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2019 -
Long-Term Fellowships - LTF

Evolutionary genetics of stomata-related climate change-adaptation through space and time

LANG Patricia (GERMANY)

Department of Biology - Stanford University - Stanford - USA

BERGMANN Dominique (Host supervisor)

Adaptation to climate change, particularly to increasing temperatures, is vital to plant survival. Stomata are the gatekeepers of plant gas exchange, balancing CO2 uptake and water vapor release, and hence obvious targets for climate change adaptation. However, while stomata formation is well characterized on the molecular level, little is known about the variation of core stomata genes across climatic gradients, and variation through time has not been investigated at all.
The central goals of this proposal are to (i) characterize the last ~200 years of stomata variation, from the start of the industrial revolution to today, in preserved historical European Arabidopsis thaliana individuals from herbaria. Combined stomata imaging of historical specimens with herbarium genomics will reveal how populations changed genetically and whether the historic stomatal changes have a genetic basis. I will then (ii) determine the temporal genetic variation in the known core stomata genes, and identify coinciding genetic variation across temporal-climatic and spatial environmental-climatic clines. Finally, I will (iii) infer expression of core stomata pathway genes (including transcriptional regulators and intercellular signaling genes) across historical timescales and determine the role of changing gene expression in stomatal adaptation, using published transcriptome data.
This work will reveal how a wild, non-domesticated plant copes with anthropogenic climate change, from historical trends to genetic mechanisms. It will provide the basis to predict future trends not only in a model weed, but also other plant species.

2019 -
Long-Term Fellowships - LTF

Mechanisms of electron transport chain supercomplex assembly during ER and nutrient stress

LATORRE-MURO Pedro (SPAIN)

Department of Cancer Biology - Dana-Farber Cancer Institute - Boston - USA

PUIGSERVER Pere (Host supervisor)

Endoplasmic reticulum (ER) stress and unfolded protein response are energetically challenging under glucose deprivation due to a decrease in glycolytic rates and protein glycosylation. Under these conditions mitochondrial respiration and oxidative phosphorylation (OXPHOS) are necessary for survival, however the mechanisms whereby these energetic requirements are regulated are unknown. This mitochondrial bioenergetic response is impaired in human mitochondrial diseases. The existence of respiratory chain supercomplexes (SC) and their organization in cells has been subject of debate for decades arising the fluid and solid-state models. To date, the function, structure and organization of SC are poorly understood. Preliminary data show that the PERK-eIF2a axis promotes SC assembly and increases OXPHOS activity. However, the mechanisms that link PERK activation and SC assembly are not known. Thus, the major goal of this application is to identify the mechanisms and molecular interactions that allow SC assembly in cells under ER stress conditions through the PERK-eIF2a axis using different in-vitro and in-vivo approaches: 1. Identification of the components that control ER and nutrient-dependent stress SC assembly through the PERK-eIF2a axis. 2. Determination of cristae architecture on SC assembly during ER stress. 3. Bioenergetic rescue of PERK activation in complex I defective mice. Outcomes from this application will provide information on the mechanisms that allow ER and nutrient stress-dependent SC assembly and electron transport chain activity with implications for the development of therapies for mitochondrial disorders.

2019 -
Grant Awardees - Program Grants

Do hydrocarbons induce membrane curvature in photosynthetic organisms?

LEA-SMITH David (UK)

School of Biological Sciences - University of East Anglia - Norwich - UK

CES Oscar (SPAIN)

Dept. of Chemistry - Imperial College London - London - UK

SHARP Melissa (DENMARK)

Instrument Division - European Spallation Source ERIC - Lund - SWEDEN

ALLISON Jane (NEW ZEALAND)

