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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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Long-Term Fellowships - LTF
Reconstructing the ancestral architecture of animal cells
DE HAAN Diede (NETHERLANDS)
Department of Cell Biology and Infection - Institut Pasteur, Paris - Paris - FRANCE
BRUNET Thibaut (Host supervisor)
Choanoflagellates, the closest living relatives of animals, have emerged as a powerful model system to study the origin of animal morphogenesis and multicellularity. These aquatic microbes share a significant portion of critical animal genes and cell architectures, such as the apical collar complex (acc), comprised of a central flagellum surrounded by a ring of microvilli. Many choanoflagellates have transient multicellular life stages, and Choanoeca flexa, a recently discovered species, is capable of emergent collective behavior. Sheet colonies of C. flexa are formed by intercellular links at the microvilli, and can switch between swimming and feeding conformations via collective apical constriction that alters collar geometry, reminiscent of mechanisms of animal tissue morphogenesis. Despite the evolutionary and functional relevance, little is known about the structure, patterning and remodeling of the acc, and the nature of intermicrovillar links in C. flexa is entirely unknown. I hypothesize that the mechanisms that govern cell and tissue architecture in animals were largely inherited from their single-celled ancestors, and can still be identified in choanoflagellates. More specifically, I hypothesize that common principles underlie acc formation, intermicrovillar adhesion and collective contractility in choanoflagellates and animals. My aim is to elucidate the processes that control choanoflagellate cell and colony shape, by investigating acc ultrastructure and formation, and characterizing the intermicrovillar links and cellular basis of colony inversion in C. flexa, respectively. I will expand the current toolbox of choanoflagellate research (predominantly comparative genomics, transcriptomics and, more recently, functional genetics) with state-of-the-art electron microscopy, to characterize high-resolution and structural aspects of different choanoflagellate life stages, and cell-cell interactions. I will use cryo-electron tomography for the ultrastructural characterization of the acc in Salpingoeca rosetta and C. flexa. Next, I will use sub-tomogram averaging to resolve the molecular composition of intermicrovillar links, within and between cells, to identify conserved and unique components that mediate the intercellular contact. Additionally, I will reconstruct whole-cell architectures of C. flexa cells and colonies in both conformations using focused ion beam-scanning electron microscopy, and quantify subcellular arrangements that mediate the switch. To gain insight into acc formation, I will use live-cell confocal microscopy to image cells during induced acc regeneration. Finally, I will perform drug screens and use high-throughput automated imaging to dissect the molecular pathways involved in acc formation. This work will provide insights into the molecular and cellular regulation of the collar complex in choanoflagellates and provide a comparative framework for the origin of cell organization in metazoans.
2024
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Long-Term Fellowships - LTF
M.I.N.D. Obesity: Microbiota, Immune system and sensory Nerves Dynamic interactions
DECOURT Charlotte (FRANCE)
Neurology - Imperial College of Science, Technology and Medicine - London - United Kingdom
DI GIOVANNI Simone (Host supervisor)
"Obesity is a global health issue due sedentary lifestyle and unhealthy diet. The adipose tissue maintains metabolic homeostasis and is the largest endocrine organ mainly localized subcutaneously in young humans. The skin, the largest innervated organ in the human body houses millions of bacteria. Studies have shown differences in skin immunity and bacterial composition between non-obese and obese individuals. However, the implications of these modifications for sensory skin innervation remain unclear. The hypothesis is that the accumulation of adipose tissue under the skin modifies the skin microenvironment by inducing an inflammatory response affecting skin innervation and function directly and indirectly by modifying the skin microbiota diversity, which would in turn modify skin immunity and innervation. The research program addresses the following questions:(1) How do modifications in the skin adipose tissue affect immunity and the microbiota in obese individuals and animals, and vice versa? (2) How does this aberrant metabolic and immune homeostasis influence sensory nerve signaling and transmission? (3) What are the molecular and cellular mechanisms underlying this bidirectional tripartite relationship?
Aim 1 is to characterize the skin bacterial microbiome in human and mice in normal-weight and obese subjects and animals.
Bacterial species will be identified by in-depth sequencing from skin biopsies from individuals and mice. Intraepidermal nerve fiber density and sensory function will be assessed from skin biopsies and with neurophysiological tests for sense of touch and nociception.
Aim 2 is to investigate the manipulation of the skin bacteria associated with obesity in mice and humans on sensory innervation and function.Loss-of-function experiments will use antibiotics to modify/deplete bacterial species in both normal-weight and obese mice. Gain-of-function experiments will use microbiota transfer onto the microbiota free skin of obese or normal-weight mice and intraepidermal nerve fiber density and sensory function will be assessed from skin biopsies and with neurophysiological tests.
Aim 3 is to evaluate how obesity-dependent modifications of the microbiota and of skin immunity affect the crosstalk between skin bacteria, immunity and sensory neuronal signaling.
Single-cell spatial multiomics of the skin and of sensory neuronal circuitry in the dorsal root ganglia and spinal cord will be carried out following manipulations of obesity-related skin bacteria and immune pathways. GCaMP (calcium) reporter mouse lines for specific sensory modalities will also be used to detect changes in neuronal activity.
