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2020 -
Long-Term Fellowships - LTF

In situ characterization of eukaryotic sodium channels using cryoEM

FAN Xiao (CHINA, PEOPLE'S REPUBLIC OF)

Department of Molecular Biology - Princeton University - Princeton - USA

YAN Nieng (Host supervisor)
Voltage-gated sodium channels (VGSC, Nav) govern membrane excitability by initiating and propagating action potentials in nerve and muscle tissues. Mutations in Nav channels are directly linked to numerous human diseases, including epilepsy, arrhythmia, and pain. Understanding the gating mechanism of Nav channels is critical for both basic research and pharmaceutical applications. In recent years, several structures of Nav channels that were purified in detergent micelles were revealed by cryogenic electron microscopy (cryoEM). However, the structure of the resting state, which requires the presence of the transmembrane electric field, has been unattainable due to the technical challenges of maintaining the membrane potential during sample preparation. Here we propose an innovative way to prepare cryo-samples of Nav channels on in situ neuronal membranes and further elucidate their resting states by sub-tomogram averaging methods. Novel systems for sample preparation and data collection will be developed to obtain high-resolution structural information on Nav channels in distinct functional states in situ. The strategy can also be generalized to investigate other membrane proteins in a native membrane environment. Achieving the proposed aims will provide unprecedented insight into the Nav channel gating function, and provide useful tools for studying the structural biology of membrane proteins in general.
2020 -
Long-Term Fellowships - LTF

Using visual proteomics to understand membrane dynamics in the malaria parasite P. falciparum

FERREIRA Josie (UK)

Centre for Structural Systems Biology - University of Hamburg - Hamburg - GERMANY

GILBERGER Tim (Host supervisor)
The malaria disease represents a significant global burden. Despite major advances in its treatment and control, rising resistance to front-line therapies makes the demand for innovative solutions more important than ever. To identify possible intervention points, we need a firm grasp on the processes that govern the parasites complex lifecycle. Central to the evolutionary success of the malaria parasite is the rapid invasion of erythrocytes and subsequent replication. During invasion, the parasite utilises intricate machinery coordinated by a sequence of receptor-ligand interactions, allowing the invagination of the erythrocyte membrane. Inside the erythrocyte, transient structures essential for invasion are rapidly disassembled. These include a double membrane structure termed the inner membrane complex. Despite their importance, our understanding of these transient structures is limited. I propose a correlative approach to understand receptor-ligand mediated erythrocyte invasion and subsequent disassembly of the inner membrane complex. I aim to directly visualise and analyse these processes in situ. This will be achieved using super-resolution fluorescence microscopy to guide specimen FIB-milling for electron cryo-tomography and subtomogram averaging. Simultaneously, studying the inner membrane complex over time in combination with mass spectrometry will allow me to identify and target key players in the disassembly process. Finally, using cryo-tomograms, I will generate a series of atlases of protein and organelle positions within the parasite and host cell. These will provide details of the alterations in the molecular landscape during and post invasion.
2020 -
Long-Term Fellowships - LTF

Relevance of lipid droplet-mitochondria contact sites for brown adipose tissue function

FISCHER Alexander (GERMANY)

Department of Genetics and Complex Diseases - Harvard Medical School - Boston - USA

