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Funding
Funding
HFSP supports novel, innovative and interdisciplinary basic research focused on the complex mechanisms of living organisms. A clear emphasis is placed on novel collaborations that bring biologists together to focus on problems at the frontier of the life sciences.
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Awardees
Awardees
In this section you find information about the awardees in the HFSP scientific programs. This includes a searchable database of HFSP awardees, information on the HFSP Nakasone Award and other achievements by HFSP awardees.
- News & Impact
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Events
Events
HFSP promotes and participates in several events every year. We are committed to bringing together the scientific community and forging new opportunities to network and have scientific discussions that help to create bridges and partnerships for the future of frontier science.
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About
About
The Human Frontier Science Program is a program of funding for frontier research in the life sciences. It is implemented by the International Human Frontier Science Program Organization (HFSPO) with its office in Strasbourg. Here you can find all you need to know about the HFSPO.
Awardees
2023
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Grant Awardees - Program
Uncovering the real paleo diet: Novel isotope analytics of amino acids from fossil hominin teeth
NEUBAUER Cajetan (.)
University of Colorado Boulder - Boulder - United States
LÜDECKE Tina (.)
Max Planck Institute for Chemistry - . - .
BAKKOUR Rani (.)
Technical University of Munich (Technische Universität München, TUM) - . - .
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
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Grant Awardees - Program
When the going gets tough: Trans-kingdom spore dormancy and revival mechanisms across scales
BALASUBRAMANIAN Mohan (.)
University of Warwick - Coventry - United Kingdom
O'SHAUGHNESSY Ben (.)
The Trustees of Columbia University in the City of New York - . - .
BEN YEHUDA Sigal (.)
The Hebrew University of Jerusalem, Jerusalem - . - .
JANSHOFF Andreas (.)
University of Göttingen (Georg-August-Universität Gottingen) - . - .
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
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Grant Awardees - Program
Mapping structural and functional connectivity of the distributed sensory system in chiton armor
LI Ling (.)
The University of Pennsylvania, Philadelphia, PA - Philadelphia - United States
BAUM Daniel (.)
Zuse Institute Berlin (ZIB) - . - .
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
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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
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Grant Awardees - Program
Evolution at the plant apex: identifying steps enabling a major organismal radiation.
HARRISON Jill (.)
University of Bristol - Bristol - United Kingdom
HETHERINGTON Alexander (.)
University of Edinburgh - . - .
FUJINAMI Rieko (.)
Kyoto University of Education - . - .
BEECKMAN Tom (.)
Ghent University (Universiteit Gent) - . - .
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
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Long-Term Fellowships - LTF
Transcriptional adaptation during vertebrate development at the single-cell level
BELLEC Maelle (FRANCE)
Dept. III - Max Planck Institute for Heart and Lung Research - Bad Nauheim - GERMANY
STAINIER Didier (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
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Grant Awardees - Program
Physics goes wild: studying the evolution of iridescence and its perception in Amazonian butterflies
DEBAT Vincent (.)
French National Museum of Natural History (Muséum national d'histoire naturelle, MNHN) - Paris - FRANCE
BELUŠIC Gregor (.)
University of Ljubljana (Slovenia) - . - .
GIRALDO Marco (.)
University of Antioquia (Universidad de Antioquia) - . - .
BRISCOE Adriana (.)
The Regents of the University of California (Irvine) - . - .
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
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Long-Term Fellowships - LTF
Viral cooperation as a novel mechanism to overcome bacterial defenses
BOMPONIS Iakovos (GREECE)
CMESS - University of Vienna - Vienna - AUSTRIA
POLZ Martin (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
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Grant Awardees - Program
New Kids on the Block: how DeNovo emerged micropeptides rewire cellular networks
CARVUNIS Anne-Ruxandra (.)
University of Pittsburgh - Pittsburgh - United States
BRUN Christine (.)
Inserm Délégation régionale Provence Côte d'Azur - . - .
BORNBERG-BAUER Erich (.)
University of Münster (Westfälische Wilhelms-Universität Münster) - . - .
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
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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
MATSUURA Tomoaki (.)
National University Corporation Tokyo Institute of Technology - . - .
GÖPFRICH Kerstin (.)
Max Planck Institute for Medical Research (Max-Planck-Institut für Medizinische Forschung) - . - .
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
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Grant Awardees - Program
The Architecture of Photosynthesis
GEITMANN Anja (.)
The Royal Institution for the Advancement of Learning/McGill University - Montreal - CANADA
DEAR John (.)
