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2023 -
Long-Term Fellowships - LTF

Deciphering the Role of Outer Radial Glia in Autism

AHMED Mai (.)

. - The Hospital for Sick Children - Toronto - CANADA

YUN Li (Host supervisor)
Autism Spectrum Disorder (ASD) is a devastating neurodevelopmental disorder that causes deficits in social interaction and behavior. To date, 1031 genes are linked to ASD, suggesting its strong genetic background. However, how perturbations in these genes contribute to ASD pathology at the cellular and molecular levels remains largely elusive. Outer radial glia (oRG) are a recently identified population of neural stem cells that is highly enriched in the brains of humans and higher primates. oRG generate the majority of human cortical neurons and contribute to cortical expansion and folding. In this project, we hypothesize that oRG are involved in the pathology of ASD based on several observations. The brains of ASD patients during early development show altered growth and folding, which suggests possible defects in oRG proliferation or differentiation. In addition, a study published by the Li lab found that a mutation in a known ASD gene led to increased proliferation of oRG. Here, I aim to employ CRISPR-based knockout screens to investigate the role of oRG in ASD pathology using human pluripotent stem cell (hPSC)-derived oRG in 2D neural cultures and 3D brain organoids. To realize my aim, I will perform CRISPR screens in arrayed and pooled formats to determine which ASD gene knockouts perturb oRG at both the functional and transcriptomic levels. Based on the results of the screens, I will select high-potential ASD genes that induced significant changes in oRG. Then, I will generate 3D cortical organoids from stable CRISPR knockout hPSC lines and examine in detail how ASD gene disruption affects oRG dynamic behavior, oRG-derived neuronal populations, and organoid development. By leveraging human stem cell models, together with the recent advances in CRISPR screens and single-cell transcriptomics, the proposed study provides a targeted large-scale approach to fill a current gap in our knowledge on the role of oRG in ASD pathology. On a global scale, my study will shed light on the different gene networks that converge within oRG for ASD pathology, which is expected to pave the road for potential biomarkers and therapeutic targets that can improve disease outcomes in ASD patients.
2023 -
Long-Term Fellowships - LTF

Profiling tumor proteolysis with genetically-encoded signaling integrators

ALGOV Itay (.)

. - Dana-Farber Cancer Institute - Boston - United States

XIN Zhou (Host supervisor)
Elevated extracellular protease activity is a hallmark of cancer, known to play an important role in shedding and activating receptors and remodeling the extracellular matrix. Technologies that allow us to understand the complexity, dynamics, and heterogeneity of extracellular proteolysis would significantly advance our understanding of how proteases impact tumor growth and metastasis, and inform how we could harness elevated proteolysis to design safer cancer drugs. It remains difficult to characterize tumor microenvironment protease activities with current molecular tools. RNAseq can determine intracellular transcript levels but doesn’t report protease activities or extracellular proteolysis. Protease sensors, such as genetically encoded reporters or small molecule probes, only allow testing of one substrate sequence at a time, which prevents us from a systematic understanding of the proteolysis landscape. To break the technology barrier for a deeper understanding of the protease activities in the tumor microenvironment, I propose to develop proteolysis signaling integrators (PSIs) that can transform a proteolysis event into a transcriptional event within a defined time window. I have designed two systems for the PSIs. The first is based on leucine zippers, alpha-helical dimerization motifs found in transcription factors. The second one is based on Protease-Activated Receptors (PARs), G protein-coupled receptors activated by proteases. In both systems, I have designed to couple a proteolysis event of a substrate sequence to release a Gal4 transcription factor (TF). The design of PSIs is modular so that a large library of substrates can be encoded and tested simultaneously. A small-molecule controllable destabilizing domain (ddDomain) will be incorporated into a PSI to control the time of expression. Tumor cells engineered to express the library of PSIs will be implanted in mice and activated for expression after the tumor grows to a specific size. If a proteolysis event happens, the Gal4 TF will drive transcription of an enhanced green fluorescent protein (EGFP), resulting in a quantitative signal of the proteolytic events. Following isolation of the tumor, cells with low, medium, and high EGFP signals will be separated and sequenced to determine the propensity of proteolysis for different substrate sequences. The development of PSIs has the potential to transform how we characterize extracellular protease activities, and the gained knowledge will inform the development of a new generation of protease-based prodrugs.
2023 -
Grant Awardees - Program

Bacterial targeting of the host epitranscriptome

ALLAIN Frédéric (.)

Swiss Federal Institute of Technology in Zurich (ETH Zurich/ETH Zürich) - . - .

HARTLAND Elizabeth (.)

Monash University - Clayton - AUSTRALIA

HELM Mark (.)

Johannes Gutenberg University of Mainz - . - .

The post-transcriptional processing and modification of cellular RNA provides an additional level of gene regulation that is known as the epitranscriptome. However, despite current knowledge of RNA modifications, the functional significance of many epitranscriptomic changes within the cell is unknown. Here we will explore the impact of bacterial infection on the host epitranscriptome using methods to identify the direct and specific modification of host RNA by bacterial pathogens. Many host-interacting bacteria use specialised protein secretion systems to inject “effector” proteins into eukaryotic cells that target various cellular processes to promote bacterial survival. Although many bacterial effector proteins are known to mediate post-translational modifications of host proteins, effectors that directly modify host RNA and alter the epitranscriptome have not been described. We hypothesise that host-interacting bacteria harbour undiscovered RNA-binding effector proteins that post-transcriptionally target eukaryotic RNA with novel modifications. Such RNA modifying effectors would offer the potential to investigate the significance of RNA modifications in host cell responses and functional biology. The specific aims are to: 1. Discover bacterial effector proteins that bind eukaryotic host RNA during infection using Legionella species as model intracellular bacteria by performing RNA-interactome capture (RIC) from host cell RNA. Epitope tagged RNA-binding effector proteins will then be used for cross-linking RNA immunoprecipitation (CLIP) of host RNA to identify RNA modifications using liquid-chromatography and mass spectrometry (LC-MS). 2. Define the host RNA targets of bacterial effectors and explore the structural basis of effector mediated RNA modifications using epitranscriptomics. Large-scale expression and purification of bacterial RNA-binding effectors with identified consensus RNA-modification motifs will be used for structural analysis of RNA-protein complexes. 3. Investigate the impact of effector-mediated host RNA modifications on the cellular response to infection by assessing bacterial mutant strains for intracellular replication defects and changes in host transcriptional responses to infection. The biodynamics of RNA-binding effectors and their modified host RNAs will be explored in vitro using novel liquid-liquid phase separation (LLPS).
2023 -
Long-Term Fellowships - LTF