FARESE Robert (Host supervisor)
Brown adipose tissue (BAT) thermogenesis is essential for survival in cold temperatures. To meet the energetic demands of this process, BAT relies on efficient energy supply from the circulation as well as from intracellular triglyceride stores in lipid droplets. The fatty acids stored in triglycerides can be liberated by lipolysis and serve as fuel for mitochondrial thermogenesis. However, high intracellular levels of free fatty acids are detrimental for cellular survival, demanding for efficient transfer processes. Microscopical analyses indicate a tight interaction between mitochondria and lipid droplets, yet even the fundamental triggers leading to the initiation of contact site formation as well as their physiological role remain elusive. In this proposal, I therefore want to examine the hypothesis that molecular complexes mediating interactions between mitochondria and lipid droplets are formed in activated BAT, and that these contact sites are critical for BAT function. To achieve these goals, microscopical interaction studies will be employed to shed light on the conditions triggering contact site formation. The molecular machinery mediating the interaction will be identified using an APEX-proximity labelling approach. Genetic manipulation will be employed to examine the role of the proteins identified in this screen for initiation and maintenance of contact sites. The relevance of these proteins for BAT function will then be analyzed using CRISPR-Cas9 technology in primary adipocytes and mice. Conclusively, the proposed approaches will not only help understanding the mechanisms involved in organelle contact site formation but also define their physiological role.
2020 -
Long-Term Fellowships - LTF

From social networks to neural networks: imaging social memory in the bat hippocampus

FORLI Angelo (ITALY)

Department of Bioengineering and the Helen Wills Neuroscience Institute - UC Berkeley - Berkeley - USA

YARTSEV Michael (Host supervisor)
From invertebrates to mammals, social behavior plays a fundamental role in the survival of species throughout the animal kingdom. In order to take advantage of past interactions with conspecifics, the brain has to encode, consolidate and recall social memories. Recent findings suggest that the hippocampal region CA2 is essential for social memory, but the nature and the stability of information stored in this circuit remains enigmatic. I will utilize the Egyptian fruit bat, a highly social mammal which develops long-term social networks within the colony, to ask how the long-term and dynamic representation of social information is encoded in CA2. I will adopt advanced behavioral measurements combined with machine learning methods to monitor and characterize social interactions and their associated vocalizations within a natural colony of bats over long periods. To investigate the existence and properties of social coding in CA2, I will take advantage of chronic wireless calcium-imaging in freely behaving and flying bats during behaviorally relevant social interactions as well as during sleep. By combining an ethological approach with cutting edge technologies for detailed measurements of long-term behavioral and neural dynamics, I will aim to uncover fundamental properties of social cognition in the mammalian brain.
2020 -
Long-Term Fellowships - LTF

Investigating the ancestral role of animal-bacterial symbiosis in epithelial morphogenesis

GARCIA DE LAS BAYONAS Alain (FRANCE)

Department of Molecular and Cell Biology - University of California, Berkeley - Berkeley - USA

KING Nicole (Host supervisor)
Animal-bacterial interactions are widespread and regulate diverse vital processes, including nutrient uptake, immune system development and tissue morphogenesis. Although crucial for animal biology, little is known about the ancestry of animal-bacterial interactions or their influence on animal origins and evolution. As the closest living relatives of animals, choanoflagellates provide key insights for reconstructing animal origins. In the model choanoflagellate S. rosetta, molecules secreted by bacteria induce two life history events – multicellular development and mating (Alegado et al. 2012, Woznica et al. 2018). However, unlike in animals in which bacterial symbionts are stably enclosed within epithelial structures, the S. rosetta life cycle responds to diffusible cues from environmental bacteria. A new choanoflagellate species, S. monosierra, discovered by the host lab forms large spherical colonies containing a stable microbiome (Hake et al., in prep). Reducing the bacterial load reduces S. monosierra colony size without reducing cell number, suggesting the microbiome regulates colony morphogenesis. This proposal seeks to harness this new bacteria-containing choanoflagellate to investigate the ancestry of animal-bacterial symbiosis and its influence on epithelial morphogenesis. First, I will define the precise symbiotic bacteria that regulate S. monosierra colony size. Second, I will investigate the molecular cues and cellular mechanisms that underlie bacterial-dependent control of S. monosierra colony size. Last, I will explore choanoflagellate diversity to assess whether a stable microbiome was present in the last common ancestor of choanoflagellates and animals.
2020 -
Long-Term Fellowships - LTF

Genomic characterization of regulatory elements associated with human breast milk production

GOLAN MAOR Yarden (ISRAEL)

