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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
2024
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Grant Awardees - Program Grants
Discovering the chemical space of bioactive modified nucleotides and their enzymatic repertoire
BELTRAO Pedro (SWITZERLAND)
- Swiss Federal Institute of Technology in Zurich (ETH Zurich/ETH Zürich) - Zurich - SWITZERLAND
CORREIA-MELO Clara (PORTUGAL)
- Leibniz Institute on Aging - Fritz Lipmann Institute e.V. - Jena - GERMANY
FUGGER Kasper (DENMARK)
- University College London Cancer Institute - London - United Kingdom
Nucleotides are basic molecules of life. A plethora of modified nucleotides (modNs) have been identified in DNA and RNA, with a few known to regulate gene expression, DNA repair, and neuronal activity. Yet, only few modNs have been identified as free monomeric nucleotides, i.e. not incorporated in nucleic acids, in nature. ModNs vary among species and exhibit diverse and striking bioactive properties such as base Z, a bacteriophage deoxynucleotide of prebiotic origin that defends against bacterial restriction enzymes, can self-repair DNA lesions and promotes read-through of stop codons in humans. Other modNs can potentiate chemotherapy or induce mutations, epigenetic changes or cytotoxic responses. To eliminate harmful modNs, species have evolved detoxifying enzymes that prevent the detrimental effects of their DNA incorporation. Despite the potential negative effects of misincorporation of bioactive modNs on organismal fitness, a systematic assessment of their chemical nature, biological sources, cross-species effects, and associated modifying and detoxifying enzymes is lacking. Here we propose a multidisciplinary approach, integrating advanced analytical chemistry, computational modeling and cell biology to: i) systematically identify and quantify modNs in human and gut microbial samples, ii) predict nucleotide modifying and detoxifying enzymes and their evolution and iii) characterize the physiological impact of identified modN on human cells, and validate the function of AI-predicted detoxifying enzymes. Undertaking this research will significantly expand our understanding of the identity, biological origins and impact of modNs, along with the evolutionary dynamics of modifying and detoxifying enzymes across the tree of life. Ultimately this research has far reaching implications from evolutionary biology to clinical therapies, whilst expanding our knowledge of chemical species-species interactions across domains of life.
2024
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Long-Term Fellowships - LTF
Neural mechanisms for dynamic action planning and execution as we move through space
BENCIVENGA Federica (ITALY)
Département de neurosciences - University of Montreal (Université de Montréal) - Montreal - CANADA
GREEN Andrea (Host supervisor)
CISEK Paul (Host supervisor)
Our understanding of the neural mechanisms underlying voluntary behavior comes primarily from experiments conducted under simplified laboratory conditions. For example, reaching has been studied mainly in seated subjects making arm movements with their body stationary. While the human neuroimaging studies conducted during my PhD contributed to this body of work, I have also become increasingly aware of its limitations. In particular, it is unclear how well the insights of this approach will generalize to the more complex scenarios encountered during natural behavior, in which we plan and perform actions in a dynamically changing environment as we move our body through space. Understanding this is crucial for new theories of brain function and clinical applications that better translate to the real world. Here, I propose to pursue a more naturalistic approach to studying voluntary movement. I will bring my expertise on frontoparietal interactions during online reach control in body-stationary human subjects to the design of new neurophysiological experiments in non-human primates (NHP) that investigate the neural mechanisms of voluntary reaching during body motion. These experiments will be conducted in the laboratories of Andrea Green and Paul Cisek (Univ. of Montréal), experts in dynamic sensorimotor control and action selection in NHPs. Under their supervision, I will perform simultaneous multi-electrode recordings in multiple areas related to reach control (primary motor, dorsal premotor, posterior parietal cortex), allowing me to examine for the first time the activity of individual neurons and the dynamics of neural populations as monkeys select, plan, and execute reaching movements while being moved around in space by a unique 3D motion system. One key goal will be to extend current motor control theories by examining how control policies are adjusted to the changing spatial relationships and reach dynamics that arise as the body moves in space. I will test the hypothesis that cortical reach circuits process body motion information in a sophisticated way, taking into account both body-limb biomechanical interactions and the context of the behavioral goal. I will also study the mechanisms that keep track of the location of potential reach goals and select between them as the body moves during planning. I will test the hypothesis that as the body moves the spatial locations of reach goals and the competition between potential actions are updated continuously within a distributed representation of reachable space. This project will move my research in a fundamentally new direction, placing me in a unique position to push theories of cognition and action towards the more dynamic scenarios we experience daily during natural behavior, with important implications for rehabilitation and neuroprosthetics. Overall, it will help launch an independent research program that shifts current experimental paradigms toward a neuroscience of natural behavior.
