aid root cause analysis Has been used to determine distribution of active ingredient in pharmaceutical tablet Imaging capabilities also include SEM with EDX for elemental mapping Optical Design & Modelling •
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Zemax modelling software, a powerful ray-­‐tracing simulation package Both sequential and non-­‐sequential modes allowing modelling of both traditional lens systems and those requiring stray-­‐light analysis Has been used to design efficient backlighting for remote control, UV illumination for water purification system Research for Industry •
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CAPPA has extensive research collaborations with both national and international companies Applying CAPPA’s photonics expertise to provide solutions to industry in areas such as telecommunications, pharmaceutical, and medical devices Projects types include direct funded, Innovation Partnerships (Enterprise Ireland), industry-­‐
focussed Research Centre (IPIC, SFI) and FP7/H2020 projects (EU) Book of Sample Projects Page 147 CIT Rísam PhD Scholarship Programme 2014 ASTRONOMY General Discipline Area: Physics and Astrophysics Name of Principal Investigator: Dr Niall Smith Email: niall.smith@cit.ie Telephone: 021-­‐4335304 CIT Blackrock Castle Observatory (CIT BCO) is home to BCOLabs, staffed by researchers from the Astronomy Instrumentation Group at CIT. These researchers operate the two robotic telescopes at CIT BCO and are engaged in developing and applying new instrumentation and technologies to support astronomy research. As well as collaborating with leading astronomy research groups, BCOLabs has worked with a number of companies on instrument development projects. The close integration of the public exhibition and the laboratories makes CIT BCO a unique centre for research and education. Book of Sample Projects Page 148 CIT Rísam PhD Scholarship Programme 2014 MARITIME, ENERGY & SUSTAINABLE ENVIRONMENT Water Management Title of project: the Irish dairy industry Demand side management of water and energy consumption in Name of Principal Supervisor: Ted Scully & Michael Murphy Brief Summary of Research Interests: Water & Energy Optimisation CIT Department: Email: Computing michaeld.murphy@cit.ie ted.scully@cit.ie Discipline Area by Frascati Classification: Telephone: 0214326747 Computer and information sciences 1. Abstract There exists an inextricable relationship between energy and water consumption in the production of milk. Optimising electricity and water consumption along with associated costs through the integration of energy and water utilisation models with Demand Side Management (DSM) technologies (algorithms that alter the farms energy and water consumption trends in order to minimise costs) in Irish milk production is becoming a topic of increasing interest for two reasons: First, the introduction of a dynamic electricity pricing system, with peak and off-­‐peak prices, will be a reality for 80% of electricity consumers by 2020. If farmers carry out their conventional milking routine during the peak period, energy costs may increase, which would impact farm profitability. Second, dairy farmers are beginning to respond to national policy frameworks and are preparing for the abolition of European Union milk quotas in 2015. These events will create an unprecedented increase in herd size, grazing area and milk processing plant capacity (milking machine, cooling tank, pre-­‐coolers and water heater), resulting in much more water and energy intensive dairy production in the near future. The agri-­‐foods sector is Ireland’s largest industry and biggest indigenous exporter with 85% of all milk produced in Ireland exported to foreign markets. The overall aim of this research is to economically optimise the mixture of energy and water consumed in on on-­‐farm milk production. Even a modest reduction in cost per litre of milk produced would have a dramatic effect on the competitiveness and success of the Irish dairy industry. 2.
Research Context and Contribution to the Research Field The ethos of the Food Harvest report is to promote growth in a smart and green manner. The vision for green agriculture includes environmental protection, energy reduction, water conservation and supply chain sustainability. The inextricable tie between energy and food prices exacerbates the industry’s vulnerability to future spikes in oil, making the energy reduction policy a high priority. Water use and energy use are inseparably linked due to the fact that large volumes of cold water are used each day on dairy farms for the purposes of milk cooling, washing and drinking (Murphy et al 2013). When farmers respond to government initiatives to increase milk production by 50% by 2020 Book of Sample Projects Page 149 CIT Rísam PhD Scholarship Programme 2014 as indicated in the Food Harvest report, research on water and energy use will become even more pertinent. Expanding farm size without cognisance of best practice in these areas will have detrimental effects on sustainability and profitability. In recent years Information and Communication Technology (ICT) has been recognized by researchers as having significant potential application in the Agricultural Sector. The overall concept of using ICT for Agriculture has become known as Precision Farming. Extensive use of ICT within a farm environment is expected to increase the level of automation and process control. This will enable the farmer to focus more on the managerial tasks, thus improving farm performance and reducing operational costs. This project will contribute to the area of Precision farming by applying a precision approach to the consumption of energy and water by dairy farms through the application of load forecasting and demand side management techniques that have already been developed (Murphy et al. 2012). This novel approach to energy and water management in milk production will result in reductions in energy costs and water consumption associated with milk production at farm level. Modern dairy farmers monitor grass growth, milk production, milk quality, milk composition, animal health and animal performance to identify inefficiencies in their production system with a view to increasing milk output while reducing input costs. These system characteristics are also compared among groups of farmers at discussion groups. Electricity consumption represents about 8% of milk production variable costs (Upton et al. 2013) however the only available metric with regard to electricity use is via a bi-­‐monthly electricity bill. This bill is often estimated on previous consumption levels rather than based on the electricity meter reading, leaving the farmer powerless to accurately distil this data into a performance indicator which can be compared with other farms. Furthermore, there exists no tangible index for totalised water consumption or for individual components. This project aims to tackle the issue of rising energy and water costs on Irish dairy farms by developing energy and water consumption models and demand side management algorithms that can be applied to any commercial dairy farm with conventional milking systems, or automatic milking systems, which will quantify energy and water costs with milk production on a daily basis while providing instruction on the optimised operation of water and energy consuming equipment to deliver minimal energy costs in the course of dairy production. 3.
Objectives •
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Develop a model to calculate dynamic water and energy consumption per litre of milk produced. Design a multi objective demand side management optimisation algorithm for water and energy utilisation. Validate the energy-­‐water model and demand side management optimisation algorithm on a selection of research and commercial dairy farms. Research Methodology Model Development Task: Develop a water-­‐energy model to simulate dynamic energy and water cost consumption litre of milk produced. Objectives. Book of Sample Projects Page 150 CIT Rísam PhD Scholarship Programme 2014 1. Utilise data mining techniques to extract high priority empirical information from existing database. 2. Carry out a meta-­‐analysis of electricity pricing tariffs based on smart metering and time of use tariff trials carried out in Ireland and Europe 3. Develop water-­‐energy model using empirical data for off-­‐line algorithm testing. Description of work to be undertaken. Model development can begin from the start of the project as all the necessary data is available from both research farms (run by Teagasc) and private commercial farms: A research test-­‐bed consisting of approximately 30 commercial farms is being managed currently by Teagasc and a commercial partner in West Cork. On-­‐farm energy and water consumption for each individual on-­‐
farm component (bulk tank, water heater, vacuum pump, water pump, plate heat exchanger, water troughs) along with milk production is being monitored and recorded. These data are being remotely monitored by a centralised network in Teagasc Moorepark. This data base will be utilised for development of the water-­‐energy model. Electricity consumption analysis of both daily and yearly consumption patterns show that dairy farmers could be exposed to higher electricity prices if a pricing structure is implemented that varies tariffs according to the load on the national grid. This task will involve using the outputs from task 1 and applying a suite of cost structures to the data in order to compute overall energy costs as well as cost per lire of milk produced per day. Prior to this cost calculation, a meta analysis of proposed smart metering and time of use tariffs will be carried out and compiled. A common methodology for applying these tariffs to the load profile will be developed so that the outputs from each tariff stream can be compared directly. The detailed data base mentioned above will give the breakdown between cow drinking water, water used for washing milking equipment and collecting yards, hot water use and plate cooler water use. These farms will form the basis for a pilot study on water use and key performance indicators, such as water used per litre of milk produced, will be used as a metric of comparison. Synergies will be made with other projects which will enable this water audit to operate in tandem with electricity audits. This will add an extra dimension to the analysis. A survey of farm management practices, collecting yard and milking machine design as well as all water supply infrastructures will be carried out on the pilot farms. For the water-­‐energy model we propose to adopt a minimal data collection approach to ensure the final system is both practical and low cost. The critical parameters to be measured and used as inputs to the model will include; milk volume (from an ultrasonic probe in the bulk tank), weather parameters (from local or on site weather instrumentation) and energy and water consumption data from each piece of equipment on the farm. This task leverages on from existing research conducted between Teagasc and the Cork Institute of Technology as the water-­‐energy model will work in tandem with existing on-­‐farm simulation systems(Murphy et al. 2014; Upton et al. 2014). Theses simulation tools will provide a virtual environment in which to develop and test demand side management optimisation algorithm for water and energy utilisation. The results of this study pertaining to electricity consumption trends and their relationship to the demand profile on the national grid will be of relevance to dairy industries internationally. Book of Sample Projects Page 151 CIT Rísam PhD Scholarship Programme 2014 DSM Optimisation Algorithm Design Task: Develop a multi-­‐objective DSM optimisation algorithm for combine water and energy cost minimisation. Objectives. 1. Utilise the water-­‐energy model as a virtual environment in which to develop experimental algorithms. 2. Investigate various control algorithms such as; Dynamic Programming, Steepest Decent, Artificial Neural Networks, Genetic Algorithms and Pareto-­‐based optimisation methods that may be used to compute optimum solutions for application of optimal energy generation systems on farms of various scales 3. Develop simulations based on reference years energy/water consumption data, milk production data and meteorological data to analyse the performance contribution over time for various optimisation algorithms. Description of work to be undertaken. Algorithm design and off-­‐line testing. On-­‐Farm Model and Algorithm Validation Task: Validate the water-­‐energy model and DSM optimisation algorithm on a selection commercial dairy farm. Objectives. 1. Validate the water-­‐energy model on a selection commercial dairy farm. 2. Implement novel optimisation algorithm on a selection commercial dairy farm. 3. Analyse the impact of algorithm introduction relative to current state of the art and quantity the economic benefits. Description of work to be undertaken. On-­‐Farm model and algorithm validation. 5.
Work Plan The intended work plan is as outlined below. Task Title Timescale Number Number of Months Book of Sample Projects Relevant information Page 152 CIT Rísam PhD Scholarship Programme 2014 1 Literature review 6 An exhaustive literature review on existing optimisation algorithms and modelling techniques for water and energy utilisation. 2 Increase knowledge in modelling and optimisation 6 Research into current model predictive control & optimization techniques. Development of water-­‐energy model 12 months – to run simultaneously to tasks 1 & 2 Develop a water-­‐energy model to simulate dynamic energy and water cost consumption litre of milk produced. 4 DSM Optimisation Algorithm Design 7 Design of novel optimization algorithms. 5 Off-­‐line testing 5 Off-­‐line testing of various optimization algorithms in a virtual environment. 7 On-­‐Farm Model and Algorithm Validation Task 6 Implementation of novel control and optimization algorithms on commercial dairy farms (on-­‐line). 6 Presentation of the conclusions established throughout the research process in multiple journal transactions and international conference proceedings. 3 8 6.
Conclusions Ethical issues It is not envisioned that any testing on Human or Animal subjects will take place in this body of research. However, we confirm that full consideration has been given to the ethical implications of this research proposal. On confirmation of the awarding of the scholarship, if needed a full ethical report and approval will be sought from a research ethical review committee, and will be submitted to the Cork Institute of Technology Research Council prior to the commencement of the Scholarship or within three months of the start date. 7. External Collaboration/Other Institutions This project will be run in coloration with several research partners including: Teagasc Moorepark, the University College Dublin Biosystems research group, the Wageningen University farm Book of Sample Projects Page 153 CIT Rísam PhD Scholarship Programme 2014 technology group and an industrial partner. Teagasc is currently funding three Walsh Fellowships in this field (two of which are in partnership with CIT) and it is hope that this research project will serve to strengthen ties between CIT and Teagasc Moorepark and lead to more collaboration in the future. Book of Sample Projects Page 154 CIT Rísam PhD Scholarship Programme 2014 Environmental/Civil Engineering Title of project: Sediment Transport in River Systems Name of Principal Supervisor: Dr. Joe Harrington Email: joe.harrington@cit.ie Telephone: 021 4335460 1. Abstract (250 words) Sediment transport in river systems is important in the context of water quality, ecology, fish life, recreation, and morphological changes. Transport mechanisms include suspended and bed load transport originating from a range of point and diffuse sources. Research into river related sediment transport is on-­‐going in the Sediments Research Group at Cork Institute of Technology at Masters and PhD level with emphasis to date on the local and complex River Bandon catchment system in the South Western River Basin District. Sediment behaviour and its impacts will be developed in this research project though on-­‐going field work, analysis of continuous monitoring data and application of numerical modelling techniques to simulate sediment behaviour and the response of the river system to a range of sediment loadings from average conditions to infrequent extreme storm events which contribute disproportionately to sediment transport patterns in the river environment. 2. Research Context and Contribution to the Research Field The research work is contributing to the on-­‐going development of new and original work for Irish River Systems from the research group at Cork Institute of Technology. 3. Objectives Summarise the key objectives of the research. 4. Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. 5. Work Plan 6. Ethical issues Book of Sample Projects Page 155 CIT Rísam PhD Scholarship Programme 2014 Title of project: An investigation into the treatment of municipal waste with energy recovery and the beneficial use of by-­‐products General Discipline Area: Environmental/Civil Engineering Name of Principal Supervisor: Dr. Niamh Power Email: niamh.power@cit.ie Telephone: 021 4335959 1. Abstract (250 words) Municipal solid waste (MSW) is a significant issue throughout Europe as the Landfill Directive (2009/31/EC) and the Waste Framework Directive (2008/98/EC) sets various targets on the quantity of waste that maybe landfilled. There are various treatment methods of MSW which have the potential to generate energy; incineration, anaerobic digestion, landfill, pyrolysis and gasification. However each of these technologies produce by-­‐products such as fly ash, digestate and leachate, but the beneficial use of these by-­‐products have not been investigated. The potential of these technologies along with an LCA, SWAT analysis and review of policy measures is required to reduce the impact MSW has on the environment. This research proposes to carry out the above investigations to determine the optimum waste strategy. Book of Sample Projects Page 156 CIT Rísam PhD Scholarship Programme 2014 Title of project: The potential of energy production from various crops in Ireland General Discipline Area: Environmental/Civil Engineering Name of Principal Supervisor: Dr. Niamh Power Email: niamh.power@cit.ie Telephone: 021 4335959 1. Abstract (250 words) The Renewables Directive (2009/28/EC) was the first Directive which set out specific sustainability criteria in terms of emissions savings and land use changes etc. In terms of energy production from crops, the optimum crop for each country or indeed within a region may vary due to climate condition, soil properties, precipitation and the knowledge of the local farming community. In addition the technology chosen to convert the crop to energy will also impact the potential for net energy; heat, CHP or transport (e.g. ethanol, biomethane or biodiesel). This research will examine the methane potential of various Irish crops (co-­‐digestion with agricultural slurries may be required) through lab testing and examine the alternative uses for these crops (e.g rapeseed to biodiesel). This research will examine a number of crops from a holistic viewpoint (growth to energy production to by-­‐products) to determine the potential energy crops and the optimum crop for Ireland. Book of Sample Projects Page 157 CIT Rísam PhD Scholarship Programme 2014 Civil & Structural Engineering Title of project: Bridges The Assessment of Transverse Load Distribution in Masonry Arch General Discipline Area: Civil Engineering Name of Principal Supervisor: John J Murphy Email: john.justinmurphy@cit.ie Telephone: 021-­‐4326741 1. Abstract (250 words) Masonry arch bridges comprise 36% of the bridge stock on national roads in Ireland [1] Due to increased traffic loads and possible deterioration of the bridge structure, it is essential that the load carrying capacity of such bridges be regularly assessed. These bridges have proven to be highly sustainable structures, with design lives (often in excess of 200 years) far surpassing those of modern bridges. Environmental benefits can be gained if their assessment provides an accurate evaluation of the capacity of the bridge, thereby avoiding unnecessary remedial work or bridge replacement. The current load model for masonry arch bridges calls for a uniform effective width of bridge to be utilized in their analysis [2]. Research carried out thus far has shown the effective width model to be simplistic [3]. LUSAS Finite Element Analysis (FEA) software has been used to create a series of 3D bridge models, which have been modelled under serviceability loads. The aim is to further extend the research by; • Carrying out an experimental phase involving the load testing of a number of bridges using inexpensive methods. The data gained will be used to verify the FEA. • Extending the FEA to include non-­‐linear properties. This will allow for transverse distribution to be studied for serviceability and limit states. • Analysing loadcases set out in the assessment codes [2]. The overall objective is to develop a new load distribution model that improves upon current methods for the design and assessment of masonry arch bridges. Book of Sample Projects Page 158 CIT Rísam PhD Scholarship Programme 2014 Title of project: Irish Grown Timber Truss Connections under Fire Conditions General Discipline Area: Structural Engineering Name of Principal Supervisor: Mr Andrew Macilwraith Email: andrew.macilwraith@cit.ie Telephone: 021 4304077 & 087 2405605 2.
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Abstract (250 words) Recent research we have carried out on Irish grown timbers shows them to have significantly different properties than their European counterparts, particularly when compared with the Nordic countries. These inherent properties will affect connection design in Irish grown timbers, and also when they become exposed to full ISO time temperature test curves. At CIT over the last number of years we have developed our fire research capability, including fire testing kilns and a bomb calorimeter. We are currently installing a larger kiln, which is surrounded by a structural steel testing frame which will allow connection testing under load, and full fire temperature profiles to be applied. Punched metal plate connections as part of prefabricated truss systems would be investigated under full fire conditions, together with various connection types in cut roof truss design. In very fast growing fires plasterboard ceiling protection systems can fail, and the truss connections can be exposed to fire. Exposed timber truss designs will also be investigated. Sustainability and carbon footprint is a very important consideration when constructing a building, and structural timber, preferably exposed, is coming to the forefront. With this in mind a detailed investigation of Irish timber connections under load in the fire condition requires to be undertaken. Furthermore much of Irish softwood is classed as C14 grade, which is currently not listed in the Eurocode tables, as they generally start at C16. An investigation of C14 grades of Irish timber, and connection design under loaded fire conditions would also be very beneficial. Research Context and Contribution to the Research Field This research work would investigate the use of Irish timber, and how it differs from the European equivalent. This is particularly relevant to all National research in structural timber design. Connection design under full fire conditions and under load can be undertaken, using Irish grown timber, and definitive results that can be used by designers will be found. Lower grade softwood timber which is excluded from the Eurocode tables, can also be investigated, with a view to providing evidence to allow more of our native home grown timber to be used structurally. Objectives Book of Sample Projects Page 159 CIT Rísam PhD Scholarship Programme 2014 •
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Ascertain inherent fire resistance times of home grown timber truss connections Compare Irish timber with European equivalents, for use in truss construction Provide additional guidance to complement the Eurocodes for Irish Grown timbers Develop fire resistant truss connection designs for Irish grown timbers. Research Methodology • Literature Search • Safety Method Statements • Eurocode Calculations – Cold Design • Eurocode Calculations – Fire Design • Truss connection tests under ambient conditions • Kiln testing of truss connections under full fire conditions • Finite Element Analysis of connections • Write papers on findings Work Plan • Masters Level 9 Research • September 2014 to September 2015 Ethical issues None Book of Sample Projects Page 160 CIT Rísam PhD Scholarship Programme 2014 Title of project: Anaeroboic Corrosion of Steel in Reinforced Concrete Construction General Discipline Area: Civil / Structural Engineering Name of Principal Supervisor: Kieran Ruane Email: joe.harrington@cit.ie Telephone: 021 4335460 kieran.ruane@cit.ie 021 4326741 1.