School of Biological Sciences - University of Auckland - Auckland - NEW ZEALAND

The cell membrane is a double layer of lipid molecules. It plays a critical role in protecting the cell from its environment and in separating the different processes that take place within its interior. Membranes must change their shape in order for the cell to function, especially during cell division, and this depends on membrane curvature. At present, cells are only known to induce curvature by accumulating lipids in one of the layers or using specialised proteins. Our goal is to investigate a new mechanism of inducing membrane curvature by accumulation of hydrocarbons in the middle of the lipid layers that has not been observed before in nature.
These hydrocarbons are like the components of diesel fuel, and are found in photosynthetic cyanobacteria and algae – some of the most abundant and widespread organisms on Earth. Production of hydrocarbons in cyanobacteria or other microbes could substitute for liquid fuels derived from petroleum. As well, cyanobacteria and algae release hydrocarbons into the environment, where they are degraded by other bacteria that clean up oil spills. However despite their environmental and biotechnological importance, the exact cellular role of hydrocarbons has not been determined.
We recently discovered that hydrocarbons are essential for maintaining optimal cell size, growth and division, processes that require cell membranes to curve and bend, and found that cells lacking hydrocarbons have lipid membranes that are less curved or flexible. We showed that hydrocarbons integrate into the cell membranes, and used computer simulations to predict that this induces membrane curvature. To investigate this further, we have assembled a team of scientists from the UK, Sweden and New Zealand. By combining our different skills, we will analyse how hydrocarbons affect the physical properties of algal and cyanobacterial membranes by 1) running computer simulations; 2) studying membranes purified from algae and cyanobacteria; and 3) carrying out experiments on live cells. Together, these simulations and experiments will allow us to explore and quantify how hydrocarbons affect curvature and other membrane properties, and so conclusively establish the role of hydrocarbons in cells. As well as improving our understanding of biology, this information will assist the use of microbes for biofuel production and oil spill cleanup.

2019 -
Long-Term Fellowships - LTF

Evolution of functional organization of the eukaryotic genome

LEE Junmo (KOREA, REPUBLIC OF (SOUTH KOREA))

- Gregor Mendel Institute of Molecular Plant Biology - Vienna - AUSTRIA

BERGER Frederic (Host supervisor)

Genomic DNA is packaged by nucleosomes assembling the four core histone components (H3, H4, H2A and H2B). Histone modifications and DNA methylations regulate specific transcriptional states in the genome, and play important roles in various cellular processes of eukaryotes. The four core histones share characteristics with the common ancestor of eukaryotes and Archaea. In eukaryotes, the primitive histones diverged as histone variants that are associated with histone modifications and DNA methylations to form functional chromatin states. In eukaryotes, chromatin states have been studied only in model species from the later diverging branches of the evolutionary tree and we know very little of their evolutionary origins. Photosynthetic eukaryotes (Archaeplastida) are the result of a primary endosymbiotic event involving a cyanobacterium that occurred ca. 1.9 Bya. Chromatin has been well studied in land plants that, in evolutionary terms, have diverged more recently (ca. 500 Mya), whereas studies are wholly lacking from their sister lineages in the Archaeplastida (i.e., glaucophyte algae containing blue-green plastids and the red algae). To understand the origin of ancestral chromatin states in photosynthetic eukaryotes, this project will elucidate ancestral chromatin states in several species of glaucophyte and red algae. This study will trace the evolutionary trajectory of chromatin organization into functional units from its archaeal origin to photosynthetic eukaryotes. The models used to dissect the evolution of chromatin states will provide platforms to study other deep branching lineages within the eukaryotic tree of life.

2019 -
Long-Term Fellowships - LTF

Functional characterization of host-microbiome interactions in a tissue-engineered mini-gut

LI Hsin-Jung (CHINA, REPUBLIC OF (TAIWAN))

Global Health Institute - EPFL - Lausanne - SWITZERLAND

PERSAT Alexandre (Host supervisor)
LUTOLF Matthias (Host supervisor)

The gut microbiome plays a critical role in human health. For example, the commensal bacterium Akkermansia muciniphila is associated with health benefits against metabolic disorders and obesity. However, clear mechanistic understanding of host-microbe interactions is lacking due to the limitations of animal models and existing in vitro systems. In vivo measurements do not capture key physiological features such as bacterial colonization dynamics and spatial organization of mucosal biofilms. In addition, no method exists for reproducing human epithelial physiology for systematic visualization of the microbiota in vitro. I propose to address these challenges by developing a micro-physiological in vitro platform based on tube-shaped gut organoids generated from primary stem cells, and perform functional and dynamic studies of microbiota down to the single cell level. I will optimize the physicochemical conditions within these engineered mini-gut organoids to facilitate stable microbiota colonization to ultimately culture defined bacterial consortia and arbitrary human microbiota. Finally, I will investigate the molecular pathways of how A. muciniphila affects host physiology and pathogen infection using imaging, spatially-resolved transcriptomics and biophysical measurements. I expect that the mini-guts will fill a crucial technological gap in microbiome studies, contributing to our understanding of the principles and regulations of bacterial colonization and host-microbe interactions, and enabling potential future clinical intervention and manipulation.

