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Life science of Pocket
Monsters - Evolution Comparative Biology Aging
Friday April 10th
9h - 17h30
Special Guests: Anthony Herrel and Michael Springer
Which type of pokemon trainers are you? How do you know your pokemon? Beyond the well-known
yellow mouse-like Pikachu, Pokémon is 720 varieties of fictional species and most of their behaviors
and properties remain unknown. This conference proposes to shed the light on the main researches
around pocket-monsters: what are the new discoveries about their evolution potential? How does
aging occur on their performances? What is the difference between the species? Our
interdisciplinary team of Kanto University will talk their new results and the consequence on the
pokemon world. Come on and discovers the pokemons as you never saw them!
Morning session (9h - 12h30)
9h - Immersion in the Pokémon world (Welcome Coffee)
9h30 - 1st Gym Battle
Master in training 1: Paula Fontanilla (M2 AIV Student)
Phenotypic observations in mice (mus musculus) of the effect of the invalidation of G15, a gene
involved in meiosis regulation.
Master in training 2: Alexis Dollion (M2 AIV student)
Profiling microsatellite loci Cape Dwarf Chameleons (Bradypodion pumilum) from the Western Cape,
South Africa
Gym Leader 1: Adrien Marck (IRMES – MSC)
A similar age-related pattern describes different physiological functions from Weedle (C. elegans) to
Ash Ketchum (Human)
10h40 - Coffee break + (Re-)Creative Time in Pokémon world
11h11 - 2nd Gym battle
Master in training 3: Marguerite Benony (M2 AIV Student)
Design of a modular and connected ant nest and quantitative study of collective motion in an ant
colony.
Gym Leader 2: Margaux Pontailler (INSERM U 970)
Tissue engineering of the right heart outflow tract by a biofunctionalized bioresorbable polymeric
valved tube
11h50 - Pokémon Champion/Special Guest: Michael Springer (Harvard Medical School)
12h30 – Lunch: Stay with Us ! O_o
Afternoon session (14h – 17H30)
14h00 - Pokémon champion/special guest: Anthony Herrel (UMR 7179 C.N.R.S/M.N.H.N.)
Analyses of morphology, physiology, and microbial diversity after a recent dietary switch in a lizard.
14h40 - Re(Creative) Pokemon Time
15h – 3rd Gym Battle
Master in training 3: Agnes Köhler (MSC)
Automatisation of Droplet Formation with Microfluidic Circuits Gym leader 3: Ameline Bardo (UMR 7179 - CNRS/MNHN)
Manipulative abilities for the same tool use task in different species of primates.
15h45 - Coffee Break
16h00 - Re(Creative) Time in Pokémon world
16h20 – 4th Gym Battle
Master in training 4: Aakriti Jain (Enzyme & Co.)
A circular design approach to elucidate material properties of bacterial cellulose and create useful
applications
Gym Leader 4: Hernán Anlló
When pikachus pika, do they mean it? Gym Leader 5: Dany Chauvin
Debugging molecular evolution, in droplets
17h30 - Happy- end in Kanto : Wine and Cheese with Ash Ketchum all his friends ???? :)
Speakers & Abstracts
Dr. Anthony Herrel
UMR7179 CNRS/MNHN: Mécanismes adaptatifs des organismes aux
communautés
Team : FUNEVOL
@ : anthony.herrel@mnhn.fr
Analyses of morphology, physiology, and
microbial diversity after a recent dietary
switch in a lizard.
Although evolution is commonly considered a slow process, recent
evidence has shown that organisms can show dramatic and
measurable phenotypic responses after introductions to novel
environments in relatively short time spans. We have previously shown how lizards (Podarcis sicula)
have rapidly evolved differences in head morphology, bite strength, and digestive tract structure
after experimental introduction onto a small island in the Adriatic Sea, Croatia. Despite the short
time scale (36 years) since this introduction, the introduced lizards became omnivores and evolved
caecal valves in the hindgut, a structure rarely observed in lizards. These changes in morphology and
performance parallel those typically documented among species and even families of lizards in both
the type and extent of their specialization. Here, we present novel data on 1) the morphology of the
cranium and its muscles using µCT scanning and 3D geometric morphometric approaches, 2) the
digestive physiology of the two populations, and 3) the diversity of the microbiomes in the hindgut
using metagenomic sequencing approaches.
Michael Springer
Harvard Medical School
Department of Systems Biology
@: michael_springer@hms.harvard.edu
Signal Processing
Signal processing and integration are fundamental features of
cellular response. We have evidence that passive transport of
sugars through hexose transporters is an under appreciated
signal integration layer that converters signals into ratios of
signals. This ratio-sensing motif can be generalized to many
other biological processes as it is analogous to competitive
inhibition. We find that when this motif is combined with
another property, mass conservation, it creates a novel
linearizing motif – it can convert Michaelian responses into
responses that are linear across their full dynamic range.