Department of Bioengineering and Therapeutic Sciences - University of California - San Francisco - USA

AHITUV Nadav (Host supervisor)
Breast milk is the optimal dietary source for infants, as it supplies all the nutritional requirements for the first six months of life. However, over 50% of mothers express concerns about insufficient milk volume or poor milk quality as pertinent to their motivation to wean their infants before six months of exclusive lactation. Human breast-milk contains macro- and micronutrients as well as numerous bioactive compounds and several different cell types, including epithelial, myoepithelial, stem cells and leukocytes. The human mammary gland is distinct from other mammals in many aspects, including milk composition, gene expression and architecture. This renders commonly used mammalian animal models non-representative systems for studying the human lactation process. During my post-doctoral fellowship, I aim to characterize the breast-milk cells transcriptome (single-cell RNA sequence), regulome (ATAC-seq and Cut&Run), and variome (genotyping arrays) and link them to create a novel and important genomic lactation dataset. I will use samples collected under both physiological (e.g., colostrum, mature milk, and involution) and pathological (e.g., low milk production) conditions, to study the mechanisms underlying different lactation pathologies and to characterize how genetic variation influences lactation outcomes and infant growth. Collectively, the results of this study will significantly impact mother and infant health worldwide and expand our toolbox to improve breastfeeding medicine and help mothers dealing with breastfeeding issues and related diseases.
2020 -
Long-Term Fellowships - LTF

A radical approach to histidine bioconjugation

GREEN Ori (ISRAEL)

The Department of Chemistry and Applied Biosciences - ETH Zurich - Zurich - SWITZERLAND

MORANDI Bill (Host supervisor)
Site-selective modifications of proteins at a predetermined location have been proven to be very useful to gather information and explore composite biological processes. In addition, these reactions give opportunities for researchers in academia and industry to prepare functional protein based materials for various applications in our daily life. Today, the chemical toolbox for site selective modifications is quite developed for targeting highly reactive amino acids residues such as cysteine and lysine, however targeting less reactive amino acids is much more challenging and therefore examples are rarer. Among the unreactive amino acids, histidine site selective modification is highly desirable. Although several reports exist for this modification there is no concrete general approach for selectively modifying histidine residues. This fact motivated us in this research proposal. Herein, we propose to develop a general strategy to selectively modify histidine residues on proteins without the need of complex genetic manipulations. We plan to leverage the exquisite functional and water group tolerance of Minisci type radical reactions to address this challenge. The bioorthogonality and feasibility of the developed reaction will be tested for drug development and fluorescent labelling of enzymes. We believe that the success of this selective histidine modification will have tremendous impact in the biomedical sciences.
2020 -
Long-Term Fellowships - LTF

Cryo-EM visualization of sister chromatid cohesion establishment at the replication fork

HENRIKUS Sarah (GERMANY)

Macromolecular Machines - The Francis Crick Institute - London - UK

COSTA Alessandro (Host supervisor)
Loss or imbalance of chromosomes can trigger various pathologies, threatening healthy cell proliferation. During the cell cycle, each chromosome is replicated, generating sister chromatids. Before cell division, duplicated chromosomes must be equally segregated and transmitted to daughter cells. Chromosome segregation is organized by cohesin, which topologically links chromatids from their synthesis onwards. Despite its vital importance, the molecular basis of sister chromatid cohesion establishment at the replication fork remains mostly elusive. A clear model is lacking of how cohesin transitions from interactions with one parental duplex DNA at the front of the replisome to two duplicated DNA strands behind the replisome. Detailed analysis of cohesin assembly at the fork is critical for the formation of a structural framework for cohesion establishment. This proposal aims to address two fundamental questions. First, I seek to describe the conformational changes that cohesin undergoes when it transitions from encircling one to two DNA molecules. Second, I aim to capture cohesin interacting with the replication fork. To tackle these questions, I will use in vitro reconstituted systems combined with cryo-EM imaging. Leveraging my expertise in chemistry and single-molecule techniques, I will develop a new DNA-affinity cryo-EM grid. This new tool will allow me to visualize cohesin and the replication machinery in a DNA-bound state, building on in vitro reconstituted systems available in the Costa and Uhlmann labs. With this multidisciplinary approach, I aim to characterize the elusive molecular intermediates of sister chromatid cohesion establishment.
2020 -
Long-Term Fellowships - LTF