Investigating the cell-matrix mechano-chemical feedback loops as determinants of tissue fate

ALLANKI Srinivas (.)

. - The Francis Crick Institute Ltd - London - United Kingdom

ERIK Sahai (Host supervisor)
Emergent tissue architecture is orchestrated by the mechano-chemical feedback interactions among the cellular and extracellular components, across scales. While the biochemical principles of tissue organization have been well studied, the mechanical and biophysical aspects remain less well understood. In a homeostatic tissue, the constituent cells both deposit and maintain the extracellular matrix (ECM), thereby determining tissue mechanics, and are responsive to the mechanical properties of the ECM. An imbalance in these processes can lead to pathologies such as fibrosis and cancer. Hence, remodeling the spatial and biochemical interactions of cells and the ECM can decide the tissue fate in between health and disease. Moreover, physiological aging is associated with changes in tissue structure and mechanics, which may relate to the development of pathologies. However, a holistic view on the in vivo principles governing tissue fate as a function of the complex feedback loops among cell types, cell states, ECM, and tissue mechanics is yet to be defined. I hypothesize that mechanical heterogeneity within the homeostatic tissue leads to the formation of stiffness-dependent cell states, which prime the cells in stiff regions to disease. Hence, the aims are – 1) to characterize the in vivo spatial arrangement of various cell types and their respective transcriptional states as a function of the surrounding ECM and tissue mechanics, and 2) to identify specific cell-matrix feedback loops that define the tissue fate. Using the homeostatic and fibrotic murine skin as models of health and disease, I will spatio-temporally map their mechano-chemical properties by combining mechanical mapping (nano-indentation) with high-resolution spatial matrisomics (imaging mass cytometry) and transcriptomics (Stereo-seq). With these data, I will uncover the spatio-temporal correlations among tissue mechanics, topology, and biochemical properties, including cellular composition, arrangement, and their transcriptomes, as well as the ECM alignment and stiffness. Next, to determine the causality of these correlations, I will manipulate the cell-matrix loops in silico using agent-based modelling and in vitro using co-cultures with stiff vs. soft matrix-generating fibroblasts. I will then systematically test these theories by using 4D live imaging coupled with nano-indentation in tissue explants. The shortlisted feedback loops will be manipulated in vivo in the homeostatic tissue using mosaic expression systems and gene-level perturbations (Perturb-seq) and assayed for the tissue fate. Finally, I will test whether these cell-matrix loops are conserved in human pathologies, including skin cancer/fibrosis. Altogether, this project will provide a comprehensive understanding of disease emergence and how local mechano-chemical feedback loops orchestrate the macroscopic tissue fate in space and time, and opens new avenues for generating preventive therapeutics.
2023 -
Grant Awardees - Early Career

Encoding motion in an interface: the shape-morphing armored skin of pufferfish

AMINI Shahrouz (.)

Max Planck Institute of Colloids and Interfaces (Max-Planck-Institut für Kolloid- und Grenzflächenforschung) - Potsdam - GERMANY

CAMP Ariel (.)

University of Liverpool - . - .


University of Southern Denmark (Syddansk Universitet, SDU) - . - .

Spiny pufferfishes, e.g., porcupinefish, defend themselves by transforming from a streamlined torpedo to a large, prickly sphere. This dramatic yet reversible shape morphing is achieved by highly mineralized hard spines anchored to a very extensible soft skin that stretches up to 40% as the body inflates. The armored skin is activated by body inflation: as the skin stretches, the sharp spines rotate into an erect position, rigidly pointing outward as a visual warning and mechanical defense. Interfacing between hard and soft tissues is ubiquitous in nature like bone and tendon, but it is very unusual for such an interface to embrace extensive, lifelong distortions while maintaining the material integrity. Remarkably, the skin-spine interface of pufferfish does exactly this function, dramatically morphing both skin and spines with every inflation-deflation cycle and using this transformation as a defense mechanism. How do puffers assemble this unlikely combination of extensible and rigid materials into a repeatedly stretched interface—without tearing themselves apart? How does the drastic skin extension drive and guide spine rotation? How do properties of soft skin and hard spine reciprocally shape dynamic movements? In this project, we integrate our expertise in mechanics, biology, and robotics to provide unprecedented insights into the multi-scale architecture and complex function of the porcupinefish’s armored skin. We will systematically investigate the dynamics of the body expansion, skin stretching, and spine erection and adapt the deployed structural and architectural strategies to create bio-inspired functional interfaces. The micromechanical experiments will reveal the secret to the integrity and performance of the interface of materials with contrasting properties. The musculoskeletal measurements, both on live animals and fresh tissues, shed light on the kinematics and functional morphology of the armored skin of pufferfish. The soft robotics model presents a cyber-physical twin for pufferfish capable of reproducing reactive behaviors consistent with its morphing behavior to verify and generate biological hypotheses. Our collaborative project unravels how the interfacial morphology of pufferfish skin encodes complex shape-morphing functions transferable to adaptive architectures for biomedical, surveillance, and environmental monitoring application.
2023 -
Grant Awardees - Early Career

Decoding the sulfation codes in the glycocalyx

ANGGARA Kelvin (.)