2019 -
Long-Term Fellowships - LTF

The molecular and cellular mechanisms underlying the sense of balance in Drosophila melanogaster

LI Kai (CHINA, PEOPLE'S REPUBLIC OF)

Department of Physiology - UC San Francisco - San Francisco - USA

JAN Yuh Nung (Host supervisor)

Sense of balance is an equilibrium reflex that relies on feedback from sensory organs to perform body posture adjustments. Maintaining proper balance is vital for animal movement. However, the molecular and cellular mechanisms of the sensory inputs in the equilibrium reflex are not well understood. The Drosophila possesses a mechanosensitive balance organ, the haltere, which detects the angular velocity-dependent force (Coriolis force) generated when the body rotates during flight. The halteres provide sensory information about rotations in three dimensions to guide the adjustments of body positions, an attractive system to dissect the mechanism underlying sensory processing in the balance control. Taking advantage of the powerful genetic tools and behavioral assays in Drosophila, I aim to identify the molecular components essential for mechanotransduction in haltere and study their functional roles in the sense of balance. I will also genetically label subpopulations of sensory neurons in halteres and characterize their coding properties in response to body rotations in different dimensions. This study should provide a basis for a molecular and cellular dissection of how balance information is detected and encoded when animals move in three-dimensional space.

2019 -
Career Development Awards

Neuronal processing of social information in freely behaving animals

LI Ying (CHINA, PEOPLE'S REPUBLIC OF)

- Chinese Institute for Brain Research - Beijing - CHINA, PEOPLE'S REPUBLIC OF

A primary goal in neuroscience is to understand how the nervous system interprets salient information from the external world and generate appropriate behaviors. Across the animal kingdom, animals respond to sensory cues emitted by conspecifics, preys or predators by initiating a repertoire of social behaviors, such as mating, fighting, prey capture, and predator avoidance. Although these behaviors are driven mainly by genetically pre-programmed instinctive circuits, they are also profoundly regulated by the animal’s internal states, suggesting an adaptive modulatory regulation of the underlying circuits. In rodents, the processing of chemical cues plays a crucial role in orchestrating essential instinctive social responses. The vomeronasal pathway, in particular, has been shown to generate sex-specific instinctive behavioral responses. Unraveling the neural mechanism underlying the processing of social cues through successive stages of the vomeronasal pathway will provide unique insights into the internal representation of social information in the brain. In primates, social behavior relies strongly upon visual and acoustic communication and, in contrast to rodents, depends minimal on chemical signaling. Studying social behaviors in primates will provide complementary insights into the neurobiology of social behaviors and emotional reactions more relate to that in humans. The marmoset, owing to its enriched social behaviors, is emerging as an ideal model for studying the neural substrates of primate social behaviors. In the long-term, we are interested in studying how the marmoset brain extracts social meaning from the environment and generate different social behaviors.

2019 -
Long-Term Fellowships - LTF

Genome-wide search for essential noncoding elements using Cpf1 tiling deletion screen

LISCOVITCH-BRAUER Noa (ISRAEL)

- New York Genome Center - New York - USA

SANJANA Neville (Host supervisor)

A major challenge of genomics has been to characterize all functional elements in the human noncoding genome, which generally lack appropriate methodologies to perturb them and measure the impact of the perturbation. Recently, CRISPR-based genome editing technologies opened new possibilities to probe noncoding regions of the genome. The easy programmability of CRISPR using short RNA guides enabled the development of high-throughput pooled CRISPR libraries for functional screens that can probe noncoding regions. However, the scale of these screens is not enough to target the entire human noncoding genome, which constitute more than 98% of the genome. Thus, a different approach is needed to engineer genome-scaled CRISPR screens over the entire noncoding genome.

We propose to develop an approach where entire chromosomes will be comprehensively screened for essential noncoding elements using tiled, overlapping deletions, generated by Cpf1 with a dual-guide delivery system. To pinpoint the genes and mechanisms through which the noncoding regions affect cell growth, we will develop a coupled deletion-single cell RNA sequencing approach which will link changes in gene expression with each deletion. This method will allow us to map essential noncoding elements at chromosome- or genome-scale and then, for these elements, map the genetic mechanisms they use to manipulate cell proliferation. Our whole genome functional noncoding screen is expected to identify many new regulatory genomic regions, with the long-term goal to create a truly genome-wide atlas of all noncoding elements that impact cell growth and to identify the genes that they modulate.