Charting the evolutionary history of a sex-specific innovation at the single-cell level

HOPKINS Benjamin (UK)

Department of Ecology and Evolution - University of California - Davis - USA

KOPP Artyom (Host supervisor)
Development is the critical link between genetic and morphological change. Thus, to understand how organisms come to differ in appearance we must understand how the developmental pathways that build them evolve. We know that changes in these pathways can drive the evolutionary loss or modification of traits. But we have so far failed to explain how new developmental pathways evolve. This is the greatest gap in our understanding of morphological diversification: innovations, such as wings, horns, and feathers, all need to evolve before they can be modified. This problem is further confounded in the most extreme parts of organismal design, sex-specific traits, which require not just the acquisition of a new developmental pathway but its limitation to a single sex. In this proposal, I develop a new analytical approach, which repurposes emerging biomedical methods, to identify for the first time the developmental genetic processes by which a novel trait, the recently-evolved Drosophila sex comb, has evolved. Combining time-series, single-cell RNA-sequencing with developmental genetic manipulations, I will use a comparative, multi-species approach to (a) reconstruct the developmental pathway that builds sex combs, (b) identify the developmental genetic changes that have driven morphological diversification, (c) elucidate how the novel pathway integrates sex-determination machinery, and (d) assess the evolvability of this innovation. Ultimately, this approach represents a new way of doing ‘evo-devo’ research – an approach that simultaneously charts trait evolution across levels of biological organisation, from gene to tissue, to understand the diversification of life.
2020 -
Long-Term Fellowships - LTF

Clonal dynamics and architecture of the blood stem cell niche

BARON Chloe (FRANCE)

Stem Cell Program - Boston Children's Hospital - Boston - USA

ZON Leonard (Host supervisor)
Hematopoietic stem cells (HSCs) are responsible for the production of all blood cells throughout life. In vivo, HSCs reside within heterogeneous microenvironments or niches able to promote their function. Understanding the mechanisms responsible for the niche ability to support HSCs is required to expand our knowledge of HSC-niche interaction in vivo in healthy conditions and after niche injury induced by chemotherapy. Additionally, it will pave the way to create in vitro niches allowing for HSC reprogramming, maintenance and expansion for therapeutic purposes. Using zebrafish, a powerful model due to its similarity to human developmental processes, hematopoietic master regulators and disease inducing mutations, I will: Aim 1: Unravel the cellular and molecular mechanisms providing niche cells the ability to support HSC using live imaging and single-cell multiomics. a- Characterize the 3D structure and the cellular dynamics of the HSC niche using live imaging of a newly generated multicolor zebrafish reporter line in healthy conditions and after cell-specific ablations. b- Decipher the niche transcriptional code responsible for HSC support combining single-cell RNA-seq, single-cell ATAC-seq and spatial transcriptomics. Aim 2: Characterize the clonal dynamics of HSCs and niche cells in the marrow in perturbed conditions using genetic lineage tracing. a- Analyze the clonal origin of HSCs and niche cells in the healthy marrow using the scGESTALT barcoding technology. b- Expose animals to sublethal irradiation and characterize the clonal dynamics of niche recovery after injury.
2020 -
Long-Term Fellowships - LTF

The molecular mechanism of sex determination in a malaria parasite

HUNZIKER Mirjam (SWITZERLAND)