Max Planck Institute for Solid State Research (Max-Planck-Institut für Festkörperforschung) - . - .

MILLER Rebecca (.)

Københavns Universitet (University of Copenhagen, UCPH) - Copenhagen - DENMARK

Large polysaccharides are widely found in nature. Arguably one of the most complex and biologically diverse groups of polysaccharides are the glycosaminoglycans (GAGs) that despite a relatively simple disaccharide repeating backbone attain enormous structural variation through decoration by sulfate groups. While many important and diverse bioactivities assigned to GAGs are believed to be directed by distinct patterns of sulfation along the large GAG chains, direct structural identification of these motifs remains largely unexplored due to analytic barriers. Therefore, our aim is to marry emerging technology advances to make a quantum leap in glycosciences with atomic-level sequencing and structural determination of polysaccharides at the single-molecule level. We hypothesize that precise genetic engineering of glycosylation in cells (RLM’s team at UCPH) will enable us to produce sufficiently homogeneous GAG chains for direct sequencing analysis by single-molecule imaging using electrospray ion-beam deposition and scanning tunneling microscopy (KA’s team at MPI). We focus on GAGs that through complex sulfation patterns orchestrated by 30 distinct sulfotransferases produce recognition landing paths - sulfation codes - for a myriad of GAG-binding proteins that serve essential functions in all metazoans. We will produce these GAGs from the library of cells, and they will be structurally characterized by imaging them one-molecule-at-a-time using scanning tunnelling microscopy to provide the visual form and shape. The images corroborated by ab initio calculations at the level of Density Functional Theory (DFT) will reveal structural GAG motifs that give rise to distinct bioactivities. We believe this interdisciplinary strategy will enable us to dissect the bioactive cues embedded in the long GAG chains. Moreover, we believe that the strategy of combining genetic glycoengineering to reduce the complexity and heterogeneity of GAGs combined with single-molecule imaging will lead to a major breakthrough in glycosciences, which will more generally open up opportunities for direct analysis of other types of polysaccharides, including bacterial lipopolysaccharides, plant polysaccharides such as chitosan, as well as more complex glycoconjugates such as proteoglycans and glycoproteins.
2023 -
Grant Awardees - Program

Understanding fundamental mechanisms governing insect cell membrane deformability

ARIOTTI Nicholas (.)

Institute for Molecular Bioscience - . - .

GEROLD Gisa (.)

University of Veterinary Medicine Hannover (TiHo) - Hannover - GERMANY

PERRIMON Norbert (.)

President and Fellows of Harvard College, Harvard Medical School - . - .

Insect cell membranes differ from mammalian membranes by deformability, lipid content, lipid distribution in microdomains and membrane leaflet asymmetry. Enveloped insect-borne viruses require intimate interactions with cellular membranes to enter cells, replicate their genomes in cells and bud from cells. Despite fundamental biophysical differences between insect and mammalian membranes, insect-borne viruses can productively infect cells from both phyla. Decades of studies on insect-borne viruses have not addressed the machinery of insect membrane deformation and its exploitation by viruses. Here we hypothesize that insect-borne viruses have evolved to biophysically manipulate membranes from both phyla and/or hijack physiological membrane properties from both phyla. Whether genes involved in membrane dynamics or deformation are genetically similar in insects and mammals or whether insects and mammals achieve similar outcomes using distinct sets of genes remains elusive to date. Therefore, our objectives are to bundle the knowledge from three disciplines to unravel fundamental membrane processes in insect cells and compare these to mammalian cells. Working at the interface of insect genetics, membrane biophysics and virology our newly formed team has assembled innovative technologies to break through this barrier in the field. Through the combined expertise of the PIs, we will: 1. Employ gene editing libraries in insect cells to identify host factors steering virus – membrane interactions; 2. Visualize membrane deformation at high-resolution upon genetic manipulation in uninfected and virus-infected insect cells using time-lapse imaging, high resolution imaging and biophysical probes; 3. Assess the impact of membrane deformation on permissiveness to insect-borne viruses by infection assays and sophisticated virological assays probing virus entry, genome replication at plasma membrane microdomains and virus budding from insect cells. 4. Compare the membrane deformation mechanisms in insect cells to those in mammalian cells. These studies will provide insight into mechanisms driving insect versus mammalian membrane shape and function. Thereby, they will revolutionize our understanding of virus adaptation across fundamentally different species.
2023 -
Grant Awardees - Program

Uncovering the real paleo diet: Novel isotope analytics of amino acids from fossil hominin teeth

BAKKOUR Rani (.)

Technical University of Munich (Technische Universität München, TUM) - . - .

LÜDECKE Tina (.)

Max Planck Institute for Chemistry - . - .

NEUBAUER Cajetan (.)