Imperial College of Science, Technology and Medicine - . - .
PEZZULLA Matteo (.)
Aarhus University (Aarhus Universitet, AU) - . - .
BRODERSEN Craig (.)
Yale University - . - .
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
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Grant Awardees - Program
Decoding the gelatinous origins of brain evolution
WOLF Fred (.)
University of Göttingen (Georg-August-Universität Gottingen) - Göttingen - GERMANY
BURKHARDT Pawel (.)
UNIVERSITY OF BERGEN - . - .
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
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Long-Term Fellowships - LTF
Gating mechanism of insect auditory transduction channels
CHAIYASITDHI Atitheb (THAILAND)
Neuroscience - University of Leicester - Leicester - United Kingdom
WARREN Benjamin (Host supervisor)
ROSATO Ezio (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.
2023
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Grant Awardees - Program
Evolution of protein multifunctionality
FEUDA Roberto (.)
University of Leicester - Leicester - United Kingdom
CHANG Belinda (.)
University of Toronto, Department of Cell & Systems Biology - . - .
MENON Anant (.)
Weill Medical College of Cornell University - . - .
GOEPFERT Martin (.)
University of Göttingen (Georg-August-Universität Gottingen) - . - .
Like moonlighting people, proteins can have several seemingly unrelated functions. How multiple functions can coexist within the sequence of a single polypeptide chain remains an open question, especially if the individual functions are not separated as in a Swiss army knife but intermingled such that selection for one function might compromise others. Merging expertise in evolutionary genomics, biochemistry, biophysics, and physiology, implemented via in silico, in vitro and in vivo approaches, we now propose to elucidate fundamental principles underlying protein moonlighting using the Drosophila melanogaster opsin protein Rh1 as a prototype. Rh1 (i) initiates visual transduction in photoreceptor cells, (ii) organizes cilia in mechanoreceptor cells, (iii) acts as a chemoreceptor protein in taste receptor cells, (iv) functions in the sensory discrimination of environmental temperature, and (v) acts as a phospholipid scramblase, contributing to membrane lipid homeostasis. We will use two approaches to scan for variants that may be important for Rh1 multifunctionality, which will then be investigated experimentally. First, we will investigate natural variation of the Rh1 sequence across populations/species and identify targets of selection. Second, we will conduct deep scanning mutagenesis experiments of Rh1 to identify all allowable variants which permit proper protein maturation and visual signaling. Allowable mutations not found in nature may be important for non-visual functions. Natural and allowable sequence variants will be quantitatively phenotyped using in vitro and in vivo analyses to determine their effects on the photo-, mechano-, chemo-, and thermosensory functions of Rh1, its scramblase activity, spectral tuning, and downstream signaling. These genetic and functional data will then be used to (i) link multiple aspects of Rh1 functions to specific amino-acid residues, (ii) determine to what extent the diverse functions make use of common residues, (iii) reveal whether the respective residues are conserved or vary in nature, (iv) elucidate the functional consequences of this variation and finally, (v) illuminate the evolutionary constraints associated with moonlighting by opsins. Thus, we will obtain a molecular understanding of how hyper-diverse functions are realized and maintained in super-multifunctional proteins.