Molecular Biology Department - Umea University - Umea - SWEDEN

BILLKER Oliver (Host supervisor)
Sexual reproduction is an obligate stage in the complex life cycle of Plasmodium parasites, the causative agents of malaria. While cyclic asexual replication of the parasite in the vertebrate host is associated with all clinical symptoms of malaria, the transmission of the disease to a new host relies on the sexual reproduction of the parasite in the mosquito. Transmission and reproductive success depend on the ability of the parasite to produce fertile male and female gametes at an optimal ratio. The molecular mechanisms of sex determination and development, therefore, hold the key to new transmission-blocking interventions and to a broader understanding of how life cycle decisions in an important group of parasites can be regulated. Recent breakthroughs have identified a master regulator of sexual commitment, but how one transcription factor can give rise to the completely different gene expression programs of male and female gametocytes remains elusive. Genetic screens and transcriptomic analyses in a rodent model have now led to the identification of a small panel of genes which I propose here will unlock the question of how sex ratio is determined. By applying a combination of state-of-the-art biochemical, cell biological and genetic techniques, I aim to characterize the function of three strongly supported, male-determining candidate genes. The obtained results will provide insights into how sex, and thus transmission, of malaria parasites is regulated. By elucidating the fascinating biology of sex determination in an ancient eukaryote that lacks sex chromosomes, the proposed work can reveal potentially novel pathways involved in the origin of eukaryotic sex.
2020 -
Long-Term Fellowships - LTF

Uncovering the molecular link between regeneration and aging in Hydra

CAMPOS RODRIGUEZ Sergio Esteban (MEXICO)

Department of Molecular and Cellular Biology - University of California - Davis - USA

JULIANO Celina (Host supervisor)
The decline in regenerative potential that follows aging is associated with organ failure ultimately leading to frailty and death. Understanding the mechanisms underlying the loss of regeneration with age may unlock novel therapies for treating age-related disease. The freshwater cnidarian Hydra vulgaris is capable of whole-body regeneration and appears to lack senescence. The closely related Hydra oligactis displays these features when cultured in normal conditions, but chemical treatment or temperature reduction induces an aging phenotype, which is accompanied by a decrease in regenerative potential. Interestingly, H. vulgaris does not age or lose regenerative potential when subjected to the same treatments. Thus, these two Hydra species present a valuable opportunity to use comparative approaches to uncover the mechanisms linking aging to a loss of regenerative potential. To accomplish this, I will use RNA-seq to profile regenerating tissue in aging and non-aging H. oligactis, and in H. vulgaris. In addition, I will profile aging H. oligactis treated with the anti-aging drug Rapamycin which promotes regeneration in aging H. oligactis. Together, these experiments will allow me to identify genes that are activated in regenerating H. vulgaris and non-aging H. oligactis, but not in aging H. oligactis after injury. I hypothesize that these genes are essential for regeneration, which I will test by knocking them down in H. vulgaris and assaying regenerative potential. The results of this proposal will contribute to understand the mechanisms of regeneration during aging and uncover potential molecular targets for the development of new anti-aging therapies.
2020 -
Long-Term Fellowships - LTF

Mapping the biogeography of the gut microbiome: from spatial ecology to disease resistance

JAHN Martin (GERMANY)

Department of Zoology - University of Oxford - Oxford - UK

FOSTER Kevin (Host supervisor)
Dense commensal microbial communities are found within the gut that protect us against pathogens. Yet, a much-discussed gap in our understanding is how these communities organise within the intestine, and how this organisation links to health outcomes. One particularly dense area of colonisation is the gut epithelial surface and associated mucus, as the region with the most permanent and intimate association with the host. My key hypothesis is that microbes at the mucus interface are particularly important for protection against pathogens that must overcome this barrier to access the epithelium in order to cause disease. I will test this in three aims: 1) I will develop new imaging methods to map the spatial organisation of microbes at the gut mucus interface facing challenge from the important pathogen Salmonella enterica serovar Typhimurium, with unprecedented throughput and detail. I will pioneer new methods for label-free pathogen and commensal identification in the gut what will allow to overcome the limited throughput in imaging-based microbiome research. 2) Based on the new imaging data, I will use custom image analysis to identify those commensal species that associate preferentially with the epithelial surface and with the pathogen. 3) Finally, I will test whether the spatial ecology of gut bacteria is predictive for colonisation resistance by assembling defined communities with different spatial organisations in gnotobiotic mice. Overall, my project promises for the first time to show how the spatial ecology of the microbiota is critical for the balance between health and disease.
2020 -
Long-Term Fellowships - LTF