University of Colorado Boulder - Boulder - United States

Accumulating evidence suggests that fossil tooth enamel is remarkably efficient in preserving amino acids (AAs). Intact AAs in fossils have the potential to reveal paleodietary isotopic proxies that may enable unique insights into the lives of even our most ancient human ancestors. While isotope studies have been a great aid for examining how diet has shaped the evolution of key human traits (e.g., brain expansion, bipedalism), current isotope ratio mass spectrometry (IRMS) is fundamentally restricted to gases. However, improved sensitivity and the ability to measure intact biomolecules would permit access to the full spectrum of paleodietary information that is encoded in organic compounds preserved in enamel. While the application of classic IRMS methods for AA analysis of bone collagen have proven valuable for food web reconstruction in ecology and archaeology, the approach is limited to relatively recent (100kya) human prehistory. This project aims to employ a new analytical paradigm based on electrospray-Orbitrap MS to access ancient biomolecules. It will measure comprehensive (compound- and site-specific) isotopic information simultaneously in biomolecules with unprecedented sensitivities. Sensitivity of the electrospray-Orbitrap for isotopes is >10,000-fold higher than isotopic NMR and at least 10 to 100-fold better than the most sensitive IRMS today. This step change makes it conceivable to attempt measuring isotopes directly within intact fossilized polar molecules, including the minute quantities of AAs preserved in hominin enamel. Our team proposes a new analytical frontier: the quantification of paleodietary signatures encoded in intact molecules (“isotopocules”) that are millions of years old. Our US group has developed initial AA isotopocule measurements. Together with fossil preparation and affinity isolation methods pioneered by our two groups in Germany, this novel technique will be validated in a modern African ecosystem (Gorongosa National Park, Mozambique), then refined and applied to hominin fossils (>1Mya). This project will establish a framework to test hypotheses and ask more nuanced mechanistic questions about early hominin food acquisition and habits. The approach we propose has significant potential to be more broadly applied in paleontology, as well as environmental and health research.
2023 -
Grant Awardees - Program

When the going gets tough: Trans-kingdom spore dormancy and revival mechanisms across scales


University of Warwick - Coventry - United Kingdom

BEN YEHUDA Sigal (.)

The Hebrew University of Jerusalem, Jerusalem - . - .

JANSHOFF Andreas (.)

University of Göttingen (Georg-August-Universität Gottingen) - . - .


The Trustees of Columbia University in the City of New York - . - .

In response to adverse conditions, organisms across the tree of life retreat into remarkable dormant states as spores. Spores of bacteria, fungi, and plants are the most resilient cell types known, and can revive following prolonged dormancy, enabling long distance organismal dispersal with significant environmental impact. Yet, the dormant state and the rapid revival remain a cell biological and physical mystery. How are cellular organization and revivability preserved without energy from nutrients? What is the biophysical nature of the dormant cytosol and its role in dormancy? What metabolic processes are required for survival? What are the mechanisms of awakening? What role is played by the spore outer layers, and how do their mechanical properties evolve during germination? What factors govern long term spore fitness? How do environmental niches impact spore physical properties? Do common principles govern spore fitness across kingdoms? To deliver a full mechanistic picture, we will combine advanced microscopy, spectroscopy, machine learning, biophysical modelling, and molecular/cell biological studies of bacterial and yeast spores, comparing dormant and nutrient-fed germinating spores. Using machine learning to analyse motions of fluorescently labelled endogenous molecules/complexes and exogenous tracer particles, we will quantify the scale-dependent relaxation kinetics of the dormant cytosol, characterize its material properties which are likely glassy as for other quiescent states, and measure entropy production to quantify metabolic activity. We will measure the cytosol-fluidizing effects of this metabolic activity using ATP uncaging, and test if this can trigger revival. Impedance spectroscopy will measure cytosol water content, a determinant of glassiness, and indentation-relaxation will probe mechanical stiffness of spore outer layers. We will encapsulate spore extracts in confined geometries (e.g. giant unilamellar vesicles) for convenient measurement and manipulation. Data from these studies will be used to develop a biophysical mathematical model of the dormant state, which will be experimentally tested. We will test the impact of diverse natural environments on our model organism spores, test if model spores and those isolated from the environment obey the same principles, and identify the parameters crucial for spore fitness.
2023 -
Grant Awardees - Program

Mapping structural and functional connectivity of the distributed sensory system in chiton armor

BAUM Daniel (.)

Zuse Institute Berlin (ZIB) - . - .

LI Ling (.)

The University of Pennsylvania, Philadelphia, PA - Philadelphia - United States

SPEISER Daniel (.)

University of South Carolina - USC - . - .

Many organisms utilize a small number of sensory organs and a centralized nervous system (e.g., the paired eyes and complex brains of vertebrates) to acquire and process information. In contrast, other species have evolved distributed sensory networks (DSNs) consisting of dispersed but interconnected sensory elements to sense and respond to external stimuli. Here, we will explore a new research frontier on nature’s strategies for designing efficient and resilient DSNs by investigating a unique model system, i.e., chitons, via a synergistic interdisciplinary collaboration. Chitons are the only extant mollusks with living tissue embedded within their biomineralized protective shell plates. This innervated tissue (aesthetes) forms a complex three-dimensional (3D) interconnected network that fills thousands of long, narrow channels. These microchannels run through the shell plates and finally extend to the shell surface. It has been shown that the aesthetes perform several sensory functions, particularly photoreception. In addition, the aesthetes of certain chiton species include visual elements with different degree of complexities, ranging from simple photoreceptive organs to eyespots that contribute to spatial vision to image-forming eyes with mineralized lenses! Thousands of these visual sensory organs are distributed across the shell plates, making the system a unique ‘hard-wired’ (embedded in mineralized shells) DSN, through which the organisms collect and process visual information and finally respond. Current knowledge of chiton DSNs is primarily focused on overall behavioral responses of animals and the fine structures of individual sensory elements. We have very limited knowledge regarding the structure and function of the chiton DSNs on the system level. How are chiton DSNs wired up? How do they function? How resilient are chiton DSNs to damage? Our international, interdisciplinary team of material scientists, biologists, and applied mathematicians will address these three fundamental questions by establishing the complete ‘connectome’ of chiton DSNs and investigating its working mechanisms and system resilience. The knowledge gained from this research will transform our current understanding of natural DSNs, which may have significant impact on a number of areas, such as distributed sensing structures, living materials, resilient swarm systems, etc.
2023 -
Grant Awardees - Program

SELFCURE: Evolutionary and cognitive processes underlying self-medication of immune-challenged bats

BECKER Daniel (.)

The Board of Regents of the University of Oklahoma (University of Oklahoma) - Norman - United States

PAGE Rachel (.)