2019 -
Career Development Awards

Neural mechanisms of vocal production control in echolocating bats

LUO Jinhong (CHINA, PEOPLE'S REPUBLIC OF)

School of Life Science - Central China Normal University - Wuhan - CHINA, PEOPLE'S REPUBLIC OF

Vocal production control, i.e. the adjustments in the timing and the spectro-temporal features of vocalizations, is fundamental to acoustic communication, including human speech. Many species of bats demonstrate the capability for precise vocal production control, raising the intriguing possibility that this animal model can yield valuable insights to the mechanisms of human speech. In this project, I propose to study the neural circuits underlying echolocation call control in freely behaving bats (Hipposideros armiger), with an integrative approach which draws upon behavioral, neurophysiological, and modeling methods. At the subcortical level, we will make extracellular neural recordings from the midbrain inferior colliculus of the auditory pathway and the midbrain periaqueductal grey of the vocal-motor pathway. These experiments will be carried out using a pendulum setup which evokes dynamic adjustments in the bat’s call production features. At the cortical level, we will make extracellular neural recordings from the motor and prefrontal cortices when individual bats are trained to perform various vocal matching tasks from a hanging stand. For both behavioral setups, two types of the auditory feedback perturbations will be introduced to study the neural mechanisms for audio-vocal integration. The auditory feedback perturbations include a Lombard condition, in which the bat listens to signals embedded in white noise, and a frequency-shift condition, in which the bat listens to frequency-shifted copies of its echolocation calls. The proposed research will offer critical insights into the brain circuits mediating vocal production control in mammals, including humans.

2019 -
Long-Term Fellowships - LTF

Deciphering the coding strategies underlying the selection of active and passive fear responses

MARTIN FERNANDEZ Mario (SPAIN)

Neurocentre Magendie, INSERM - University of Bordeaux - Bordeaux - FRANCE

HERRY Cyril (Host supervisor)

The recruitment of distinct neuronal populations to generate specific behavioral responses is a fundamental property of the central nervous system. However, understanding how defined neuronal sub-circuits encode different behavioral responses is still a major challenge of modern neuroscience. In this project I aim to elucidate how neuronal populations of the dorsomedial prefrontal cortex (dmPFC) encode the selection of active and passive fear responses. To achieve this goal, I will perform large-scale recordings of spiking and oscillatory activity in the dmPFC during conditions that will trigger either passive or active fear behavior, aiming to identify behavior-specific neuronal populations, assemblies and oscillations and the mechanisms mediating their interaction. Then, I aim to elucidate the projection patterns of the dmPFC neurons involved in active and passive fear and their targets in different brain regions. Finally, I will use optogenetics to manipulate specific neuronal populations in a phase specific manner aiming to reveal temporal encoding of fear behavior. Using these approaches, my goal is to demonstrate the role of specific coding mechanisms governing circuit selection during active and passive fear. This will largely expand our understanding of how particular neuronal circuits are selected based on environmental information and how specific fear coping strategies are coded. Anxiety disorders are a major health problem in western societies. It is estimated that 14% of the European adult population suffers anxiety disorders. Understanding the neural circuits involved in fear behavior will potentially lead to future therapies targeting anxiety disorders.

2019 -
Long-Term Fellowships - LTF

Reconstituting and deciphering the TCR signaling apparatus by DNA nanotechnology

MASUBUCHI Takeya (JAPAN)

Section of Cell and Developmental Biology - UC San Diego - San Diego - USA

HUI Enfu (Host supervisor)

T cells are a type of lymphocyte that are able to recognize and destroy pathogens and tumor cells. The initial step in T cell activation is the binding of the major histocompatibility complex (MHC) presented antigen peptide to the T cell antigen receptor (TCR), which causes Lck mediated phosphorylation of its associated CD3 chains, including a CD3z/CD3z homodimer, a CD3g/CD3e heterodimer, and a CD3d/CD3e heterodimer. It is well established that CD3z/CD3z homodimer recruits ZAP70, a key cytosolic kinase, upon tyrosine phosphorylation. While much research has focused on CD3z, the roles of other CD3 chains are poorly understood. It is not clear why they are needed, what cytosolic proteins they recruit, and why they exist in a well-defined stoichiometry and geometry. To determine the role of the TCR architecture, I propose to assemble CD3 subunits on synthetic lipid bilayers with precisely controlled stoichiometry and inter-subunit distance using DNA nanotechnology. Using our recently developed fluorescence and microscopy readouts, I will dissect how the TCR architecture affects the recruitment of ZAP70 and other T cell signaling proteins. I will begin with a simple membrane reconstitution system to recapitulate each of the three types of CD3 dimerization, and determine their respective effect on signaling. I will then assemble the whole CD3 complex by precisely controlling the organization of CD3 dimers using a DNA scaffold. By exploring the potential geometry reported previously, this highly innovative approach may allow me to uncover the fundamental design principle of the TCR-CD3 complex and provide a mechanistic basis for designing better T cell-based immunotherapies.