This study is expected to provide a novel understanding of the mechanisms underlying the bidirectional relationships among the skin microbiome, immunity, and innervation and their implications in sensory function in obesity. It could also have significant implications for obesity associated diseases of the peripheral"
2024
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Grant Awardees - Program Grants
Decoding invisibility: from genome evolution to tissue optical properties in transparent fish
DEL BENE Filippo (ITALY)
- Institut de la Vision - Paris - FRANCE
JOHNSEN Sonke (United States)
- Duke University - Durham - United States
RAMIALISON Mirana (Madagascar)
- Murdoch Childrens Research Institute - Parkville - AUSTRALIA
The "invisibility superpower" is an extreme camouflage adaptation widespread among animals living in pelagic environments, which have evolved transparency to avoid detection by both predators and prey. In teleost fish, transparency has evolved multiple times, partly mediated by a loss of pigmentation. However, the question of how internal organs and tissues, such as muscles and digestive glands, become transparent by minimizing light scattering and absorption remains unanswered. Studies in certain invertebrates and tetrapod vertebrates have shown that internal transparency is sometimes an actively maintained physiological process. Here, our aim is to investigate the adaptations that allow animals to achieve transparency, with a particular focus on the teleost subfamily of Danionin fish. Within this subfamily, multiple species have independently evolved transparency. To achieve this, we will leverage the experimental accessibility of the non-transparent zebrafish (Danio rerio) and the highly transparent Danionella cerebrum. Our research will be structured around three main objectives. Firstly, we will investigate the tissue properties of Danio rerio and Danionella cerebrum through ultrastructural and optical studies. We will examine factors such as blood vessel and red blood cell distribution, skin cell structure, and musculature myofibril structure. All ultrastructural findings will be incorporated into optical models aimed at exploring the effects of tissue modifications on transparency. Concurrently, we will employ comparative genomic approaches to several available Danionin species to identify genomic loci associated with whole-body transparency in these fish. Additionally, we will perform spatial transcriptomics studies to assess the spatial expression levels of candidate transparency genes in both zebrafish and D. cerebrum. Finally, building on these results, we will functionally test the genetic and genomic changes associated with transparency in these two model systems using genome editing techniques. The outcomes of this genetic manipulation will be quantitatively evaluated by assessing animal transparency through optical coherence tomographic microscopy. Overall, this proposed project will provide us with a deeper understanding of the genetic, anatomical, histological, and ultrastructural differences underlying tissue transparency in vertebrates.
2024
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Grant Awardees - Program Grants
Cross-talk between the skin microbiome, immunity and sensory innervation in neurophysiology
DI GIOVANNI Simone (ITALY)
- Imperial College of Science, Technology and Medicine - London - United Kingdom
ELINAV Eran (ISRAEL)
- Weizmann Institute of Science - Rehovot - ISRAEL
FAN Rong (United States)
- Yale University - New Haven - United States
This team aims to investigate the cross-talk between microbial-dependent immunity in the skin, the largest and most innervated organ in our body, and the peripheral nervous system, for the control of sensory signals affecting nociception and spinal sensorimotor integration across the lifespan. How exposure to the diversity of the skin microbiome affecting immunity in the skin could drive peripheral and central nervous system physiological responses and how these can in turn influence skin immunity and the skin microbiome is unknown. This research program aims to address the following fundamental questions: (i) how does the microbiome that shapes immunity in the skin regulate neural signaling and activity? (ii) how does neural activity in turn regulate the skin immune and microbial microenvironments? (iii) what are the neurophysiological implications of this cross-talk? Our studies will reveal a new biological paradigm for bidirectional cell-cell communication across systems, barriers, and species within the well-defined anatomical system stemming from skin innervation. Given the profound effect of aging on neural activity and immunity affecting homeostatic processes, this program will investigate these mechanisms across the lifespan, in young and aged animals and individuals. This will expand its relevance and timeliness for the understanding of age-dependent changes in neurophysiological responses underpinned by neuro-immune interactions. Last but not least, technologies including single cell/nuclei sequencing, bacterial metagenomics, spatial transcriptomics and epigenomics, chemo and optogenetics to modulate neuronal activity currently allow us to soundly experimentally investigate the immune-neuronal cross-talk in our well-spatially and functionally defined model system. Therefore, we believe that this research program will be extremely novel, while feasible, timely, and relevant to the understanding of neuroimmune interaction regulating fundamental physiological functions. It will also bear critical implications for human health for the regulation of nociception and sensorimotor function.
2024
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Grant Awardees - Early Career
A tale of tails – reconstructing evolutionary transition between archaeal and eukaryotic chromatin
TAKEMATA Naomichi (JAPAN)
- Kyoto University - Kyoto - JAPAN
DODONOVA Svetlana (Russian Federation)
- European Molecular Biology Laboratory (EMBL-Heidelberg) - Heidelberg - GERMANY
In eukaryotes, histone proteins play critical roles in chromatin organization by forming its fundamental structural unit called nucleosome. DNA accessibility can vary depending on the 1D nucleosome spacing and their 3D arrangement, enabling regulation of chromatin-based processes such as transcription. Eukaryotic chromatin regulation strongly depends on disordered N-terminal regions, “tails,” of the histones. These tails serve as foci for post-translational modifications, mediate interactions between nucleosomes, and recruit various effector proteins, readers, writers, and remodellers. Archaeal histones are ancestral to eukaryotic histones. However, most of them have no tails, which are crucial for eukaryotes. This raises key questions in the chromatin-evolution field: How did eukaryotes evolve histone tails and tail-based regulatory mechanisms from an archaeal ancestor, and what role could the tails play in proto-eukaryotic chromatin? In this research proposal, we aim to answer these questions by creating the first synthetic model of proto-eukaryotic chromatin. We will fuse eukaryotic histone tails with an archaeal tail-less histone and test how this affects the molecular properties of the histone, its interactions with the DNA, and how it influences chromatin architecture in the test tube and inside the cell. Within our proposed research, we will create and characterize multiple chimeric constructs that mimic a proto-eukaryotic histone in vitro. These constructs will be further introduced into archaeal cells for in vivo characterization. By employing biochemistry, biophysics, genetic engineering, and state-of-the-art sequencing and cryo-ET/EM technologies, we will investigate the structural and functional effects of tail acquisition by an archaeal histone on genomic and molecular scales. Our study will provide insight into how the emergence of histone tails impacted proto-eukaryotic chromatin and how it led to the subsequent evolution of tail-based regulatory mechanisms in the eukaryotic lineage.