Abstract (250 words) The developed world is moving from a state of infrastructure construction to a state of infrastructure maintenance. Sustainability is the key driver for the development of modern maintenance strategies. A tangible outcome of this focus on sustainability is the extension of life span of existing infrastructure. This reduces pressure on existing natural resources arising from the construction of replacement infrastructure. Improvments are required to our understanding of the degradation of construction materials to maximise the effectiveness of maintenance strategies. The study proposed here focusses on a rarely reported degradation mechanism of reinforced concrete – anaerobic corrosion . Reinforced concrete is the most commonly used building material in the world for civil infrastructure. Steel corrosion of concrete reinforcement is an active area of research. Corrosion of steel is an electrochemical process requiring a supply of oxygen in the presence of moisture. Steel corrosion product usually occupies a much larger volume than the un-­‐ corroded steel resulting in cracked or spalled concrete. If the supply of oxygen is restricted, black rust may be formed by the process of anaerobic corrosion. Black rust is not expansive, which makes it particularly difficult to detect in reinforced concrete. Limited literature is available on anaerobic corrosion of steel in concrete and the formation of black rust. There is little, or no, knowledge amongst practising engineers of the existence of anaerobic corrosion of concrete reinforcement. Engineers are trained to observe for the surface signs of internal reinforcement corrosion and the lack of surface signs associated with anaerobic corrosion is problematic. The purpose of the research proposed here is to quantify the extent of anaerobic corroision as a degradation mechanism in reinforced concrete construction and to develop assessment methods to detect its presence which will be of use to practising engineers worldwide. 2. Research Context and Contribution to the Research Field Anaerobic corrosion of steel reinforcement in concrete is rarely reported in literature. Studies of anaerobic corrosion of steel construction in general have involved diverse areas such as nuclear waste repositories, boiler feed water systems, underground pipe lines and archaeological samples [1]. A three year study in to the deterioration of reinforced concrete in the marine environment conducted in CIT from 2010 to 2013 [2] resulted in the first recorded instance of anaerobic corrosion to concrete reinforcement in Ireland [3]. As part of that study anacedotal evidence was collected of several other examples of anaerobic corrosion particularly in reinforced concrete structures in a marine environment. Book of Sample Projects Page 161 CIT Rísam PhD Scholarship Programme 2014 Anaerobic corrosion in reinforced concrete is thought to occur when the oxygen supply is limited at active anodes typically resulting in non-­‐expansive corrosion products. Corrosion under oxygen deficient conditions is considered to be more serious than normal aerobic corrosion (red rust), as it may be active for some time before there is any visible evidence at the surface of the concrete [4], [5]. Black rust is described as being a spongy product, and soluble in water. The black rust is not a crystalline material and it will occupy voids in concrete spaces without exerting expansive pressure on the concrete. Rust staining may occur on the concrete surface. It is a relatively unstable product and readily converts to ferric oxide (red rust, Fe O ) when exposed to oxygen. 2 3
Therefore, the initial period following the breakout of concrete may be crucial if the presence of anaerobic corrosion is to be correctly identified [6], [7], [8]. The obvious danger of anaerobic corrosion in reinforced concrete is that there may be little or no surface sign of corrosion meaning that it can go undetected eventually leading to structural failure. There is a need to quantify the extent of anaerobic corrosion in our infrastructure, to increase awareness of it as a degradation mechanism and to improve inspection standards and guidelines. Further research into the formation of black rust is warranted so that methods for its detection, identification and treatment may be developed. [1] F. King, Technical Report 08-­‐12 corrosion of carbon steel under anaerobic conditions in a repository for SF and HLW in Opalinus Clay, Nagra, October 2008. [2] R.O’Donovan. B.D. O’Rourke. K.D. Ruane. J.J. Murphy, Reinforced Concrete Deterioration of a 100 year old Structure in a Marine Environment, Proceedings of Bridge and Concrete Research in Ireland Conference, September 2012. [3] R.O’Donovan. B.D. O’Rourke. K.D. Ruane. J.J. Murphy, Anaerobic Corrosion of Reinforcement, 3rd International Conference of Damage Assment of Material and Structures (DAMAS), September 2012. [4] C. Arya, L.A. Wood, The Relevance of Cracking in Concrete to Corrosion of Reinforcement, Concrete Society, Technical Report No. 44, 1995. [5] A. Karimi, N.R. Buenfeld, Service life prediction of concrete structure based on automated monitoring, Imperial College London, 2007. [6] R.J. Cope, Concrete Bridge Engineering: Performance and Advances, Elsevier Applied Science, 1987. [7] J.P. Broomfield, Corrosion of Steel in Concrete – Understanding, investigation and repair, E & FN Spon, 2003. [8] H. Fatemi, M. Moore, R. Khatri, Importance of Detection of Black Rust Formation, th Proceedings of Austroroads 8 Bridge Conference, June 2011. 3.
Objectives Book of Sample Projects Page 162 CIT Rísam PhD Scholarship Programme 2014 There are 4 key objectives to this research project: • To produce a state-­‐of-­‐the-­‐art literature review in the area of anaeroboic corrosion of steel in reinforced concrete construction which shall include recorded instances of the phenomema, detection techniques, exposure and environmental triggers, electro-­‐
chemical and phenomenological models, and remediation measures; 4.
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To undertake a quantitative examation of a large sample set of reinforced concrete construction in the marine environment to detect the presence of anaerobic corrosion; •
To update the state-­‐of-­‐the-­‐art review to include the findings of a statistiscal analysis of the quantitative examination described above; •
To increase awareness in the industry of the presence of anaerobic corrosion as a degradation mechanism in reinforced concrete construction through the dissemination of papers and inspection guidelines. Research Methodology The research methodology is tailored to the 4 objectives as follows: • Literature review using traditional research methods; •
Quantitative examination requiring the examination of a large sample set of existing marine structures in reinforced concrete and the application of a range of tests to the sample set including, inter-­‐alia, concrete core removal, local break-­‐out, half-­‐cell potential testing, chloride content etc. Permission shall be sought from owners of the marine structures for testing. Owners are likely to be local authorities, Department of the Marine and Port Authorities. There are a number of specialist test firms who conduct reinforced concrete examinations of this nature and it is anticipated (based on informal discussions to date) that these firms will allow the PhD student to review their historic test data to search for recordings of anaeroboic corrosion; •
The application of statistical methods to the data set described above so that hypotheses may be tested and conclusions may be drawn in relation to the national and international stock of marine structures in reinforced concrete; •
Dissemination through peer reviewed journal and conference papers. Presentations to national bodies such as the Department of Marine to influence publications of national guidelines for infrastructure inspection, maintenance and repair. Work Plan • This is a 36 month project and the anticipated work plan is: • 0-­‐6 months: literature review, preparation for quantitative examination phase; •
6-­‐24 months: on-­‐going literature review, site based reinforced concrete testing, data gathering; Book of Sample Projects Page 163 CIT Rísam PhD Scholarship Programme 2014 6.
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24 – 30 months: data analysis and statistical review; •
30-­‐36 months: preparation and finalisation of thesis. It is noted that this study may be of interest to graduates of all engineering and physical / chemical science disciplines. Ethical issues None Book of Sample Projects Page 164 CIT Rísam PhD Scholarship Programme 2014 Architecture Title of project: Optimization of the combined energy performance of a building Name of Principal Supervisor: Katherine Keane Email: Telephone: 021 433 5950 Katherine.keane@cit.ie 1. Abstract (250 words) moving forward there will be a huge emphasis on embodied energy, alongside reduced operational energy. We are now getting close to the point where reducing operational energy has almost bottomed out. Any further decrease could inevitably trigger a greater increase in energy consumed, based on increased embodied energy within the materials. It would be interesting to see where the cross over occurs and at what point the 'combined' energy consumption (embodied + operational) begins to increase due to the law of diminishing returns. Testing based on the specific location is also crucial, as I only have 2 Irish climate datasets available at the moment and I have an almost 20% variation in the same dwellings operational performance in these 2 locations. Book of Sample Projects Page 165 CIT Rísam PhD Scholarship Programme 2014 Title of project: Post-­‐occupancy energy evaluation in Institutional context General Discipline Area: Energy / Interior Architecture Name of Principal Supervisor: Email: Dr Garrett O’Sullivan Garrett.OSullivan@cit.ie Telephone: 021 433 5153 NOTE: A FULL PROPOSAL HAS SEPARATELY BEEN SUBMITTED BY DR. O’ Sullivan 1. Abstract (250 words) Energy research is continually compounding the urgent need to craft innovative design strategies to assist in the quest in achieving optimum balance between human and environmental ingredients. Fundamental to achieving this synergistic balance is a two-­‐ fold equation. In the first instance, the design of the building is paramount. This provides a vehicle which can be programmed and monitored. Secondly, behavioural use patterns and the interface between the user and the building are pivotal. Appreciating the defined and somewhat under researched significance of the User / Building interface, this research aims to investigate post –occupancy energy usage in an institutional context. In executing this empirical research, the methodological framework first explores un-­‐regulated energy usage patterns. Having established a ‘Real World’ perspective and delimited the responsive behavioural parameters, the research forwards an ‘Energy Efficient Model’ and charts the variances as determined by low budget and morphed behavioural dynamics. 2. Research Context and Contribution to the Research Field The research work is contributing to the on-­‐going development of new and original work for Post –occupancy energy evaluation from the research group at Cork Institute of Technology. 3. Objectives Summarise the key objectives of the research. 4. Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. 5. Work Plan 6. Ethical issues None Book of Sample Projects Page 166 CIT Rísam PhD Scholarship Programme 2014 Title of project: Can interior design material specification adversely impact IAQ in Naturally ventilated low energy office buildings General Discipline Area: Energy / Interior Architecture Name of Principal Supervisor: Email: Marc O’ Riain Marc.oRiain@cit.ie Telephone: 021 433 1. Abstract (250 words). 7. Research Context and Contribution to the Research Field The research work is contributing to the on-­‐going development of new and original work for Interior Architecture from the research group at Cork Institute of Technology. 8. Objectives Summarise the key objectives of the research. 9. Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. 10. Work Plan 11. Ethical issues None Book of Sample Projects Page 167 CIT Rísam PhD Scholarship Programme 2014 Title of project: Can Interior Architectural acoustic solutions be used to improve productivity and Interior Office Environments General Discipline Area: Energy / Interior Architecture Name of Principal Supervisor: Email: Marc O’ Riain Marc.oRiain@cit.ie Telephone: 021 433 1. Abstract (250 words). 2. Research Context and Contribution to the Research Field The research work is contributing to the on-­‐going development of new and original work for Interior Architecture from the research group at Cork Institute of Technology. 3. Objectives Summarise the key objectives of the research. 4. Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. 5. Work Plan 6. Ethical issues None Book of Sample Projects Page 168 CIT Rísam PhD Scholarship Programme 2014 HEALTH & EXERCISE Social Studies Title of project: Residential Child-­‐Care Skills Audit Name of Principal Supervisor: Áine de Róiste (Dr.) & Ms. Roisin Lane Brief Summary of Research Interests: Developmental Psychology; Social Care CIT Department: Email: Applied Social Studies aine.deroiste@cit.ie Discipline Area by Frascati Classification: Telephone: 021-­‐4335313 5.9 1. Abstract (250 words) The objectives of this research is to undertake a skills audit of social care workers in the residential child care sector in order to identify current skills required to work at both junior and senior levels in these sectors. The aim is for this to be undertaken in the light of the HETAC Social Care Awards and Standards Framework. This document outlines the broad standards of knowledge, skill and competence across levels 6, 7 8, and 9 of the National Framework of Qualification for the social care qualification in general. This would be original in drawing clear relationships between what the particular work place sector of residential child care sees as necessary for education and training to cover to equip students optimally to work in residential child care in particular. A mixed methodology will be used including interviews with Residential Managers and Human Resource Managers initially and later with key informants (such as representatives from CORU, HETAC, Social Services Inspectorate), focus groups with social care residential child care staff and social care lecturers in the Institute of Technology sector and a questionnaire with social care BA (Hons) students. 2.
Research Context and Contribution to the Research Field Social Care has undergone rapid professionalization in recent decades. The formation of HIQA, the Social Services Inspectorate as well as the National Standards for Residential Child Care, reflect the progress of such professionalization. The establishment of the Health and Social Care Professionals Council (CORU) which will regulate registration of Social Care professionals and others is central to this. CORU was established under the Health and Social Care Professionals Act 2005 and is the umbrella body responsible for protecting the public by regulating health and social are professionals. With reference to CORU and educational institutions, HETAC developed its awards standards framework for Social Care in 2010 which sets out learning outcomes (Knowledge, Know-­‐how & Skill, Competence) according to the National Framework for Qualifications. This document (http://www.hetac.ie/docs/B.2.9-­‐5.5_Awards_Standards_Social_Care_Work_2010.pdf) will provide the framework for the current research but rather than identifying generic social care knowledge and skill outcomes, this research seeks to identify knowledge, skills and competence according to this framework specific to the field of residential child care. Currently there are over 5,000 children in care in Ireland. Residential care includes high support Book of Sample Projects Page 169 CIT Rísam PhD Scholarship Programme 2014 and special care units and there are private and public residential child care units. Within the context of these units the ranges of needs of children in residential care are changing as a result of but not exclusively because of changes in the demographics and circumstances of families in modern Ireland. As such this skills audit will need to take cognisance of current needs but also look at identifying future needs based on the changing nature of Irish society. 3.
Objectives (a) To identify the specific skills and knowledge base required for optimal residential child care work and to depict these on the NFQ thereby formulating a residential child care specific competency framework and milestone training/education plan. (b) To identify and suggest pertinent pedagogical and assessment methods on such skills and knowledge. (c) To guide and inform teaching on skills and knowledge residential child care practice and career guidance in social care. (d) To identify current trends and develop new competencies necessary to meet the ever changing needs of the client groups identified. 4.
Research Methodology A mixed methodology comprising of qualitative (interviews, focus groups) and quantitative (survey) methods will be used drawing from the expertise of different stakeholders in the residential Child Care sector; Residential care managers, Social Care practitioners, Social Services Inspectorate and other bodies concerned with developing and assessing standards as well as focus groups with other interested parties: CORU, HEA/QQI, academics, social care staff and students Work Plan Sept 2014-­‐Feb. 2015 Literature review including international skills audits in residential child care/social care. Collection of job specifications, application forms as well as annual reports and inspectorate reports in residential child care. Database formation and initial contact with centres. Sampling strategy formation. Development of an Interview Schedule March-­‐July 2015 August-­‐December 2015 Jan.2016-­‐June 2016 July-­‐Dec 2016 Jan-­‐June 2017 Book of Sample Projects Development of a skills audit framework Interviews with Residential Managers (n=8-­‐12) & HR managers (n= 6-­‐8) in residential child care Data analysis of interviews Focus groups (n=4-­‐6) with social care staff Questionnaire development and piloting Focus group analysis Questionnaire administration and analysis Revision of skills audit and NFQ Identification of potential key informants Key informant interviews (n=4-­‐6) on revised NFQ Focus groups (n=4) with social care lecturers Write-­‐up and research presentations Page 170 CIT Rísam PhD Scholarship Programme 2014 Ethical issues Informed consent: All participants will be professionals and will be informed about the research content and purpose. Freedom to withdraw: All participants will have the right to withdraw at any time. Confidentiality and anonymisation: No participant will be identifiable from the research. All data will be anonymised. Debriefing and cross-­‐validation of findings: Participants will be debriefed about the results of the research and will be afforded the opportunity to cross-­‐validate their contributions. Harm minimisation: No potential harm is envisaged from the research. Data Protection: Data will be collected, analysed, stored and destroyed in accordance with the Data Protection Act (2003). 5. External Collaboration/Other Institutions Social Care Ireland will be contacted in determining the sampling frame. Book of Sample Projects Page 171 CIT Rísam PhD Scholarship Programme 2014 Health Sciences Title of project: Quantifying GAA Footballers physiological performance using Cork Senior Footballers GPS data Brief Summary of Research Interests: Applied mathematics and statistics Name of Principal Investigator: Email: sean.lacey@cit.ie CIT Department: Email: Dr Seán Lacey Telephone: 021-­‐4335917 Mathematics sean.lacey@cit.ie Discipline Area by Frascati Classification: Telephone: 021-­‐4335917 Statistics/Health Sciences 1. Abstract (250 words) In recent years, professional sports have all benefitted from the use of GPS devices to analyse player and team performance and to help avoid player injury. Sports such as Australian Rules football, soccer and rugby are using GPS devices extensively to gather information about their players and teams in an effort to have a competitive advantage over their opponents. Gaelic football teams, in particular men’s senior inter-­‐county teams, are now also starting to use GPS to gain a competitive edge over opponents, and to help win the Senior All-­‐Ireland Championship. 2.
Research Context and Contribution to the Research Field GPS technology allows managers to get a more accurate reading of how a player is performing physiologically, their fitness level, and have their team in the best possible physical shape prior to matches. 3.
Objectives The purpose of this project will be to look at the physical exertions of the Cork Senior Inter-­‐County Gaelic footballers using Global Positioning System (GPS) and tackle counts during competitive games. The aspects that will be included in the study will be distances run at 5 various speed zones, number of sprints during a game and the number of tackles a player is involved in. Using these variables, the project will try and generate an effort score and stress score for each player after a game. Theses scores should capture how much a player has worked during a particular game, so Book of Sample Projects Page 172 CIT Rísam PhD Scholarship Programme 2014 management can monitor a players work rate and exertion during a game, and also establish a more individualised post game training/recovery plan. 4.