Characterizing the translation-initiation modes of operons in bacteria

CHEMLA Yonatan (ISRAEL)

Biological Engineering - MIT - Cambridge - USA

VOIGT Christopher A. (Host supervisor)
Despite the central role operons play in prokaryotic genome organization, their origin, evolution, function and unique characteristics are not well-understood. The primary difference between operons and the comprehensively-studied monocistronic mRNAs is that operonic cistrons frequently overlap with one another. These overlaps mandate that the translation initiation of a distal cistron must occur within the coding region of the upstream proximal cistron. This process does not allow for independent translation initiations, a fact inadequately explained by the current paradigm for translation initiation, the 30S binding mode, as it necessitates constant interference between elongating and initiating ribosomes. Recently, a new mode of translation-initiation, the 70S scanning mode, was experimentally observed, and it offers a challenge to the existing paradigm. However, it remains unknown which initiation mode occurs at each cistron, nor how to perform measurements that differentiate between the two modes and capture their genomic distribution inside a living cell. Moreover, it is not known what processes are involved in the ribosomal initiation mode-decision or its mechanism of regulation. Herein, we propose an experimental framework based on ribosomal titration assays followed by ribosome profiling, which will enable us to identify the genome-wide distribution of initiation modes, and measure and map their ribosome-mRNA affinity landscape. Using this data, we will study and characterize the mechanisms that govern the mode of initiation, and build synthetic operons to validate our findings and enable precise prediction and utilization of the operon unique characteristics.
2020 -
Long-Term Fellowships - LTF

Engram epigenetics – A CRISPR-based approach to identify genes for the treatment of fear memories

CODA Davide (ITALY)

Neuroepigenetics Laboratory - Brain and Mind Institute - Lausanne - SWITZERLAND

GRÄFF Johannes (Host supervisor)
The experience of traumatic, life-threatening events gives rise to some of the most enduring forms of fear memories, which can degenerate into a devastating pathological state known as post-traumatic stress disorder (PTSD). Yet, surprisingly little is known about how long-lasting memory are formed and stored. Likewise, the neural and molecular mechanisms of how to best overcome remote fear memories remain unknown. The aim of this project is to identify the transcriptional and epigenetic changes occurring at a single cell level during remote fear memory attenuation, and to validate their functional relevance. To this end, I will use a mouse line in which the promoter of a neuronal activity marker (c-Fos) drives a tetracycline inducible system that allows for the identification of the neuronal subpopulation underlying fear memory attenuation. FACS cell sorting coupled with single cell RNA-seq, ChIP-seq and ATAC-seq will capture the genome-wide changes in gene expression and chromatin organization occurring within the tagged subpopulation of cells. Finally, spatiotemporally controlled CRISPR approaches will be used to dissect what gene-specific alterations, either transcriptional or epigenetic, are responsible for remote fear attenuation. I anticipate that this proposal has the groundbreaking potential to uncover the molecular mechanisms behind the overcoming of remote fear memories, providing precious insights for the treatment of PTSD. In extension, showing how the modulation of epigenetic marks in a cell type and locus-specific manner can impact neuronal function and memory capacity will represent a major step forward for the entire field of molecular neuroscience.
2020 -
Long-Term Fellowships - LTF

Investigation of the rules governing plasma cell transition between short and long-lived states