2024
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Long-Term Fellowships - LTF
The neuronal mechanisms underlying state-dependent odor preference
DORON Adi (ISRAEL)
Cell Biology - Harvard Medical School - Boston - United States
LIBERLES Stephen (Host supervisor)
Internal states, such as hunger and thirst, are strong motivational forces that drive us to pursue goals and meet our basic needs. To induce adaptive behavior, specific sensory information needs to be integrated with the internal cues regarding the state of the animal. For example, in my host lab it was shown that mice exhibit hunger-dependent food odor preference, which involves neuropeptide Y (NPY) release in the paraventricular thalamus (PVT) from hypothalamic hunger neurons (AGRP neurons). The PVT is a midline thalamic structure that plays a vital role in various motivated behaviors and is also associated with arousal and valence processing. The PVT is highly interconnected, receiving inputs from multiple brain regions, including the hypothalamus and the brainstem, and has reciprocal connections with several cortical regions. This extensive anatomical connectivity underscores the potential role of the PVT as a hub for linking internal states and external information to drive behavior. Importantly, the PVT consists of heterogeneous cell populations, with subgroups of neurons showing distinct connectivity and transcriptomes. In proposed research, we will investigate neuronal mechanisms within the PVT that drive odor-preference behavior under various internal states. We anticipate that our findings will contribute to a better understanding of the neural circuits and mechanisms underlying the interaction between internal state and external sensory cues.
2024
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Grant Awardees - Program Grants
Mechanoradicals as a novel form of mechanosensing: from protein stretching to animal aging
ZAIDEL-BAR Ronen (ISRAEL)
- Tel Aviv University - Tel Aviv - ISRAEL
GRÄTER Frauke (GERMANY)
- Heidelberger Institut für Theoretische Studien - Heidelberg - GERMANY
DUNN Alexander (United States)
- The Board of Trustees of the Leland Stanford Junior University - Stanford - United States
Over a century of work shows that synthetic polymers, even under pre-failure stretch, undergo ruptures of chemical bonds, leading to the formation of radicals. Whether these mechanoradicals formed in biological material was, until very recently, unknown. Recent in vitro experiments demonstrated that collagen, the major structural component in connective tissues and the most abundant protein in the human body, also forms mechanoradicals when exposed to sufficient mechanical loads. Our hypothesis is that mechanically-generated chemical radicals form within the extracellular matrix of living systems and affect their physiology. Our strategy is to test this hypothesis in two in vivo model systems with unique individual advantages while leveraging synergies: C. elegans to show mechanoradicals in a full organism that can be genetically modified and imaged live, and intact ‘living’ mouse tendon to work with a closer human relative and for full mechanical control.
In this collaborative project, which blends expertise in live-imaging of biosensors, molecular dynamics simulations, micromanipulations, and genetic engineering, we will pursue the following aims: 1) Detect ROS in vivo in the C. elegans cuticle and extracellular matrix of mouse tendon with genetically-encoded and chemical sensors; 2) Correlate extracellular ROS formation with forces on collagen measured with a molecular tension sensor in mechanically-manipulated worms and tendons; 3) Build molecular models of C. elegans collagens and computationally predict rupture-prone and ROS scavenging residues in C. elegans and tendon collagens and variants thereof ; 4) Perturb mechanoradical formation through mutagenesis of predicted residues or with cell-impermeant scavengers; and 5) Examine the effect of reduced or increased mechanoradical formation on cell, tissue, and animal physiology and healthspan. These experiments will uncover mechanoradicals as a hitherto unrecognized molecular species in life that converts tension into ROS, with implications for tissue homeostasis and organism health.
2024
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Grant Awardees - Early Career
S3: Securing shifting sands – from genes to geoengineering
DUNNING Luke (United Kingdom)
- University of Sheffield - Sheffield - United Kingdom
REIJERS Valerie (NETHERLANDS)
- Utrecht University (Universiteit Utrecht, UU) - Utrecht - NETHERLANDS
WENGROVE Meagan (United States)
- Oregon State University - Corvallis - United States
Interactions between the physical environment and living organisms can drive the formation of biogeomorphic landscapes. Coastal sand dunes are one such landscape, where shifting sands are secured into stabilised dunes by specialised coastal grasses. Whilst we know that different species produce different dune morphologies, our understanding of how sand dunes and the species responsible for their bioengineering have co-evolved is incomplete.
This interdisciplinary project combines expertise in evolutionary genetics, coastal ecology, and sediment transport with the ultimate aim of understanding how variation at the molecular level translates into whole landscape changes in terms of topography and resilience. Our molecular approaches will identify the genetic basis of key dune building traits (e.g. rhizome architecture and lignin content), and generate heritability and evolutionary rate estimates for these phenotypes using genome wide data. Field measurements, manipulative experiments and wind tunnel experiments will determine how plant phenotypic variation impacts wind flow dynamics, the ecological limits of the dune grasses, and how this is linked to sediment dynamics. Finally, we will combine our experimental and molecular results with geomorphological models to determine the effect this variation has on coastal morphodynamics.
This ambitious project will investigate how molecular variation can ultimately impact whole landscapes. This will advance our fundamental knowledge of evolution, but also has potentially important applied outcomes. Coastal dunes protect a third of all shorelines from flooding, and our results will enable us to determine the adaptive potential this system has to mitigate the effects of climate change including sea level rise and the increased magnitude of storm surges. If our results show that dune grasses lack the capacity to adapt to changing conditions in a short space of time we may need to adopt mitigation strategies to avoid the collapse of our coastal defences in the future.