Smithsonian Tropical Research Institute, Washington, DC - . - .

SIMON Ralph (.)

Nuremberg Zoo, Behavioral Ecology and Conservation Lab - . - .

Plant medicinal properties are used by a diverse range of animal taxa. Chimpanzees consume hairy Aspilia leaves when suffering from intestinal parasites, Kodiak bears use Ligustium roots against ectoparasites, and monarch butterflies prevent infection in their offspring by laying their eggs on milkweed, a plant toxic to protozoans. Self-medication behaviors provide an effective mechanism to minimize infection load. But despite its eco-evolutionary importance, we lack clear understanding of how behaviors associated with self-medication evolve. Importantly, animals may possess either an innate mechanism to search for medicinal food items, or they may learn individually or through others to associate specific foods with specific cures. Bats are a especially relevant group to study the mechanisms underlying self-medication. They harbor diverse parasites, feed on a wide variety of foods and, due to their cognitive capacities and extraordinary longevity, have high potential to learn to associate specific food resources with curative properties. Phyllostomid fruit bats in particular are ideal for investigation given the wide variety of plants that they have access to in the Neotropical rainforest. Using state-of-the-art tracking techniques, AI-based individual recognition, and targeted and -omics approaches for characterizing immunity and parasites, we propose to investigate the mechanisms underlying self-medication in phyllostomid bats. First, we will determine the immune state, parasite diversity, and nutritional diversity of wild bat populations and investigate potential links between immunity, infection, and certain food plants. Next, by testing immune-challenged and control-treated individual bats on natural and artificially-created medicinal food preferences, we will shed light on the role of learning vs innate mechanisms in self-medication. By tracking groups of bats through a rainforest site that has been studied long-term with fully mapped fruiting tree species, we have the unique opportunity to assess whether immune-challenged individuals switch to a diet with medicinal compounds. Finally, by tracking experimentally immune-challenged and experimentally cured bats trained on artificial sonar beacons indicating the presence of medicinal foods in the wild, we will assess how information regarding self-medication can spread through a bat social network.
2023 -
Grant Awardees - Program

Evolution at the plant apex: identifying steps enabling a major organismal radiation.


Ghent University (Universiteit Gent) - . - .

FUJINAMI Rieko (.)

Kyoto University of Education - . - .


University of Bristol - Bristol - United Kingdom

HETHERINGTON Alexander (.)

University of Edinburgh - . - .

The origin and rise to dominance of vascular plants massively impacted the Earth System and led to an explosive radiation in biodiversity, but how vascular plants originated and diversified to form lycophytes, ferns and seed plants with complex shoot and root systems is unknown. Answers to these questions hinge on apical growth, a key innovation enabling persistent stem cell activity in plants’ growing tips. Like living mosses, the earliest land plants lacked apical growth, and were short lived with tiny stems terminating in the development of spore-producing sporangia. We hypothesise that the origin of apical growth involved the relocation of sporangia from terminal to lateral positions, and the juxtaposition of stem cell and proliferative regions, as seen in the apices of living vascular plants. However, mosses and vascular plants are distantly related with widely divergent forms, and ancestral patterns of apical growth shown by ancient pro-vascular and vascular plant fossils are unknown. Moreover, living vascular plants have diverse patterns of apical growth, and the changes enabling shoot and root evolution are unknown. To test our hypothesis, we propose an innovative research plan that combines morphological data from fossils and living plants at either side of the origin of apical growth with developmental and genetic data from mosses, lycophytes, ferns, and seed plants through four interlinked work packages. WP1 will use a forward genetic screen in a moss and establish functional reverse genetic analysis in a lycophyte to identify genes involved in the origin of apical growth. WP2 will determine structure of fossil apices preserved during the emergence of vascular plants to identify ancestral patterns of apical growth. WP3 will evaluate cell proliferation patterns in a moss and a range of vascular plants and compare apical organizations between living plants and fossils to identify stepwise changes during the evolution of apical growth. WP4 will use transcriptomic and reverse genetic methods to identify conservation and divergence in the genetic networks for apical growth. As an integrated whole, the research will lead to a step change in our understanding of apical growth, a key innovation enabling the radiation of today’s dominant vascular plant flora.
2023 -
Long-Term Fellowships - LTF

Transcriptional adaptation during vertebrate development at the single-cell level

BELLEC Maelle (.)

. - Max Planck Institute for Heart and Lung Research - Bad Nauheim - GERMANY

DIDIER Stainier (Host supervisor)
The development of a multicellular organism requires the precise control of gene expression in space and time so that cells adopt their correct identity. However, genetic mutations can alter this complex process. Recently, a transcriptional adaptation (TA) has been uncovered as one of the mechanisms underlying genetic compensation in zebrafish, mouse cells in culture, and C. elegans1,2. TA refers to the phenomenon by which mutated genes (with mRNA-destabilizing mutations) trigger the transcriptional up-regulation of other genes, called adapting genes. Mutant mRNA degradation, e.g., via Nonsense-Mediated Decay (NMD), has been shown to be required for TA3,4. However, little is known about the spatial and temporal characteristics of adapting gene regulation. Yet, TA would be required to be fast and regulated at all the different steps of gene expression in order for the embryo to develop correctly. Recent technological advances have made it possible to access the dynamics of transcription but only a few have been implemented in vertebrates thus far. This project aims to decipher when and where the TA occurs in the context of the developing zebrafish embryo. Aim 1 will test the hypothesis that TA is initiated during the zygotic genome activation and that there are several possible modes of transcriptional upregulation of the adapting genes. To test this hypothesis, I will use mutant alleles of early expressed genes that have been shown to exhibit TA including vcla, aldh2 and alcama. These genes and their corresponding adapting genes will be tagged with different live reporter arrays (e.g. MS2, PP7 loops) using standard genome editing tools in order to monitor transcription in live embryos with high-end microscopy followed by quantitative image analysis. This approach will allow us to determine the time-scale at which TA occurs and also help us understand the different modes of transcriptional upregulation of the adapting genes. Aim 2 will test the hypothesis that mutant mRNA degradation occurs in specialized organelles that are critical for TA. To test this hypothesis, I will use high resolution microscopy to look at the localization of NMD components as well as membrane-less organelles, such as P-bodies granules, together with the mutated and the wild-type mRNA. To test the importance of these granules, I will use mutants defective in P-granule formation and look at the effects on TA in terms of transcriptional output. Until now, TA has been mostly investigated on pooled populations of cells, therefore we lack the understanding of this phenomenon at a cellular level. This project will be important to fill this gap and get a better understanding of the spacio-temporal characteristics of genetic compensation which help the robustness of vertebrate development. 1. Rossi, A. et al. Nature 524, 230–233 (2015). 2. Ma, Z. et al. Nature 568, 259–263 (2019). 3. El-Brolosy, M. A. et al. Nature 568, 193–197(2019). 4. Serobyan, V. et al. Elife 9, e50014(2020).
2023 -
Grant Awardees - Program