2024
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Long-Term Fellowships - LTF
Investigating the effects of chronic stress on gut-brain interactions
BIGLARI Nasim (GERMANY)
Bioelectronics Group - Massachusetts Institute of Technology - MIT - Cambridge - United States
ANIKEEVA Polina (Host supervisor)
Stress can lead to or exacerbate several dysfunctions within the gastrointestinal tract which may manifest as alterations in motility, permeability, secretion, as well as visceral hypersensitivity and hyperalgesia. First level response to stress activates the autonomous nervous system releasing catecholamines, such as adrenaline and noradrenaline. If the stressor persists, the hypothalamic–pituitary–adrenal axis is engaged and cortisol is released from the adrenal glands. Actions of the opposing parasympathetic system are mainly mediated via the vagus nerve. Its afferent fibers, relay sensory information from the periphery to the brain, while vagal efferents carry instructions from the brain. Vagal efferents, inhibited by stress, are a major component of parasympathetic activity and act to decrease intestinal inflammation and strengthen intestinal barrier function, as shown in animal and human studies. In mice, mild chronic stress increases hypersensitivity in sensory gastric vagal afferents. Although the inhibitory effect of stress on vagal activity is known, the exact mechanisms of dysfunction remain elusive. Since vagal neurons are heterogenous, I aim to decipher which cell-types are implicated in the dysfunction that occurs after long-term stress exposure, whether cell-types can be attributed to a particular feature of dysfunction such as hypersensitivity and motility and how these alterations are reflected in the brain leading to efferent activity modulation. I plan to utilize refined experimental tools developed in the group of Prof. Anikeeva (MIT) to remotely induce magnetothermal stimulation of corticosterone-release in mice chronically and non-invasively. Macro and micro-scale criteria of gut dysfunction will be monitored via assessment of structural, barrier integrity and motility changes. To identify implicated afferent subtypes that exhibit altered activity after chronic stress exposure, I will perform single cell sequencing of the nodose ganglion (where cell bodies of vagal afferents converge) and compare the immediate early gene expression patterns to that of the control mice. Based on the identified altered activity patterns, I subsequently intend to investigate whether cell-type targeted optogenetic modulation of the identified affected vagal afferent subtypes are necessary and/or sufficient for inducing or inhibiting parameters of dysfunction. Additionally, to identify how stress exposure is reflected in the brain, I will look for neuronal activation markers using whole-brain clearing and imaging, with a particular focus on projection targets of vagal neurons. To conclude, I aim to understand which part(s) of the gut-brain circuitry are affected by chronic stress, where the information relay to the brain is disrupted and to identify the neuronal and hormonal junctions that mediate gut hypersensitivity and altered function.
2024
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Cross Disciplinary Fellowships - CDF
Coupling massive gene synthesis with generative sequence models to decipher antibiotic resistance
BISARDI Matteo (ITALY)
Michael Smith Laboratories - University of British Columbia - Vancouver - CANADA
TOKURIKI Nobuhiko (Host supervisor)
The spread of bacteria expressing beta-lactamase enzymes, which hydrolyze beta-lactam antibiotics, poses a substantial threat to health systems worldwide. Despite the huge diversity of natural beta-lactamases, our knowledge of their sequence-function relationship focuses only on a handful of clinical isolates and is limited to single-mutational scans. My aim is to characterize the whole sequence landscape of antibiotic-specific resistance, by iteratively combining cutting-edge generative sequence models with high-throughput gene synthesis and functional assays. Protein language models are usually trained on unlabeled data. As a consequence, they are totally blind to function and only rely on statistical patterns to make predictions. To increase the accuracy of the models and endow them with biological meaning, I propose to develop functionally informed generative models by integrating in vivo measurements of thousands of diverged natural and artificially generated beta-lactamases. The experiments will span all four beta-lactamase classes (A, B, C, and D) and use different bacterial species and beta-lactam antibiotics to reproduce clinically relevant conditions. To overcome the prohibitive costs needed to synthesize the libraries of long genes required by our project, I will exploit the expertise of the Tokuriki lab with DropSynth, a cutting-edge multiplexed technique that uses microfluidic droplets to assemble oligo DNA sequences at very low prices. To generate artificial sequences for the first experimental round, I will employ a pre-trained autoregressive protein language model that will be initially fine-tuned on a curated dataset of beta-lactamase sequences extracted from public sequence databases. The function of natural and artificial enzymes will be quantified by linking it to bacterial fitness in a high-throughput fashion, which will be used to enrich the models with functional context. Comparison between functional and inactive sequences will permit the identification of sequence patterns encoding functional specificity and go beyond the statistics of sequence alignments. Moreover, I will exploit the species- and substrate-specificity information by adding dedicated tokens at the beginning of the sequences and conditioning on them during the generative process in a further fine-tuning step. The same procedure will be repeated in a second generative and experimental round to test the quality of the sequence landscape and refine the model once again. The result will be a multidimensional, context-aware sequence landscape of antibiotic resistance for beta-lactamases. We anticipate that my work will shed light on beta-lactamase evolution, and insights into the sequence space that encodes functional specificities will allow fast and inexpensive detection of novel emerging multidrug-resistant beta-lactamases.
2024
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Grant Awardees - Early Career
Quantifying the 4-dimensional microenvironment to explain the coexistence of social insects
BISHOP Tom (United Kingdom)
- Cardiff University - Cardiff - United Kingdom
DAVIES Andrew (SOUTH AFRICA)
- President & Fellows of Harvard College - Cambridge - United States
SENIOR Rebecca (United Kingdom)
- School of Biological & Biomedical Sciences, Durham University - Durham - United Kingdom
JANION-SCHEEPERS Charlene (SOUTH AFRICA)
- University of Cape Town - Cape Town - SOUTH AFRICA
We seek to understand how microclimatic variation in 4D contributes to the coexistence of competing ant species. We will do this by integrating high-resolution environmental, topographic, physiological, and behavioural data from the diverse South African Karoo ecosystem using a combination of techniques that the research team has developed and pioneered.
Few places on Earth are dominated by a single species, instead, most are rich mosaics of coexisting species. Traditionally, coexistence has been explained by niche differentiation and the different resource requirements of species. Many species, however, coexist despite their similar requirements and alternative hypotheses are needed to explain, predict, and understand their coexistence patterns.
We propose a simple, yet untested, explanation for the coexistence of diverse ecological communities: the microclimate-maze hypothesis. This hypothesis posits that climatic variability at the micro-scale effectively isolates individuals and species from each other within a landscape. This isolation prevents competition and promotes coexistence. The microclimate-maze is a simple idea, but the high-resolution, spatiotemporally explicit environmental and biological data required to test it is challenging to obtain.
Here, the complementary expertise of our team will test the microclimate-maze hypothesis relative to classic coexistence theories across five subprojects:
- First, we will empirically measure the microclimate across sixteen 0.25 ha plots in the South African Karoo.