Paula Fontanilla-Ramirez
Laboratoire de développement des
gonades(LDG)
Under the guidance of Gabriel Livera
@: Paulafontanillar@gmail.com
Phenotypic observations in mice (mus musculus) of the effect of the
invalidation of G15, a gene involved in meiosis regulation.
Meiosis is a universal process used by all eukaryote; thesetwo rounds of cellular division preceded by
a single DNA replication produce haploid gametes.The fusion of male and female gametes at the time
of fertilization will allow reestablishing the proper number of chromosome and mix maternal and
paternal genetic information generating diversity.Additionally during the first step of meiosis genetic
exchanges also occurs between homologous chromosome generating even more diversitythose
exchanges are initiated by DNA Double Strand breaks (DSBs) induced by the topoisomerase Spo11.
Surprisingly, despite meiosis being a key process forfertility and evolution, many actors involved in
vertebrate meiosis are still unknown. A transcriptome study performed by the lab identified several
new candidate meiotic genes. RT-qPCR analysis of one of these, G-15, defined an expression profile
well correlated to male and female meiosis. The G15-knock out (KO) mice were thus generated and
the first analyses identified a change in size and structure of gonads and a major defect of fertility in
those with a likely arrest during meiotic progression. In this context the study was focused on going
further on the phenotype characterization. Mice were raised and mated, and gonads were isolated.
Tail DNA was extracted to define the genotype of the animals by PCR. Histology and
immnunostaining were performed. The phenotype analyses performed in adult males showed that in
KO, the meiosis is arrested at an early stage of prophase I and a percentage of the testicular
tubulescontained nomeiotic stages (only mitotic cells, spermatogonia). Observation of histological
sections show a particular feature in all stages of KOtestes: abnormal metaphases; these are cells
with a blackberry like structure. To understand whether cell death was involved in the G15-KO
phenotype we measured two markers of apoptosis,ISEL and cleaved caspase 3. The percentage of
tubules with apoptotic cells is 5-15 % less in the wild type compared to the KO showing that the
absence of G-15 induced cell death during meiosis. Abnormal metaphases were stainedneither for
ISELnor for Cleaved Caspase 3. We also investigated whether meioisis was initiated at the proper
timing using an early marker of meiosis (γ -H2Ax that detects DBS) at the stage at which the first
meiotic stages are expected to appear,10 days post-partum (dpp). The percentage of tubules stained
was thesimilar for both wild type and KO however later at the 16 dpp,this percentage decreases by
half for the KO. This likely indicates that though there is no overt delay in the meiotic process
something rapidly interrupt the process. Lastly to determine whether the phenotype of the G15KO
was dependent or not of DSB we analyzed G-15/Spo11 double KO. These analyses performed in
females suggest that G15 acts independently from Spo11. Altogether this work confirms that G-15 is
a gene involved in meiosis albeit its mechanism of action remains enigmatic. The high conservation
of this gene throughout evolution prompt for further study which should provide a better
understanding of the regulation of meiosis in mammals.
Key words: Meiosis. Knock out. Apoptosis. Abnormal metaphase. Double strand breaks.
Alexis Dollion
South-African National Biodiversity Institute (SANBI), Departement: Applied biodiversity research,
Molecular lab
Under the guidance of Pr. Krystal Tolley
@: dollion.alexis.14340@gmail.com
Profiling microsatellite loci Cape Dwarf Chameleons (Bradypodion
pumilum) from the Western Cape, South Africa
Monitoring and assessing statutes of threatened
species is nowadays a priority. To do so molecular
biology techniques, like profiling is usually used to
test gene flow between populations, paternity and
Hardy-Weinberg
equilibrium
(population
equilibrium). Here, we worked on the threatened
species, the Cape Dwarf Chameleon (Bradypodion
pumilum), to test 4 new microsatellites loci (Bth76,
Bth161, Bme45and Bme58; developed and
Picture from Krystal Tolley
optimized in 2012 by Feldeheim and co-workers for
the species complex B. melanocephalum –
thamnobates) on 4 different population of B.
pumilum occurring in the Cape Town region. These kinds of studies are really important to provide
new microsatellites loci, tools, for population genetics and conservation biology.
Our preliminary results suggest that at least Bth76, Bth161 and Bme45 are good candidate for
population genetics in the Cape Dwarf Chameleon.