2019 -
Long-Term Fellowships - LTF

Investigating collinear bursts of HoxD genes transcription through live imaging of gastruloid body

MAYRAN Alexandre (FRANCE)

ISREC - EPFL - Lausanne - SWITZERLAND

DUBOULE Denis (Host supervisor)

Hox clusters are uniquely regulated, their collinear transcriptional patterns specifies an anterior-posterior axis of mammalian body plans reflecting their order on the genome. Spatio-temporal cues regulates the unique expression of these genes. Genetic disruption of the cluster uncovered multiple levels of cis-regulation. Two enhancer “archipelagos” in gene deserts surrounding the cluster control gene activation. Further, CTCF boundary elements separate the cluster in two TADs that target each archipelago to specific portions of the cluster.
Using transgenic constructs in drosophila embryos, it was shown that transcription occurs by series of bursts. The “static” view provided by classical approaches such as RNAseq or in situ hybridization limits our ability to dissect gene regulation. Thus, the specific contributions of each layer of gene regulation is still poorly understood.
Recently, part of the Duboule laboratory switched to the culture of "gastruloid" from mouse ES cells. These objects fully implement Hox collinear expression, providing a unique access to visualization of gastrulation-like patterning events that are normally obscured by implantation of the mammalian embryo.
I propose to analyse bursting using gastruloids and to follow Hox transcription through live imaging. First, we will assess how spatiotemporal cues regulate bursting at the cellular level. Then, we will dissect the functional consequences on bursting after disruption of the enhancers or loss of boundary elements.
This will provide us with a unique system to uncover mechanistic contributions of enhancer-promoter contact and boundary elements to the unique pattern of Hox gene expression.

2019 -
Career Development Awards

Molecular mechanisms for protein synthesis dependent, long-term memory

MIKUNI Takayasu (JAPAN)

Department of Cellular Neuropathology - Niigata University Brain Research Institute - Niigata - JAPAN

Memory is a fundamental function in animals and humans. Memories can be classified into short-term memory that lasts for minutes to hours, and long-term memory that lasts for hours, days or even a lifetime. Different molecular mechanisms underlie these two types of memory: trafficking and modification of pre-existing proteins are sufficient for short-term memory, while synthesis of new proteins is required for long-term memory. Although the mechanism for short-term memory has been intensively studied, less is known about the mechanism for long-term memory. This is due to the lack of a good method to monitor and manipulate specific synthesized proteins in brain tissue. In this proposal, I aim to understand when, where and how protein synthesis mediates long-term memory in the mouse brain. Toward this aim, I will first develop a high-throughput method to image and control distinct synthesized proteins in brain tissue. For this, I will use my previously established genome editing methods (Cell 2016, Neuron 2017) as well as chemical labeling and optogenetic techniques. Using this method combined with two-photon imaging, electrophysiology and behavioral analysis, I will comprehensively understand the spatio-temporal dynamics and role of a number of newly synthesized proteins in long-lasting synaptic plasticity in vitro as a cellular model of long-term memory, and long-term memory in behaving mice in vivo. My proposed research will provide (1) a new platform to understand the molecular mechanism for various brain processes that depend on protein synthesis, and (2) new insight into the molecular mechanism for long-term memory from synaptic, cellular to systems levels.