- Second, we will generate high-resolution, 4D maps of microclimate by combining the empirical data with drone-based LiDAR via heat and vapour transfer equations.
- Third, we will rapidly estimate the physiological thermal and hydric performances of over 40 different ant species using novel infrared detection methods.
- Fourth, we will intensively monitor the nesting, foraging, and dietary preferences of ants living in the study plots.
- Finally, we will combine these data in a spatiotemporally explicit framework to test the microclimate-maze hypothesis.
A greater understanding of how species coexist in the same landscapes is a fundamental goal of biological science and will be crucial to understanding when, if, and why ecosystems change in response to environmental fluctuations.
2024
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Long-Term Fellowships - LTF
Structural basis of the human spliceosome quality control
BOREIKAITE Vytaute (LITHUANIA)
Plaschka group - Research Institute of Molecular Pathology (Forschungsinstitut f molekulare Pathologie GesmbH, IMP) - Vienna - AUSTRIA
PLASCHKA Clemens (Host supervisor)
"Splicing of newly synthesized precursor messenger RNAs (pre-mRNAs) is essential for eukaryotic gene expression and involves the removal of introns and subsequent ligation of exons to produce a mature protein-coding mRNA. In humans, splicing is carried out by over 150 proteins and five small nuclear RNAs that assemble into a dynamic multi-megadalton complex called the spliceosome. A single round of splicing requires an exceedingly complex series of conformational and compositional transitions within the spliceosome. With so much room for error, how is aberrant splicing prevented? Recent evidence suggests that mechanisms for spliceosome quality control (QC) exist, but their molecular basis remains unknown.
QC mechanisms have evolved at every step of gene expression to ensure the faithful execution of genetic instructions. By analogy with the well-studied QC mechanisms in protein translation, I hypothesize that the spliceosome can form aberrant conformational and compositional states that, if unresolved, may result in faulty mRNAs and a depleted pool of spliceosome components, impeding gene expression. Thus, while canonical splicing events are increasingly well understood, elucidating how aberrant off-pathway spliceosomes form, how they are recognized and dealt with represents a major knowledge gap. With this project, I aim to expand our mechanistic understanding of pre-mRNA splicing beyond canonical events by elucidating the molecular basis of human spliceosome QC using a combination of structural and functional approaches. Understanding spliceosome QC may shed light on the molecular basis of diseases linked to aberrant splicing and may also reveal the role of QC factors in alternative splicing."
2024
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Grant Awardees - Program Grants
Probing the evolutionary ecology of cognition through High-Density Diffuse Optical Tomography
BOTERO Carlos (United States)
- The University of Texas at Austin - Austin - United States
CULVER Joseph (United States)
- Washington University in St.Louis - St. Louis - United States
GÜNTÜRKÜN Onur (GERMANY)
- Ruhr University Bochum (Ruhr-Universität Bochum) - Bochum - GERMANY
How did advanced cognition and general intelligence evolve? This fundamental question remains largely unanswered because brain anatomy and function have only been studied in a surprisingly small number of species. Recent advances in imaging technology have enabled the characterisation of individual patterns of brain functional connectivity creating a new opportunity for comparing across species and studying the evolution of cognition. However, existing tools like fMRI are expensive, non-portable and tend to require sedation (which disrupts neural networks). This project will bridge these critical gaps by developing a portable, cost-effective optical tool for imaging awake whole-brain functional connectivity in birds and using this groundbreaking tool to study how the architecture and properties of neural networks (i.e., the blueprints of cognition) vary in relation to morphology, ecology, and behaviour. Our research plan involves: (1) Transferring existing Diffuse Optical Tomography (DOT) technology from mammals to birds and validating the performance of these instruments with existing connectivity data on pigeons, advanced computational simulations, and parallel fMRI studies; (2) Developing advanced algorithms for processing, characterising, and comparing functional connectivity networks to ensure the robustness and accuracy of large scale interspecific comparisons; and (3) Applying our new imaging technology to study functional connectivity differences in four major avian clades with well-known differences in ecology and cognitive ability to demonstrate the feasibility of our approach. The successful completion of these goals will transform the eco-evolutionary study of cognition by enabling the characterisation of functional connectivity patterns in large numbers of species over relatively short timescales. Additionally, it will represent a major step forward in the fields of evolutionary neuroscience, cognitive ecology, and cognitive psychology by enabling a shift in focus from comparing singular brain regions to comparing the complex neural networks that actually drive cognitive functions. In terms of brain imaging, this project will also deliver critical improvements to our ability to sample functional connectivity repeatedly, non-invasively, and in the wild at a fraction of current costs.
