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, Pokemons are 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 share their new results. Come on and discover the pokemons as you never saw them! 9h -‐ Immersion in the Pokémon world 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 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. 10h30 -‐ Coffee break 10h50 -‐ (Re-‐)Creative Time in Pokémon world: Special brainstorming 11h20 -‐ 2nd Gym battle Gym Leader 1: Adrien Marck (IRMES – MSC) A similar age-‐related pattern describes different physiological functions from Weedle (C. elegans) to Ash Ketchum (Human) Gym Leader 2: Margaux Pontailler (INSERM U 970) Tissue engineering of the right heart outflow tract by a biofunctionalized bioresorbable polymeric valved tube 11h40 -‐ 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. 12h30 – Lunch: Stay with Us ! 14h00 -‐ Pokémon champion/special guest: Michael Springer (Harvard Medical School) 14h40 -‐ Re(Creative) Time in Pokémon world: Drawing :o 15h15 – 3rD Gym Battle Master in training 4: Agnes Köhler (MSC) Automatisation of Droplet Formation with Microfluidic Circuits -‐ Master in training 5: Aakriti Jain (Enzyme & Co., ) A circular design approach to elucidate material properties of bacterial cellulose and create useful applications Master in training 6: Guillaume Terradot High Throughput Identification of Public Goods producing genes in Escherichia Coli 16h15 -‐ Coffee Break 16h30 -‐ Re(Creative) Time in Pokémon world: Surprise ! 17h – 4th Gym Battle Gym leader 3: Ameline Bardo (UMR 7179 -‐ CNRS/MNHN) Manipulative abilities for the same tool use task in different species of primates. Gym Leader 4: Hernán Anlló (LSCP) 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 ???? :) Speakers & Abstracts Dr. Anthony Herrel UMR7179 CNRS/MNHN: Mécanismes adaptatifs des organismes aux communautés Team : FUNEVOL @ : [email protected] 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 @: [email protected] 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 @: [email protected] 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 @: [email protected] 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. Marguerite Benony Lab: MSC, Université Paris Diderot Under the guidance of Pascal Hersen @:[email protected] 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. 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 @: [email protected] 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 bi-‐
exponential 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. Margaux Pontailler INSERM U 970, laboratoires de recherches biochirurgicales, Paris Under the guidance of Philippe Menasché @ : [email protected] 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 @: [email protected] 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. Aakriti Jain Enzyme & Co. Under the guidance of Guillian Graves @: [email protected] 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 post-‐
processing 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. Guillaume Terradot @: [email protected] High Throughput Identification of Public Goods producing genes in Escherichia Coli The study of the evolution of cooperation or public good games in game theory, has faced for many years the heady issue of this simple rhetoric -‐ Public goods production is costly, thus the fitness of cooperators is lower than those of the cheaters, thus cheaters only should survive -‐ consequently it is hard to imagine how can cooperation be a stable evolutionary strategy. This argument, is a reformulation of the well known public goods game in game theory, in which even though the total payoff of a population of individuals is maximized when each individual contributes to the public pool, the Nash equilibrium is 0. Through the past decades, it has been suggested that reputation [5], population spatial dynamics -‐ migration -‐ [3] or Simpson’s paradox [4] could explain the sustainability of cooperation on evolutionary time scales. A strong focus in microbiology is to unveil the behaviour of isolated clonal populations of cells. Though, those populations are rarely found in nature, where heterogeneous genetically population of different bacteria share similar ecological niches. In that context, finding what can be used as public goods is of a particular interest, both to understand the mixed microbial dynamics and be able to tune cooperation level in synthetic biology [1]. In this study, we hope to identify potential gene candidates for the production of public goods, thus complementing existing reports [2] in Escherichia Coli. For that purpose we analyse the growth phenotype of a microbial mix containing two strains A and B. The B strain is always a W T fluorescent GF P strain whereas A includes all the knocked out strains of the keio collection [6]. References [1] Edwin H. Wintermute et al. Dynamics in the mixed microbial concourse. Genes & Development, 2010. [2] Edwin H. Wintermute et al. Emergent cooperation in microbial metabolism. Molecular Systems Biology, 2010. [3] Joe Yuichiri Wakano et al. Spatial dynamics of ecological public goods. PNAS, 2009. [4] John S. Chuang et al. Simpson’s paradox in a synthetic microbial system. Science, 2009. [5] Martin A. Nowak et al. Fairness versus reason in the ultimatum game. Science, 2000. [6] Tomoya Baba et al. Construction of escherichia coli k-‐12 in-‐frame, single-‐gene knockout mutants: the keio collection. Molecular Systems Biology, 2006. Ameline Bardo UMR7179 CNRS/MNHN: Mécanismes adaptatifs des organismes aux communautés Team : FUNEVOL Under the guidance of Dr. Emmanuelle Pouydebat @ : [email protected] 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. 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 @: [email protected] 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 droplet-‐
based 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).