2019 -
Long-Term Fellowships - LTF

Exploring the human fetal microbiome and its role in immune system development

MISHRA Archita (INDIA)

Singapore Immunology Network - A*STAR - Singapore - SINGAPORE

GINHOUX Florent (Host supervisor)

Growing evidence on the indispensability of microbiome in human-health suggests human development is intimately linked with microbial-symbiosis. However, when and where human-body encounters its first microbial-species remains elusive. The task of differentiating between the commensal and pathogenic-microbes lies with the immune system and recent reports show that its developmental programming starts quite early during fetal-growth. Advances in the field made the picture more complex, evincing early embryonic origin of tissue-specific immune cells, that are independent of bone marrow. We hypothesize that during fetal-development, selective microbial species may cross the placental-barrier and colonize fetal-tissues where they interact with the tissue-resident immune cells, selectively priming them for future functionality/tonicity. This project will identify the fetal microbial-colonizers in different organs, their spatiotemporal dynamics and crucial interactions with the developing immune-system, in human fetuses. Notably, we will also investigate the fetal brain microbiome and gut-brain axis to capture the role of microbes in defense mechanisms in brain. We will employ single-cell RNA-seq and microbial-genomics to identify unique fetal-determinants that condition the immune-system for establishing tissue-specific microbiome. This could be a key determinant in human immune-system development, with life-long implications for immune-homeostasis, memory and microbial-symbiosis. These investigations will be transformative for research in fetal development, host-pathogen interactions, and immune-modulatory interventions in various aspects of human health and disease.

2019 -
Grant Awardees - Program Grants

Decoding the biomechanics of flight-tone based acoustic communication in mosquitoes

MITTAL Rajat (USA)

Dept. of Mechanical Engineering - Johns Hopkins University - Baltimore - USA

GIBSON Gabriella (USA)

Dept. of Agriculture, Health and Environment - University of Greenwich - London - UK

The aerial courtship “dance” of mosquitoes has fascinated entomologists for over 150 years. This dance involves highly controlled variations in the frequency and intensity of flight-tones (i.e. sounds generated by the flapping wings) with concurrent changes in flight speed and direction, and enables recognition of conspecifics, display of fitness and transmission of mating interest. However, despite over a century and a half of research, significant knowledge gaps continue to exist in our understanding of this behavior. To decipher this courtship dance, entomologists have to integrate acoustic, energetic and flight information for untethered, free-flying mosquitoes, but the tools that can provide these data have, so far, not been available. In the current project, the two investigators combine their respective expertise in computational biomechanics and acoustics, and behavioral entomology, to generate unprecedented data and insights into the biomechanics and physics of courtship-associated acoustic communication in mosquitoes. In particular, by combining computational modeling with biological assays, the team will generate six-dimensional soundscapes of free-flying mosquitoes engaged in courtship and determine how these soundscapes are actively modified during courtship. We will also estimate for the first time, the energetic costs of courtship and mate-chasing, and the potential constraints this places on courtship behavior. Finally, the team will characterize the degree to which, carefully tailored exogenous sounds can alter and even disrupt courtship. The success of this novel approach could be transformative for future research into comparative auditory mechanisms of communication across a wide range of flying insects. In addition, the insights gleaned here could form the scientific foundation for novel insecticidal/surveillance traps and also lead to environmentally friendly strategies for diminishing mating success in mosquito species that are vectors for malaria, Zika fever and other devastating mosquito-borne diseases.

2019 -
Grant Awardees - Program Grants

Unravelling an unusual biomineralization from nano to macro scale using advanced technologies

MOAZEN Mehran (UK)

Dept. of Mechanical Engineering - University College London - London - UK

VICKARYOUS Matthew (CANADA)

Dept. of Biomedical Sciences - University of Guelph - Guelph - CANADA

ABZHANOV Arkhat (USA)

Dept. of Life Sciences - Imperial College London - Ascot - UK

HERREL Anthony (BELGIUM)

Dépt. Adaptations du Vivant - UMR 7179 C.N.R.S/M.N.H.N - Paris - FRANCE

Osteoderms are hard calcified tissues that form within the skin of some animals. They resemble bone, hence the name, but are fundamentally different in several respects. Crocodile and armadillo skin plates, and turtle shells are among the most familiar examples, reportedly forming a protective armour against external predators and aiding locomotion. However, although less visible, osteoderms are also present in many lizards.
In terms of their shape, spatial distribution, and interaction, lizard osteoderms show the highest diversity in the animal kingdom, yet we know little about what drives this extraordinary diversity, how it is controlled, or how it originated. It could be a biproduct of other genetic differences or, more likely, a natural optimization to enhance osteoderm function, protective or otherwise, under conditions specific to each lizard type.
This project brings together a multidisciplinary team of expert engineers, developmental and evolutionary biologists from the UK, Canada and France to investigate the mechanisms underlying the development, patterning, and evolution of osteoderms in lizards. The team will use a range of advanced techniques (e.g. genetic analysis, material testing, imaging, and computer simulations) to investigate lizard osteoderms from the first molecular signalling events and cellular interactions, through to organismal level. Osteoderm mechanical properties will be characterised both as single units and as sheets so as to understand their function during feeding and locomotion.
This is a basic science project focused on a novel biological tissue and its evolutionary implications, but with a systems approach that may shed light on pathological calcifications, as well as aiding the development of biomimetic materials and structures. Most importantly it will train the next generation of scientists, in a multidisciplinary and international setting, providing them with a fundamental knowledge of biological tissues and a diverse skillset with which to address the global challenges of 21st century.