2024
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Long-Term Fellowships - LTF
Protein dynamics and function in the evolutionary history of the CO2 fixing enzyme Rubisco
BUCHANAN Charles (UK)
Evolutionary Biochemistry - Max Planck Institute for Terrestrial Microbiology - Marburg - GERMANY
HOCHBERG Georg (Host supervisor)
Traditionally, protein function is thought to be determined solely by structure. However, biomolecules are not always confined to one structural conformation, and it has long been conjectured that motions between different conformations can explain differences in function where there are no differences in ground state structures. Advances in Nuclear Magnetic Resonance spectroscopy (NMR) allow such motions to be probed across many different time-scales, even in complexes up to 1 MDa using selective isotopic labelling schemes. The promise of this capability has not yet been fully realised, as it is generally impossible to causally link particular motions to specific differences in protein function. In this proposal, I intend to make this connection by retracing how protein function and dynamics changed in concert across evolutionary history. To establish this paradigm, I will use the socio-economically relevant model system Ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco). Rubisco is responsible for almost all current carbon fixation. During its history and evolution Rubisco’s catalytic mechanism has undergone important changes, almost certainly caused by differences in its motions and dynamics. Firstly, Rubisco has an undesired side-reaction with oxygen, whose product has to be detoxified in a set of reactions that lead to agriculturally significant losses of carbon and nitrogen. Plant Rubiscos distinguish between CO2 and O2 better than their bacterial precursors, but how they accomplish this remains unknown; both kinds of Rubisco have identical active sites in available crystal structures. Secondly, plant Rubiscos depend on a specific ATPase (a so called activase) to periodically remove sugar phosphates other than its native substrate from its active site. This kind of ‘metabolic repair’ is unnecessary in older forms of Rubisco, where the molecules diffuse out of its active sites unaided. The central hypothesis of this proposal is that these important differences in function are ultimately caused by differences in protein motions. I will prove this causal link by first retracing the evolution of these functional changes using ancestral sequence reconstruction and functional characterization of resurrected enzymes (both established in the Hochberg lab). I will then use NMR techniques that probe motions from pico- to micro-second dynamics in large proteins (which I used and developed during my DPhil) to test which dynamical changes are associated with historical substitutions that led to changes in Rubisco’s catalytic properties. This work will create a new paradigm for how the dynamical underpinnings of protein function can be unravelled and reveal the biophysical basis for geochemically significant changes in the function of one of life’s most central enzymes, which may ultimately help rationally improve Rubisco. It will also be a first step in my long-term ambition to illuminate causal links between protein dynamics and function.
2024
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Grant Awardees - Program Grants
Deciphering the role of ion distribution in mitochondria for long-term memory formation
BUSCH Karin (GERMANY)
- University of Münster (Westfälische Wilhelms-Universität Münster) - Muenster - GERMANY
TOMKINSON Nicholas (United Kingdom)
- University of Strathclyde - Glasgow - United Kingdom
JONAS Elizabeth (United States)
- Yale University - New Haven - United States
Long-term potentiation (LTP; memory formation) involves stimulation of neurons and enlargement of specific synapses. Surprisingly, LTP requires an increase in metabolic efficiency (an increase in ATP produced/oxygen molecules consumed). Mitochondrial energy metabolism is controlled by the proton motive force (PMF) across the inner mitochondrial membrane (IMM), which drives ATP synthesis. The PMF consists of an electrochemical gradient, but its exact ionic composition is not known. Furthermore, the IMM is not absolutely tight for ions but shows a certain conductance. We hypothesize that an increase in metabolic efficiency to provide ATP for LTP is based on an optimization of usage of PMF. We propose two mechanisms: a) structural alteration in cristae compartments that optimize the PMF usage and OXPHOS coupling and b) a decrease of the leakiness of the IMM for ions, e.g. through closure of a large ion channel contained within the ATP synthase c-subunit ring. We suggest that this closure is due to an internal conformational change that includes the reorganization and movement of ATP synthase F1 toward FO resulting in ATP synthesis onset and thus an increase in ATP production efficiency. To test this hypothesis, structural changes of the IMM as well as dynamic ion distributions on both sites of the IMM before and after LTP will be determined. N. Tomkinson will design and synthesize bioanalytical fluorescent sensors for monovalent and divalent ions (H+, Ca2+, K+, Na+) and test them first in HEK-293 cells. Suitable IonS will then be used in neurons to record potential changes across the IMM. To place the sensors accordingly, they will be chemically conjugated to substrates of self-labeling tags, such as the Halo-tag. These so-called ion sensor HaloTag ligands (IonS-HTL) are used by K. Busch and E. Jonas to dope Halo-tagged proteins in the intracristae space and matrix of neurons to monitor changes in ion concentrations due to LTP. To account for ultrastructural changes and reorganization of ATP synthase during LTP, K. Busch and E. Jonas will conduct high resolution imaging using cristae specific dyes and Halo-tagged ATP synthase for single molecule tracking and localization. This will allow us to test whether increased efficiency in ATP synthesis after LTP stimulation is due to a reorganization of ATP synthase, leak closure and/or changes in the cristae structure.
2024
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Grant Awardees - Program Grants
3D-bioprinting meets machine learning: a novel tool to decipher the determinants of viral tropism.
CASTRILLO Gabriel (SPAIN)
- University of Nottingham - Nottingham - United Kingdom
VALLI Adrian (ARGENTINA)
- Spanish National Research Council (Consejo Superior de Investigaciones Científicas, CSIC) - Madrid - SPAIN
STEGMAYER Georgina (ARGENTINA)
- National University of the Littoral (Universidad Nacional del Litoral, UNL) - Santa Fe Capital - ARGENTINA
Similar to humans, plants can be infected with a variety of viruses producing diseases, including plant death. These infection outcomes are determined by the viral tropism, the specificity of a virus for a cell type, tissue or species. This unique virus characteristic is regulated by the host immune system, the site of entry, and the cell types infected. Thus, knowing determinants of viral tropism is critical to predict and control the spreading of a viral infection and its outcome. In humans, this information is available for a high number of viruses because of the existence of novel tissue and organ models, like organoids, that facilitate the generation of this knowledge. Unfortunately, in plants similar technologies have not yet been developed, slowing down the study of viral tropism and the design of novel strategies to tackle virus infection. With this project, we will take a major step to correct this oversight by deciphering why a virus can colonise a cell type and not others. This is achievable now because we have a unique multidisciplinary team composed by experts in plant sciences, biomaterials, virology, imaging and machine learning methods from four different countries. This team will collaborate to demonstrate our hypothesis that similar to human organoid models, it is possible to reproduce plant organ characteristics in vitro to develop organ models to study viral tropism. We will do this via an innovative approach that includes the use of novel self-assembling materials combined with key macromolecules and living cells from the different plant organs (leaf, stem, and root) that enable 3D-printing of artificial plant organ tissues (objective 1). These models, that reproduce 3D characteristics of different plant tissues will be infected with a collection of labelled viruses to study viral tropism. So, we will know which cell types from each organ can be colonised by a virus and which genes they induce (Objective 2). This data will be used to predict the viral ability to colonise intact plant tissues via machine learning methods and will be validated in real plants (Objective 3). This technology will open new avenues to understand the impact of viral tropism on plant health, a central aspect of all crop breeding programs and will help us design novel antiviral strategies to increase crop performance under current and future climate conditions.