DE CARVALHO Renan (BRAZIL)

Laboratory of Lymphocyte Dynamics - The Rockefeller University - New York - USA

VICTORA Gabriel (Host supervisor)
Long-lived plasma cells (LLPCs) produce durable antibodies against a wide variety of pathogens, and are associated with long-lasting immune protection. LLPCs arise from T cell-dependent structures in secondary lymphoid organs known as germinal centers, whereby naïve B lymphocytes undergo rapid proliferation and mutate their Immunoglobulin genes. Cells that successfully generate high-affinity antibodies are selected to live, becoming either memory B cells or plasma cells (PCs), which in turn give rise to two main populations: short-lived plasma cells (SLPCs) and LLPCs. SLPCs are found in secondary lymphoid organs, bone marrow and mucosal tissues, where they eventually become LLPCs. Despite the importance of this cell type for protective responses throughout life, the factors driving each PC population is not fully understood. Moreover, a still unaddressed question in the field is why only a few clones of SLPCs convert into LLPCs, and the mechanisms driving this differentiation. Thus, this project aims to define the rules governing SLPC-LLPC transition. Through the combination of transgenic PC-reporter mice, cutting-edge techniques and tools available in Victora’s Lab, we will be able to specifically track SLPCs and LLPCs, providing important clues about their specific niches, clonal composition and patterns of gene expression. Taken together, the innovative approaches presented in the current proposal will faithfully address unsolved mysteries about the biology and dynamics of plasma cells, generating knowledge that will help to better understand the mechanisms driving tissue homeostasis, effective humoral responses and the development of better vaccine-based strategies.
2020 -
Long-Term Fellowships - LTF

Molecular and physical mechanisms of gamete binding and fusion in zebrafish

DENEKE Victoria (EL SALVADOR)

- Research Institute of Molecular Pathology - Vienna - AUSTRIA

PAULI Andrea (Host supervisor)
Fertilization is a dynamic process that involves the approach, binding and fusion of haploid gametes, the sperm and the egg. To date, only three proteins have been shown to be essential for fertilization in vertebrates: Izumo1, Juno, and CD9. In mammals, the binding of Izumo1 and Juno mediates sperm and egg interaction, yet many key regulators of fertilization have likely been missed, possibly due to redundant functions, since this process involves the coordination of multiple proteins. Therefore, it is instrumental to apply new tools to uncover new molecular regulators of fertilization. I propose to use a multifaceted approach that includes subcellular proteomics, quantitative in vivo imaging and genetics to gain a comprehensive understanding of the dynamics and molecular mechanisms regulating fertilization. Such approaches are technically challenging in the mammalian system, where fertilization occurs internally and access to a large number of eggs is limited. The zebrafish model provides many advantages for fertilization studies, since fertilization occurs externally, and many eggs and sperm can be collected from adults for proteomic studies. High resolution imaging studies are facilitated in the zebrafish (Danio rerio) system due to the presence of the micropyle, the single sperm entry site in the zebrafish egg. These features result in the ability to address long-standing questions in the field with emergent methodologies that will provide a new mechanistic and biophysical understanding of gamete binding and fusion.
2020 -
Long-Term Fellowships - LTF

From vision to camouflage: behavioural computations in the cuttlefish

EVANS Dominic (UK)