2019 -
Long-Term Fellowships - LTF

Microbiome manipulation by the host: lessons from early-divergent plant immunity

MONTE Isabel (SPAIN)

Department of Plant and Microbial Biology - University of Zurich - Zurich - SWITZERLAND

ZIPFEL Cyril (Host supervisor)

Colonization of land by plants about 450 million years ago was one of the major evolutionary breakthroughs of the history of Earth. During terrestrialization, plants developed sensory systems to detect friends and foes in their new environment. In flowering plants, emerging evidence suggests that the subfamily XII of leucine-rich repeat receptor kinases (LRR-RKs) specialized in the innate immune perception of bacteria. Notably, this subfamily is not present in algae, and likely appeared in the common ancestor of all land plants. The liverwort Marchantia polymorpha has recently emerged as an ideal model plant for evolutionary studies. In this project, I will characterize the Marchantia LRR-RK XII subfamily through a combination of genetics, biochemistry and proteomics. In addition, I will use Marchantia as a tool to assess the impact of innate immune receptors on microbiome dynamics. Microbiome profiling of Swiss Marchantia accessions will be employed to design synthetic bacterial communities (SynCom). Inoculation of immunity-related Marchantia mutants with SynCom followed by phenotypic characterization and microbiome profiling will demonstrate how host immunity modulates bacterial populations. I will thus unveil the molecular basis of innate immunity against bacteria in early-divergent land plants and provide insights into the evolution of plant immunity, and more generally in RK signalling in land plants. The conclusions of this work will ultimately expand our knowledge on the evolution of plant innate immunity as well as on the interplay between plants and their microbiomes.

2019 -
Grant Awardees - Program Grants

Imaging viral RNA genome assembly with high spatial and temporal resolutions inside infected cells

NAFFAKH Nadia (FRANCE)

Dept. of Virology - Institut Pasteur - Paris - FRANCE

CISSE Ibrahim (NIGER)

Dept. of Physics - Massachusetts Institute of Technology - Cambridge - USA

FONTANA Juan (SPAIN)

Faculty of Biology and Astbury Centre for Structural Molecular Biology - University of Leeds - Leeds - UK

Sporadically, novel and potentially devastating pandemic influenza A viruses (IAVs) are generated through genome reassortment between human and animal co-infecting IAVs. Such pandemic viruses emerge as a consequence of the segmentation of IAVs genome into a bundle made of 8 distinct viral RNAs (vRNAs). However the molecular mechanisms of vRNA intracellular transport and assembly into vRNAs bundles, which are critical for reassortment, remain largely unknown. Our project aims to elucidate these fundamental aspects of IAV life cycle by developing innovative approaches.
We challenge the original model that newly synthesized vRNAs, in the form of viral ribonucleoproteins (vRNPs), are transported across the cytoplasm on Rab11-dependent recycling endosomes. Based on our recent work, we hypothesize that the concomitant transport and assembly of vRNPs is driven by their physical association with remodelled endoplasmic reticulum (ER) membranes and Rab11-dependent transport vesicles distinct from recycling endosomes.
We will set up a cellular system which resembles the natural respiratory tissue targeted by IAVs, while being amenable to simultaneous imaging of the endogenous Rab11 protein and tagged vRNAs. We will develop two cutting-edge and complementary imaging methods: dual-color single molecule fluorescence in situ hybridization (FISH) in live cells for the tracking of distinct vRNAs that diffuse concomitantly, and cryo-Focused Ion Beam combined with electron microscopy in situ hybridization (EMISH) to image individual vRNPs and their transport vesicles at molecular resolution. We will further assess the role of cellular ER-shaping proteins by performing CRISPR/Cas9-mediated knockdowns, and by monitoring changes in the viral-induced remodelling of ER and biogenesis of vRNP transport vesicles by live fluorescence imaging and cellular EM.
The proposed research will require the very close collaboration between three partners with distinct but complementary expertise. The approaches developed jointly are poised to revolutionize our understanding of IAV multi-RNA genome transport and bundling, and thus help in the broader goal of achieving better prevention and treatment of influenza disease. Additionally, the proposed technical developments in live cell FISH and cellular EM, will have impact on other fields of studies well beyond the scope of the proposed project.