Research Methodology The study will try determining that position requirements are statistically different. Measuring the effort and stress scores should allow for positional requirement comparison, player comparison and also monitor the teams overall scores from game to game. The project will establish a worst case scenario of each position so that management can design training programs to better prepare players for worst case scenarios in a game. Using GPS technology and scoring systems will help teams monitor their performance and assist with match preparation so players are in the optimal physical shape before a game. 5.
Work Plan • Clean the data -­‐ On some occasions the GPS units can be turned on before the match and as a result there were too many GPS minute recordings per game. Similarly, at times a player on the bench wears a GPS unit and therefore the data will be irrelevant. • Calculate and assess the load, from aforementioned variables, required by each position. • Assess player’s weaknesses and strengths along with mapping game demands of each variable. • Investigate various factors on game performance, for example venue (Home/Away) and result (Win/Loss/Draw). 6.
Ethical issues N/A External Collaboration/Other Institutions Mr Brian Cuthbert, Cork Football Manager. 7.
Book of Sample Projects Page 173 CIT Rísam PhD Scholarship Programme 2014 Title of project: Fatigue Prediction of Rugby Players using Munster Rugby GPS Data Name of Principal Supervisor: Dr Seán Lacey Brief Summary of Research Interests: Applied mathematics and statistics CIT Department: Email: Mathematics sean.lacey@cit.ie Discipline Area by Frascati Classification: Telephone: 021-­‐4335917 Statistics/Health Sciences 1. Abstract (250 words) In recent years, professional sports have all benefitted from the use of GPS devices to analyse player and team performance and to help avoid player injury. Sports such as Australian Rules football, soccer and rugby are using GPS devices extensively to gather information about their players and teams in an effort to have a competitive advantage over their opponents. It appears that technology is now capable of venturing into the challenge of predicting fatigue, with variables called Metabolic Power (MP) and Critical Power (CP). Metabolic power measures the energy involved in getting up to certain speed zones and can be reported in real time. Critical power is the power-­‐asymptote of the hyperbolic relationship between power output and time-­‐to-­‐
exhaustion. Munster Rugby does not currently have the units that give MP and CP live. But they wish to obtain the information retrospectively and start testing and are prepared for when the technology becomes available to them. 2.
Research Context and Contribution to the Research Field Physiologically, the CP represents the boundary between the steady-­‐state and non-­‐steady state exercise intensity domains and therefore may provide a more meaningful index of performance than other well-­‐known landmarks of aerobic fitness such as the lactate threshold and the maximal O2 uptake. Despite the potential importance to sports performance, the CP is often misinterpreted as a purely mathematical construct which lacks physiological meaning and only in recent years has this concept begun to emerge as valid and useful technique for monitoring endurance fitness. Interventions including training, pacing and prior exercise can be used to alter the parameters of the power-­‐time relationship. The challenge of this project is in optimising such interventions in order to positively affect the parameters of the power-­‐time relationship and thereby enhance sports Book of Sample Projects Page 174 CIT Rísam PhD Scholarship Programme 2014 performance in specific events. 3.
Objectives There have been many attempts to monitor fatigue real-­‐time in team sports. The simplest one was to use heart rate (HR) data and see if the players were getting tired by checking if the HR was getting higher and higher. HR has subsequently proven to be a poor indicator to fatigue. With the development in technology like GPS used for position tracking of the players, sport scientist showed that the distance covered and distance covered at higher velocities in the last minutes of the game is dropping down. It was believed that it had to be due to fatigue! Subsequently, it has been shown that no matter the fitness level of the player, everybody experiences a drop in performance during the last minutes of the game due to game tactics. Depending on the score, the leading team will try to put the ball in the corners, protect the ball or get it out-­‐of-­‐bounds. In other words slow down the game. So the drop in distance covered has nothing to do with fatigue, but rather game demand. This project aims to show that combining the internal (HR) and external work (GPS) will give some insight regarding the cost of activity. If HR gets higher for the same level of external work, that should indicate fatigue. This project will aim to present a method of how to combine what is known of a players potential and the expression of this potential in the game – i.e., derive a metabolic and power model to predict fatigue. 4.
Research Methodology The relationship between power output and critical power can be used to determine the amount of limited anaerobic reserve or W' (read W prime) been depleted. Using known CP and W' for an individual can make it possible to predict distance times and exhaustion times. According to the CP/W' model, exhaustion happens when one spends all of his/her W'. The more W' you spend, the more you are tired. The original real time monitoring idea comes from Philip Skiba. He used this approach in cycling because it is easy to measure power output on the bike. Knowing CP/W' of the cyclist can enable one to visualise loss in W' and make appropriate adjustments in pace. Power output is not measured in rugby currently. Through analysis of retrospective GPS data from Munster Rugby, this project will try to determine a method to quantify power output. Book of Sample Projects Page 175 CIT Rísam PhD Scholarship Programme 2014 5.
Work Plan This project will entail using calculus in R and working with the following variables: •
Critical Power/Critical speed – max speed of power that can be sustained for a long periods of time; •
Capacity/W’ – Anaerobic reserve; •
Metabolic power from GPS measured in J/Kg or cal/kg. Throughout the project validity studies and reliability studies on the statistics will be produced by Munster Rugby. 6.
7.
Ethical issues N/A External Collaboration/Other Institutions Mr Will Douglas, Munster Rugby Mr Bryce Cavanagh, Melbourne Rebels Book of Sample Projects Page 176 CIT Rísam PhD Scholarship Programme 2014 Title of project: Rating residential properties for assisted and independent living Name of Principal Supervisor: Dr Alex Vakaloudis Brief Summary of Research Interests: Independent Living, e-­‐learning, security CIT Department: Email: Nimbus/TEC alex.vakaloudis@cit.ie Discipline Area by Frascati Classification: Telephone: 021 4335163 Social biomedical sciences 1. Abstract (250 words) As life expectancy increases, the number of aged people in need of care also grows. Assisted and independent living is a research area looking into the provision of an environment suitable for aged or disabled people. Within this context, an active research question is building or converting accommodation fit for this purpose. The research question of this proposal is to define a fully quantifiable rating framework for residential properties in regards to their rightness for assisted and independent living. This is an interdisciplinary effort and input should be taken not only from technology areas (electronics, multimedia) but also from architectural, medical, social and occupational therapy experts. It is a framework rather than a simple rating system due to the complexity of parameters involved, for instance the different needs depending if person is on the early or late stages of Alzheimer’s or living alone or not. The ultimate outcome would a method to objectively portray the suitability of a residence for assisted and/or independent living, highlighting its deficiencies and measuring the effort required to achieve acceptable standards. 2. Research Context and Contribution to the Research Field Currently, there are efforts to define what an ideal environment for assisted and independent living should be. Most approaches however are driven by a single discipline and fail to come up with optimised, global solution. For instance, occupational therapists do not succeed in making best use of sensors (technology and money wise) and vice versa technical people do not have the expertise to deploy high-­‐tech solutions properly. As a result it is difficult to determine first the shortcomings of an effort and or how it could be easily be improved. The main contribution of this work is to define a rating mechanism for residential properties regarding the suitability for assisted and independent living. Since caring for aging people is becoming a major issue, the selection of a residence is a major factor towards providing them with proper care. Moreover new houses to be built for these specific cases will have a standard to abide with. A property has in our days a BER and we seek to identify a similar rating. Book of Sample Projects Page 177 CIT Rísam PhD Scholarship Programme 2014 3.
Objectives 1. To specify the actors and the main use-­‐cases from a medical perspective (e.g. early/late stage dementia, people living with/without a spouse) and to define the requirements posed by each use-­‐case 2. To classify the technological, architectural and communal solutions and constraints for responding to these requirements in flexible manner to cater for future advances. 3. To formulate a ranking framework for surveying a property and ranking for assisted and independent, possibly determining technological, architectural and communal sub rankings 4. To provide cost estimates for improving the ranking of a property. 4. Research Methodology The main element of this proposal is the formulation of the ranking framework. This requires analytical skills and understanding on the principles of building a rating framework. Moreover, knowledge from diverse domain experts needs to be retrieved. As a result the first step will sequentially contacting experts in psychiatry, occupational therapy, architecture and electronics with the objectives to understand the medical needs, the opportunities/limitations by architecture and the offerings of technology. Based on this information, the different sub-­‐rating categories will be identified and a rating framework will be formalised. Along with this activity, pilot studies will be contacted to verify results and ensure the framework’s performance. 5. Work Plan WP1: Examine the main “pains” or people in need of assistance for their living, the levels of support required to achieve certain standards of life. WP2: Survey existing residential establishments and identify critical points from an architectural and communal perspective WP3: Study technological solutions in terms of sensors, devices, user experience techniques and finally systems for assisted and independent living. WP4: Define rating framework to match medical “pains” against coverage by a property WP5: Contact study to verify the validity of framework. WP6: Writing up and dissemination As we intend to satisfy both generic and specialised usages we need to adopt an agile-­‐based approach with iterations as illustrated in the following table Year 1 Year 2 WP1 WP2 Book of Sample Projects Year 3 Page 178 CIT Rísam PhD Scholarship Programme 2014 6.
7.
WP3 WP4 WP5 WP6 Ethical issues Since surveys of properties, interviews with residences and consultations with domains experts will be carried out, there are issues of privacy and confidentiality. The following actions will be implemented 1. Contact methods and techniques will be submitted to CIT for approval 2. All data collected will be anonymised and protected against identification by deduction 3. No location or hint of location will be disclosed. External Collaboration/Other Institutions We expect to collaborate with experts in CIT and UCC and explore collaborations with leaders in assisted and independent living in other countries (e.g. Dementia villages in Holland, Nursing homes in UK, Independent living houses in Norway) so as to take into account local cultural principles Book of Sample Projects Page 179 CIT Rísam PhD Scholarship Programme 2014 Working Title of project: ‘Project Spraoi’: to improve fundamental movement skills, physical activity levels and nutritional behaviour in school children Name of Principal Supervisor: Dr Tara Coppinger, Dr. Con Burns Brief Summary of Research Interests: Physical activity promotion, obesity prevention, school aged children, nutrition, fundamental movement skills CIT Department: Email: Department of Sport, Leisure & Childhood Studies con.burns@cit.ie; tara.coppinger@cit.ie Telephone: Discipline Area by Frascati Classification: 021-­‐4335321 3.3 Health Sciences 1. Abstract (250 words) Summarise the objectives, the main expected originality and the research methodology to be used. ‘Project Spraoi,’an intervention which aims to improve the health and wellbeing of children by increasing physical activity (PA) and improving nutrition, is currently being implemented by a team of researchers from Cork Institute of Technology, in four primary schools in Cork city and county (n=1,030). The project is based on international best practice (Project Energize, New Zealand) and links closely with the Healthy Ireland Framework (2013), which has identified the health and wellbeing of the nation as a national priority. Recent research suggests that fundamental movement skills (FMS); actions such as hopping, skipping, throwing, catching and kicking, are the building blocks for movement, as they provide the foundation for the acquisition of more complex skills. Yet, evidence suggests low levels of FMS proficiency among children and insufficient data is available outlining the FMS proficiency of Irish primary school children. The Spraoi research team aims to address this paucity by (i) measuring FMS proficiency and (ii) implementing and evaluating an FMS intervention amongst two (one rural, one urban) primary schools in Cork city and county that are currently participating in ‘Project Spraoi’. FMS proficiency data will be collected from the same age children (senior infants, fourth class) that are currently being evaluated (N=107) in ‘Project Spraoi’ and in order for comparison, the same protocol of measurements will also be collected from pupils from two schools (N=127) that will not receive the intervention. Height, weight, body composition measures (waist circumference, percentage body fat) and PA, assessed by accelerometry, will also be measured. 2.
Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. Fundamental movement skills (FMS) are basic observable patterns of behaviour present from childhood to adulthood. FMS include running, hopping, skipping (locomotor), balancing, twisting, dodging (stability), throwing, catching and kicking (object control) (Department of Education Book of Sample Projects Page 180 CIT Rísam PhD Scholarship Programme 2014 Victoria, 1996; Gallahue and Ozmun, 2006; Stodden et al., 2008). Recent research, underpinning the necessity of a physically active lifestyle, suggests that FMS are the building blocks for movement as they provide the foundation for the acquisition of more complex skills in the specialised sport specific movement stage (Gallahue and Ozmun, 2006; Hardy, King, Espinel, et al., 2010). Research commissioned by the Victorian Department of Education (1996) states that all FMS can be mastered by 10-­‐11 years. Okely et al. (2001) have argued that the mastery of FMS in relation to their transfer to sport specific skills is an important contributing factor to physical activity (PA) participation amongst youth. The rationale for promoting the development of FMS in childhood relies on the recent findings from a systematic review (Lubans et al., 2010) of the current and future benefits associated with the acquisition of FMS in children. This systematic review found a relationship between FMS competency and eight potential benefits; namely global self-­‐concept, perceived physical competence, cardio-­‐respiratory fitness (CRF), muscular fitness, weight status, flexibility, PA and reduced sedentary behaviour. Despite the associated physiological, psychological and behavioural outcomes for FMS proficiency and their positive impact on public health, it is apparent that a lot of children do not have these basic patterns of movement. The evidence would suggest that while levels of FMS vary from country to country, performance levels remain consistently low across the spectrum with the majority of children and adolescents failing to surpass 50% mastery in most skills (Mitchell et al., 2013). In terms of increasing children’s PA, the school environment has the potential to make important differences and presents a number of opportunities for intervention (Lavelle et al., 2012; Van Sluijs et al., 2008; Vasques et al., 2013; Ward et al., 2007). A recent report by Sallis et al., (2012) highlighted that in the past two decades, evidence-­‐based school curricula have shown significant differences in moderate to vigorous physical activity (MVPA) during and outside of school hours. The school environment presents many opportunities for targeting children directly, with many studies suggesting the importance of targeting ecological domains beyond the individual (Kahn et al., 2002; Perry et al., 2012; Sallis et al., 2012). Effective school environments present opportunities to embody a culture of care, and to be fully inclusive of the individual regardless of the existing racial or socio economic background differences (Cavanagh et al., 2012). The development of evidence-­‐based school programmes has seen the acceptance of Physical Education (PE) as an efficacious resource (Sallis et al., 2012). As a viable change agent to increase PA in the school-­‐aged population, PE is considered a very important provider of PA (McKenzie and Lounsbery, 2009; Payne and Morrow, 2009; Scheerder et al., 2008; Ward et al., 2007). PE also gives children an opportunity to learn physical and behavioural movement skills (Haerens et al., 2007; McKenzie and Lounsbery, 2009; Mitchell et al., 2013; Van Beurden et al., 2003). A recent meta-­‐analysis of the effectiveness of motor skill interventions illustrate a significantly positive association between participation in school based motor skill programmes and FMS proficiency (Logan et al., 2011). Furthermore, intervention programmes such as “Move it Groove it” and “Project Energize” highlight that both PA and FMS can be integrated during the provision of PE (Mitchell et al., 2013; Van Beurden et al., 2003). In October 2013, researchers from the Department of Sport, Leisure & Childhood Studies at Cork Institute of Technology commenced ‘Project Spraoi.’ The aim of the programme is to improve the overall health and to reduce weight gain of primary school aged children by increasing their PA and encouraging healthy eating. This is the first intervention of its kind ever to be introduced in Ireland. The programme is delivered by three ‘Energizers,’ in four intervention and three control schools in Cork city and county. It is based on the best-­‐practice model of ‘Project Energize’ in New Zealand (NZ) (http://www.projectenergize.org.nz/) and receives full support from the NZ team. Initial findings of the process evaluation have been positive, with excellent levels of school involvement Book of Sample Projects Page 181 CIT Rísam PhD Scholarship Programme 2014 and participation. Furthermore, feedback from a recent national conference (The All Ireland Postgraduate Conference in Sport Science and Physical Education, University of Limerick, 24th January 2014) identified the value of’ Project Spraoi’ in its approach to concentrate research on evidence based international best practice. The next proposed phase to ‘Project Spraoi’ is the inclusion of an FMS intervention. The research aims to evaluate the intervention effect after 9 months (end of academic school year 1) and 21 months (follow-­‐up/end of academic year 2) amongst a primary school cohort (senior infants, fourth class). Two schools (one rural, one urban) will receive the FMS intervention over the course of two school years, and FMS proficiency will then be compared to two control schools, who will only receive their usual PE programme for the same period. The evaluation aims to ascertain if the intervention groups demonstrate significant increased levels of FMS proficiency over time, when compared to the control groups. Secondary aims will assess if the intervention had a positive impact on minutes of daily physical activity (PA), correlates of physical activity as well as standard anthropometric characteristics (height and weight) and body composition measures (waist circumference and percentage body fat via bioelectrical impedance analysis). 3.
Objectives The objectives of the proposed research are to: (i)
Assess the FMS proficiency of primary school children participating in ‘Project Spraoi’, a physical activity and nutrition health promotion intervention being delivered to primary school children in Cork city and county. (ii)
Evaluate the efficacy of a school based intervention aimed at improving FMS among primary school children in Cork city and county after 9 months (end of academic year 1) and 21 months (follow up/end of academic year 2). (iii)
Evaluate the efficacy of a school based intervention aimed at improving FMS among primary school children in Cork city and county on levels of habitual PA, correlates of activity and body composition. 4.