- Max Planck Institute for Brain Research - Frankfurt am Main - GERMANY

LAURENT Gilles (Host supervisor)
Understanding how vision guides behavior is a key goal of neural systems research. This project will use long-term behavioral assays and electrophysiology to investigate the perceptual rules and neural dynamics underlying camouflage behavior in the cuttlefish – an animal which uses vision and neural control of skin patterning to ‘match’ itself to the background visual scene. As the cuttlefish skin provides a readout of the animal’s perceptual state, this system presents an unparalleled opportunity to study visual processing and complex motor control in the behaving animal. Using large-scale high-resolution imaging techniques to record and reveal the dynamics of skin ‘pixels’ across the body, I aim to determine the behavioral rules and visuomotor computations that govern camouflage behavior. First, I will map the transformation of visual input into skin pattern output by systematically varying the visual scene of the animal’s home environment during long-term behavioral recordings. This will reveal which statistical properties of visual stimuli are reproduced in skin patterns, at single chromatophore resolution, and how chromatophore motor units are dynamically orchestrated to assume these patterns. Next, I will investigate the neural mechanisms of pattern generation using ex vivo electrophysiology in the pathway purported to control this behavior. I am convinced that the study of visually-guided body patterning behavior will yield fundamental principles of visual perception and complex sensorimotor processes in general.
2020 -
Long-Term Fellowships - LTF

Structural and biochemical investigation of Xist-mediated X-chromosome inactivation

KUMAR Ananthanarayanan (INDIA)

Department of Molecular, Cellular and Developmental Biology - Yale University - New Haven - USA

PYLE Anna Marie (Host supervisor)
The majority of the human transcriptome encodes non-coding RNAs that are not translated into protein. Long ncRNAs (LncRNAs) are 200 nucleotides or longer, and are involved in many cellular processes, including embryogenesis and DNA damage repair. Xist is an evolutionarily conserved LncRNA that plays a key role in dosage compensation in eutherian females. It does so by recruiting protein complexes that deposit repressive marks on histones on one X chromosome (XC), thereby leading to heterochromatin formation. Recent computational and biophysical studies suggest that Xist, as well as other LncRNAs, adopt higher order tertiary structures similar to ribozymes and group-II introns. Nonetheless, no high-resolution 3-D structures of Xist and its associated protein complexes have been determined. Thus, the precise molecular mechanism of XC inactivation remains unclear. In this proposal, I aim to biochemically identify and reconstitute Xist ribonucleoprotein (RNP) complexes involved in spreading and silencing of the XC. I will then determine the 3-D structures of Xist-protein complexes using a combination of electron cryomicroscopy and X-ray crystallography. In combination with biochemical and biophysical assays, I will characterize the native proteome associated with Xist, as well as the contributions of Xist tertiary structure towards recruitment of protein machineries including the polycomb complexes. These studies aim to elucidate molecular mechanisms of how Xist carries out gene silencing of the XC.
2020 -
Long-Term Fellowships - LTF

Deciphering the functions and mechanisms of brain-wide motor representations

LEV Itamar (ISRAEL)

Department for Neurobiology - University of Vienna - Vienna - AUSTRIA

ZIMMER Manuel (Host supervisor)
Brain-wide representations of ongoing behavior were recently observed in neuronal activity patterns measured form various organisms such as worms, flies, and mice. Surprisingly, also primary sensory areas, like the V1 visual cortex in mice, previously thought to exclusively represent sensory information are also strongly modulated by behavioral variables like running speed. While this phenomenon seems to be prevalent, its functions and underlying neuronal mechanisms are elusive. I hypothesize that motor commands are integral components of sensorimotor transformations. Like others have suggested for the V1 area, I propose that this sensorimotor integration allows behavior-dependent sensory gain control, and more speculatively also involves predictive coding, i.e. that perception is tuned to unexpected outcomes of the animal's explorative movements. To address these hypotheses, I will use the tractable model organism C. elegans which is amendable to the cutting-edge whole-brain calcium imaging technology. I will develop new whole-brain imaging assays in freely-moving worms. I will then use these assays to search for gain-control circuits where the sensitivity of sensory neurons is modulated by different behavioral states. I will also look for predictive-coding circuits involving error-coding neurons, sensitive to unexpected stimuli. To study the behavioral relevance of these mechanisms, e.g. during navigation, I will interfere with the neuronal activity of the relevant circuits via optogenetics and other transgenic inhibition tools. Therefore, by combining these different approaches I aim to uncover generalizable functions and mechanisms of brain-wide motor representations.