2023
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Long-Term Fellowships - LTF
Functional exploration and machine learning of the solute binding domain transcription factors
CHEN John (CANADA)
Chemistry - The Australian National University - Canberra - AUSTRALIA
JACKSON Colin (Host supervisor)
The LacI superfamily of Transcriptional Regulators (TRs) are common in bacteria and allow for the sensing of molecules to regulate gene expression. TRs have a DNA binding domain and a solute binding protein (SBP) domain, which binds specifically to a variety of small metabolites. Ligand binding results in conformational change and allosteric control of the TR’s DNA binding affinity, coupling small molecule binding to gene regulation. The recent explosion in genomic and metagenomics sequencing has unveiled a wealth of sequence diversity. However, only a handful of TR sequences have been characterized, leaving the vast majority of the metabolite binding sequence space unexplored; we estimate that >95% of sequences clusters are ‘orphans’, with no closely related (>35% sequence identity) sequences of known function. Thus, there is great opportunity to expand our understanding of TRs and molecular recognition in general, as there is a plethora of undiscovered ligand binding solutions with unknown mechanisms. In this project, I propose to survey the unexplored sequence space, by characterizing and functionally mapping orphan TR sequences, followed by a multifaceted machine learning approach to predict ligand binding throughout the rest of the family. We will first generate a sequence similarity network (SSN) of the ~1 million TRs collected from the NCBI database, which clusters sequences by sequence identity. Using the SSN, we will identify approximately 200 diverse ‘orphan’ TR clusters, then synthesize and clone approximately 200 of these sequences into expression vectors. To characterize each TR in terms of their function as an activator or repressor, each gene will be co-expressed into a library of reporter plasmids expressing an On/Off selection system that contains a binding site with randomized DNA promoter sequence; this system selects (by survival) for transcriptional activation or repression. The TRs will then be screened using a small molecule library (~1,000s of compounds), where each gene/DNA library is screened with and without the small molecule, and co-selected for active or repressed expression of the reporter. Finally, each condition in which activation/repression is observed will be identified with a molecular barcode, pooled and sent for deep sequencing, allowing mapping of all DNA recognition sequences and all responsive ligands for every screened TR by highlighting the surviving DNA/ligand combinations under On/Off selection. We will analyze novel TRs using protein crystallography, structure prediction (alphafold) and phylogenetic analysis. Most importantly, this data will be used to train machine learning algorithms to allow us to accurately predict both DNA binding specificity and ligand binding throughout the entire superfamily. We expect this project to greatly enhance our knowledge of gene regulation and molecular recognition, allowing for further expansion of the fundamental study of prokaryotic gene regulation.
2023
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Cross Disciplinary Fellowships - CDF
Highly parallel determination of protein identity and function with single-molecule resolution
CHOI Hansol (KOREA, REPUBLIC OF (SOUTH KOREA))
PCMM - Boston Children's Hospital - Boston - United States
WONG Wesley (Host supervisor)
While advances in single cell RNA sequencing (scRNA-seq) technology have revolutionized biomedical research (Papalexi et al., Nat. Rev. Immunol., 2017), equivalent approaches for proteomic analysis remains a challenge. Two significant reasons why analyzing proteins is more challenging than analyzing DNA or RNA 1. The high complexity of the proteome: proteins show higher complexity than genes not only due to the increased diversity of their building blocks, but also due to diversification during translation. 2. Lack of technology that can efficiently identify and characterize proteins in trace samples: unlike DNA which can be easily amplified with polymerase chain reaction (PCR), proteins cannot be easily replicated. To meet these challenges, the development of high-throughput single-molecule approaches is a promising avenue, which should enable the deciphering of complex proteomes, including the high heterogeneity between cells that can arise in cancer. Furthermore, proteins can provide additional information to scRNA-seq technology since they contain information that arose during translation. In addition to measuring posttranslational modifications, proteomics methods can also characterize protein conformation, which cannot be inferred from scRNA-seq data and is closely related to its functionality, with misfolded proteins potentially leading to various diseases (Cohen et al., Nat., 2003). Because misfolded proteins cannot easily be purified or labeled, protein conformation would ideally be analyzed using single-molecule approaches. However, conventional approaches for studying protein conformation are often lacking or limited in terms of throughput or their ability to analyze trace samples (Serebryany et al., bioRxiv, 2022; Aebersold et al., Nat., 2016). The overall goal of this proposal is to develop a high-throughput, single-molecule proteomics technology with the potential to revolutionize cancer proteomics. The highly parallel protein profiling and structural analysis technology that we develop will complement more traditional single-cell profiling approaches such as scRNA-seq. Compared to mass spectrometer (MS)-based and ELISA-based single cell proteomics, our single-molecule approach should have advantages in sensitivity and multiplexity, respectively (Labib et al., Nat. Rev. Chem., 2020).
2023
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Grant Awardees - Program
Deciphering the role of dynamics in vascular network remodeling and determination
KATIFORI Eleni (.)
University of Pennsylvania, Philadelphia, PA - Philadelphia - United States
JONES Elizabeth (.)
Catholic University of Leuven (Katholieke Universiteit Leuven, KU Leuven) - . - .
CORNELISSEN Annemiek (.)
Laboratoire Matière et Systemes Complexes, CNRS, UMR 7057 - . - .
Vascular networks in animals are constantly in flux, remodeling their topology and architecture during development and adulthood, to respond and adapt to different stimuli and environmental conditions. The resulting topologies are typically complex, involving several levels of hierarchy, and display features that can be inconsistent with steady flow adaptation models, like suppression of vascular shunting. In this project, we will explore how these biological transport networks are built and maintained. In particular, we will combine our expertise in theoretical and computational fluid dynamics, soft matter physics, and experimental developmental biology of two very different animal classes, mammals and jellyfish, to understand how pulsatility and other dynamics influences the long-term adaptation and remodeling of the vascular system. Pulsatility is present in all living organisms and yet our understanding of the role this stimulus plays is minimal. We propose that pulsatility is vital to the organism, playing an essential role in preserving vascular loops and preventing shunting.