Adrien Marck
IRMES, Institut de Recherche bioMédicale et d’Epidémiologie du Sport & Laboratoire MSC Matière et
Systèmes Complexes
Under the guidance of Jean-Marc Di Meglio & Jean-François Toussaint
@: Adrien.MARCK@insep.fr
A similar age-related pattern describes different physiological
functions from Weedle (C. elegans) to Ash Ketchum (Human)
The development, the rise and the decay of
physiological functions and performances through life
is a common feature shared by a lot of living
organisms. In Homo sapiens at the prism of sport
performances several studies described the relation
between performance trajectories and age. Dan. H.
Moore developed such a description with a biexponential equation to describe the top performances
development in track and field events (Dan H. Moore,
Nature 1975). The function described the record
progression for each age on a few running and throwing events for men and women. This function
was recently adjusted to an extended range of different sports revealing a deterministic
asymmetrical envelope for these different maximal human physiological performances. Using this
previous function we have investigated the relation between performance and age for different
species and performance traits. The dynamics of growth and decay processes revealed a same
asymmetric envelope with a growth phase shorter and faster than degeneration. This investigation
underlines the similarity of these envelopes and paves the way for an extending exploration through
the description of different maximal performance traits by age in different species and at different
scales.
Marguerite Benony
Lab: MSC, Université Paris Diderot
Under the guidance of Pascal Hersen
@:marguerite.benony@gmail.com
Design of a modular and connected ant nest and quantitative study
of collective motion in an ant colony.
Ants are an archetype of sophisticated coordination and organizational patterns. They are considered
as a superorganism. Here we propose a novel experimental approach, namely a modular, connected
ant nest, to study how social insects react individually and collectively to controlled spatio-temporal
perturbations of their environment.
We have started to develop a modular ant nest using 3D printers. We printed several connectible
squared chambers, which can contain corridors, mazes, large and small rooms, dead-ends etc…. Once
all chambers are connected, we can quickly and easily restructure the topology of the nest. We are
also building an app to remotely control and observe the nest.
With that modular tool, we aim study the adaptation of ant colonies with respect to topology
restructuration, and controlled time-varying environmental perturbation. Chambers will be
instrumented to perform at least one action on the nest (changes of temperature, humidity, light,
vibration) in order to perform local perturbations in space and time. Later, we will also develop
image acquisition and analysis tools to ensure that we can track one individual ant with high
resolution while recording all ants movements.
We used design methods to design and build the nest. It is therefore printable not only by
researchers but also by anybody who is interested by observing and studying ants behaviors.
Margaux Pontailler
INSERM U 970,
laboratoires de recherches biochirurgicales, Paris
Under the guidance of Philippe Menasché
@ : margaux.pontailler@wanadoo.fr
Tissue engineering of the right heart outflow tract by a
biofunctionalized bioresorbable polymeric valved tube
Approximately 42% of infants’ mortality in the world is
related to congenital heart defects (prevalence: 8-12/1000
births). Over 1/3 require the reconstruction of the right
ventricular outflow tract (RVOT) by surgical procedures
which currently use inert materials without any growth
potential. Consequently, multiple reoperations are often
required, with their attendant high risk of mortality and
morbidity.
The TEH-TUBE project will address these limitations by
creating a novel bioabsorbable biomaterial using a
polymeric valved tube either seeded with autologous
adipose tissue derived stem cells (ADSC) or functionalized
by a peptidic sequence triggering homing of the host cells
onto the scaffold to make it a living self-populated
structure.
The main objectives of the project are:
• Compare 3 different polymers processed by electrospinning (ES) to generate a competent valved
tube
• Compare, in the selected polymer, ADSC seeding and peptide grafting using in vitro mechanical and
biological tests as well as in vivo animal experiments (primarily rats)
• Validate the ultimate combination (polymer + cells or peptides) in a clinically relevant large animal
model (in this case, the growing lamb to specifically assess the regenerative and growth potential of
the composite construct)
Agnes KÖHLER
MSC, Université Paris Diderot
Under the guidance of Dr. Gaelle Charron
@: koehler.agnes@gmail.com
Automatising of Droplet Formation with Microfluidic Circuits
Understanding and controlling processes is an
interesting topic to any researcher. This knowledge
could be useful in other domains such as chemistry,
for example to some experiments as exploring the
thermodynamics of a reaction between two
components A and B, e.g. titration or synthesis of
nanoparticles.
The idea is to build an automated titrator, that is a
system of reservoirs, pipes, pumps and spectrometer
for the optical readout that will mix A and B in various
proportions, read the result optically and will infer
from that readout how much A and B have reacted
together. Such systems already exists BUT they are
very expensive (several k€). Also there is computer
piloting but no proper control, that is no intelligent
investigation of the mixture compositions. The composition space is screened linearly. Furthermore
they consume quite a lot of reagents A & B which means that it might not be possible to investigate
reactions involving costly or rare compounds, like antibodies or enzymes, or get many replicates of
the measurements.