Research Methodology Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. (i)
Development of Intervention Relevant intervention material used in ‘Project Energize’ has already been made available for use in ‘Project Spraoi’s’ study, and only minor adjustments to the protocol have been applied in order to make it relevant to the Irish setting. ‘Project Energize’ has also developed and validated an international best practice FMS intervention, which has had a positive impact in NZ. This intervention will be adapted for use in an Irish setting and evaluated using schools that are currently enrolled in the ‘Project Spraoi’ intervention. These schools were originally recruited using group randomised controlled trial methods (ISRCTN global register http://www.controlled-­‐
trials.com/ISRCTN92611015/). The 21 month intervention will target all children (N=481) in two schools (one urban, one rural) in Cork. The evaluation of the intervention will include the same age children (senior infants and fourth class) that are currently being evaluated (N=107) as part of ‘Project Spraoi’. This includes pupils (N=127) from two schools that are acting as controls, in that they do not receive any of the Book of Sample Projects Page 182 CIT Rísam PhD Scholarship Programme 2014 programme but still undertake the same protocol of measurements as the intervention schools, in order for comparisons to be made. Six year old and ten year old children will be included, based on children of these age ranges being at the advent of important ages for forming and understanding health habits. (ii)
Intervention Implementation Central to the recruitment of the RISAM scholar, is their ability to act as an ‘Energizer’ in the intervention. The ‘Energizer’ will support the class teachers by leading processes, modelling classes, and providing resources on FMS to help them achieve their goals. Therefore, in addition to the postgraduate researcher being recruited via appropriate academic methods, they will also be selected using the NZ Energizer recruitment protocol. This requires ‘Energizers’ to be teachers/ graduates in the fields of exercise, nutrition and/ or P.E. At induction, and then each month, the ‘Energizer’ will undertake combined training with members of the ‘Project Spraoi’ team (postgrad supervisors, other academic staff in CIT, external collaborators and postgraduate students), in order to share experience, resources and skills. (iii)
Intervention Evaluation Protocol An impact evaluation (e.g. change in anthropometric measures) and process evaluation (assessing the process of programme implementation) will form the two major constituents of the intervention evaluation. These methods of evaluation provide insight into how successful an intervention is and how they are interpreted and responded to by different groups of people. They also identify whether the strategies are reaching the intended target group. Such findings will be of great use for further implementation of the ‘Spraoi’ programme nationally and for new school-­‐based obesity prevention strategies based in Ireland. Such research has the potential to change the habitual activities of children across the nation. Specific measurements of this research will be outlined below. As some of these measures are currently being undertaken as part of the broader ‘Project Spraoi’ programme, a more detailed explanation of these is provided in the Appendices. Measurements Baseline measures will be taken at the beginning of the school year in September 2015 (pre), and follow up testing will occur at the end of the intervention in May 2017. Periodic measurement tests will also be conducted during the intervention period. The project’s collaborator, Dr Wesley O’Brien, will administer periodic training workshops to the researcher, to ensure that measurement assessment standards are met continuously during data collection. FMS will be assessed in conjunction with the guidelines from the Test of Gross Motor Development (TGMD) and the ‘Energizer’ will receive formal training in FMS proficiency. The specific 15 gross motor skills to be assessed include: run, skip, gallop, slide, leap, hop, horizontal jump and vertical jump (locomotor; maximum score of 66); kick, catch, overhand throw, strike, underhand roll and stationary dribble (object control; maximum score of 48); balance (stability; maximum score of 10). Participants will perform the skill on 3 occasions including 1 familiarisation practice and 2 performance trials. Video cameras will be used to record each participant’s performance and execution of the selected 15 FMS. The TGMD will be administered by the Energizer before and after the FMS intervention, with approximately five to six children at a time. If the child is able to perform all components of the skill correctly, (s)he will be graded as proficient in that skill. The pretesting information will then be presented to class teachers in a report and used to identify the skills that require the most attention. Book of Sample Projects Page 183 CIT Rísam PhD Scholarship Programme 2014 Height and weight will be measured, in order to calculate body mass index (BMI) (weight(kg)/height(m2)) and Cole et al. (2000) cut off points will applied to the data in order to calculate BMI classification (normal, overweight, obese). PA will be measured using ActiGraph GT1M and GT3X accelerometers, at 5 second epochs to capture the intermittent and sporadic behaviour of youth and to avoid underestimation of time in moderate and vigorous activity that may occur when longer epochs are used. Each participant will be asked to wear an accelerometer during all waking hours, for seven consecutive days. Correlates of physical activity will be measured using an adapted version of a previously validated questionnaire developed in previous research which has found to have validity and reliability (Burns et al., 2014). FMS intervention The FMS intervention will be tailored to the needs of each school, based on the pretest/ baseline information gathered by the researcher/ ‘Energizer’. The ‘Energizer’ will then provide and discuss with each class teacher, models and plans for targeted physical education classes and provide specific material sourced from the Kiwidex (Sport and Recreation New Zealand, 2005) and SPARC, Developing Fundamental Movement Skills manuals (Sport and Recreation New Zealand, 2007). These skills and activities will then be included in their PE/PA sessions. In addition, after the baseline testing, each child will set their own goals for the skills that they want to improve. Control Children in control schools will not receive any of the intervention components. They will, however, undertake all physical measurements, have their FMS assessed and their PA quantified, at the same time points as the intervention participants. Sample Size Two intervention and two control schools have already been recruited as part of ‘Project Spraoi’. A total of 107 (58 senior infants, 49 4th class) participants from intervention schools and 127 (65 senior infants, 62 4th class) participants from control schools will be tested pre and post intervention. Data Analysis Data will be analysed using SPSS version 21.0 for Windows and in conjunction with the other data collected as part of the broader ‘Spraoi’ project. Descriptive statistics for the anthropometric characteristics and objective daily PA over time (pre and post) will be calculated. Individual two-­‐way repeated measures ANOVA’s will be conducted to explore the impact of gender and school type (intervention group relative to control) over time (pre and post) on objective daily PA minutes and FMS gross motor skill proficiency. Statistical significance will be set at p<0.05. FMS scores will be calculated for all 15 FMS tests for the intervention group, relative to the control, using paired sample t tests. In order for international comparisons to be made, the results will be directly compared to those obtained in Project Energize (Mitchell et al. 2013 http://www.ncbi.nlm.nih.gov/pubmed/23697592). Work Plan Present the research work plan, outlining the main research tasks and timing. Book of Sample Projects Page 184 CIT Rísam PhD Scholarship Programme 2014 PhD Year 1 GANTT Chart Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Literature Review Training on testing procedures Training on intervention procedures Recruitment of intervention and control schools Dissemination of consent forms Pilot testing of intervention Present review paper Annual monitoring Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Data collection (baseline) Baseline analysis Write up of baseline analysis findings Intervention implementation Year 1 post test & process evaluation Present paper of year 1 findings Annual monitoring Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug PhD Year 2 GANTT Chart PhD Year 3 GANTT Chart Task Book of Sample Projects Page 185 CIT Rísam PhD Scholarship Programme 2014 Intervention implementation Post testing Process evaluation Write up Thesis Final paper/viva voce 5.
Ethical issues If the proposed research directly involves human or live animal subjects, discuss the ethical issues involved and the actions that will be taken to ensure compliance with CIT ethics guidelines and with the CIT Child Protection Policy (if children are involved). On 2nd October 2013, the Research Ethics Committee at Cork Institute of Technology granted ethical approval for the postgraduate research team in the department to proceed with ‘Project Spraoi’. A separate ethics application will be submitted for the FMS aspect of the research. 6. External Collaboration/Other Institutions • Professor Elaine Rush, Auckland University of Technology, Auckland, New Zealand. • Ms Stephanie McLennan, Project Energize Manager, Sport Waikato, Hamilton, New Zealand. • Dr Wesley O’Brien, University College Cork, Cork, Ireland. References Burns, C., Murphy, J., Vaughan, J., MacDonncha, C., 2014 Year in school and physical activity stages of change as discriminators of variation in the physical activity correlate profile of adolescent females. Journal of Physical Activity and Health, in press Cavanagh, T., Macfarlane, A., Glynn, T., Macfarlane, S., 2012. Creating peaceful and effective schools through a culture of care. Discourse: Studies in the Cultural Politics of Education 33, 443–455. Cole, T.J., Bellizzi, M.C., Flegal, K.M., Dietz, W.H., (2000). Establishing a standard definition for child overweight and obesity worldwide: International survey. BMJ 320, 1240–1243. Department of Education Victoria, 1996. Fundamental motor skills: A manual for classroom teachers. Melbourne, Australia. Gallahue, D.L., Ozmun, J.C., 2006. Understanding motor development: Infants, children, adolescents, adults., 6th ed. Mc-­‐Graw Hill, New York, NY. Hardy, L., King, L., Espinel, P., Cosgrove, C., Bauman, A., 2010. NSW schools physical activity and nutrition survey (SPANS). Full Report. Sydney: NSW Ministry of Health. Book of Sample Projects Page 186 CIT Rísam PhD Scholarship Programme 2014 Kahn, E.B., Ramsey, L.T., Brownson, R.C., Heath, G.W., Howze, E.H., Powell, K.E., Stone, E.J., Rajab, M.W., Corso, P., The Task Force on Community Preventive Service Service, 2002. The effectiveness of interventions to increase physical activity: A systematic review. American Journal of Preventive Medicine 22, 73–107. Lavelle, H.V., Mackay, D.F., Pell, J.P., 2012. Systematic review and meta-­‐analysis of school-­‐based interventions to reduce body mass index. Journal of Public Health 34, 360–369. Lubans, D.R., Morgan, P.J., Cliff, D.P., Barnett, L.M., Okely, A.D., 2010. Fundamental movement skills in children and adolescents: Review of associated health benefits. Sports Medicine 40, 1019–1035. McKenzie, T.L., Lounsbery, M.A.F., 2009. School physical education: The pill not taken. American Journal of Lifestyle Medicine 3, 219–225. Mitchell, B., McLennan, S., Latimer, K., Graham, D., Gilmore, J., Rush, E., 2013. Improvement of fundamental movement skills through support and mentorship of class room teachers. Obesity Research and Clinical Practice 7, e230–e234. Mitchell, J.A., Pate, R.R., España-­‐Romero, V., O’Neill, J.R., Dowda, M., Nader, P.R., 2013. Moderate-­‐
to-­‐vigorous physical activity is associated with decreases in body mass index from ages 9 to 15 years. Obesity 21, e280–e286. Okely, A.D., Booth, M.L., Patterson, J.W., 2001. Relationship of physical activity to fundamental movement skills among adolescents. Medicine and Science in Sports and Exercise 33, 1899–1904 Payne, V.G., Morrow, J.R.J., 2009. School physical education as a viable change agent to increase youth physical activity. The President’s Council on Physical Fitness and Sports Research Digest 10, 1–
8. Perry, C.K., Garside, H., Morones, S., Hayman, L.L., 2012. Physical activity interventions for adolescents: An ecological perspective. The Journal of Primary Prevention 33, 111–135. Sallis, J.F., McKenzie, T.L., Beets, M.W., Beighle, A., Erwin, H., Lee, S., 2012. Physical education’s role in public health: Steps forward and backward over 20 years and HOPE for the future. Research Quarterly for Exercise and Sport 83, 125–135. Scheerder, J., Vanreusel, B., Beunen, G., Claessens, A., Renson, R., Thomis, M., Vanden Eynde, B., Lefevre, J., 2008. Lifetime adherence to sport and physical activity as a goal in physical education. In: Seghers, J., Vangrunderbeek, H. (Eds.), Physical education research what’s the evidence. Utigeverij Acco, Leuven, pp. 29–40. Sport and Recreation New Zealand. Kiwidex manual (2005). Wellington: SPARC Sport and Recreation New Zealand. Sport and Recreation New Zealand. Developing fundamental movement skills manual (2007). Wellington: SPARC Sport and Recreation New Zealand. Van Beurden, E., Barnett, L., Zask, A, Dietrich, U., Brooks, L., Beard, J., 2003. Can we skill and activate children through primary school physical education lessons? “Move it Groove it”—a collaborative Book of Sample Projects Page 187 CIT Rísam PhD Scholarship Programme 2014 health promotion intervention. Preventive Medicine 36, 493–501. Van Sluijs, E.M.F., McMinn, A.M., Griffin, S.J., 2008. Effectiveness of interventions to promote physical activity in children and adolescents: Systematic review of controlled trials. British Journal of Sports Medicine 42, 653–657. Vasques, C., Magalhaes, P., Cortinhas, A., Mota, P., Leitao, J., Lopes, V.P., 2013. Effects of intervention programs on child and adolescent BMI: A meta-­‐analysis study. Journal of Physical Activity and Health, (iFirst Article). Ward, D.S., Saunders, R.P., Pate, R.R., 2007. Physical activity interventions in children and adolescents. Human Kinetics, Champaign, IL. Appendices ‘Project Spraoi’ Evaluation Methodology The anthropometric measures include: PA, fitness and nutritional knowledge and attitudinal questionnaires. Established longitudinal guidelines will be followed in taking these measurements. Baseline and 2 year (0 and 24 months +/-­‐ 1 month) measurements include: • Height and mass, which will be measured using a calibrated stadiometer and scales, respectively. • Body Mass Index (BMI), which will be calculated by dividing body mass in kg by height in metres squared. • Waist circumference, which will be recorded using standardised methods, with an inelastic tape measure. • Blood pressure and heart rate -­‐ duplicate measurements of arterial blood pressure will be taken using a mercury sphygmomanometer after the subject has rested in a seated position for five minutes. A second reading will be taken after a further two minutes and the average of the two readings will be recorded. • Body fat percentage measurement will be recorded via the validated Impedimed DF50 hand-­‐to-­‐
foot bio-­‐impedance analysis (BIA) system. • Aerobic fitness will be assessed using the 550 metre run/walk test. • Nutrition will be assessed using questionnaires that are deemed valid and reliable by the NZ research team and piloted for use with Irish schoolchildren. These include: (i) The Household Questionnaire which is completed by parents and has been developed from a number of sources (Children’s Nutritional Survey New Zealand, Diet History Questionnaire New Zealand, Children and Young People Survey), (ii) School stocktake which is completed by the school and (iii) Knowledge and Attitudes questionnaire which is completed verbally by the children. The following measurements will be recorded at six monthly intervals (6, 12, 18 months +/-­‐ 2 weeks) for all participants: •
•
•
Height Mass BMI calculation PA and sedentary behaviour will be measured via Actigraph accelerometers for a period of 7 days to provide quality objective PA and sedentary behaviour data. Actigraph accelerometers have been found to be a valid measure of PA amongst children using doubly labelled water. These are small (3 Book of Sample Projects Page 188 CIT Rísam PhD Scholarship Programme 2014 cm x 3 cm) electronic devices that give an indication of frequency, duration and intensity of movement and which are validated for use in children. To be included in the analysis, participants will be required to wear the accelerometer for a minimum of 600 minutes on four separate days; as recommended by the literature. Time spent in PA of different intensities is based on the application of count thresholds. These count thresholds are derived from calibration studies that classify accelerometer output to measured activity energy expenditure. Moderate and vigorous activity count thresholds will be calculated using the age specific equations. Due to the nature of activity among youths (i.e. short bursts of intermittent activity of different intensities), data will be collected at 5 second epochs to avoid underestimation of time in moderate and vigorous activity that may occur when longer epochs are used. The process evaluation (Exposure, Reach, Satisfaction, Delivery, Context and Fidelity) component will allow for the perceptions and reaction of those involved in the intervention’s strategies to be considered. This will include focus groups that will be administered by the primary researchers with relevant staff members from participating schools that have responsibility for co-­‐ordinating intervention activities. Direct comparisons will be made with the NZ dataset of waist circumference, blood pressure and heart rate, body fat percentage measurement (via bioelectrical impedance analysis), PA (accelerometry), aerobic fitness (via 550 metre run/walk test), sedentary behaviour (accelerometry) and the questionnaire responses. More general comparisons of PA and dietary behaviour will be made with the national Health Behaviour of School Children (HBSC) and “Growing Up in Ireland” studies currently taking place here in Ireland. Book of Sample Projects Page 189 CIT Rísam PhD Scholarship Programme 2014 Working Title of project: An investigation into the relationship between training load and markers of wellness among elite hurling players Name of Principal Supervisor: Dr. Con Burns & Dr. Cian O’Neill Brief Summary of Research Interests: Sports coaching and pedagogy, human performance measurement, CIT Department: Email: Department of Sport, Leisure and Childhood Studies con.burns@cit.ie Discipline Area by Frascati Classification: Telephone: 021-­‐4335321 3.3 Health Science 1. Abstract (250 words) Summarise the objectives, the main expected originality and the research methodology to be used. Season long competition schedules in sport create challenges for coaches in balancing the requirements of recovery, developing and maintaining physical fitness as well as adjusting the training load before every game (Gastin et al. 2013). Ensuring adequate rest and recovery is important in the avoidance of overtraining and the achievement of optimal performance, therefore it is recommended that training load and recovery be continually monitored during the training year (Kellman et al., 2010). Various subjective player monitoring tools as well as objective GPS devices have been used to record and monitor athlete training load and wellness. Elite Gaelic games (GAA) players may be at increased risk of overtraining as these players tend to play on multiple teams (club, college, county) and multiple sports (football, hurling). Furthermore, previous research has reported that elite GAA players have been found to report significantly higher levels of emotional and physical exhaustion compared to non-­‐elite players (Burns et al. 2014). While limited previous research has investigated training loads and wellness in other sports (Gastin et al., 2013) research of this nature has not been carried out with elite GAA players. Therefore the proposed research aims to investigate training load and markers of wellness using a subjective player monitoring tool and objective GPS devices. Data will be collected across playing seasons with players from inter county minor, third level college and senior inter county hurling teams. 2.