To do this, we will first build computation models that calculate the flow dynamics in complex elastic networks. We will test these models with real in vivo measurements of whole mouse embryos and jellyfish. We will then use experiment and computation to study how short-term dynamics in the flow and variations in the pumping force that propels the fluid are propagated by fluid structure interactions of the elastic vascular walls. We will investigate mechanisms, both on the physiological and genetic level, including gain-of-function and loss-function models. The earlier is obtained by increasing vessel stiffness, both in jellyfish and mouse, thereby generating faster and larger pulse waves. The latter takes advantage of recently developed mechanical assist devices for the heart that create continuous flow in the vasculature. Our final aim is to to understand the role of wave reflection and additive/subtractive effects of the pulse wave forms and perform a comparative analysis of our findings in jellyfish and mouse, to eventually uncover the fundamental biological rules that shape vascular network architectures.
2023
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Grant Awardees - Program
Electrogenetic control of bacterial metabolism, communication, and biofilm formation
MALVANKAR Nikhil (.)
Yale University - New Haven - United States
CRAIG Lisa (.)
Simon Fraser University - . - .
FRANCETIC Olivera (.)
Institut Pasteur, Paris - . - .
SALGUEIRO Carlos (.)
Faculdade Ciências e Tecnologia, Universidade Nova de Lisboa - . - .
Electrogenetics is an emerging biotechnology platform that uses electric fields to control gene expression. Current electrogenetic methods rely on diffusive ions which become ineffective due to high fluid flow present in most environments. To achieve fast and directional electron transport, soil microbes including Geobacter have evolved long thin proteinaceous “nanowires” capable of ultra-fast delivery of excess metabolic electrons to external mineral acceptors or to other microbes in a process called Direct Interspecies Electron Transfer (DIET). DIET is crucial to prevent toxic electron build-up in the anaerobic habitats where Geobacter lives in biofilm communities with other microbe species. Crucially, many archaea capture these electrons via DIET and use them to produce methane (methanogens) or to degrade methane (methanotrophs). Nanowires and DIET thus have a major impact on the global levels of methane, a greenhouse gas 30 times more potent than CO2 in trapping heat. Despite their global importance, the conditions and mechanisms driving nanowire biogenesis and function in DIET are poorly understood. Recently, PI Malvankar showed that nanowires are polymers of cytochromes that are secreted to the Geobacter cell surface via an unusual type IV pilus machine. Electric fields induce nanowire production by upregulating expression of genes involved in their biogenesis. Thus, the Geobacter system is an ideal model to study electrogenetics. To elucidate how the electric fields control nanowire biogenesis and signalling, we will identify Geobacter genes upregulated during DIET in co-cultures of Geobacter donor and acceptor species. We will deploy solid-state physics, spectroelectrochemistry, biochemistry, structural biology and genetics to characterize nanowire secretion and assembly, electron wiring and transport in DIET, and its effects on gene expression. By reconstituting nanowire secretion and assembly in Escherichia coli we can characterize their biogenesis and function. This information can be used to design nanowire-based electrogenetics systems that form conductive biomaterials, generate energy (biofuels) and produce biological products. Importantly the Geobacter system can be paired with methane-utilizing microbes to investigate electrogenetics in these species, with the long term goal of controlling DIET to reduce atmospheric carbon levels.
2023
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Long-Term Fellowships - LTF
Structure of the Synaptic Vesicle
DAS Poulomi (INDIA)
Neurology - The Regents of the University of California, San Francisco - San Francisco - United States
EDWARDS Robert (Host supervisor)
STROUD Robert (Host supervisor)
Synaptic transmission is crucial for brain function and defects are associated with many neuropsychiatric disorders. Presynaptic mechanisms regulating neurotransmitter release decode the information stored in neural firing, and functions have been assigned to several of the key proteins involved in synaptic vesicle docking, Ca++ sensing and membrane fusion. However, the mechanisms, regulation and coordination are not well understood. The function of many other synaptic vesicle proteins also remains unknown. Indeed, previous work has focused on the function of individual proteins without considering the larger context, leading to the assumption that membrane proteins are randomly distributed on the synaptic vesicle. However, interactions between several of them suggest organization which would have profound implications for neurotransmission, behavior and disease.