2024
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Grant Awardees - Early Career
How predictable is evolution? Eco-evolutionary dynamics of fungi across biological scales
MANHART Michael (United States)
- Rutgers Biomedical and Health Sciences - Newark - United States
WORTEL Meike (NETHERLANDS)
- University of Amsterdam - Amsterdam - NETHERLANDS
CHARLEBOIS Daniel (CANADA)
- University of Alberta - Edmonton - CANADA
Evolutionary biology has traditionally focused retrospectively on the natural history of life, but new tools and challenges (such as climate change and drug resistance) have precipitated the need for evolution to become a predictive science. The repeatability of evolutionary processes is a key concept for making these predictions. While previous studies have uncovered some of the basic theory and examples of repeatable evolution in single-species microbial populations, it is not clear what these results mean for repeatability in multispecies communities where microbes naturally exist. Furthermore, the relationship between species diversity and repeatability may depend on the biological scale we consider, but we lack general principles for how evolutionary repeatability varies across scales.
We have assembled an interdisciplinary team, combining experiments on communities of Candida yeast (led by DC), multiscale modeling (led by MW), and bioinformatics/theory (led by MM), to address how eco-evolutionary feedbacks affect evolutionary repeatability across biological scales. The main hypothesis of our project is that greater species diversity decreases evolutionary repeatability. Candida yeasts are an ideal system to address this hypothesis, as Candida naturally occur in multispecies communities and rapidly evolve resistance to antifungal drugs. The project is structured into four interconnected objectives, each involving collaborations between PIs. We will empirically (Objective 1) and computationally (Objective 2) explore how antifungal resistance is affected by communities, ploidy, and drug concentrations. Empirical data will inform multiscale models (including genotypes, phenotypes, and environment) and model predictions will be verified by experiments. These models (Objective 2) will then inform conditions for evolution experiments (Objective 3) and produce evolutionary simulations to test repeatability across interspecies diversity. Both the empirical and computational evolutionary outcomes will be analyzed with a novel framework to quantify repeatability across biological scales (Objective 4), and hypotheses about the underlying mechanisms will be validated in simulations (Objective 2). Altogether this project will make a fundamental advance toward evolutionary predictions of microbes in ecologically-relevant environments.
2024
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Long-Term Fellowships - LTF
Targeted epigenome editing using induced proximity-based small molecules
CHIBA Kosuke (JAPAN)
Department of Chemistry, Department of Molecular and Cell Biology - The Regents of the University of California, Berkeley - Berkeley - United States
NOMURA Daniel (Host supervisor)
Epigenetic modifications modulate gene expression and suppression, which strongly affect embryonic development, cell differentiation, and many genetic diseases including cancer. While DNA methylation has been widely studied as one of the important epigenetic modifications, there is no universal tool to artificially edit DNA methylation to specific loci. Recent work has demonstrated that a dead Cas9 (dCas9) fused to a catalytic domain of DNA methyltransferases (DNMTs) successfully induced DNA methylation in loci-specific manner using guide RNA (Nunez J. K. et al. Cell, 2021). These tools are powerful to study epigenetics, however, it faces packaging and delivery challenges because of their huge molecular weight. This project aims to develop a small-molecule-based DNA methylation platform as a tool for selective epigenome editing at specific loci. This platform will enable us to study the effect of DNA methylation in stem cells and patient-derived cells with high modulating efficacy because small molecule has good cell permeability. Furthermore, it could also be applied to study tissue-specific effects of epigenomics in vivo. Herein, we propose to use covalent chemoproteomic platforms to find small-molecule covalent recruiters targeting allosteric non-functional sites within DNMTs as well as within demethylases (TETs). Upon identifying suitable recruiters which retain the catalytic activities of their respective enzymes, we will take two orthogonal approaches: (1) a small-molecule based approach to conjugate our DNMT or TET recruiters to small molecule ligands for transcription-related factors, such as p300, BRD4, and EZH2, or onto G-quadruplex targeting ligands previously reported in literature. (2) a bioconjugation approach wherein our DNMT or TET recruiters are attached to dCas9 with guide RNA or pyrrole-imidazole polyamide (PIP), which could recognize target DNA in a sequence-specific manner. In the case of concept (1), we hypothesize that these conjugates will recruit DNMTs or TETs to actively transcribed or transcriptionally repressed genetic loci to methylate or demethylate these sites to suppress or activate transcription of these sites, respectively. This approach could be useful as a chemical tool for modulating transcription or even a therapeutic approach for diseases such as cancer, in which cancer cells often show aberrant activation of oncogenic loci and suppression of tumor-suppressor loci. Concept (2) will enable more control of methylation and transcriptional regulation at specific genetic loci. It could be useful for studying cell development or differentiation by changing the translation state of specific loci. Our tools will elucidate which DNA methylation or demethylation is lethal for embryonic failure, and which loci is relevant for oncogenesis or cell differentiation. We expect this approach could also be applied to other editing strategies such as histone acetylation or RNA epitranscriptomics.