Research Context and Contribution to the Research Field Describe the broad context of the research, including a brief review of the current state of the art in the topic of the proposed research, and the overall contribution which it will make to the general field of research. The goal in training competitive athletes is to provide training loads that are effective in improving performance (Meeusen et al., 2013). To achieve this and to maximize high level of performance in elite sport a clear strategy needs to be developed to manage, manipulate and monitor players fatigue (Van Winckel et al., 2014). Season long competition schedules in sport create challenges for Book of Sample Projects Page 190 CIT Rísam PhD Scholarship Programme 2014 coaches in balancing the requirements of recovery, developing and maintaining physical fitness as well as adjusting the training load before every game (Gastin et al. 2013). Management of this fatigue becomes more challenging when athletes are involved in multiple teams e.g. club inter county, club, senior and multiple sports e.g. Gaelic football and hurling. Playing competitive Gaelic games involves varying levels of exercise induced muscle damage (EMID) (Van Winket et al., 2014). This EMID is characterized by delayed onset muscle soreness (DMOS), decreased muscle function, impaired performance, and increased perceived fatigue (Van Winkle, 2014). Gould and Dieffenbach (2002) demonstrated that chronic failure to adequately recover from the stress of training induces a state of overtraining which may result in eventual burnout. Furthermore, previous research has reported an association between higher training loads over a season and increased risk of injury (Gabett et al., 2012). Athlete overtraining and burnout has been highlighted as an area for concern for sporting organizations due to the potential negative consequences to sports participation and athlete welfare (Cresswell and Eklund 2004). Overtraining has been defined as ‘an accumulation of training and/or non-­‐training stress resulting in long term decrement in performance capacity with or without related physiological and psychological signs and symptoms of maladaptation in which restoration of performance may take several weeks or months’ (Meeusen et al., 2013). Burnout is an experiential syndrome with 3 main characteristics: (i) physical and emotional exhaustion, (ii) reduced sense of athletic self-­‐accomplishment and (iii) sport devaluation (Raedeke 1997). The occurrence and existence of burnout has been hypothesized to result in decreased performance, and the eventual withdrawal from organized sport participation (Cresswell and Eklund 2004). Burnout has been found to be a dynamic experience which is influenced by factors such as playing position, injury, starting status and level of participation (Cresswell and Eklund 2006). It has been argued that high level sport performers may be particularly susceptible to burnout, however to date limited evidence has examined this hypothesis (Hill et al. 2008). A recent study of the correlates of sport participation among Irish adolescents assessed levels of burnout among elite sport participants and non-­‐elite sport participants (Burns et al., 2014). Levels of burnout was measured using a validated ‘Athlete Burnout Questionnaire ‘which assessed (i)reduced accomplishment, (ii) emotional/ physical exhaustion and (iii) ‘devaluation’ of sports performance (Raedeke and Smith, 2001). Elite GAA participants were found to exhibit greater levels of emotional and physical exhaustion compared non elite sports participants (P <.05). To the authors knowledge no previous study has monitored training load among GAA participants and more research is warranted to assess and monitor training load. An ability to monitor training load is critical to the process of quantitating training plans (Foster et al., 2001). A recent development in sports coaching has been the development of player monitoring tools to provide coaches with subjective information on player wellness (Killen et al., 2010). The monitoring of players training load as well as markers of wellness have the potential to reduce periods of overtraining among sports participants. Monitoring tools have assessed training load using rate of perceived exertion (RPE) x time (mins), these scores have been found to correlate with heart rate scores (Wallace et al., 2009). Practitioners have been encouraged to incorporate these tools into some form of monitoring questionnaire or training diary (Meeussen et al., 2013). While these tools have potential to inform quality coaching there is a dearth of research which has examined the effectiveness and validity of these tools and more research is warranted (Gastin et al., Book of Sample Projects Page 191 CIT Rísam PhD Scholarship Programme 2014 2013). Global positioning systems (GPS) are gaining popularity in field based sports as a means for coaches to assess movement demands for their athletes in training and competition (Peterson et al., 2010, Wisbey et al., 2009). GPS has been found to provide a valid, reliable measure of movement demands in team sports (Coutts and Dutfield et al., McLeod et al., 2009). GPS devices can provide information relating to distance covered, maximum velocity, high acceleration efforts and distance covered at specified speed zones (Wisbey et al., 2009). Increased knowledge of movement demands of the game assists coaches plan recovery and training programmes for their athletes. Maximising athlete performance is a primary goal in sports coaching. To make informed decisions as a coach it is necessary to have knowledge of factors such as athlete fatigue, wellness, injury and training load. Furthermore, to effectively plan and prepare athletes for elite sport it is necessary to have an in-­‐depth analysis of the movement demands associated with the specific sport. The proposed research aims to increase the body of knowledge relating to (i) player monitoring, (ii) movement demands in Gaelic games. The research aims to monitor daily training load, prevalence of injury and markers of wellness among Gaelic games participants at minor, third level colleges and senior inter county. In conjunction, the proposed study will provide in depth objective analysis (GPS) of the movement demands of minor, third level colleges and inter county teams. This level of analysis has not previously been undertaken and it will assist coaches to develop specific training programmes relevant to the needs to the game. Research on the usefulness and validity of player monitoring tools has the potential to increase the use of these inexpensive, non-­‐invasive tools in the coaching context. 3. Objectives Summarise the key objectives of the research. The objectives of the proposed research are to: 1. Investigate the training loads and markers of wellness during competitive seasons among inter county minor, third level colleges and senior inter county hurling teams. 2. Analyse objectively measured movement demands associated with hurling games at inter county minor; third level colleges and senior inter county levels. 3. Assess the relationship between objectively measured training load and: (i) subjective markers of wellness and (ii) subjective rating of training load over a competitive season. 4. Evaluate the impact of wellness on weekly playing performance in elite hurling teams over a competitive season. 4.
Research Methodology Book of Sample Projects Page 192 CIT Rísam PhD Scholarship Programme 2014 Describe the methodology to be used in the proposed research and why it is appropriate to the research objectives. The proposed research consists of three related studies monitoring player wellness and training load across a playing season. A brief outline methodology of each study is provided. Study 1: A comparison of training loads and markers of wellness among elite minor, third level colleges and senior inter county hurling players Due to the nature of elite GAA, players tend to be involved with multiple teams (club, third level college, inter county) and multiple sports (hurling and Gaelic football). As a result it is difficult for coaches to effectively monitor players training load and to ensure adequate rest. Participants in the proposed research are (i) an inter county minor hurling team; (ii) a third level college hurling team and (iii) a senior inter county hurling team. In this study players on each team will be asked to complete ‘Squadplus’ player monitoring tool for a competitive season (http://www.squadplus.com/). With this tool data is entered before any scheduled activity, usually in private and at a constant time each morning. This online tool asks players to subjectively record training load on the previous day and to rate their wellness scores. Training load is calculated based on time spent in training/ games x perceived intensity based on the rate of perceived exertion (RPE) scale. Subjective wellness scores are based on rating sleep, energy, mood, appetite, soreness and sickness on a daily basis from 1 (bad as possible) to 5 (good as possible). ‘Squadplus’ was piloted with the Cork Institute of Technology Fitzgibbon hurling team during the 2013-­‐2014 season. Adherence rate to the completion of the daily monitor was over 70% which is similar to a study of professional Australian football players (Gastin et al., 2013). The purpose of this study is to investigate the relationship between training load and markers of wellness during competitive season among each group of participants. Study 2: An analysis of objectively measured movement demands of the game of hurling using elite minor, third level colleges and senior inter county teams. Knowledge of the movement demands of the sport will assist coaches to plan more specific training sessions that meet the demands of the game. The use of integrated technology such as GPS devices can contribute to significant improvements in the preparation training and recovery aspects of field based sports (Dellaserra et al. 2014). GPS has been found to provide a valid, reliable measure of movement demands in team sports (Coutts and Dutfield et al., McLeod et al., 2009). Variables measured using GPS include distance covered, maximum velocity, high acceleration efforts and distance covered at specified speed zones. While large scale research has examined the movement patterns in sports such as Australian rules and soccer (Dellaserra et al. 2014), there is a dearth of research which has focused on the movement patterns in Gaelic games. Furthermore, to the author’s knowledge no previous research has examined differences in movement patterns between different levels of elite performance (minor, third level college, senior inter county). Players on each participating team will be asked to wear VX 230 GPS tracking devices for all competitive games and a selection of training sessions during a competitive season. Therefore the purpose of this study is to Book of Sample Projects Page 193 CIT Rísam PhD Scholarship Programme 2014 investigate the movement demands in hurling of inter county minor, third level colleges and senior hurling teams using GPS tracking devices Study 3: Relationship between objective GPS data and subjective player monitoring among elite hurling players Perceptions of wellness are often used by coaches to assess adaptive responses to training (Gastin et al., 2031). These tools have numerous benefits such as being easy to use, inexpensive, non-­‐invasive and the provision of data on each player to a coach. While these monitoring tools are increasing in popularity literature contains little in terms of the usefulness or validity of these tools (Gastin et al., 2013). One study has indicated that subjective ratings of physical and psychological wellness were sensitive to previous weekly training load manipulations, periods of unloading and individual player characteristics in Australian Rules football (Gastin et al., 2013). The current study aims to build on this research in GAA and to assess the relationship between (i) objectively measured training loads (GPS) and player and coach perception of training load measured using RPE, (ii) objectively measured training load (GPS) and markers of wellness throughout a competitive season, (iii) weekly playing performance recorded as a single performance score derived from game statistics and markers of wellness scores. It is envisaged that this research will add to the body of knowledge relating to coaching science and will inform future coaching in the area of Gaelic games. References Burns, C., Murphy, J.J., Vaughan, J., MacNamara, A., MacDonncha, C. (2014). Correlates of adolescent sports participation. Department of Sport Leisure and Childhood Studies, Cork Institute of Technology and The Gaelic Athletic Association, Dublin, Ireland. Cresswell, S. L. & Eklund, R. C. (2004). The athlete burnout syndrome: possible early signs. Journal of Science and Medicine in Sport, 7(4), 481-­‐487. Coutts, A., & Duffield, R. (2010). Validity and reliability of GPS devices for measuring movement demands of team sports. Journal of Science and Medicine in Sport, 13, 133–135 Dellaserra, C.L., Gao, Y., Ransdell, L. (2014). Use of integrated technology in team sports:a review of opportunities, challenges, and future directions for athletes. Journal of Strength and Conditioning Research, Feb, 28(2), 556-­‐73. Gray, A.J., Jenkins, D., Andrews, M.H., Taaffe, D.R, Glover, M.L. (2010). Validity and reliability of GPS for measuring distance travelled in field-­‐based team sports. Journal of Sports Science, Oct, 28(12), 1319-­‐25. Foster, C., Florhaug, J.A., Franklin, J., Gottschall, L., Hrovatin, L.A., Parker, S.,Doleshal, P., Dodge, C. (2001). A new approach to monitoring exercise training. Journal of Strength and Conditioning Research, 15(1), 109-­‐15. Gabbett, T.J., Ullah, S. (2009). Relationship between running loads and soft-­‐tissue injury in elite team sport athletes. Journal of Strength and Conditioning Research, 26(4), 953-­‐60. Book of Sample Projects Page 194 CIT Rísam PhD Scholarship Programme 2014 Gastin, P,B., Fahrner, B., Meyer, D., Robinson, D., Cook, J.L. (2013). Influence of physical fitness, age, experience, and weekly training load on match performance in elite Australian football. Journal of Strength and Conditioning Research, May, 27(5), 1272-­‐9. Gastin, P.B., Meyer, D., Robinson, D. (2013). Perceptions of wellness to monitor adaptive responses to training and competition in elite Australian football. Journal of Strength and Conditioning Research, Sep, 27(9), 2518-­‐26. Hill, A. P., Hall, H. K., Appleton, P. R. & Kozub, S. A. (2008). Perfectionism and burnout in junior elite soccer players: The mediating influence of unconditional self-­‐acceptance. Journal of Psychology Sport and Exercise, 9(5), 630-­‐644. Kellmann, M. (2010). Preventing overtraining in athletes in high-­‐intensity sports and stress/recovery monitoring. Scandinavian Journal of Medicine and Science in Sport, Oct, 20 Suppl 2, 95-­‐102. Killen, N.M., Gabbett, T.J., Jenkins, D.G. (2010). Training loads and incidence of injury during the preseason in professional rugby league players. Journal of Strength Conditioning Research, 24(8), 2079-­‐84. Macleod, H., Morris, J., Nevill, A., & Sunderland, C. (2009). The validity of a non-­‐differential global positioning system for assessing player movement patterns in field hockey. Journal of Sports Sciences, 27, 121–128. Meeusen, R., Duclos, M., Foster, C., Fry, A., Gleeson, M., Nieman, D., Raglin, J., Rietjens, G., Steinacker, J., Urhausen, A. (2013). European College of Sport Science; American College of Sports Medicine. Prevention, diagnosis, and treatment of the overtraining syndrome: joint consensus statement of the European College of Sport Science and the American College of Sports Medicine. Medicine and Science in Sports and Exercise, 45(1), 186-­‐205. Petersen, C. J., Pyne, D. B., Dawson, B., Portus,M., & Kellett, A. (2010). Movement patterns in cricket vary by both position and game format. Journal of Sports Sciences, 28, 45–52. Van Winckel, J., Tenney, D., Helsen, W., McMillan K., Meeert, J.P., Bradley, P. (2014). Fitness in Soccer: The science and practical application. Moveo Ergo Sum: Leuven. Wisbey, B., Montgomery, P. G., Pyne, D. B., & Rattray, B. (2009). Quantifying movement demands of AFL football using GPS tracking. Journal of Science and Medicine in Sport, Sep, 13(5), 531-­‐6 Wallace, L.K., Slattery, K.M., Coutts, A.J. (2009). The ecological validity and application of the session-­‐
RPE method for quantifying training loads in swimming. Journal of Strength and Conditioning Research, 23(1), 33-­‐8. 5. Work Plan Present the research work plan, outlining the main research tasks and timing. PhD Year 1 GANTT Chart Task Book of Sample Projects Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Page 195 CIT Rísam PhD Scholarship Programme 2014 Literature Review Ethical Approval Training on testing procedures Recruitment of teams Dissemination of consent forms GPS data collection third level college team Data analysis phase 1 Present review paper Annual monitoring Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Literature review GPS data collection third level college team GPS data collection –inter county teams Data analysis phase 2 Present paper 2 Annual monitoring Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Data analysis – phase 2 GPS data third level college team PhD Year 2 GANTT Chart PhD Year 3 GANTT Chart Book of Sample Projects Page 196 CIT Rísam PhD Scholarship Programme 2014 Preliminary results Present paper 3 Write up thesis Final paper/viva voce 6.
Ethical issues If the proposed research directly involves human or live animal subjects, discuss the ethical issues involved and the actions that will be taken to ensure compliance with CIT ethics guidelines and with the CIT Child Protection Policy (if children are involved). The proposed research seeks to follow the highest ethical standards in the research design. Key CIT ethical guidelines relating to honesty, integrity, openness, accountability and fairness will inform all research practice. As the proposed research will involve human subjects, the following steps will be taken: • Prior to beginning the study ethical approval will be granted from the Cork Institute of Technology Ethics Committee • All athletes willing to participate in the research will be provided with an information sheet and required to sign a consent form • Signed parental consent will be required for any athletes under the age of 18 years • Participation in the research will be anonymous, no reference to individual participants names will be made when publishing material from the research • Results gathered will be stored confidentially, only the primary investigators will have access to this data • There is no risk, pain or discomfort foreseen to participants participating in the research • All participants will have the right to withdraw from the research at any time. • Data will be collected, analysed, stored and deleted at the end of the research 7. External Collaboration/Other Institutions Indicate any external collaboration envisaged. • Mr Aidan O’ Connell, Strength and Conditioning Coach, Munster Rugby. • Mr. Pat Daly, Head of Games Development and Research, Croke Park. • Dr. Mark Lyons, Lecture in Strength & Conditioning, University of Limerick, Limerick • Mr. Pat Mulcahy, Fitzgibbon Cup Manager, Cork Institute of Technology. Internal Collaborators: • Dr. Sean Lacey, Department of Mathematics, Cork Institute of Technology. • Mr. Noel Collins, Department of Sport Leisure and Childhood Studies, Cork Institute of Technology. Book of Sample Projects Page 197 CIT Rísam PhD Scholarship Programme 2014 Title of project: An investigation to performance attributes and performance development pathways in elite age grade squads in the game of Gaelic football Name of Principal Supervisor : Dr. Cian O’ Neill Brief Summary of Research Interests: Coaching Science, Human Performance Evaluation, Elite Sports Performance CIT Department Email: cian.oneill@cit.ie : Dept. of Sport, Leisure & Childhood Studies Telephone: 021 4335823 Discipline Area by Frascati Classification: 3.3 Health Sciences (Sport & Fitness Sciences) 1. Abstract (250 words) There has been a significant amount of research conducted in the area of performance measurement in many sports. To date there has been studies with this focus conducted in Australian Rules Football (Young et al., 2005), Rugby League (Gabbett, 2002), Soccer (le Gall et al., 2008), American Football (Sierer et al., 2008) and many of the other popular field sports. Much of this research has examined the physical performance attributes that are required to perform at the various levels of participation, while some also examined technical aspects of performance (i.e. skill). Several research studies have examined the changes in physical performance attributes that occur at various time points across the season (e.g. Pre-­‐season, end pre-­‐season and prior to the start of competition across the season) and also between age grades within the respective sports (Argus et al., 2009; Silvestre et al., 2006). However, there is a dearth of such research within the sports of the Gaelic Athletic Association (GAA), and in particular the game of Gaelic football (Collins et al., 2007). This project aims to address the lack of research in these areas by conducting a thorough examination into the differences present in performance variables associated with the game of Gaelic football by examining squads at different levels of participation (U/14, U/16, U/18, U/21 and senior inter county) and also by monitoring their performance levels across the competitive season. 2. Research Context and Contribution to the Research Field ‘Development Squads’ and ‘Academies’ are common place in most counties. These structures have been put in place with the aim of providing these developing athletes with the opportunities to reach their full potential in a holistic manner (i.e. sport-­‐specific, but also socially, emotionally, etc.). Within these developmental structures, the young athlete should be developed tactically, technically, psychologically and physically. To date there has been no performance standards established for these developmental athletes to reach, nor are there any published studies that define minimum or recommended standards that young athletes should be aspiring to in their respective sports (Murphy, 2012). With no existing performance standards established, the management and backroom staff have no (a) generic and/or (b) specific standards from which to measure the current status of their players and also have no baseline scores to compare their ongoing development. This lack of research can be a limiting Book of Sample Projects Page 198 CIT Rísam PhD Scholarship Programme 2014 factor in their performance development pathway, which can in turn hinder their general game-­‐
related development. It is not just the developmental structures that will benefit from this research. In recent years there has been a huge emphasis on improving the physical performance of Gaelic footballers at adult level both club and county. With the professionalism of the support structures in place in the sport of Gaelic football, it is important that the benefits of research that players in professional sports experience are afforded to the GAA athlete (Reilly & Collins, 2008). It is very important that the key attributes that are required to reach optimal performance in the sport of Gaelic football are established to enable the back room staff to provide a programme where optimal performance can take place (Brick & O’ Donoghue, 2005). Another important area of human performance research is tracking the athlete’s physical performance across the season in order to ensure the athletes reach the level of peak performance at the required time. Again, there is a lack of research in this area in the sport of Gaelic football; this research will establish performance standards at various time points across the season, e.g. pre-­‐season, post pre-­‐season and pre-­‐championship. From these performance standards, it will be possible to establish if the players are at the optimal level of performance for that respective phase of the season. In short: •
This research will provide a thorough understanding of the performance attributes that are possessed by the Gaelic football athlete. The research will identify strengths and weaknesses of the athlete in terms of their physical/technical performance. •
The data collected will identify the physical performance attributes that are related to higher levels of playing performance (i.e. elite level as reflected in the sample population). This will provide important information to those responsible for player development pathways. •
Performance standards will be established for senior inter county, minor inter county and County Development Squads (U/14 & U/16) at three time points across the competitive season. The three time points will be the beginning of the pre-­‐season, post pre-­‐season and immediately prior to the competitive championship phase of the season. •
Comparisons into how the respective squads change in terms of physical/technical performance across the season will be conducted. This will enable a detailed examination of how players at each level change in terms of their performance during a competitive season. 3.
Objectives Aim To provide an insight into the physical and technical attributes required for optimum performance at various stages of development in the sport of Gaelic football Book of Sample Projects Page 199 CIT Rísam PhD Scholarship Programme 2014 Objectives 1. To examine the differences in performance attributes present between elite athletes of different age grades within the sport of Gaelic Football (U/14, U/16, U/18, U/21, Senior inter county) 2. To examine and monitor changes in physical/technical attributes that occur across the season in the elite Gaelic football player 3. To examine the changes in performance attributes that occur across the season between athletes of different age grades (i.e. pre-­‐season/post pre-­‐season/pre-­‐championship) 4.