Physics goes wild: studying the evolution of iridescence and its perception in Amazonian butterflies

BELUŠIC Gregor (.)

University of Ljubljana (Slovenia) - . - .

BRISCOE Adriana (.)

The Regents of the University of California (Irvine) - . - .

DEBAT Vincent (.)

French National Museum of Natural History (Muséum national d'histoire naturelle, MNHN) - Paris - FRANCE

GIRALDO Marco (.)

University of Antioquia (Universidad de Antioquia) - . - .

Iridescence is a fascinating optical property induced by complex nanostructures that evolved multiple times in a wide diversity of organisms. Yet, how iridescence is perceived and how it co-evolves with visual perception is unknown. Here, we aim at identifying the selective forces shaping the evolution of wing iridescence and its perception in the emblematic Morpho butterflies. The genus Morpho is ideal to study the evolutionary drivers of iridescence, because striking variation in iridescence occurs within and among its 30 species, associated with contrasted ecologies. We will test two main hypotheses: (1) Morpho iridescence evolves under selection by predators, the blue flashes produced during escape flight increasing their difficulty of capture. (2) Iridescence facilitates species and mate recognition, in part dependent on the light environment. These hypotheses imply a co-evolution of Morpho coloration with flight and color vision. To test these hypotheses, we will combine the skills of experts from complementary scientific disciplines. (1) Physics: we will quantify iridescence and polarization in both sexes for the whole genus, through microspectrophotometry, imaging scatterometry and spectrogoniometry. (2) Behavioral ecology: we will use state-of-the-art videographic and kinematic analyses to quantify flight behavior during escape, courtship and male-male competition and assess its effect on dynamic color signals. (3) Molecular biology: we will assess the evolution of opsins throughout the genus and assess their expression in both sexes in blue and non-blue Morpho species, using RNA-seq, immunohistochemistry and in situ hybridization. (4) Electro- and optophysiology: sensitivity of the photoreceptors will be assessed using single cell recordings; optical pupillograms will characterize retinal mosaic structure, and recordings of optic lobes will identify the neuronal pathways involved in iridescent color vision. This original interdisciplinary approach will allow us to decipher the factors shaping the evolution of iridescence and polarization in Morphos, from the joint perspective of signal production and reception. Filling this knowledge gap will be a major contribution to our understanding of the diversity of structural colors in the living world.
2023 -
Long-Term Fellowships - LTF

Viral cooperation as a novel mechanism to overcome bacterial defenses

BOMPONIS Iakovos (.)

. - University of Vienna (Universität Wien) - Vienna - AUSTRIA

MARTIN Polz (Host supervisor)
Bacterial viruses (phages) outnumber bacteria by an order of magnitude in the oceans, and they are thought to heavily influence the abundance and diversity of bacterial populations. Yet this view is hard to reconcile with the dilute nature of the ocean environment and the extremely narrow host range of most phages, owing to the vast diversity of bacterial anti-phage defenses. Here, I hypothesize that cooperative co-infections by different phages can overcome defenses to effectively broaden their host range. This hitherto overlooked mechanism is suggested by recent observations of frequent recombination among co-occurring phages, even though these are unable to lyse the same bacterial hosts, and may explain how phages collectively overcome the sum of the bacterial anti-phage defense systems. I propose to establish a phage co-infection matrix to (i) identify cooperative lysis of bacteria by phage pairs as well as cooperative defense of different defense genes within hosts, (ii) use the co-infection matrix to computationally predict genes and genetic elements guiding cooperative interactions, and (iii) experimentally test these predictions using molecular genetics. This work is enabled by the Nahant collection, the largest fully genome sequenced cross infection matrix of co-occurring phages and their hosts, consisting of >1,300 marine Vibrio isolates and 251 lytic phages. This matrix, constructed by using individual phage isolates, showed sparse infection due to multiple anti-phage defense systems in each bacterial strain residing on diverse mobile phage defense elements (PDEs), so that solitary phages can only infect one Vibrio strain on average. Importantly, PDEs are absent from lab-domesticated bacteria (presumably due to their fitness costs in the absence of phages), highlighting the value of the Nahant collection in studying native phage-bacteria interactions. Using a high-throughput liquid co-infection assay, I will identify phage cooperation by infecting PDE-containing Vibrios with binary phage-combinations, to find phage-pairs that lyse their hosts upon co-infection (but not independently). I will receive training in analyzing phage genomes and metagenomes, to select syntenic phages from distinct groups. Cooperative infections between syntenic viruses will enable me to computationally pinpoint the cooperation-guiding genes, as the unique genetic fragments should be encoding complementary anti-defense systems. Because these phage-host interactions are important beyond the ocean, my novel approach will not only allow me to reveal cooperation as a main driver of one of the most prevalent ecological interactions, but also to guide rational phage therapy design that already relies on combining multiple different phages for unknown (but perhaps cooperative) reasons.
2023 -
Grant Awardees - Program

New Kids on the Block: how DeNovo emerged micropeptides rewire cellular networks


University of Münster (Westfälische Wilhelms-Universität Münster) - . - .