2024
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Long-Term Fellowships - LTF
Understanding the role of co-factor mediation in co-transcriptional RNA splicing
FALEEVA Maria (CYPRUS, EU PART)
Sir Peter MacCallum Department of Oncology - University of Melbourne (Melbourne University) - Parkville - AUSTRALIA
DAWSON Mark (Host supervisor)
Transcription factors (TF) bind regulatory elements at specific genes via their DNA binding domains and recruit cofactors using their transactivation domains (TADs) to facilitate transcription. In higher eukaryotes, some genes may span 100kb and include large introns that hinder the processivity of RNA polymerase II (Pol II). As transcription and splicing occur concurrently, the interaction between the spliceosome and transcriptional machinery is highly topical, particularly because mutations in splicing factors are prominent in developmental diseases and cancer. The specific transcriptional coactivators that facilitate Pol II processivity across exon-intron boundaries and facilitate co-transcriptional splicing remain largely unknown; addressing this fundamental biological question has important implications in diverse streams of biology involving plants / animals. This project aims to address this question by selectively recruiting the TAD of nine TFs to a specific integrated promoter to drive transcription of a split GFP reporter system. The efficient transcription &splicing of GFP will enable a fluorescent readout of efficient co-transcriptional splicing and provide the opportunity to identify the major cofactors involved with unbiased CRISPR screens. This rich dataset will provide us with several lines of orthogonal evidence to uncover cofactors required for efficient co-transcriptional splicing. The molecular mechanism underpinning how the identified cofactors facilitate Pol II processivity and co-transcriptional splicing will be the primary focus of the final aim of this project. The central hypothesis is that specific transcriptional coactivators are recruited to facilitate Pol II processivity across exon-intron boundaries and regulate co-transcriptional mRNA splicing. Initial CRISPR screens will be conducted using Human K562 cells with a Gal4-UAS reporter system. Gal4 is fused in-frame with the TAD of a specified TF and recruited to an integrated chromatinised reporter containing 5xUAS binding sites immediately up-steam of a CMV promoter. This drives expression of GFP-PEST cDNA split by a large intron of interest. We will use a bespoke CRISPR library that includes all known transcriptional co-factor proteins to identify targets that specifically disrupt Pol II processivity and co-transcriptional splicing of an intron containing gene. These targets will be validated in human, mouse, and D. melanogaster cell lines. To identify the molecular mechanisms underpinning the results we will modulate the cofactors of interest via rapid degradation via the dTAG and Auxin systems and shall assess the rate of Pol II elongation, splicing and chromatin recruitment of the co-factors. This innovative proposal addresses how co-factors regulate Pol II processivity and co-transcriptional RNA splicing across exon-intron boundaries. The results have significant implications for normal development and cell fate decisions in various biological context.
2024
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Long-Term Fellowships - LTF
Microbial Consortia with Direct Electron Transfer: in situ Visualization of Community Robustness
FINK Justus Wilhelm (GERMANY)
Divison of Geological and Planetary Sciences - California Institute of Technology - Pasadena - United States
ORPHAN Victoria (Host supervisor)
Multi-species consortia of microbes shape human health and environment. Their chemical output emerges from the specialized metabolism of consortia members and the interactions between cells in a close physical grid. Thanks to recent discoveries, we now know that microbial consortia in anaerobic conditions can use electricity to exchange energy between cells. The direct transfer of electric current by nanowires and cytochromes provides these consortia with a low-loss, high-specificity mechanism of exchange that spans larger distances than the exchange of diffusible compounds. This way, direct electron transfer has emerged as a fundamentally different mode of interaction in microbial ecology. Current research with example consortia focuses on the molecular mechanism of electron transfer and the spatial patterns of cell activity at steady state. How such sophisticated interaction networks respond to an environmental perturbation remains an open question. Importantly, this response cannot be predicted from the principles that currently exist. My aim is to address this question directly for methane-metabolizing communities, measuring the response to nutrient concentration both at the level of the population as well as for single cells. To do so, I will leverage the expertise of the sponsor lab to observe single cells responding to nutrient pulses in their original aggregate structure. I will connect these two levels of observations with a quantitative, predictive modeling framework, building on my previous theory work on nutrient limitation. I hypothesize that the response to environmental perturbation emerges in two layers: Firstly, the spatial structure of the aggregate defines a base access of each cell to electron transfer with the partner species. Secondly, cells may experience limitation for diffusible nutrients like nitrogen or vitamins, especially if they are close to a partner cell and the base limitation from electron transfer is relatively weak. To resolve the environmental perturbation in a spatial setting, we need to quantify the relative strength of response for a set of nutrients and do so for single cells. I will test these hypotheses in a naturally evolved system of direct electron transfer: the granular aggregates of anaerobic methanotrophic archaea (ANME) and their sulfate-reducing bacterial partners (SRB) that work together in the deep-sea environment to remove 80% of all methane released from the seafloor. I will apply a nutrient-pulse with stable isotope tracers to map the single cell response within aggregates using the analytical imaging techniques from the sponsor lab (FISH-nanoSIMS). In conclusion, the work here will test the impact of direct electron transfer on community response in an environmentally relevant microbial consortium, enable me to transition from theory to experiments and provide analytical tools to visualize the cell response in a large range of structured microbial aggregates for future research.