2024
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Grant Awardees - Program Grants
Unambiguous Biosignatures for Life Detection
CLEAVES Henderson (United States)
- Howard University - Washington - United States
VAN ZUILEN Mark (FRANCE)
- French National Centre for Scientific Research (Centre national de la recherche scientifique,CNRS) - Plouzané - FRANCE
MCMAHON Sean (United Kingdom)
- University of Edinburgh - Edinburgh - United Kingdom
What distinguishes living from non-living matter? Organisms (and their fossil and otherwise degraded remains) differ from non-biological entities in important ways. It is particularly notable that natural selection favors certain materials, morphologies, and metabolic processes, which have evolved many times independently, likely because they represent “optimality peaks” on the landscape of evolutionary fitness and because these peaks may be (onto)genetically accessible from multiple starting points and evolutionary histories. We propose to apply state of the art machine-learning methods and analytical tools from paleontology and organic geochemistry to discriminate biological and non-biological materials, patterns and processes. Our first major goal is to improve our ability to recognize proxies for life (“biosignatures”) in environments far removed from us in time (e.g. billions of years old terrestrial samples), in space (e.g. in extraterrestrial solar system materials), or in physicochemical conditions (extreme environments on the modern Earth). Our second goal is to address the question of how and why biological materials differ systematically from non-living ones. This aligns with HFSPO’s mission “to fund basic research focused on the elucidation of the sophisticated and complex mechanisms of living organisms”.
2024
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Grant Awardees - Program Grants
Optogenetic control of organelle “chatter” and effects on calcium dynamics in human cardiomyocytes
ENTCHEVA Emilia (United States)
- The George Washington University - Washington - United States
SATO Moritoshi (JAPAN)
- The University of Tokyo - Tokyo - JAPAN
COLMAN Michael (United Kingdom)
- The University of Leeds - Leeds - United Kingdom
Excitation-contraction coupling (ECC), linking electrical events to calcium release and mechanical contraction, is central to the heart’s function. Current ECC theories focus on the sarcoplasmic reticulum, SR, as the main intracellular calcium store with optimized location and molecular makeup for reliable calcium cycling to translate electrical triggers into mechanical work. As highly metabolically active cells, cardiomyocytes have a densely populated and intricately structured cytosol, full of organelles with their own calcium cycling machinery. These non-SR organelles include the mitochondria, lysosomes, endoplasmic reticulum (ER). Recent imaging data suggest proximity and possibility for communication (“chatter”) between these organelles in synchronizing calcium release via nanospaces. To fill a gap in our understanding of the contribution of non-SR compartments to cardiac ECC, we will develop and deploy new cardiomyocyte-tailored optogenetic “magnet” tools to dynamically bring organelles together while tracking calcium release and wave dynamics. Human pluripotent stem cell derived cardiomyocytes, iPSC-CMs, will serve as an experimental model for this project. Effectiveness of tethering of different organelles by light will be assessed using fluorescence reporter co-localization, as well as optogenetics-enabled fast-freezing electron microscopy of ultrastructure. The functional consequences of light-induced nanodomains between key calcium stores and increased “chatter” between them will be systematically quantified by voltage and calcium dynamics measurements using global and organelle-specific optical sensors. These experimental observations will be used to formulate new inclusive models of ECC that reflect organelle proximity and “chatter” to better capture pathological states and to potentially provide new anti-arrhythmic therapeutic options. Some organelle tethering will also aim to induce a more mature state in the iPSC-CMs, i.e. compensate for the lack of T-tubules or initiate T-tubule formation by light for enhanced ECC. Overall, this interdisciplinary work will contribute to our fundamental understanding of calcium dynamics in the heart, by providing an updated quantitative view of ECC including non-SR compartments.
2024
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Grant Awardees - Program Grants
Illuminating Microbial Communication Networks: The Phycosphere lab (COUDRET, Christophe)
COUDRET Christophe (FRANCE)
- CNRS Délégation occitanie - Toulouse - FRANCE
TUVAL Idan (SPAIN)
- CSIC - Esporles - SPAIN
RAINA Jean-baptiste (FRANCE)
- University of Technology Sydney - Sydney - AUSTRALIA
WHEELER Glen (United Kingdom)
- Marine Biological Association of the United Kingdom (MBA) - Plymouth - United Kingdom
Marine microbial communities play a central role in global carbon and nutrient cycling. In these complex communities, chemically mediated signaling between phytoplankton and their neighboring microbes mediates important trophic interactions. However, recent studies suggest that light-based communication may also contribute to microbial intra- and inter-species communication and influence community structure and function in the phycosphere (the microenvironment surrounding microalgal cells). Yet, the nature of such communication is currently completely unknown. We will examine how microorganisms in the phycosphere use light-based communication to influence the structure and function of their surrounding community. More specifically, we aim to answer: What forms of light-mediated communication exist between microbial communities (i.e., chlorophyll fluorescence, bioluminescence)? Are bacteria able to sense light generated from their phytoplankton hosts? What are their physiological responses to light sensing (i.e., phototaxis or secretion of nutrients and infochemicals)?
2024
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Grant Awardees - Early Career
Resurrecting the Multiple Origins of Tyrosine Kinase Activity and Phosphotyrosine Recognition
CREIXELL Pau (SPAIN)
- The Chancellor, Masters, and Scholars of the University of Cambridge - Cambridge - United Kingdom
METZGER Brian (United States)
- Purdue University - West Lafayette - United States
A longstanding goal in biology is to understand how nature innovates or, in other words, how it introduces capabilities that previously did not exist. The experimental tractability of molecular systems containing multiple biochemical functions makes them particularly suited to address this fundamental question, yet we generally do not understand the individual molecular steps that give rise to each molecular function nor their relative evolutionary order.