BRUN Christine (.)

Inserm Délégation régionale Provence Côte d'Azur - . - .

CARVUNIS Anne-Ruxandra (.)

University of Pittsburgh - Pittsburgh - United States

De novo genes emerge in non-coding DNA and code for entirely novel de novo proteins (DNPs) with evolutionarily unexplored sequences, structures and functions. DNPs have been recognized recently and are intensely studied as they describe a hitherto unknown mode of molecular innovation and may reveal species specific functional differences. However, most studies so far ignore that DNPs do not emerge or evolve in isolation, but in the context of an already established complex system. This project will study how DNPs integrate and potentially reshape pre-existing protein interaction networks and, conversely, how networks adapt in response to these “new kids on the block”. Most DNPs may not be retained over several speciation events or even fixed in the whole human population, yet lurk in our cells and may pose disease risks. We focus on short proteins that have very recently emerged or are currently spreading in the human lineage. We will deploy an array of computational and experimental approaches to identify human DNPs and map their protein interaction landscapes throughout evolution . We will first define a comprehensive set of thoroughly verified human DNPs. Next, we will determine their evolutionary history by comparative genomics and reconstruct, wherever possible, their most likely ancestral sequences. We will computationally predict biophysical properties such as structure, intrinsic disorder and aggregation propensity of DNPs. Potential protein binding motifs and likely interactors of DNPs will be predicted and confirmed experimentally using yeast-2-hybrid and phage display. By combining evolutionary analyses of DNPs and their interactors with graph theoretical modeling of network behavior in response to DNP addition, we will learn if DNPs preferentially attach to proteins of the network with particular topological, functional or evolutionary properties. Our experiments and analyses will lead to understanding if DNPs evolved to adapt to the interaction network, if the existing network adapted or, alternatively, if the network has evolved resilience towards incoming additions. Overall, we aim to dissect the molecular bases and derive corresponding rules governing how DNPs integrate cellular networks to engender novel beneficial functions or novel disease risks that are specific to humans.
2023 -
Grant Awardees - Program

Autonomous evolution of synthetic cells under non-equilibrium conditions

BRAUN Dieter (.)

Ludwig Maximilian University Munich (Ludwig-Maximilians-Universität München, LMU) - Munich - GERMANY

GÖPFRICH Kerstin (.)

Max Planck Institute for Medical Research (Max-Planck-Institut für Medizinische Forschung) - . - .

MATSUURA Tomoaki (.)

National University Corporation Tokyo Institute of Technology - . - .

Fascinating biology originates from the Darwinian evolution of cellular life. Mechanisms to create the evolvability of cellular systems remain a fundamental open question. We will reveal how out-of-equilibrium conditions could be used as a driving force to create an autonomously evolvable synthetic cell. While providing highly efficient ways to evolve synthetic protocells in the future, the approach will also address how cells could have emerged in the first place. We will use thermal gradients at air-water interfaces and freeze-thaw cycles to assemble and replicate cells. Selection will be performed based on the ability of the cell to express either peptide-based or RNA-based dimerizing transmembrane units and associate and sediment. The autonomous nature of the process will allow us to select only cells that could incorporate a functional transcription and translation system. We will proceed along three subprojects: i. Autonomous vesicle assembly. Components essential for transcription and translation will be encapsulated into unilamellar lipid vesicles through thermal trapping at a heated air-water interface and accumulation by freeze-thaw-cycles. This will demonstrate the autonomous out-of-equilibrium emergence of both biomolecule accumulation and encapsulation to recreate cellular compartments. ii. Transmembrane domain for the selection by sedimentation. Based on the information encoded on the DNA, synthetic cells will display either an RNA-based or a protein-based surface molecule to trigger aggregation and subsequent sedimentation. This function will be first established in GUVs and then moved to systems which select the aggregated cells by autonomous sedimentation, providing the selective signal that the transcription/translation system was functional. iii. Autonomous amplification of the sedimented cells. Sedimented cells will be brought back to the next rounds of evolution by picking the sedimented colonies, replicating the DNA, refeeding the transcription/translation system and recreating the vesicle compartments. Besides establishing the processes in tubes, the selection and refeeding will be continuously performed in a heated air-water interface microfluidics or a thermally oscillated freeze-thaw cycle. The whole-cell selection and reformation of cells will create an autonomous evolution of proto-cellular systems.
2023 -
Grant Awardees - Program

The Architecture of Photosynthesis


Yale University - . - .

DEAR John (.)

Imperial College of Science, Technology and Medicine - . - .


The Royal Institution for the Advancement of Learning/McGill University - Montreal - CANADA

PEZZULLA Matteo (.)

Aarhus University (Aarhus Universitet, AU) - . - .