2024
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Cross Disciplinary Fellowships - CDF
Elucidating electrophile-sensor signaling proteins at the contact sites between bacteria and host
FRIDIANTO Kevin Timothy (INDONESIA)
Institute of Chemical Sciences and Engineering - École Polytechnique Fédérale de Lausanne (EPFL) - Lausanne - SWITZERLAND
AYE Yimon (Host supervisor)
The rise of antimicrobial resistance necessitates the development of innovative strategies. Burgeoning evidence hints that upon adherence of bacteria, host cells release antimicrobial lipid-derived electrophiles (LDEs) that are counteracted by pathogen-specific proteins (1), rendering the process a promising source of novel therapeutic targets. Nonetheless, investigations toward bacteria–host LDE-signaling remain underexplored due to the lack of high-throughput precision tools to probe such events at the cell-to-cell-surface contact sites. I will address this need by functionally adapting the Aye group’s REX (reactive electrophiles and oxidants) technologies (2–4) that leverage HaloTag as an anchor of custom-designed Halo-targetable photocaged-LDE (Ht-PE) probes to map electrophile-responsive proteins with spatiotemporal precision upon light exposure. If successful, my approach will discover novel electrophilic ligand/target pairs of functional importance in bacteria–host LDE-signaling. I will first use the E. coli–HeLa system as proof-of-concept and extend it to other disease-specific contexts, e.g. L. monocytogenes and human colorectal adenocarcinoma Caco-2 (5) as follows: • Build and functionally validate a novel split-HaLo-REX. Using established cloning/transgene-expression tools, I will fuse a fragment of Halo ‘Ha’ on bacterial cell surface protein, and the other fragment ‘Lo’ on mammalian cell surface protein. Assembly of active HaLo that can bind Ht-PE only upon cell-to-cell contact-site formation will be confirmed using imaging and functional assays. • Map LDE-actionable protein players involved in E. coli adhesion to HeLa cells using the newly-developed split-HaLo-REX. By engineering a panel of Ht-PEs comprising both natural LDEs and structural analogs, execution of split-HaLo-REX in the designated co-culture followed by quantitative proteomics target-ID will enable ranking of both E. coli-& HeLa-originated LDE-responder proteins exclusively operative at the adherence sites. • Validation and mechanistic studies of novel target–ligand pairs. The top-hit responders will be validated for on-target specificity using the established validation method T-REX (2). I will further study how electrophile labeling of top-hits alters their functions on host–bacteria adhesion and downstream changes at both systems (e.g. RNA-Seq) and pathway/mechanistic levels (e.g. host immune response, cell proliferation, DNA damage response, lipid signaling) using methods routinely used in the Aye lab. My project uniquely innovates precision chemical probes and bioengineering design to interrogate biological interactions with spatiotemporal and context-specific control inaccessible by current technologies. It promises to spotlight new approaches to disease treatment. 1.eLife 10, e59295 (2021) 2.Nat. Protoc. 11, 2328–2356 (2016) 3.Nat. Protoc. 18, 1379–1415 (2023) 4.Proc. Natl. Acad. Sci. 119, e2120687119 (2022) 5.Cell 111, 825–836 (2002)
2024
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Grant Awardees - Program Grants
Elucidating physico-chemical forces setting the limit of bacterial growth
HWA Terence (United States)
- The Regents of the University of California, San Diego - La Jolla - United States
VAN TEEFFELEN Sven (GERMANY)
- University of Montreal (Université de Montréal) - Montreal - CANADA
PILIZOTA Teuta (United Kingdom)
- University of Edinburgh - Edinburgh - United Kingdom
FRITZ Georg (GERMANY)
- University of Western Australia (UWA) - Perth - AUSTRALIA
Vibrio natriegens (Vnat) is one of the fastest growing organisms, doubling more than 50% faster compared to Escherichia coli, Bacillus subtilis, and many closely related Vibrio species in rich and minimal medium. The origin of this supercharged growth is enigmatic, but it is clear that it cannot be explained by a simple molecular mechanism. Pilot studies indicate that Vnat’s enzymes, including its ribosomes, work faster. Since the proteomic composition of Vnat is similar to slower growing Vibrios and also to E. coli, faster growth does not only require faster ribosomes but also faster upstream enzymes that synthesize amino acids and other precursors for growth. Strong homology of Vnat with slower Vibrios (e.g., > 97% AA identity with V. campbellii which grows 50% slower) disfavors independent adaptation of individual enzymes. We thus hypothesize that Vnat’s intracellular environment is modified to increase enzymatic rates globally, analogous to increasing the ambient temperature.
To reveal important physico-chemical variables responsible for the higher effective temperature of Vnat, we will study the response of Vnat and its enzymes to various environmental and genetic perturbations. We will also characterize the intracellular environment, measuring, e.g., biomass density, osmolyte concentration, pH, membrane potential, and enzymatic rates, before mimicking those conditions in vitro for direct measurements of enzymatic rates. We will use various techniques including physiological and metabolic approaches (Hwa), genome engineering (Fritz), and single-cell based measurements of biomass density, intracellular diffusion (van Teeffelen), energetics and transport (Pilizota). Comparative genomics between Vnat/V. campbellii and other closely related fast/slower growing Vibrio species (Fritz), together with mathematical model of physiology, will ultimately link the physico-chemical factors of faster growth to their genetic driver(s). Finally, we will demonstrate our understanding by moving the genetic driver(s) of fast growth from Vnat to its slower-growing sister to make it grow faster. Our findings will shift cell growth studies from the current focus on regulation and signaling to understanding to physico-chemical properties of the cytoplasmic environment, and thus open up a new, active area of research of interest to the entire life sciences community.