Research Methodology Squads from four different age-­‐grade levels (U/14, U/16, U/18, U/21), in addition to the elite Senior inter county squad will undertake a series of physical and technical performance tests. The battery of physical tests will include measures of flexibility, speed, agility, leg power, upper body power, local muscular endurance, body composition, anaerobic capacity and aerobic capacity. The technical tests will consist of performing the basic skills of the game (hand pass, kick pass and sprint solo) in a pressurised situation incorporating decision-­‐making where appropriate. The latter point is to make the challenge more game-­‐specific. A series of comparisons will be explored between the various squads to provide an insight into any significant differences present between age grade performance levels. Further comparisons will also be conducted between the senior inter county and the minor inter county squads, which will provide a greater insight into the performance differences between the senior elite and junior elite sample population. All squads will be tested at three stages throughout the competitive season. The stages will be (1) at the beginning of pre-­‐season, (2) post pre-­‐season and (3) immediately prior to the competitive championship phase of the season. Data will be analysed in order to monitor changes across the season for each respective squad, and also the rates of such change of each squad. Data Analysis Data analysis will be carried out on SPPS (version 21 for windows). All data will be examined for normality of distribution to ensure that there are no violations of the assumptions required for respective statistical procedures. For test-­‐retest analysis of pre-­‐season to post pre-­‐ season to championship data, a repeated measures ANOVA with one grouping variable (time) will be used. This analysis will be conducted for each respective squad. With regards to between subject group analysis i.e. examining the relationship between the selected squads, a repeated measures ANOVA with 2 grouping variables (time X age grade) will be used. Book of Sample Projects Page 200 CIT Rísam PhD Scholarship Programme 2014 5.
Work Plan Gantt Chart – Year 1 (14/15) Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Ethical approval X Training on Test Procedures X Literature Review X X X X X U/14 Testing X X X U/16 Testing X X X U/18 Testing X X X U/21 Testing X X X Senior Testing X X X Preliminary Results 1 X X X Conference Presentation X Review Paper 1 X X Gantt Chart – Year 2 (15/16) Task Literature Review Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug X X U/14 Testing X X X U/16 Testing X X X U/18 Testing X X X U/21 Testing X X X Senior Testing X X X Preliminary Results 2 X X X Conference Presentation X X X Review Paper 1 Book of Sample Projects Page 201 CIT Rísam PhD Scholarship Programme 2014 Review Paper 2 X X Gantt Chart – Year 3 (16/17) Sept Task Review Paper 2 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug X U/14 Testing X X X U/16 Testing X X X U/18 Testing X X X U/21 Testing X X X Senior Testing X X X Preliminary Results X X X Conference Presentation X X Review Paper 3 X X Gantt Chart – Year 4 (17/18) Sept Task Review Paper 3 Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug X Conference Presentation X Submit Draft Document X X Submit Final Document X 6.
Ethical issues Ethical approval will be sought from the Cork Institute of Technology ‘Research Ethics Committee’ prior to the commencement of testing. As all risks associated with this proposed study are (1) minimal in nature and (2) in all cases, the selected physical/technical tests are not more strenuous or intense than any physical exertion that participants would encounter in playing their own sport of Gaelic football, it is anticipated that there will be no issues with this approval application. As the study will require the participation of individuals under the age of 18, parental consent will need to be attained for these population subgroups in addition to that of the respective team managements. Book of Sample Projects Page 202 CIT Rísam PhD Scholarship Programme 2014 7.
External Collaboration/Other Institutions • Professor Phil Jakeman Professor of Physiology, University of Limerick, Limerick, IRELAND • Dr. Brian Carson, University of Limerick, Limerick, IRELAND Lecture in Sports Physiology, University of Limerick, Limerick, IRELAND -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐ References • Argus, C.K., Gill, N.D., Keogh, J.W.L., Hopkins, W.G. & Beaven, C.M. (2009). Changes in Strength, Power, and Steroid Hormones during a Professional Rugby Union Competition. Journal of Strength and Conditioning Research, 23 (5), 1583-­‐1592. • Brick, N. and O'Donoghue, P.G. (2005). Fitness profiles of elite players in Hurling and three football codes: Soccer, Rugby Union and Gaelic Football, Science and Football V (Edited by Reilly, T., Cabri, J. and Araujo, D.), London: Routledge, 166-­‐171. • Collins, K., Reilly, T., MacLaren, D., & Reeves, S. (2007). A physiological comparison of two •
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inter-­‐county hurling teams. Journal of Sports Sciences, 25, 257. Gabbett, T.J. (2002). Physiological characteristics of junior and senior rugby league players. British Journal of Sports Medicine, 36 (3) 334-­‐339. Le Gall, F., Carling, C., Williams, W. & Reilly, T. (2008). Anthropometric and fitness characteristics of international, professional and amateur male graduate soccer players from an elite youth academy. Journal of Science and Medicine in Sport, 13 (1), 90-­‐95. Murphy, A. (2012). An investigation into the variation that exists between the physical performance indicators of hurling players at different levels of participation, Unpublished MSc. Thesis, University of Limerick. Reilly, T & Collins, K. (2008). Science and the Gaelic sports: Gaelic football and hurling. European Journal of Sports Science, 8 (5), 231-­‐240. Sierer, S.P., Battaglini, C.L., Mihalik, J.P., Shields, E.W. & Tomasini, N.T. (2008). The National Football League Combine: Performance Differences Between Drafted and Nondrafted Players Entering the 2004 and 2005 Drafts. Journal of Strength and Conditioning Research, 22 (1), 6-­‐12. Silvestre, R., Kraemer, W.J., West, C., Judelson, D.A., Spiering, B.A., Vingren, J.L., Hatfield, D.L., Anderson, J.M. & Maresh, C.M. (2006) Body composition and physical performance during a national collegiate athletic association division I men’ soccer season. Journal of Strength and Conditioning Research. 20 (4), 962-­‐970. Young, W., Newton, R., Doyle, T., Chapman, S., Cormack, S., Stewart, T. & Dawson, B. (2005). Physiological and anthropometric characteristics of starters and non-­‐starters and playing positions in elite Australian Rules football a case study. Journal of Science and Medicine in Sport, 8 (3), 333-­‐345. Book of Sample Projects Page 203 CIT Rísam PhD Scholarship Programme 2014 Title of project: An investigation into the role of training load on elite Gaelic Football players and the associated relationship with injury prevention management Name of Principal Supervisor : Dr. Cian O’ Neill & Dr. Con Burns Brief Summary of Research Interests: Coaching Science, Human Performance Evaluation, Elite Sports Performance CIT Department Email: cian.oneill@cit.ie : Dept. of Sport, Leisure & Childhood Studies Telephone: 021 4335823 Discipline Area by Frascati Classification: 3.3 Health Sciences (Sport & Fitness Sciences) 1. Abstract (250 words) Gaelic football is an intermittent high-­‐intensity sport in which activities that rely on maximal strength, speed, and power are interspersed with periods of lower intensity aerobic activity and rest. It is a contact-­‐based field sport requiring high levels of endurance, strength, power, agility, and speed as well as proficiency with game-­‐related skills. These components comprise the training modalities used at the elite Gaelic football level and the monitoring of such a vast range of modalities is central to performance. Training for success is a balance between achieving peak performance and avoiding the negative consequences of excessive training. Gaelic Football players at the elite level have little recovery time between sessions and as a result the psychological and physiological demands associated with excessive training have led to many injuries (GAA, 2007). Training volumes and intensities that are not optimal do not have the desired physiological adaptations, whereas those that are excessive increase injury risk and impair sporting performance. An appropriate periodization of the training stimulus applied to a player is important to obtain optimal sporting performance. The aim of this project is to explore and monitor an elite Gaelic football team over a three-­‐year period. This research will examine the applied science of elite Gaelic football, with a particular focus on (1) the applied physiology of elite Gaelic football and (2) injury incidence and training load within the game and its associated training/match programmes. 2.
Research Context and Contribution to the Research Field Many studies have stressed the importance of the training load in enhancing athletic performance and the changes in performance attributable to varying periods of intense and light training (Banister & Calvert, 1980; Foster et al., 2001; Gabett & Jenkins, 2010; Lambert & Boressen, 2010). These practicalities are reflected in the practice of coaches who design highly detailed periodised training models. Although periodised training programmes are quantitative in nature, there has been great difficulty in finding a way to effectively quantitate training using a single term. Endurance athletes generally use standard training volume (kms’ per week) as an Book of Sample Projects Page 204 CIT Rísam PhD Scholarship Programme 2014 index of training with reasonable effectiveness. However, measurement of training volume ignores the critical training variable of ‘intensity’. The ability to monitor training is critical to the process of quantitating training periodisation plans. To date, no method has proven successful in monitoring training during multiple types of exercise (Lambert et al., 2010) as high-­‐intensity exercise training is particularly difficult to quantitate. The demands of different sports vary and therefore the methods of assessing training need to vary accordingly. There is a precedent for this consensus approach with scientists having previously done so for the assessment of physical activity, and for defining injuries in rugby, football and cricket (Lambert et al., 2010). Standardising such methods has resulted in the quality of research in these areas increasing exponentially; therefore further examination needs to take place using evidence-­‐based methods for assessing training loads specific to Gaelic Football, Ireland’s most widely played team sport. In this study, an evaluation of the the ability of the session rating of the rate of perceived exertion (RPE) method will be conducted to quantitate training, along with measures of heart rate and blood lactate, in addition to the use of a global positioning system (GPS). In addition, there is also a dearth of evidence related to the transfer of standard physiological profiling of players (e.g. speed, power, aerobic/anaerobic test results, etc.) to competition-­‐
based running performance (i.e. during training/matches) across the various levels of competition (pre-­‐season/league/championship). This can lead some coaches to ‘over-­‐train’ their players due to their acute lack of awareness of what training loads and levels of intensity are required to optimally prepare their players for competitive performance. Consequently, there is accumulating evidence to suggest that ‘burnout’ in talented young GAA players is a serious issue that needs to be urgently addressed by the Association. (Report of the Task Force on Player Burnout: GAA 2007). This issue of ‘burnout’ is most prevalent in the youth population playing Gaelic games and the result of the psychological and physiological demands associated with excessive training and the number of games has led to many young players dropping out of their respective sports (Gaelic football and/or hurling). This is something that is increasingly challenging the GAA as an association through cost constraints, time commitments being placed on amateur members, physical impact on players, player’s work commitments, player’s short and long term health, physical impact on retired players and on the GAA culture in general. The old saying, “where does it all end?” is often quoted on the ground at GAA club/county training sessions all over the country”. Therefore, this area is not merely an area of interest in the field of coaching science and performance, but is also a core area within the GAA’s strategic research plan based in the association’s headquarters at Croke Park. 3.
Objectives 1. To examine the player demands on elite Gaelic football players based on respective positioning on the field of play Book of Sample Projects Page 205 CIT Rísam PhD Scholarship Programme 2014 2. To investigate whether there are significant relationships between the physiological demands of the game and fitness profiles of the players as measured using a physiological test battery 3. To create a training analysis and quantification system whereby classification categories of training activities can be devised for squads of all levels of performance to inform best practice in programme design and implementation 4. To monitor prospective player loading across multiple seasons to inform injury prevention protocols and management and to support the creation of an ‘Injury Prediction Model’ based on the accumulation of measured variables 4.
Research Methodology Study (Objective) 1 Thirty (N=30) elite male Gaelic Football players from an inter-­‐county squad will be recruited for this study. A global positioning system (GPS) analysis will be completed during training sessions and matches with players who have been pre-­‐assigned to one of the five outfield positional groups representing the line-­‐up on a Gaelic football field (i.e. full forwards, half forwards, midfielders, halfbacks and fullbacks). The training data collated over a 10-­‐month period will include all pre-­‐season and in-­‐season skill, conditioning, repeated high-­‐intensity effort exercise, and game-­‐based training sessions. Repeated high-­‐intensity effort activities that will include repeated sprinting and tackling will also be included in the training programme. Exercise-­‐to-­‐rest ratios, based on the most demanding passages of play expected during competition, will be used for these drills. Game-­‐based training/conditioning activities (e.g. small-­‐sided training games played on a reduced-­‐sized pitch) will be used to improve physical qualities, technical skill, and decision-­‐making aspects of the participant’s game. Recovery skill sessions and final team sessions before competitive matches will be excluded from the analysis as they will not meet the required intensity and/or challenge to meet the inclusion criteria of sessions as stated above. Study (Objective) 2 Sixty (N=60) elite male Gaelic Football players from 2 different inter-­‐county squads will be recruited for this study. All players will be highly motivated as they will be competing for selection in their respective inter-­‐county match day squads. A battery of physiological and anthropometric performance measures (e.g. flexibility, speed, power, agility, strength and endurance) will be recorded at various intervals across the season (i.e. pre-­‐season, post pre-­‐
season, pre-­‐championship). Performance in the physiological and anthropometric tests will be explored in the context of training and match-­‐day data recorded via the GPS system (see Study 1). Study (Objective) 3 Thirty (N=30) elite male Gaelic Football players from an inter-­‐county squad will be recruited for this study. Testing will be performed in the pre-­‐competitive phase of the season after players have completed a 3 month pre-­‐season skills and conditioning programme. All participants will be in optimal physical condition for this phase of the season and must be free from injury at the Book of Sample Projects Page 206 CIT Rísam PhD Scholarship Programme 2014 time of testing. Participants will be requested to abstain from strenuous physical exercise for 72 hours prior to testing, as described below: (A) Small-­‐Sided Games This study will be completed over 2 training sessions, performed 2 days apart. Two small sided games, commonly used in Gaelic football, will be played in each session. Field sizes will be determined by the researcher, based on field dimensions commonly used for the small sided games relative to the numbers available on any given day (i.e. factoring in injuries, etc.). On Test Day 1, two teams will play an 8 minute small-­‐sided game on a small field (approx. 20 X 40m), while the remaining two teams play the small-­‐sided game on a larger sized field (approx. 40 X 70m). On Day 2, the groups will rotate and compete in the opposite field of play. (B) Physiological Demands Player movement will be recorded by a GPS unit sampling at least 5Hz. The GPS signal will provide information on speed, distance, position, and acceleration. The GPS unit will also include tri-­‐axial accelerometers and gyroscopes sampling at 100Hz, to provide greater accuracy on speed and acceleration. The unit will be worn in a small vest, on the upper back of the players. Study (Objective) 4 Sixty (N=60) elite male Gaelic Football players from 2 different inter-­‐county squads will be recruited for this study. Participants will have completed a 4-­‐week active recovery off-­‐season period, and will be free from injury at the commencement of the study. A periodised game-­‐
specific strength and conditioning programme (gym-­‐ and field-­‐based) will be implemented, with training loads progressively increased in the general preparatory phase of the season (i.e. November to February) and reduced during the competitive phase of the season (i.e. March to October). The training programme will progress from high volume-­‐low intensity activities during the pre-­‐season conditioning period, to low volume-­‐high intensity activities during the in-­‐season conditioning period. Each player will participate in 5 structured training sessions each week (gym-­‐ and field-­‐based) across the season. Training load and injury data will be recorded for every session. The intensity of individual training sessions will be estimated using a modified rating of perceived exertion (RPE) scale. Training load will be calculated by multiplying the training session intensity by the duration of the training session and will be reported in arbitrary units. Intensity estimates will be obtained 30 minutes after completing the training session. When compared to heart rate and blood lactate concentration, the RPE scale has been shown to provide a valid estimate of exercise intensity (Foster et al., 1996). In addition, prior to commencing the study, the relationship between heart rate and RPE, and blood lactate concentration and RPE, on a subset of 30 subjects during a typical field session will be examined (e.g. skills drills, small-­‐sided games, and repeated effort). A subset of players (n = 15) will also complete two identical off-­‐season training sessions, performed one week apart, prior to the commencement of the study, to determine test-­‐retest reliability. 5.
Work Plan Book of Sample Projects Page 207 CIT Rísam PhD Scholarship Programme 2014 Gantt Chart – Year 1 (14/15) Task Sept Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Ethical approval X Training on Test Procedures X Literature Review X X X Study 1 X X X X X X X X X Study 2 X X X Study 3 Study 4 X X X X X X X X X Preliminary Results 1 X X X Conference Presentation X Review Paper 1 X X Gantt Chart – Year 2 (15/16) Oct Nov Dec X X Study 1 X Study 2 X X X Study 3 Study 4 X X X X X X X X X X Preliminary Results 1 X X X Conference Presentation X X Review Paper 1 X X Review Paper 2 X X Task Literature Review Sept Jan Feb Mar Apr May Jun Jul Aug Gantt Chart – Year 3 (16/17) Book of Sample Projects Page 208 CIT Rísam PhD Scholarship Programme 2014 Sept Task Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Literature Review X X X Study 2 X X X Study 3 X Study 4 X X X X X X X X X X Preliminary Results 1 X X X Conference Presentation X X Review Paper 2 X X Review Paper 3 X X Gantt Chart – Year 4 (17/18) Sept Task Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Study 4 X Review Paper 3 X Review Paper 4 X X Conference Presentation X Submit Draft Document X X Submit Final Document X 6.