Phosphotyrosine signaling is a molecular system that evolved relatively recently and regulates processes ranging from proliferation and differentiation to cell-to-cell communication. Tyrosine Kinases (TKs), which phosphorylate tyrosine residues (i.e., phosphotyrosine “writers”), and SH2 domains, which recognize and bind phosphorylated tyrosine residues (i.e., phosphotyrosine “readers”), are two key components of this signaling toolkit. Whereas SH2 domain-containing proteins are found throughout eukaryotes and are thought to be relatively ancient, the dogma was that TK had evolved just prior to the emergence of metazoans. However, relatively recent evidence of TKs in many pre-metazoan species directly challenges this dogma and raises new questions about the timing and molecular steps underlying the origins and evolution of phosphotyrosine “writing” and “reading”, both individually and in relation to one another. Moreover, we have recently shown that signaling downstream of a subset of TK that are capable of “writing” twin phosphotyrosine marks antagonizes canonical single phosphotyrosine pathways. The emergence and evolution of this non-canonical TK activity has remained equally unclear.
On top of the canonical branching leading to most TKs, phosphotyrosine “writers” have evolved multiple times independently during eukaryotic evolution. This provides us with a unique opportunity to determine the extent to which the evolution of new molecular functions is dictated by biophysical constraints, contingent on evolutionary origins, or merely one of many possible evolutionary solutions. Here we propose to combine high-throughput biochemistry with ancestral protein reconstruction to address two broad questions: 1) when and how did single and twin phosphotyrosine kinases and binders evolve, 2) how interchangeable are the different “solutions” for TK activity among the various evolutionary origins of this function?
2024
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Long-Term Fellowships - LTF
Analysis of molecular changes of the nervous system in C. elegans upon circadian rhythm entrainment
DAHL Kristin (USA)
Biozentrum - Biozentrum University of Basel - Basel - SWITZERLAND
SPANG Anne (Host supervisor)
Caenorhabditis elegans are ectothermic and are thus subject to diurnal and seasonal changes in temperature, specifically soil temperature where they naturally reside. C. elegans sense temperature changes through specific thermosensory neurons and respond through changes in intracellular signaling. These neurons are essential for the regulation of longevity (Lee & Kenyon, 2009). In the laboratory setting, single and multiple, short-term heat shocks have been shown to increase lifespan in C. elegans (Zhou et al, 2011). The phosphoproteome of adult C. elegans after short-term mild heat stress showed a wide range of signaling changes, notably to proteins associated with lifespan determination (Huang et al, 2020). C. elegans can be entrained to a circadian rhythm by the application of temperature cycles (Olmedo et al, 2012). However, it remains unclear if temperature-induced circadian rhythms have a protective effect on longevity compared to a single short-term heat shock. Thus, we aim to elucidate whether circadian rhythms entrained by temperature cycling have a positive effect on longevity through the analysis of the changes to mRNA expression and the proteome, specifically in the nervous system. Hypothesis: Circadian rhythm temperature shifts increase C. elegans longevity and result in mRNA and proteome changes to the nervous system. Aim1: How do oscillating circadian-like temperature shifts affect C. elegans longevity? We will use an automated platform with precise temperature control (Le et al, 2020). We will employ circadian rhythm paradigms that mimics naturally occurring temperature oscillation from to 12°C to 22 °C and compare those to a constant state as well as a single heat shock to determine their impact on C. elegans longevity. Longevity will be assessed by measuring locomotion, touch response, and pharyngeal pumping. We will determine the circadian entrainment paradigm that has the most beneficial effect on longevity, which will be used in Aim 2. Aim2: Which pathways are activated/repressed in the nervous system during and after circadian temperature entrainment? We will utilize Ribotag technology with RNAseq and TurboID fused to a fluorescent protein with LC/MS to identify actively translating mRNAs (Wester et al, 2023) and proteins and post-translational modifications, respectively in the nervous system using neuron-specific promoters. Inducible TurboID in C. elegans is established (Artan et al, 2021). We will determine the overlap between the RNA and proteome datasets and perform pathway analyses using computational tools. Promising candidates will be validated by tissue-specific RNAi, CRISPR-Cas9 technology and functional assays to elucidate underlying mechanisms. Conclusion: We will elucidate neuronal molecular mechanisms regulating the responses to naturally occurring temperature oscillations and their effect on the animal’s lifespan.
2024
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Grant Awardees - Program Grants
Understanding the molecular basis of animal cold thermosensation
VIANA Felix (SPAIN)
- Miguel Hernandez University (Universidad Miguel Hernández de Elche) - Elche - SPAIN
DOMENE Carmen (United Kingdom)
- University of Bath - Bath - United Kingdom
DALEN Love (SWEDEN)
- Stockholm University - Stockholm - SWEDEN
SOBOLEVSKY Alexander (Russian Federation)
- The Trustees of Columbia University in the City of New York - New York - United States
Temperature is an important natural stressor, driving selection to survive in particular environments. Environmental temperature is sensed by specialized proteins, known as temperature-sensitive TRP ion channels (thermo-TRPs), expressed at sensory nerve endings. TRPM8 is the key cold sensor in mammals and birds. How cold temperature is translated into ion channel structural changes is unclear. We propose a multidimensional characterization of thermo-TRPs in animals evolutionary adapted to different thermal environments, including extreme cold temperatures, to gain insight into structural basis of temperature-dependent gating. Likewise, comparison of thermo-TRPs from mammals and birds, with a distinct evolutionary history of > 300 million years, offers another temporal dimension.
The scientific consortium is formed by four international teams with complementary expertise. Using comparative genomics and bioinformatics, we will characterize DNA sequences of thermo-TRPs in evolutionary related species occupying different thermal niches. We will identify amino acid sequence changes unique to cold-adapted species, including extinct woolly mammoths and steppe bison, as well as extant ptarmigan and lemmings, and compare them with relatives from warm temperate climates. Functional analysis of resurrected proteins expressed in mammalian cells, including neurons, using advanced electrophysiological techniques will show whether they have different thermal sensitivities. Using reverse genetics, we will examine how engineering specific nucleic acid sequence affects the phenotype of the mutated proteins. Best candidates identified during genomic and functional tests will be subjected to single-particle cryo-EM for 3D structure determination, further refined by molecular dynamics simulations to gain insight into the molecular processes underlying thermal sensitivity. Based on structural comparisons and the results from computer simulations, we will propose a molecular mechanism of temperature sensation. This mechanism will be critically tested using mutagenesis and functional recordings.