2024
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Long-Term Fellowships - LTF
Uncovering the secret world of microbial enzymatic decorated nanowires
GABEL Clinton (USA)
Synmikro Center for Synthetic Microbiology - Philipps-Universität Marburg - Marburg - GERMANY
SCHULLER Jan (Host supervisor)
Acetogenic bacteria subsist at the thermodynamic limit of life under extremes of temperature, salinity, food scarcity, and anaerobic environments. They utilize the conserved, phylogenetically ancient Wood-Ljungdahl metabolic pathway (WLP), where hydrogen is the electron donor and carbon dioxide is the terminal electron acceptor. Their comparatively alien metabolic machinery utilizes redox-reactions where molecular machines employ metalloclusters for electron transfer and act as catalytic centers. Through our active research on modularity, where domains act in electron donor modules while others transmit electrons to catalytic acceptor modules, the Schuller Lab discovered hydrogen dependent CO2 reductase (HDCR), the first enzyme of the methyl branch in the WLP from T.kivui, forms enzymatic, protein decorated nanowires. Filamentation and modularity increases enzyme stability, explaining HDCR’s unsurpassed catalytic activity. HDCR catalyzes formate synthesis from CO2 a 1000-fold more effectively than chemical catalysts, relying on iron-sulfur cluster networks created by nanowire formation. HDCR filaments bundle in cells, forming ring structures attached to the plasma membrane – an untapped discovery with functional and physiological implications. We aim to understand membrane anchoring mechanisms and the ring structures’ biological role. We hypothesize this is an adaptation to low CO2 levels, acting as a carbon concentration mechanism, inducing efficient CO2 capture and utilization. Identification of proteins in HDCR-membrane interactions will be performed through in vivo protein crosslinking paired with genetic manipulation and cryoET complemented by in vitro assays. We hypothesize this effective architecture is not unique, and diverse, biological nanowires are ubiquitous in nature. We identified the A. aromaticum AOR enzyme as an HDCR-type nanowire (Winiarska et al. 2023), indicating more biological nanowires are awaiting discovery. Our work will demonstrate that nanowires are crucial adaptations for anaerobic life to respond to stress and endure environmental extremes. Our aim is to identify new biological nanowires through collaboration with Dr. Georg Hochberg, a local expert in phylogenetic and evolutionary biochemistry. New nanowires will be discovered through data mining, phylogenetic analysis, and protein-structure prediction methods. After identification, organism cultivation using our lab’s resources, native isolation, enzymatic characterization, and cryoEM will be achieved with our established biophysics and biochemistry pipelines. Our goal is to discover new modular redox functions linked to nanowire cores and elucidate their formation, illuminating how anaerobes adapt and survive at the extremes of life. Novel redox functions and nanowires can be adapted for carbon capture and biotechnology applications, addressing industrial and environmental needs while expanding the synthetic chemistry toolkit's reach for reduction reactions.
2024
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Grant Awardees - Program Grants
Deciphering the Impact of Viral Infections on Human Neurocognitive Functions ex vivo
GAUDIN Raphael (FRANCE)
- University of Montpellier (Université de Montpellier) - MONTPELLIER - FRANCE
IKEUCHI Yoshiho (JAPAN)
- The University of Tokyo - Tokyo - JAPAN
GOWRISHANKAR Ganesh (INDIA)
- CNRS Languedoc-Roussillon - Montpellier cedex 5 - FRANCE
The brain is the command center of neurocognitive functions achieved through complex circuitry. Viral exposure is associated to significant risk of neurodevelopmental and neurodegenerative diseases as well as children intellectual disabilities. Yet, mechanistic details underlaying these observations remain unknown. Investigations on human neurocognitive symptoms suffers from the lack of in vitro models that replicate the complexity of brain’s organization and plasticity. Here, we built an interdisciplinary team to explore the impact of neuroinfection on neuronal circuitry and functions. We will develop a method to innervate human brain explants with axons extended from cerebral organoids to investigate impairment of intra/inter-regional circuits. To emulate environmental interactions by the organoid-slice circuits in real time, we will setup a novel hybrid brain organoid-slice model associated to a microfluidic robotic system. This ambitious project will enable the first in vitro closed-loop human brain model that will provide novel conceptual insights on virus interactions with the interwoven circuitry of the brain and set seminal molecular bases underlying neural plasticity and cognition in health and disease.
2024
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Grant Awardees - Program Grants
Vibrational information transfer between living cells in the extracellular matrix
LESMAN Ayelet (ISRAEL)
- Tel Aviv University - Tel Aviv - ISRAEL
MORTIMER Beth (United Kingdom)
- University of Oxford - Oxford - United Kingdom
ZAERA POLO Ramon (SPAIN)
- Carlos III University of Madrid (Universidad Carlos III de Madri, UC3M) - Leganes - SPAIN
GENIN Guy (United States)
- Washington University in St.Louis - St. Louis - United States
The ability of cells to transmit mechanical cues between themselves through the extracellular matrix (ECM) has been recently recognized as a mechanism of long-range cell-cell communication, with implications in a variety of physiological and disease states. Previous works have focused on quasi-static forces (variations over minutes to hours), whose transduction drives cells to remodel both themselves and the ECM. However, cells can sense and respond to rapid forces in the form of vibrations (e.g., time-dependent at higher frequencies, much faster than the characteristic time of ECM homeostatic remodeling or turnover). Whether cells themselves transfer information to neighboring cells via vibrational waves in the ECM is yet unknown. We hypothesize that vibrations, primarily delivered by longitudinal waves along remodeled (stretched, oriented and tensed) collagen tracks, affect signaling cascades associated with both healing and the onset of fibrosis through information transfer between fibroblasts. Our international team of experts in vibrational animal communication, vibration modeling, in vitro cellular systems, and mechanobiology will explore the propagation of dynamic cues through collagen-based materials and establish whether cells generate, transfer and sense information via transient waves. Manipulation of these mechanical cues may possibly be harnessed to accelerate wound healing and impede fibrosis.