Photosynthesis is the metabolic process that sustains all life on Earth. Understanding how vascular plants reconcile leaf structural optimization for both light capture and photosynthetic gas exchange with architectural stability required to withstand gravity and wind has been an intractable challenge. While the anatomy of the inner leaf tissues should optimize gas exchange through a porous microstructure that augments the net absorptive interface, such an optimization should also come with a cost to the architectural stability of thin planar leaves. This interdisciplinary project leverages a combination of expertise in cell biology, ecophysiology, and mechanical engineering to investigate the functional trade-off between gas exchange and leaf mechanics. Based on engineering concepts, the biomechanics of plant leaves and the porous properties of its inner tissues will be analyzed at multiple length scales to gain insight into evolutionary pressures that have shaped laminar leaves over millions of years. Our approach will reconcile how and why leaves are structured the way they are and identify the critical design principles of highly productive species capable of sustaining maximum photosynthetic performance. We also aim to understand the construction costs and minimal investments needed to produce a laminar leaf that is biomechanically robust while still meeting the demands to serve as the cellular scaffold for photosynthesis. Collectively, the data and new methodology developed in this collaborative project will 1) provide novel insight into the evolutionary trajectory of land plants, 2) identify the key design elements of the internal three-dimensional cellular geometry, 3) facilitate the interdisciplinary exchange of ideas, tools, and theory to make a major advancement in our understanding of plant biomechanics and materials science, and 4) identify a set of key traits that could be used for the development of next-generation biomimetic materials with inspiration from nature, as well as new crop varieties that are more efficient in terms of resource allocation, photosynthetic performance, and resilience.
2023 -
Grant Awardees - Program

Decoding the gelatinous origins of brain evolution



WOLF Fred (.)

University of Göttingen (Georg-August-Universität Gottingen) - Göttingen - GERMANY

The origin of first brains was key in animal evolution as it allowed them to rapidly integrate environmental cues, coordinate responses to threats or opportunities, and form internal models of the world to make decisions and guide behavior. However, the evolutionary origin of animal brains remains mysterious. Ctenophores are marine organisms and strong candidates for one of the first animal lineages developing an elementary brain to navigate through the ocean. Intriguingly, ctenophores possess a unique type of neuronal integration center called the aboral organ that in juvenile animals contains about 80 nerve cells and functions as a multi-sensory integration center controlling complex behaviors. The ctenophore aboral organ presumably evolved independently of centralized nervous systems in bilaterians and likely preserves biophysical and molecular mechanisms characteristic of the first nervous systems. Ctenophores therefore offer a unique opportunity to elucidate the cellular mechanisms, behavioral capacities, and adaptive values relevant to the evolutionary invention of animal nervous systems. Here, we propose to uncover the neural circuit basis of ecologically important behaviors of a fierce planktonic predator, Mnemiopsis leidyi, a ctenophore that can disrupt entire marine ecosystems when displaced or out of control, contributes to the production of “ocean snow”, transferring carbon to the abyss, and harbors perhaps the most alien brain of any predatory animal on the planet. We will build on recent breakthroughs in organismal biology, molecular neuroscience, connectomics, neural circuit inference and neurotechnology to establish a data-driven account of Mnemiopsis’ neural brain circuits and behavior, to all-optically read and interrogate the state of its brain, and to test and validate computational models of its neuronal processing by cellular-resolution whole-brain imaging. Dense behavioral videography data in free-ranging animals will be used to construct data-driven quantitative models of 3D animal postural and movement dynamics during hunting, propulsion and steering. Together, these studies will allow us to understand Mnemiopsis’ brain and behavior by bridging levels from the molecular and biophysical architecture of nerve cells to ecologically important behaviors and shed new light on the very origin of biological brains.
2023 -
Long-Term Fellowships - LTF

Gating mechanism of insect auditory transduction channels


. - University of Leicester - Leicester - United Kingdom

BENJAMIN Warren (Host supervisor)
EZIO Rosato (Host supervisor)
Insect hearing can match and even outperform their vertebrate counterparts, for instance, a species of moth can hear up to a few hundred kHz or ten times greater than that of humans (1). However, insect auditory organs operate at microscopic scales making it difficult to understand how they work. The site where sound is converted into electrical signals are membrane protrusions termed cilia. They are so small that they are at the diffraction limit of light. The cilium contains mechanically sensitive ion channels (2,3) that open when they are displaced by sound. Not only is the identity of the channels disputed, but the mechanism by which the insect mechano-electrical transduction (MET) machinery operates is largely speculative. These two complementary questions form the two aims of this fellowship proposal. 1. Identify the MET channels using CRISPR-Cas9-mediated mutations of the two channel candidates. There are two contenders for the MET channel in insects: NompC that resides near the ciliary tip (4) and Nanchung-Inactive located at the base of the cilium (5). My host lab has recently established the experimental workflow for CRISPR-Cas9 edited genetic mutants in the desert locust. I will individually mutate Nanchung, Inactive and NompC and measure the resulting transduction current. These will constitute the first transduction current measurements from insect auditory neurons with genetically mutated transduction channels and will finally reveal which of these two channels is the bona fide auditory transduction channel. 2. Characterise sub-micrometre displacements of cilia with a dynamic super-resolution imaging. Sound-induced movements of the cilia are hypothesised to be less than 200 nm (6) putting it below the resolution of light microscopy. Working at the interface of biology and physics, I will characterize internal motions of cilia in the auditory organ of the desert locust by measuring the proportional activation of photosensors from live images of the cilium projected onto a high-speed (10,000 frames per second) and high photon-efficiency (95% photon capture) CMOS-based camera. My host lab has established proof-of-concept of this imaging system down to the resolution of 10 nm. Live imaging of the cilium, in response to sound, will be combined with electrophysiological measurements of the MET currents from individual auditory neurons (a technique pioneered by the host lab (7)). I will combine the two physiological techniques offered by the host lab with my background in the biophysics of hearing to reveal how the cilium is activated through sound and solve an enduring enigma for the field of mechanotransduction. REFERENCES 1. Moir HM, et al. BioLett. 2013, 9:4. 2. Field LH, et al. AdvInsectPhys. 1998. 3. Vavakou A, et al. PNAS. 2021, 118:39. 4. Liang X, et al. Cytoskeleton. 2011, 68:1. 5. Kim J, et al. Nature. 2003, 424:6944. 6. Moran D, et al. PNAS. 1977, 74:2. 7. Warren B, et al. JNeurosci. 2018, 38:15.