Hence we started to build up a microfluidic autotitrator using droplet microfluidics, which consume
less reagent and can be coupled to a microscope for optical readout. In order to do so, we designed a
microfluidic droplet generator and mixer, by printing a 3D plastic mask with photopolymerization,
assembling the device made of PDMS and connecting it with syringe pumps with water as solution A
and oil as carrier fluid. The following step is to inject a precise amount of B. As a starting point A and
B will be different dyes that should be mixed at different concentrations and a microscope connected
to a camera as an optical read-out. This setup implements a closed feedback loop that could then be
further modified according to the precise task the circuit should perform.
Ameline Bardo
UMR7179 CNRS/MNHN: Mécanismes adaptatifs des organismes aux communautés
Team : FUNEVOL
Under the guidance of Dr. Emmanuelle Pouydebat
@ : ameline.bardo@gmail.com
Manipulative abilities for the same tool use task in different species
of primates
Primates have highly developed capacities for
gripping and manipulation that differ between
species. In this context, the human hand is
considered as unique based on its functional
characteristics. However, the real dynamic
manual abilities of primates remain poorly
known. The purpose of this study is to compare
the manipulative strategies in different species
of primates (humans, bonobos, gorillas,
orangutans), during the same tool use task. This
task requires the useof a tool to recover a static food item (e.g. walnut) in a wooden maze while
facing many obstacles; the wire netting between the subject and the maze, and the obstacles inside
the maze. All species were in the same experimental conditions allowing us to compare across
species. We here focus on the functional strategies used during this task by the different species and
quantify the grip types and the in-hand movements involved to reposition the tool in the hand. We
found common strategies despite the differences in hand morphology but also strategies specific to
some species. We discuss the results in the context of the evolution of manipulative behaviors and
highlight the importance of novel methods to better understand the manual specificities of each
species.
Aakriti Jain
Enzyme & Co.
Under the guidance of Guillian Graves
@: aakriti.jain24@gmail.com
A circular design approach to understand and elucidate material
properties of bacterial cellulose
In this project, I aim to explore the intersection of biology and design by investigating natural
bioprocesses and understanding possible use cases for these bioprocesses. At the beginning of the
investigation, I was intrigued by several such processes - biocalcification by urea consuming bacteria,
the use of mycelium growth to create aesthetically and functionally pleasing pieces and the
fermentation process through which bacterial cellulose can be produced. In the end, I narrowed
down my investigation to growing a symbiotic colony of bacteria and yeast (SCOBY) under various
design-specific conditions in order to understand how we can utilize the produced bacterial cellulose
in the way the material can be shaped, colored, molded, and transformed. The idea is to cut postprocessing as much as possible and be able to create a finished or almost-finished product just by
growing it. We have also designed a prototype of a house-hold object that can be used for this type
of systemic growth of products where the input can be sugar-rich wastes and the output would be an
almost finished product.
Hernán Anlló
hernan.anllo@cri-paris.org
When pikachus pika, do they mean it?
What is consciousness? How did we develop it? Do non-human
animals have a sense of agency? What about babies? Is the whole
spectrum of emotions that Pikachu display a bold overstatement
of animal consciousness, or are pocket monsters right on the
money when it comes to represent animal emotion?
Dany Chauvin
Laboratory of Biochemistry, ESPCI Paristech
Under the guidance of Clément Nizak
@: dany.chauvin@live.fr
Debugging molecular evolution, in droplets
A laboratory technique mimicking Darwinian
evolution called Directed Evolution is broadly
used to improve the biochemical properties
(activity, stability, etc) of proteins of interests.
Nonetheless, this technique often fails to achieve
high improvement owing to the large size of
sequence space, non-additivity of mutational
effects, and other unknown reasons. To
overcome this problem, we propose to study
molecular evolution from two different
perspectives using high-throughput dropletbased microfluidics. First, we will decipher what is
the relationship between the starting point of the
directed evolution experiment and its outcome.
We will generate a genotype/phenotype mapping
of millions of mutants of a promiscuous aminopeptidase enzyme and assess the evolutive potential
of each one of them by measuring the biochemical properties of their neighborhoods in sequence
space. Then, we will generate all possible single mutations and all possible pairs of mutations of a
protein sequence, that of the rat-trypsin enzyme (more than 30 millions mutants). For each mutant
we will measure its biochemical properties, and then determine the pairs of positions that are
correlated. We aim to identify networks of correlated positions in the three dimensional structure of
the protein and to relate them to their different biochemical properties, in the spirit of the "potein
sectors" previously predicted by our collaborators (Halabi et al. Cell 2009).