2024
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Cross Disciplinary Fellowships - CDF
Is quantum coherence important in coupling the antenna system to the photosystem in cryptophytes?
GRÜNING Gesa (GERMANY)
School of Physics - University of New South Wales (UNSW) - Sydney - AUSTRALIA
CURMI Paul (Host supervisor)
Cryptophytes are single-celled, aquatic algae faced with the challenge of limited photons which demands a very efficient light-harvesting process. Cryptophytes possess an antenna comprised of phycobiliproteins (PBPs) that increases the photon absorption area and the accessible spectral range of the incoming photons. The incoming photon creates an electron-hole pair called an exciton, which needs to move from the antenna to the photosystem quickly and efficiently. Evidence of quantum beats suggests that this process of moving the exciton via several PBPs employs quantum coherence. However, the most efficient way for the exciton transferal is a mixture of coherent and incoherent transfer steps. The intra-protein interactions are probably based on coherent excitation transmission while the transfer process between PBPs is incoherent. We hypothesize that the PBP linking the antenna with the photosystem operates coherently. Recently, it has been discovered that PBPs come in two different quaternary structures: the open and the closed form. The closed form exhibits coherent beats while open form does not. The main goal of this project is to determine the role of quantum coherence in the light harvesting systems of cryptophytes. Specifically, we plan to investigate the quantum mechanical nature of the linking protein that connects the antenna proteins with the photosystem in cryptophytes. To achieve this objective, we will employ a combination of experimental and computational methods. First, we plan to determine the single particle structure of this linking protein between the photosystem and the antenna proteins using state-of-the-art in situ cryo-electron microscopy (cryo-EM). In the next step, we would build a molecular dynamics simulation based on this newly found structure and perform quantum mechanics/molecular mechanics (QM/MM) computations to evaluate possible exciton transfer pathways. In conclusion, by investigating the quantum coherence in the linking protein between the antenna and the photosystem, our research project aims to uncover the missing piece in the interplay of coherent and incoherent exciton transfer. These kinds of linking proteins between antenna structures and the photosystems are not unique to cryptophytes, for example the FMO protein in green sulphur bacteria is also thought to employ quantum coherence. We hope to uncover the reason for this apparently general requirement for linking proteins to function in a coherent way and discover how the linking protein is able to uphold the long-lived quantum coherence against the thermal motion of its surroundings. Understanding the quantum biological nature of the linking protein holds immense promise for unlocking the quantum secrets of cryptophytes and shedding light on the fascinating interplay of coherent and incoherent exciton transfer in several species, with potential applications in quantum technologies and bio-inspired design of efficient energy harvesting systems.
2024
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Long-Term Fellowships - LTF
Vocal communication and the evolution of hyper-cooperative societies
HERSH Taylor (USA)
School of Biological Sciences - University of Bristol - Bristol - United Kingdom
KING Stephanie (Host supervisor)
Humans are extremely “hyper-cooperative”: we regularly engage in long-term and strategic cooperation with non-kin. This propensity for working together has allowed us to dominate the planet, and the key to our success is language. However, humans are not the only animals capable of hyper-cooperation. In Shark Bay, Australia, unrelated male bottlenose dolphins work together in an extensive network of nested alliances—“partners” in “teams” in “clubs”—to control reproductive access to females. Given that dolphins also display remarkable vocal complexity via diverse repertoires of whistles, is vocal communication the mechanism behind hyper-cooperation in this society as well? Or did dolphins evolve a different way of building and maintaining hyper-cooperative relationships? I aim to discover how the rare but powerful phenomenon of hyper-cooperation unfolds in an unconventional, underwater study system. I hypothesize that dolphins, like humans, rely on vocal communication to mediate the interactions underlying their hyper-cooperative society. I predict this will be accomplished through alliance-specific whistle repertoires. First, I will quantify similarities and differences in whistle usage among many alliances. Second, I will evaluate what specific vocalisations mean by playing different whistles to individuals and recording their behavioural and acoustic responses in the field (via drone video footage and underwater microphones, respectively). Third, I will use social and behavioural datasets spanning >40 years to determine whether variations in whistle usage impact long-term fitness (e.g., number of paternities, female consortship rates) of individuals and alliances. Finally, I will build mechanistic agent-based models to explore the interplay between vocal communication and hyper-cooperation over evolutionarily timescales. The models’ agents will be parameterized to behave like real-world male dolphins. The emergent property will be social network structure (i.e., nested alliances). The manipulated condition will be whether agents can vocally signal, and the form that such signalling takes (i.e., able to signal to single individuals vs. groups). Comparative research is crucial to understand how and why hyper-cooperation so rarely evolved. The alliances of male dolphins in Shark Bay are the largest and most complex hyper-cooperative network known beyond humans. Supported by 40 years of research, these dolphins offer an exceptional opportunity to understand the vocal mechanisms that underpin hyper-cooperative behaviours. This ambitious project synergises my quantitative skills, Dr. King’s expertise in dolphin communication, and the University of Bristol’s research facilities, enabling me to move into exciting and challenging fields (e.g., playbacks, modelling). With HFSP’s support, I will answer unresolved, big-picture questions about the role of vocal communication in the evolution and persistence of hyper-cooperative societies.