The long-term objective of this project is to develop a holistic understanding of the diverse mechanisms involved in neurotransmitter release and their role in information processing. The strategy is to determine the structure and organization of proteins embedded in the synaptic vesicle membrane at near-atomic resolution and test the functional implications of the most salient findings.
I hypothesize that the organization of synaptic vesicle membrane proteins serves to coordinate their function in neurotransmitter release. Previous work on individual proteins involved in synaptic vesicle docking and fusion has suggested interactions between several of them. For instance, membrane fusion requires multiple SNARE complexes, and the synaptic vesicle contains many copies of the principal v-SNARE VAMP2. The Ca2+ sensor synaptotagmin 1 has been suggested to link these complexes into a ring, which may confer cooperativity. The synaptic vesicle also contains t-SNAREs that may act in cis to regulate interaction in trans with t-SNAREs at the plasma membrane. Determining the organization of these proteins will help to understand their role in release. This work will also provide a foundation to understand how synaptic vesicles interact with other elements of the release machinery such as plasma membrane docking sites and presynaptic Ca++ channels.
Synaptic vesicles isolated by differential centrifugation and gradient fractionation will be used for structure determination by Cryo-electron tomography, in collaboration with the Stroud lab. The issue of heterogeneity will be addressed by selective immunoisolation and/or class averaging. Imaging and electrophysiology in primary neuronal cultures will be used to test the predictions for synaptic vesicle exocytosis and neurotransmitter release.
The results will provide a framework to understand the function, regulation, and interactions among synaptic vesicle proteins, providing a broad context to understand neurotransmitter release, its role in information processing, behavior, and dysfunction in disease.
2023
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Long-Term Fellowships - LTF
Investigation of uropathogenic E. coli virulence mechanisms in a human bladder microtissue model
DE BENTO FLORES Carlos Eduardo (PORTUGAL)
Biozentrum - Biozentrum University of Basel - Basel - SWITZERLAND
DEHIO Christoph (Host supervisor)
Urinary tract infections (UTIs) are among the most common infections in the world and the primary cause for the prescription of antibiotics. WHO has recently highlighted UTI treatment as a critical exacerbating factor in the global antimicrobial resistance (AMR) crisis. However, the pathophysiological mechanisms underlying UTI and its frequent recurrence remain largely understudied, hindering the development of effective therapeutics. The vast majority of UTI research has been performed in mouse models or cancer cell lines using uropathogenic E. coli (UPEC) as the predominant agent. However, the obtained results often cannot be fully translated to humans due to differences in bladder ultrastructure, physiology/function and immunity.
Therefore, the main goal of this project is to unveil the main strategies and virulence factors underlying UPEC colonization and persistence using a physiologically relevant human microtissue bladder model. The following hypotheses will be addressed: i) Does bacterial adhesion, invasion and the formation of intracellular bacterial communities occur in the human model as previously described for the mouse model?; ii) Which virulence factors (e.g. flagella, type I- or P-pili) are critical for the establishment and persistence of UTI?; iii) What is the role of the innate immune response (e.g. diapedesis and phagocytosis) for the outcome of the infection (persistence vs. clearance); iv) Which of these strategies and molecular mechanisms are shared between different UPEC strains?
A multidisciplinary approach will be taken by the in-depth characterization of a perfused, urine-tolerant, fully stratified 3D-human bladder microtissue model, that is under development in the host lab at Biozentrum, Univ. of Basel. Bladder biopsies and urine from UTI patients obtained from the University Hospital Basel will be used for validation purposes. The initial assessment of pathophysiological mechanisms will be performed using UPEC strain CFT073 (broadly used in mice infection models), together with mutants in virulence factors identified by a genome-wide CRISPRi screen in the host lab. To depict the general infection strategies (adhesion, intracellular communities, etc.), I will also address mechanistic aspects of the underlying virulence processes, targeting host compartments and bacterial factors (e.g. flagella, pili, etc.) at single cell resolution using 4D spinning disk live cell imaging. Selected clinical UPEC isolates will be used as comparison and immune cells (i.e., neutrophils) will be added to the model to assess UPEC clearance.
Overall, this project will allow the study of basic pathways underlying UTIs and mimic recurrence in a powerful platform, serving as a crucial complement (or even alternative) to the current mice models that dominate the field. We will be able to dissect with high-resolution the specific mechanisms and players involved in the UTI establishment and its persistence, which is a current demand.