2019 -
Grant Awardees - Young Investigator Grants

From self-reproduction to evolution in the RNA world

NGHE Philippe (FRANCE)

Laboratoire de Biochimie - ESPCI - Paris - FRANCE

HAYDEN Eric (USA)

Dept. of Biological Sciences - Boise State University - Boise - USA

SMERLAK Matteo (FRANCE)

Group Structure of Evolution - Max Planck Institute for Mathematics in the Sciences - Leipzig - GERMANY

RAMESH Arati (INDIA)

Dept. of Biochemistry Biophysics and Bioinformatics - National Center for Biological Sciences - Bangalore - INDIA

Is evolution possible in the absence of template-based replication?
Evolution, in life as we know it, relies on the copying of DNA with errors, providing the basis of reproduction with heredity and variation. Likewise, in the hypothetical RNA world, copying of RNA with errors is thought to have played the same role. However, the high complexity of RNA polymerases suggests that replication must have been preceded by reproduction and evolution based on simpler catalysts. Reproduction can occur by autocatalytic synthesis of single ribozyme species from RNA fragments, or by collective autocatalysis of multiple ribozyme species, all denoted AutoCatalytic Systems (ACS). For ACS to evolve in an open-ended way, theory indicates that there must exist a large diversity of such ACS throughout the sequence space. Further conditions for evolution are that ACS must amplify within compartments (enabling reproduction with heredity), propagate to other compartments as a function of their differential amplification (selection), and that rare events trigger the appearance of novel ACS (variation).
We aim to test the hypothesis that RNA reproduction based on ACS is widespread in the sequence space, and from this diversity, demonstrate that evolution in ACS is indeed possible.
For this, we will generate a large landscape of self-reproducing molecules using the natural group I intron family as an input for statistical inference methods. Self-reproducers will be constructed by fragmentation of these ribozymes by generalizing the strategy formerly applied to a ribozyme from the Azoarcus bacterium, and developing innovative in vitro screening methods with droplet microfluidics. We will show how the autocatalytic dynamics of individual self-reproducers, and their propensity to catalyse the formation of other self-reproducers or self-reproducing networks, allow to implement the properties of reproduction with heredity and variation underlying evolution.
Evolution will be tested in bulk and in compartmentalized populations, by submitting ACS to cycles of incubation and propagation. Finally, the probability of emergence of evolution in ACS and its open-ended character will be assessed based on the density of functional reproducers and their evolutionary accessibility in the sequence space.

2019 -
Long-Term Fellowships - LTF

The neuronal and genetic regulation of sleep and arousal in zebrafish

NICHOLS Annika (AUSTRALIA)

Biozentrum - University of Basel - Basel - SWITZERLAND

SCHIER Alexander (Host supervisor)

Humans spend approximately one third of their lives asleep, but the genetic and neural circuits underlying this state are poorly understood. Sleep and wake are two disparate physiological and neural states. Therefore, arousing- and sleep-promoting circuits must interact to ensure that the correct state is efficiently established and maintained. To better understand sleep and arousal regulation in vertebrates, I will use two approaches to identify circuits and genes underlying these processes in zebrafish.

Aim 1: Restless leg syndrome (RLS) is a sensorimotor disorder that causes leg movements especially during periods of rest or sleep and is a leading cause of insomnia. Genes linked to RLS provide an entry point into the circuits that promote arousal and disrupt sleep. Zebrafish homolog knockouts of the RLS-linked genes Meis1 and Skor1 induce hyperactivity and sleep fragmentation. I will identify what circuit changes underlie these phenotypes.

Aim 2: I will develop a novel and non-invasive neuronal activity recording system to identify sleep- or wake-active cells. This system will convert neuronal activity into patterns of CRISPR/Cas9-mediated editing of a DNA barcode during inducible time windows. I will combine single-cell RNA-sequencing and activity recording to identify neurons that regulate sleep and wake.

Together, these aims will identify sleep and arousal circuits and provide the foundation for my long-term goal of understanding how sleep and wake states are generated and maintained.