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Ethical issues Ethical approval will be sought from the Cork Institute of Technology ‘Research Ethics Committee’ prior to the commencement of testing. As all risks associated with this proposed study are (1) minimal in nature and (2) in all cases, the selected physical/technical tests are not more strenuous or intense than any physical exertion that participants would encounter in playing their own sport of Gaelic football, it is anticipated that there will be no issues with this approval application. External Collaboration/Other Institutions Book of Sample Projects Page 209 CIT Rísam PhD Scholarship Programme 2014 •
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Dr. Giles Warrington Programme Chair, Dept. of Sport Science & Health, Dublin City University, Dublin, IRELAND Dr. Mark Lyons Lecture in Strength & Conditioning, University of Limerick, Limerick, IRELAND Dr. Gary Walker Manchester United Football Club, Strength & Conditioning Coach Mr. Aidan O’ Connell Munster Rugby, Strength & Conditioning Coach -­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐-­‐ References •
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Banister, E.W. & Calvert, T.W. (1980). Planning for future performance: implications for long term training. Canadian Journal of Applied Sport Sciences, 13, 170–176. Buckley, J.P., Eston, R.G. & Sim, J. (2000). Ratings of perceived exertion in braille: validity and reliability in production mode. British Journal of Sports Medicine, 34, 297–302. Collins, K., Doran, D. & Reilly, T. (2011). Small-­‐Sided Games Present and Effective Training Stimulus in Gaelic Football [Web log post]. Retrieved April 3rd, 2014, from http://www.kierancollins.com/Index/Blog/Entries/2011/5/26_Small-­‐
side_games_present_an_effective_training_stimulus_in_Gaelic_football.html Comyns, T. & Flanagan, E.P. (2013) Applications of the Session Rating of Perceived Exertion System in Professional Rugby Union. Report: Irish Institute of Sport, National Sports Campus, Co. Dublin, Ireland; and Irish Rugby Football Union (IRFU). Dunbar, C.C., Robertson, R.J. & Baun, R. (1992). The validity of regulating exercise intensity by ratings of perceived exertion. Medicine & Science in Sports & Exercise, 24, 94–99. Foster, C., Daines, E., Hector, L., Snyder, A.C. & Welsh, R. (1996). Athletic performance in relation to training load. Wisconsin Medical Journal, 95, 370–374. Foster, C., Florhaug, J.A. & Franklin, J. (2001). A new approach to monitoring exercise training. Journal of Strength & Conditioning Research, 15, 109–15. Gabbett, T.J. (2004). Reductions in pre-­‐season training loads reduce training injury rates in rugby league players. British Journal of Sports Medicine, 38, 743–749. Book of Sample Projects Page 210 CIT Rísam PhD Scholarship Programme 2014 •
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Gabbett, T.J. & Jenkins, G.D. (2010). Relationship between training load and injury in professional rugby league players. School of Exercise Science, Australian Catholic University, Australia and School of Human Movement Studies, The University of Queensland, Australia Gabbett, T.J. & Domrow, N. (2007) Relationships between training load, injury, and fitness in sub-­‐elite collision sport athletes. Journal of Sports Sciences, 25, 1507–19. Gaelic Athletic Association (2007). Report of the Task Force on Player Burnout. Dublin: Croke Park Press Gibbs, N. (1993). Injuries in professional rugby league: a three-­‐year prospective study of the South Sydney professional rugby league football club. American Journal of Sports Medicine, 21, 696–700. Herman, L., Foster, C., Maher, M.A., Mikat, R.P. & Porcari, J.P. (2006). Validity and reliability of the session RPE method for monitoring exercise training intensity. Scandinavian Journal of Sports Medicine, 18, 14–17. •
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Lambert, M.I. & Borresen, J. (2010). Measuring Training Load in Sports. International Journal of Sports Physiology and Performance, 5, 406-­‐411. Lamberts, R.P., Rietjens, G.J., Tijdink, H.H., Noakes, T.D. & Lambert, M.I. (2010). Measuring submaximal performance parameters to monitor fatigue and predict cycling performance: a case study of a world-­‐class cyclo-­‐cross cyclist. European Journal of Applied Physiology, 108, 183–190. Laukkanen, R.M.T. & Virtanen, P. (1998). Heart rate monitors -­‐ state of the art. Journal of Sports Sciences, 16, 53–57. Mahon, J. (2000). A History of Gaelic Football. Dublin: Gill & Macmillan O’Brien, J. (2000). A Pocket History of Gaelic Games. Dublin: Gill & Macmillan. Townshend, A.D., Worringham, C.J. & Stewart, I.B. (2008). Assessment of speed and position during human locomotion using nondifferential GPS. Medicine & Science in Sports & Exercise, 40, 124–132. Book of Sample Projects Page 211 CIT Rísam PhD Scholarship Programme 2014 BUSINESS Entrepreneurship General Discipline Area: Entrepreneurship Title of project: Gender, Entrepreneurial Self-­‐Efficacy, and Entrepreneurial Career Intentions: Implications of Female Role Models for Entrepreneurship Education. Name of Principal Supervisor: Email: breda.kenny@cit.ie Dr Breda Kenny Telephone: 021 4335427 1. Abstract (250 words) Within the context of entrepreneurship education and entrepreneurial role models, this research explores the impact of gender. Guided by self-­‐efficacy, entrepreneurship and entrepreneurship education theory three main research objectives are proposed. Firstly, to examine and assess how entrepreneurship education is delivered from primary school level education to third level education. Secondly, to explore the role and input of female role models in the entrepreneurship education system. Thirdly, to assess the effects of female role models on the entrepreneurial self-­‐efficacy and career intentions of students. This study is an exploratory study based on theory building and as such a qualitative approach will be used. Data will be collected mainly by methods such as: in depth interviews, focus groups as well as surveys. A qualitative approach of data gathering and analysis will be used. Structured observations of day-­‐to-­‐day classroom practice will be conducted. Field notes will be maintained to achieve appropriate contextual indicators of the visited schools and colleges. Qualitative interviews will be conducted with teachers, academics, students as well as female entrepreneurs and role models. The outcomes of this research will provide insights into how entrepreneurship is delivered in the modern classroom as well as the impact of female role models on the entrepreneurial mindset and career intentions of students. Research Context and Contribution to the Research Field The concept of female entrepreneurship is gaining traction in the academic as well as the practitioner community. Indeed, Henry et al’s (2012) review of extant gender and entrepreneurship literatures demonstrates a recent and significant proliferation of female entrepreneurship empirical research, as evidenced by the fact that 214 (64%) of 335 articles were published between 2003 and 2012. Furthermore, 40% were published within the previous five years alone, suggesting that gender had now become a legitimate area of scholarly inquiry within the entrepreneurship field. Hughes et al (2012) feel it more appropriate to characterize women’s entrepreneurship research as being at the brink of adolescence. In the practitioner field, female entrepreneurship programmes and support Book of Sample Projects Page 212 CIT Rísam PhD Scholarship Programme 2014 measures are now offered by a range of enterprise support agencies, business incubators and the banking sector. Women play an increasingly important role in entrepreneurship and economic development throughout the world (Tegtmeier and Mitra, 2014). For 24 innovation-­‐based countries worldwide, the Global Entrepreneurship Monitor (GEM) identifies an average rate of 4.8% of all adult women who were nascent or young entrepreneurs in 2012 (Sternberg et al., 2013). In the European Union, the rate of Total Entrepreneurial Activity among women in 2012 was 5% (Xavier et al., 2013). Estimated with population statistics by the European Commission (2013), this rate represents about 8.3 million women who were in the process of starting a business in the European Union in 2012. The GEM report 2012 shows that men are far more active in early stage entrepreneurship in Ireland than their female counterparts. The rate of early stage entrepreneurship for men in Ireland is currently at a rate of 10.3 per cent (two and a half times more than the rate of early stage entrepreneurship among women) which is currently at a rate of 4.2 per cent. This rate of early stage entrepreneurial activity amongst women is similar when compared with the EU (5.1 per cent) and the Organization for Economic Co-­‐operation and Development (OECD) which has a rate of 5.8 per cent. However countries like Australia (8.4 per cent) and the US (10.4 per cent) are far superior to Ireland in terms of female entrepreneurial activity. Table 1 below shows that rates in female entrepreneurship in Ireland grew in 2006 and 2007 before taking a sharp decline in 2008, and a further decrease in the years 2010 and 2011. Table 1: Female Entrepreneurship in GEM 2012 Source: Entrepreneurship in Ireland 2012, Global Entrepreneurship Monitor (GEM) Self-­‐Efficacy and Entrepreneurship Defined as ‘people’s beliefs about their capabilities to produce designated levels of performance that exercise influence over events that affect their lives’, the Banduran concept of self-­‐efficacy has been shown to powerfully influence the way people think, feel and behave (Bandura, 1994, p.71; Pajares, 1996). According to Bandura, the potency of these beliefs is such that a person’s ‘level of motivation, affective states and actions are based more on what they believe than on what is objectively true’ (Bandura, 1997, p.2). Book of Sample Projects Page 213 CIT Rísam PhD Scholarship Programme 2014 Thus, a person’s self-­‐efficacy is said to determine their perceptions of whether certain goals are achievable, how much task-­‐specific effort they apply in pursuit of them and how long they persist in the face of adversity (Bandura, 1977, 1986; Gist and Mitchell, 1992). Moreover, efficacy-­‐beliefs also influence the degree of anxiety an individual experiences as they engage in a task and the level of accomplishment realised once fulfilled. Highly efficacious people are seen to set more challenging goals and maintain a stronger commitment to them, heighten their efforts in the face of failure, recover more rapidly from setbacks and attribute failure to a lack of effort or knowledge which they believe they can acquire. When goals are achieved, self-­‐efficacy is reinforced, leading to positive appraisals and higher aspirations for the future (Herron and Sapienza, 1992; Lent and Hackett, 1987). More specifically, entrepreneurial self-­‐efficacy (ESE) has been identified as playing an instrumental role in the new venture creation process. Defined as ‘the strength of a person’s belief that he or she is capable of successfully performing the various roles and tasks of entrepreneurship,’ ESE is seen as an important antecedent to entrepreneurial action (Chen et al, 1998, p. 295). A growing body of literature supports the idea that an individual’s intention to start a company is formed in part by their perception of the expected outcome (Boyd and Vozikis, 1994; Chen et al, 1998; Zhao et al., 2005; Barbosa et al., 2007). Moreover, across the literature, ESE is linked with a variety of entrepreneurial behaviours such as opportunity recognition and innovation and as an important variable in determining not only the strength of entrepreneurial intentions but the probability that such intentions will lead to actions (Bird, 1988; Krueger and Braezel, 1994; Kruger et al.,, 2000). In support of this, Zhao et al provide empirical evidence that supports the thesis that individuals choose to become entrepreneurs most directly because they are high in entrepreneurial self-­‐efficacy. Self-­‐efficacy is posited as playing a critical mediating role between entrepreneurial intentions and three of the four antecedent variables, namely: formal learning, entrepreneurial experience and risk propensity (2005). We know that entrepreneurial self-­‐efficacy is among the most important antecedents of entrepreneurial intentions and activity (Ajzen, 1991; Krueger and Carsrud, 1993; Kolvereid, 1996; Krueger et al., 2000; Liñán and Chen, 2009; Moriano et al., 2012; Jaén and Liñán, 2013) and that women’s ESE is generally lower than that of men (Kickul et al., 2008; Kourilsky and Walstad, 1998; Gatewood et al., 2002). The Global Entrepreneurship Monitor Women’s Report 2012 reveals that for the developed countries in Europe 33% of the women population report having the skills for an entrepreneurial activity while 50% of the male population do so (Kelley et al., 2013). Entrepreneurial Role Models Since entrepreneurial role models provide a positive image of entrepreneurship as well as support by providing information, knowledge and second hand experience, a link between entrepreneurial roles and ESE can be assumed (Peterman and Kennedy, 2003). Moreover, we know from intention based models that ESE and attitude interact (Ajzen, 1991). Book of Sample Projects Page 214 CIT Rísam PhD Scholarship Programme 2014 Moreover, the entrepreneurial process is found to be highly complex and dependent on the individual’s environment. Entrepreneurial role models are one of these factors, which can be found in a wide range of empirical studies (Clercq and Arenius, 2006; Chen et al., 1998; Crant, 1996; Krueger et al., 2000; Scherer et al., 1989). For example, Scherer and colleagues (1989) show that entrepreneurial role models have an impact on entrepreneurial career preference. They also demonstrate that not only the role model’s pure existence matters, moreover its performance is important as well (Scherer et al., 1989). Although the popular media frequently uses role models and the importance has been stressed by various scholars (Gibson, 2003; Bandura, 1997; Lockwood and Kunda, 1997), research specifically on role models in entrepreneurial activities remains scant. In this research the focus is on the impact of female role models in the entrepreneurship education context. The definition of a role model used in this research is a description by Gibson (2003 pp. 199.): ‘‘A role model is a person an individual perceives to be similar to some extent, and because of that similarity, the individual desires to emulate (or specifically avoid) aspects of that person’s attributes or behaviors.’’ The definition of a role model can be divided into two basic components, it is a combination of ‘‘role’’ and ‘‘modeling’’. Katz and Kahn (1978) define ‘‘roles’’ as forms of behavior and sets of activities, with part of status positions, such as a manager, leader or teacher. The idea of ‘‘modeling’’ is explained by Bandura (1986) as the psychological matching of cognitive skills and patterns of behavior between a target and an observing individual. Demographic and personal characteristics are influential and can determine whether an individual has a role model. This research will take these factors into consideration. Arenius and Minniti (2005) stress the importance of personal characteristics and the environment of an individual when choosing to become an entrepreneur. Entrepreneurship Education The past decades have witnessed a rapid increase in entrepreneurship courses at all levels of education, from primary school to university (Blenker et al., 2011). Some 25 years ago, numerous researchers (see, for example, Hills, 1988; McMullan and Long, 1987; Sexton and Bowman, 1984; Vesper et al, 1989) highlighted the confusing variety of approaches to and accepted paradigms of entrepreneurship education with their associated myriad purposes, methods and learning goals. This concern is no less valid today, with the increasing number of courses reflecting a multitude of paradigms with different ontological views on the nature of entrepreneurship and different didactic approaches to education (Béchard and Grégoire, 2005; Gartner and Vesper, 1994; Honig, 2004). In light of this variety of approaches, a fundamental question has arisen among researchers in entrepreneurship education: what constitutes entrepreneurship education? Attempts to answer this have led to many reports and studies laying out the current landscape of entrepreneurship education in different Book of Sample Projects Page 215 CIT Rísam PhD Scholarship Programme 2014 areas and educational levels. Prior research has been conducted on entrepreneurial self-­‐efficacy, gender research into gender roles in entrepreneurship as well as a large amount of literature on entrepreneurship education. There does however seem to be a gap in combining these theories together to recognise the effect that education in entrepreneurship has on female students in particular as well as examining the effect of female role models on the entrepreneurial mind-­‐set of students. The outcomes of this research will provide insights into how entrepreneurship is delivered in the modern classroom as well as the impact of female role models on the entrepreneurial mindset and career intentions of students. Objectives This study will examine and assess how entrepreneurship education is delivered from primary school level education to third level education and the input from females in the world of innovation and entrepreneurship. This research aims to: • Examine and assess how entrepreneurship education is delivered from primary school level education to third level education • Explore the role and input of female role models in the entrepreneurship education system. • Assess the effects of female role models on the entrepreneurial self-­‐efficacy and career intentions of students. Research Methodology This study is an exploratory study based on theory building and as such a qualitative approach will be used. The unit of analysis in this study is the student in the education system in Ireland to include primary schools, secondary schools and third level colleges. Interviews will also be conducted with economic developing agencies such as Enterprise Ireland and the Enterprise Boards to gather data on female entrepreneurship trends as well as the involvement of these agencies with schools and colleges to promote entrepreneurship to students. Data will be collected mainly by methods such as: in depth interviews, focus groups as well as surveys. A qualitative approach of data gathering and analysis will be used. Structured observations of day-­‐to-­‐day classroom practice will be conducted. Field notes will be maintained to achieve appropriate contextual indicators of the visited schools and colleges. Qualitative interviews will be conducted with teachers, academics, students as well as female entrepreneurs and role models. Qualitative research encompasses a variety of methods that can be applied in a flexible manner, to enable respondents to reflect upon and express their views or to observe their behaviour. Whereas quantitative research incorporates methods that seek to quantify data and typically apply some form of statistical analysis Cooper, D and Schlinder, P (2003) best Book of Sample Projects Page 216 CIT Rísam PhD Scholarship Programme 2014 describe this as “qualitative research refers to the meaning, the definition or analogy or model characterising something, while quantitative assumes the meaning and refers to a measure of it”. Work Plan Initial Registration and Orientation September 2014 Design of a research plan October 2014 Gaining access/getting permission to work in a particular area/have access to data. June – September 2014 Literature review November 2014– July 2015 Defining of sampling and setting up of selection criteria. July 2015 Design and testing of interview templates. August-­‐ September 2015 Design and organisation of interview and focus group schedules, etc. October 2015 Completion of Focus Groups and Interviews. November-­‐ March 2016 Editing of completed Interviews and Focus Groups, grouping and coding of data, entering data into a computer April 2016 – August 2016 Design and testing of NVivo (software for qualitative research) September 2016 Raw tabulations/draft analysis of all qualitative data gathered. October – December 2016 Analysis of data January-­‐ April 2017 Book of Sample Projects Page 217 CIT Rísam PhD Scholarship Programme 2014 Presentation of final research thesis to supervisor May 2017-­‐ September 2017 Ethical issues As the research involves human subjects, the following ethical considerations are relevant: 1. Selecting informants for the research –Key informants for this research will be state support agencies such as Enterprise Ireland, Schools and Colleges as well as academics, teachers and students. 2. Gaining access to /contact/approach potential informants-­‐ The sampling frame will consist of education institutions, educators, academics, students as well as state support agencies. Telephone and email contact will be made to a sample of these possible participants to inform them of the purpose of the study and to obtain their consent to participate. Contact will also be made with the relevant school authorities in relation to parental consent where necessary. 3. Anonymity and confidentiality – This research study not require respondents to provide personal information. The cover letter/email inviting respondents to interview will state that the information provided will be dealt with in strictest confidence and will be used for academic purposes only. 4. Arrangements to ensure that informants know the purpose of the research and what they are going to inform about?-­‐ Informants will be informed of the overall purpose of the research during the initial telephone and email contact and during the in-­‐depth interviews and focus groups. 5. Ensure that informants are aware of their right to refuse to participate or withdraw at any time? Both the telephone contact and written correspondence informs them that participation in the research study is voluntary. An opt-­‐out facility will be in place at each stage of the research. 6. Storing the information -­‐ Hard copies of the interview notes and related files will be stored in a locked cabinet in postgraduate room on the CIT Bishopstown Campus in Cork. Soft and audio copies of the data will be stored in encrypted format on personal drive on dedicated project laptop. References Ajzen, I. (1991): The Theory of Planned Behavior. In: Organizational Behavior and Human Decision Processes 50 (2), 179–211. Bandura, A. (1977). Social Learning Theory. New York: General Learning Press. Bandura, A. (1978): The self system in reciprocal determinism. In: American Psychologist: Journal of the American Psychological Association (Apr.), 344–358. Bandura, A. (1986). Social Foundations of Thought and Action: A social cognitive theory. Book of Sample Projects Page 218 CIT Rísam PhD Scholarship Programme 2014 Englewood Cliffs, NJ: Prentice-­‐Hall. Bandura, A. (1989). Human agency in social cognitive theory. American Psychologist, 44, 1175-­‐1184. Bandura, A. (1994). Self-­‐Efficacy. In V. S. Ramachaudran (Ed.) Encyclopedia of human behaviour (Vol. 4, pp. 71-­‐81). New York: Academic Press (Reprinted in H. Friedman [Ed.], Encyclopedia of mental health. San Diego: Academic Press, 1998). Bandura, A. (1997). Self-­‐efficacy: The exercise of control. New York: W. H. Freeman and Company. Barbosa, S., Gerhardt, M. and Kickul, J. (2007). The role of cognitive style and risk preferenceon entrepreneurial self-­‐efficacy and entrepreneurial intentions. Journal of Leadership and Organizational Studies, 13 (4), 86-­‐104. Béchard, J.P., and Grégoire, D. (2005), ‘Entrepreneurship education revisited: the case of higher education’, Academy of Management Learning and Education, Vol 4, No 1, pp 22–43. Bird, B. (1988). Implementing entrepreneurial ideas: The case for intention. Academy of Management Review, 13(3), 332-­‐453. Boyd, N.G.; Vozikis, G. S. (1994): The influence of self-­‐efficacy on the development of entrepreneurial intentions and actions. In: Entrepreneurship Theory and Practice 18 (4), 63–