In the context of rapid climate change, unraveling the function of ion channels involved in temperature sensing and thermoregulation has significant relevance. These findings could help identify novel interventions to minimize the effects of temperature on animal physiology and survival.
2024
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Long-Term Fellowships - LTF
Genetically Encoded Voltage Indicators to uncover the role of Golgi cells in Pattern Classification
DAVOINE Federico (URUGUAY)
Institut de Biologie de l'ENS - Dieudonné Lab - Institut de Biologie de l'Ecole Normale Supérieure, IBENS - Paris - FRANCE
VILLETTE Vincent (Host supervisor)
DIEUDONNÉ Stéphane (Host supervisor)
We all rely on the cerebellum to refine our movements, whether it is a surgeon performing a complex procedure or a farmer lifting a box of vegetables. However, the cellular mechanisms underlying the encoding and recognition of sensorimotor sequences within the cerebellar cortex are not well understood. Classical theories propose that sparse activation of Granule Cells (GrCs) is essential for pattern classification of sensorimotor information coming through Mossy Fibers (MFs). Yet, recent in vivo recordings have revealed extensive activity of GrCs, challenging the current understanding of cerebellar function. This proposal aims to investigate the hypothesis that inhibitory Golgi Cells (GoCs) play a key role in shaping patterns of GrC activity, by encoding relevant behavioral information. GoCs provide a major source of inhibitory input to GrCs and have extensive connectivity, with synaptic inputs from MFs and Parallel Fibers (GrCs’ axons), re-entry loops from Purkinje Cells (via inhibitory Lugaro Cells) and inhibitory neurons from Deep Cerebellar Nuclei (DCN), as well as spillover-mediated input from Climbing Fibers (CFs). Furthermore, paired patch-clamp recordings and computational simulations suggest that electrical coupling between GoCs may enable them to both synchronize and desynchronize during behavior, thus adding more complexity to the system. My objective is to study the functional relevance of these connections to GoCs, using the Genetically Encoded Voltage Indicator (GEVI) JEDI-2P, during postural adjustments of head-fixed mice, a cerebellar-relevant behavior. The host lab has developed viral expression strategies and custom-made multiphoton optical technologies to optimize GEVI recordings, suited to record the fast kinetics of GoCs spikes and their subthreshold activity, as well. In particular, the combination of GEVI and Ultrafast Local Volume Excitation, in a random access microscope, enables to overcome major limitations inherent to all-optical interrogations of neuronal circuits in behaving animals. My proposal aims to address the following questions: Q1: Do GoCs population encode specific sensorimotor features or the general behavioral context? Q2: How plastic is the functional extent of electrical connectivity between GoCs? Q3: Are there clusters of GoCs shaped by CFs spillover? Q4: How do re-entry loops participate in shaping GoCs activity? Depending on the question being investigated, a red-shifted Genetically Encoded Calcium Indicator will also be expressed by MFs or GrCs (Q1), CFs (Q3), Lugaro cells or DCN neurons (Q4). Optogenetic stimulation will be used to measure electrical coupling in vivo for Q2. Computational simulations might be performed as a supplementary approach. This project will provide insights into the dynamics of inhibitory patterning and the role of electrical coupling in the mammalian brain, during circuit-specific relevant behavior, with unprecedented spatial and temporal resolution.
2024
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Grant Awardees - Program Grants
Mechanisms and origins of glycosylation in giant viruses
FISCHER Matthias (GERMANY)
- Max Planck Institute for Medical Research (Max-Planck-Institut für Medizinische Forschung) - Heidelberg - GERMANY
DE CASTRO Cristina (ITALY)
- University of Naples Federico II (Università degli Studi di Napoli Federico II) - Napoli - ITALY
OGATA Hiroyuki (JAPAN)
- Kyoto University, Uji Campus - Uji - JAPAN
Viruses typically rely on host enzymes for modifying their proteins after translation, but the so-called “giant viruses” not only have exceptionally large particles and genomes, they also encode unique biosynthetic machineries including various carbohydrate-modifying enzymes. Initial studies have shown that their capsids are decorated with diverse glycan structures, most of which were unknown from the study of cellular organisms. However, the function, biosynthesis, and evolutionary origin of glycan diversity in giant viruses remain unknown. Here, we will address these questions by studying cultured virus-host systems of marine phototrophic and heterotrophic protists, and corresponding giant viruses that encode dozens of predicted sugar-modifying enzymes. We will follow a holistic approach to dissect the glycomes of three giant viruses, by addressing these fundamental tasks: 1) Which glycans compose the capsid? 2) How are these glycans assembled? 3) What is the evolutionary origin and trajectory of viral glycogenes?
The first task is key to defining the viral glycan structure and will be addressed by combining chemical and spectroscopic methods. The second task will assign functions to predicted viral glycan-modifying enzymes by siRNA knockdown and structural analysis of the resulting virus capsids. It will also address the assembly of glycans during the infection process by feeding the host with selected sugars labeled with an azido-group, which can later be coupled to a fluorophore or chemical bait to monitor the subcellular localization or to isolate biosynthetic intermediates.
Finally, the third task will re-trace the evolutionary path of viral glycosyl-manipulating genes by large-scale comparative genomics and phylogenetic analysis.
The overall outcome of this project will enable an unprecedented insight into the glycobiology of giant viruses and advance our understanding of enzymatic diversity in nature.