77. Blenker, P, S Korsgaard, H Neergaard and C Thrane (2011), The Questions we care about: Paradigms and progression in entrepreneurship education, Industry and Higher Education, Vol 25, No. 6 pp 417-­‐ 427 Chen, C. C.; Greene, P. G.; Crick, A. (1998): Does entrepreneurial self efficacy distinguish entrepreneurs from managers? In: Journal of Business Venturing 13 (4), 295–316. European Commission: eurostat – Your key to European statistics, available at: http://epp. eurostat.ec.europa.eu/portal/page/portal/eurostat/home (accessed September 27, 2013). Gartner, W.B., and Vesper, K.H. (1994), ‘Experiments in entrepreneurship education: successes and failures’, Journal of Business Venturing, Vol 9, No 3, pp 179–187. Gatewood, Elizabeth J.; Shaver, Kelly G.; Powers, Joshua B.; Gartner, William B. (2002): Entrepreneurial Expectancy, Task Effort, and Performance. In: Entrepreneurship Theory and Practice, 27 (2), 187–206.Gist, M.E. and Mitchell, T. R (1992) Self-­‐Efficacy: A Theoretical Analysis of its Determinants and Malleability. Academy of Management Review 17 (2), 183-­‐
211. Book of Sample Projects Page 219 CIT Rísam PhD Scholarship Programme 2014 Global Entrepreneurship Monitor Report (2012), Paula Fitzsimmons, Colm O’Gorman 2011, [Online] Available at: http://www.enterprise.gov.ie/en/Publications/GEM-­‐Report.pdf [Accessed 20 February 2014] Henry, C L Foss and H Ahl, (2012), Parallel Lines? A Thirty-­‐Year Review of Methodological Approaches in Gender and Entrepreneurship Research, paper presented at the ISBE Conference, DCU, Dublin, Ireland, Nov 6-­‐8th. Herron, L. and Sapienza, H. J. (1992) The entrepreneur and the initiation of new venture launch activities,Entrepreneurship Theory and Practice 17 (1), 49-­‐55 Hills, G.E. (1988), ‘Variations in university entrepreneurship education: an empirical study of an evolving field’, Journal of Business Venturing, Vol 3, No 2, pp 109–122. Honig, B. (2004), ‘Entrepreneurship education: toward a model of contingency-­‐based business planning’, Academy ofManagement Learning and Education, Vol 3, No 3, pp 258–
273. Hughes, K.D., Jennings, J.E., Brush, C.G., Carter, S. and Welter, F. (2012): Extending women's entrepreneurship research in new directions. Entrepreneurship Theory and Practice, 36 (3), 429-­‐442. Jaén, I. and Liñán, F. (2013): Work values in a changing economic environment: The role of entrepreneurial capital. International Journal of Manpower, 34, In press. Kelley, D. J., Brush, C. G., Greene, P. G., Litovsky, Y. (2013): Global Entrepreneurship Monitor 2012 Women’s Report, Global Entrepreneurship Research Association. Kickul, J.; Wilson, F.; Marlino, D.; Barbosa, S. D. (2008): Are misalignments of perceptions and self-­‐efficacy causing gender gaps in entrepreneurial intentions among our nation's teens? In: Journal of Small Business and Enterprise Development 15 (2), 321–335. Kolvereid, L. (1996): Prediction of employment status choice intentions. In: Entrepreneurship Theory and Practice 21 (1), 47-­‐57. Kourilsky, M. L.; Walstad, W. B. (1998): Entrepreneurship and female youth: knowledge, attitudes, gender differences, and educational practices. In: Journal of Business Venturing 13, 77–88. Krueger, N. F., and Brazeal, D. V. (1994). Entrepreneurial potential and potential entrepreneurs. Entrepreneurship Theory and Practice, 18(3), 91-­‐104. Krueger, N. F., Jr.; Carsrud, A. (1993): Entrepreneurial intentions: Applying the theory of planned behavior. In: Entrepreneurship and Regional Development 5 (4), 315-­‐330. Book of Sample Projects Page 220 CIT Rísam PhD Scholarship Programme 2014 Krueger, N. F., Jr.; Reilly, M. D.; Carsrud, A. L. (2000): Competing models of entrepreneurial intentions. In: Journal of Business Venturing 15 (5-­‐6), 411-­‐432. Lent, R. W., and Hackett, G. (1987). Career self-­‐efficacy: Empirical status and future directions. Journal of Vocational Behavior, 34, 279-­‐288. Liñán, F.; Chen, Y.-­‐W. (2009): Development and cross-­‐cultural application of a specific instrument to measure entrepreneurial intentions. In: Entrepreneurship Theory and Practice 33 (3), 593–617. McMullan, W.E., and Long, W.A. (1987), ‘Entrepreneurship education in the Nineties’, Journal of Business Venturing, Vol 2, No 3, pp 261–275. Moriano, J. A.; Gorgievski, M.; Laguna, M.; Stephan, U.; Zarafshani, K. (2012): A cross-­‐
cultural approach to understanding entrepreneurial intention. In: Journal of Career Development 39 (2), 162–185. Scherer, R. F.; Adams, J. S.; Carley, S. S.; Wiebe, F. A. (1989): Role Model Performance Effects on Development of Entrepreneurial Career Preference. In: Entrepreneurship Theory and Practice 13, 53-­‐71. Sexton, D.L., and Bowman, N. (1984), ‘Entrepreneurship education: suggestions for increasing effectiveness’, Journal of Small Business Management, Vol 22, No 2, pp 18–26. Tegtmeier S and J Mitra ( 2014) , Determinants and Measurement of Entrepreneurial Self-­‐
efficacy –Evidence for Women Entrepreneurs, RENT XXVII Entrepreneurship, Institutions and Competitiveness, ISM University of Management and Economics, Vilnius, Lithuania, November 20-­‐22. Vesper, K.H., McMullan, W.E., and Ray, D.M. (1989), ‘Entrepreneurship education: more than just an adjustment to management education’, International Small Business Journal, Vol 8, No 1, pp 61–65. Xavier, S. R., Kelley, D., Kew, J., Herrington, M., Vorderwülbecke, A.: Global Entrepreneurship Monitor 2012 Global Report, Global Entrepreneurship Research Association. Zhao, H. S.; Seibert, S. E.; Hills, G. E. (2005): The Mediating Role of self-­‐efficacy in the Development of Entrepreneurial Intentions. In: Journal of Applied Psychology, 90, 1265-­‐
1272. Book of Sample Projects Page 221 CIT Rísam PhD Scholarship Programme 2014 Title of project: Risk Perception and Risk Management in the Irish Dairy Industry General Discipline Area: Agricultural Economics Name of Principal Supervisor: Dr Declan O Connor Email: declan.oconnor@cit.ie Telephone: 021-­‐4335527 1. Abstract (250 words) EU dairy policy continues to undergo considerable change largely driven by a desire to make
the Common Agricultural Policy (CAP) more market focused and the need to reform the CAP
to fit within potential future WTO constraints. These policy reforms will reduce the extent to
which the EU dairy sector is insulated from global dairy markets. This means that the price
volatility that exists on world markets will increasingly be observed in the EU where the
variation in milk prices and dairy commodities can be expected to become more pronounced.
This increase in volatility translates into increased risk for all participants in the Irish dairy
industry. While a considerable body of research and analysis exists in relation to the many
price risk management tools which are available (e.g. diversification, insurance, risk pooling,
futures, options, hedges and production contracts amongst others), little attention has been
paid to how these tools may be adopted and used by industry participants in Ireland. This
research will first quantify the effect of increased price risk on Irish dairy farmers. Following
this the risk management tools that could be implemented to manage and or minimise this
risk will be explored. The perception, understanding and attitude of Irish dairy farmers and
dairy processors towards price risk and the implementation of price risk management tools
will be ascertained by means of surveys, questionnaires and game theory. Finally their
suitability in an Irish context will be assessed.
The identification and adoption of suitable risk management tools will help to ensure that
the Irish dairy industry remains competitive and profitable in an uncertain future. In
essence, this analysis will inform all industry participants, policy makers, academics and
those who wish to provide private market solutions to price risk management for the dairy
industry.
2.
Research Context and Contribution to the Research Field Up to recent times the policy instruments employed by the EU have very successfully
isolated internal EU dairy prices from the greater volatility associated with world prices. As a
consequence dairy industry participants in the EU have had little incentive to develop and use
price risk management tools. However recent movements towards lower levels of CAP
support prices, reduced intervention and a more liberal global agricultural trading system has
Book of Sample Projects Page 222 CIT Rísam PhD Scholarship Programme 2014 resulted in much greater price volatility for dairy commodities. This increase in volatility
translates into an increase in risk for dairy industry participants. This is acknowledged by the
European Commission in its current CAP negotiations where the issue of risk management
now features prominently.
A number of tools may be utilised to manage risk in agricultural markets (e.g. diversification,
insurance, risk pooling, futures, options, hedges and production contracts amongst others).
However the success of the EU in isolating its dairy industry from price volatility has meant
that many industry participants have had limited recourse to these tools and thus may have
limited understanding of their value and applicability. This lack of familiarity with these tools
coupled with the anticipated cost of consolidation both at farm and processing level post
dairy quota may leave the industry particularly vulnerable in the current economic climate.
Consolidation in many cases will lead to specialisation and thus increased risk. This is
recognised by the fact that global futures markets exchanges (EUREX, LIFFE and NZX)
have recently begun to offer of a number of dairy futures products. Likewise the CAP now
allows for the subsidisation of insurance products and mutual funds with a view to the EU
itself withdrawing from its role of risk management. However the success of these
instruments in managing risk for the dairy industry will lie in their ability to meet the needs
of the industry participants which in turn depends on the ability of industry participants to use
them correctly.
In light of the expected development of new insurance products and the adoption of futures
markets it is timely to consider how these instruments might address the future needs of the
Irish dairy industry. In order to achieve this goal the following questions will be answered:
•
Which tools are currently employed to manage price risk in the Irish dairy industry
•
What is the level of understanding of price risk management tools within the industry
•
Which tools are likely to be employed to manage risk in the future
•
What barriers exist in relation to adopting price risk management tools in the industry
It should be noted that these represent the initial issues to be addressed and as they are
addressed a number of further hypotheses may be considered in order to explain the empirical
results. Furthermore the methodology will allow the samples to be stratified and thus allow
comparisons of the strata. For example it will be possible to establish if larger farmers have
Book of Sample Projects Page 223 CIT Rísam PhD Scholarship Programme 2014 greater recourse to certain tools or if age is a factor in adopting these tools. Likewise, for
example, it will be of interest to determine whether processor structure (Co-op versus PLC) is
a significant determinant in the adoption of these tools.
In essence this research will address a field of research which to date has received little
attention in Ireland or the larger EU, thus filling a knowledge gap. Those involved in the
dairy industry will be introduced to a suite of tools which may potentially aid them in
managing risk in a more effective manner. This research will help industry participants by
informing them of a suite of tools which may contribute towards providing them with a more
stable income despite operating in a more volatile market environment and thus underpin the
viability of the dairy sector. Furthermore it is imperative that policy makers and industry
leaders are in a position to lead change from an informed position. This research will provide
a valuable insight to those policy makers, industry leaders and those wishing to provide
private market solutions to price risk in the Irish dairy industry.
3.
Objectives This research aims to: (i)
To describe how the changes in EU and World trade policy are leading to increased
price volatility for the Dairy industry in Ireland and outline how price risk globally and
in the EU in particular may develop.
(ii)
To provide a literature review of the development and operation of price risk
management tools in the agri-food sector.
(iii) Review risk management tools adopted in other countries where price risk is already a
major issue for the dairy and related sectors.
(iv) To provide examples of how these tools may benefit dairy industry participants.
(v)
To provide an analysis of the tools currently employed in the industry.
(vi) Ascertain the attitude and perception towards price risk at farm and processor level.
(vii) Conduct quantitative and qualitative analysis to evaluate the suitability of price risk
management tools in an Irish context.
(viii) Rank the tools in terms of their suitability across a range of criteria.
(ix) To highlight the barriers to adoption which exist for certain tools.
(x)
To introduce a postgraduate student to the field of dairy economics and finance and
train them in current research methodologies with particular reference to survey
analysis and experimental game analysis.
Book of Sample Projects Page 224 CIT Rísam PhD Scholarship Programme 2014 4.
Research Methodology The changes, and proposed changes, to EU dairy policy and global trade and their potential
effects on the EU dairy industry are well documented by the EU Commission, academics and
the print media. The potential significance of these changes in relation to price risk in the
industry provides the motivation for this study and will be presented at the outset. To
complete this background analysis the role of dairy industry in the EU and the significance
and uniqueness of the Irish industry within this sector will be outlined. This analysis will be
based on the vast literature and datasets which exist and the challenge for the researcher will
be to synthesise this information. The researcher will be able to draw on the considerable
experience of his supervisor whose fields of research include dairy economics and dairy
policy.
The research will next review the use of development of price risk management tools. These
instruments have a long history and their development and use is again well documented in a
large number of finance textbooks and academic publications. In particular the use of these
instruments in the US is well documented and the student may rely on a number of
publications from the University of Wisconsin-Madison amongst others. The supervisor has
built a relationship with the University of Wisconsin-Madison and Cornell University, and in
particular professors Ed Jesse and Andrew Andrew Novakovic, both of whom have published
extensively on this topic. Again the challenge for the researcher will be to synthesise this
information.
The survey and interview methodology used is popular and well critiqued in a large number
of textbooks and academic journals. The supervisor has experience of supervising post
graduate students, a number of which have used survey and interview methodologies. In
addition he has conducted surveys for the European Dairy Association and as part of an EU
wide research team. From his teaching experience the supervisor has a good knowledge of
statistical software and analysis. He has experience of creating databases and this will greatly
aid the student. The questions posed in the interviews and survey will be informed by the
industry experts with whom the supervisor has continued contact and also by similar work
undertaken in Norway and Poland by Flatena et al (2005) along with Klocko-Gajewski and
Sulewski (2008) respectively.
The supervisor is confident that some of his industry contacts will volunteer for pilot
Book of Sample Projects Page 225 CIT Rísam PhD Scholarship Programme 2014 interviews and surveys as their feedback would be informed and critical where necessary.
While the surveys and interviews will provide insights into the understanding of various risk
management tools and the perception of price risk in the Irish dairy one needs to be cautious
and address the gap that often exists between intentions and actions. As the tools are new data
on their uptake is not available in order to address this gap experimental games which mimic
market circumstances will be conducted. This approach will follow the one used in a number
of recent IPRI studies which considered the uptake of a number of weather based insurance
derivative products. Prof. Dr. Andreas Thümmel, a lecturer in Hochshule Darmstadt, with
both teaching and practical experience in conducting such experimental games has offer to
give advice and co-supervise this element of the research.
Having completed this study the researcher will have an in depth knowledge of;
•
EU dairy policy
•
the Irish and EU dairy sectors
•
the use of price risk management tools in the EU and US
•
survey design
•
experimental games
•
the presentation of survey data using statistical software
•
analysis of survey data using statistical software
•
how to conduct interviews
•
analysis of interview data using statistical software
•
presentation of results
The researcher will also learn a number of skills including the ability to;
•
undertake a literature review
•
design a survey and conduct interviews
•
create a database
•
formulate and test hypotheses
•
use survey and statistical software
•
design experimental games
Book of Sample Projects Page 226 CIT Rísam PhD Scholarship Programme 2014 •
present finding to peers and industry
The supervisor has developed relationships with key industry participants from Irish Dairy
Board, FcStone, IBEC, Teagsac, AIB and the Department of Agriculture. In all cases these
organisation were very favourably disposed to this and any similar research. Furthermore, it
is probable that this collaboration will generate results which will lead follow-on and
sustained research into this nationally strategic field of research. The relationships formed
and experience gained in this project would prove invaluable in such endeavours.
Work Plan T
Title
Timescale
Other relevant information
ask
1
A review of past and current
(4 months)
This will provide the student with
dairy policy in the EU and a
an essential background in dairy
review of the structure of the
policy and the Irish dairy industry
Irish dairy sector
thus highlighting the motivation for
this research. This data will also
inform
the
representative
selection
samples
for
of
the
survey. This review will lead to a
thesis chapter.
2
A review of price risk
(4months)
This review will outline the historic
management in agricultural
development
of
price
risk
markets.
management in agricultural markets.
A descriptive analysis will then
outline the more appropriate tools to
use and their possible uses from an
Irish
perspective.
Comparative
studies in other countries will be
presented
and
analysed.
This
analysis will determine the nature of
the questions posed in the surveys.
Book of Sample Projects Page 227 CIT Rísam PhD Scholarship Programme 2014 This part of the research will result
in a completed literature review
chapter.
3
Preparation and piloting of
(2 months)
As stated tasks 1 and 2 above will
farm survey and processor
inform the questions posed in the
interview.
survey. A pilot survey will be
distributed, completed and analysed.
Following analysis the final survey
will be agreed and distributed to the
selected
samples.
Two
pilot
interviews with industry personnel
will be conducted. Likewise the
sample
of
processors
to
be
interviewed will be selected at this
point.
4
Distribution and collection of
(6 months)
This task will require the posting of
survey to farmer sample.
the surveys and the creation of a
Survey analysis.
database on their return. Using
appropriate software such as Excel
and SPSS the data will be presented,
analysed and interpreted.
The
output will be an empirical thesis
chapter.
5
Conduct interviews with the
(6months)
This task will require the student to
selected processors and
interview the selected processors.
analysis of results.
The data will be presented, analysed
and interpreted. The output will be
an empirical thesis chapter.
6
Design and execution of risk
perception game
Book of Sample Projects (6 months)
This task will require the student to
conduct
an
review
of
extensive
the
literature
design
of
Page 228 CIT Rísam PhD Scholarship Programme 2014 experimental games in the field of
risk perception. Next the student
will have to design the experimental
game both in pilot and final format
7
Execution of risk perception
(6 months)
game and analysis of results.
This task will require the student to
conduct the experimental games and
analyse and interpret the results.
The output will be an empirical
thesis chapter.
8
Write up and redrafting of
remaining chapters of thesis
(2 months)
This will result in the presentation
of a completed thesis and a peer
reviewed journal paper.
Ethical issues Standard practices in relation to survey analysis and interviews will be adhered to. Result will
not be published where the information provided is deemed to be of a sensitive commercial
nature and may be attributable to a single individual or entity. However this will be an
exception as it is envisage that the samples will be large and anonymous. In all cases the
purpose and nature of the study will be clearly before the commencement of any data
collection.
Book of Sample Projects Page 229