2024
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Cross Disciplinary Fellowships - CDF
Molecular mechanism of sister chromatid resolution in replicated human chromosomes
HIDAKA Takuya (JAPAN)
Daniel Gerlich Group - Institute of Molecular Biotechnology (Institut fuer Molekulare Biotechnologie GmbH. IMBA) - Vienna - AUSTRIA
GERLICH Daniel (Host supervisor)
"Faithful transmission of genetic information across cell progeny requires disentanglement and separation of extremely long DNA molecules after replication. Sister DNA molecules are first resolved and packaged into separate bodies by condensin-mediated DNA loop extrusion and DNA strand crossing mediated by topoisomerase II (TOP2A in vertebrates), followed by long-range movement mediated by the mitotic spindle. While spindle mechanics are understood in great detail, it has remained unclear how condensin and TOP2A cooperate in sister chromatid resolution. While TOP2A resolves inter-chromatid entanglements, it also induces intra-chromatid entanglements to enhance the mechanical stability of chromosomes during mitosis. How these two activities are coupled with condensin-mediated DNA looping is not known, as no method can simultaneously detect condensin and TOP2A activities in the same cell to assess sister chromatid topologies.
In this project, I aim to develop a new method for genome-wide mapping of TOP2A activities within and across sister chromatids along with DNA contacts mediated by condensin at the single-cell level. To achieve this, I will combine my chemical ligation-based DNA barcoding technology to retain nuclear and spatial information of genomic DNA fragments and antibody-coupled DNA tags with the host lab’s sister-chromatid-specific nascent DNA labeling strategy using a thymidine analogue. After sequencing the barcoded library, the barcodes enable the reconstruction of genomic sites undergoing strand passing by TOP2A and loop extrusion by condensin, whereby sister chromatids can be distinguished based on the DNA label mapping to plus or minus strands. The chemical ligation-based approach will significantly reduce barcode length compared to enzymatic ligation, which is essential for reading sufficient lengths of genomic DNA for efficient sister-chromatid-specific mapping.
With this technique, I will determine the extent by which DNA loop extrusion constricts entanglements behind condensin to promote decatenation, how much chromosome compaction by condensin affects local concentration of TOP2A and intra-chromatid catenation, and whether other potential sister chromatid resolution activities are involved.
This study will reveal how condensin and TOP2A cooperate in folding and resolving replicated chromosomes, a process fundamental to all life forms. The method developed in this project captures multiple targets and pairwise/multiway interaction at the single-cell level, thereby providing a powerful means to investigate the coordination of other molecular processes such as DNA replication, cohesion establishment, and DNA repair. This project will, therefore, advance technology and biological insights with implications for cell division and genome architecture."
2024
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Grant Awardees - Program Grants
Physical forces and mechanotransduction during mouse embryo implantation
TREPAT Xavier (SPAIN)
- Fundacio Institut de Bioenginyeria de Catalunya (Institute for Bioengineering of Catalonia) - Barcelona - SPAIN
HIIRAGI Takashi (JAPAN)
- Hubrecht Institute - Utrecht - NETHERLANDS
Implantation marks a key transition in mammalian development, establishing essential interactions between the embryo and uterine tissue. Upon implantation, mammalian embryos undergo major morphological transformations to form the egg cylinder and establish body axes. However, current understanding of the underlying mechanisms remains limited for two main reasons. First, the process of embryo implantation is inaccessible in the uterus. Second, the physical forces that drive this process have never been measured neither ex-vivo nor in-utero. In this proposal we hypothesize that 1) embryos generate and experience dynamic force as they establish adhesion to the uterine surface; 2) the mechanical interaction at attachment induces changes in the inner cell mass position and/or embryo orientation; 3) this orientation in turn influences the embryo morphogenesis into an egg cylinder. To test these hypotheses, this project aims to map 3D forces and mechanotransduction pathways driving cellular decisions and morphological changes both ex-vivo and in-utero. In Objective 1, we will study the mechanics of mouse implantation ex-vivo by directly measuring the traction forces and intercellular stresses as the blastocyst adheres to substrates with tunable elasticity, viscoelasticity, non-linearity and degradability. Simultaneously, we will examine how the mechanical properties of the substrate affect embryo orientation and development. We will compare our ex-vivo findings from mouse embryos with those of monkey embryos which differ from mice in terms of position of the inner cell mass and morphogenesis. In Objective 2, we will study how the mechanical cues that the embryo experiences during implantation are transduced to impact three main processes: interactions at the uterine-embryo interface, embryo orientation upon attachment, and morphogenesis into the egg cylinder. The results will be integrated into a mechanical model of embryo implantation. Finally, in Objective 3, we will test model predictions in-utero and verify the mechanisms of embryo-uterus interactions during implantation across cell/tissue scales by combining intravital microscopy with novel tools for force measurement. This project will provide an understanding of how physical forces and mechanobiological signals drive mammalian implantation in-utero.
2024
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Long-Term Fellowships - LTF
Unmasking the Role of Nuclear Antioxidant Systems in Human Disease
HSU Sheng-Chieh (CHINA, REPUBLIC OF (TAIWAN))
The University of Texas Southwestern Medical Center (UT Southwestern) - The University of Texas Southwestern Medical Center (UT Southwestern) - Dallas - United States
GARCIA-BERMUDEZ Javier (Host supervisor)
DEBERARDINIS Ralph (Host supervisor)
Human metabolism heavily relies on oxygen (O2) as a primary electron acceptor in around 150 metabolic reactions, essential for processes like mitochondrial respiration. However, the involvement of O2 in metabolism can lead to the generation of reactive oxygen species (ROS), unwanted molecules that have the potential to oxidize and damage various cellular components, including nucleotides, proteins, and lipids. To counteract the harmful effects of ROS, aerobic organisms have developed antioxidant systems, primarily localized within the subcellular spaces where ROS-generating enzymes are prevalent. Mitochondria, being a major source of cellular ROS, possess specific isoforms of enzymes that help dissipate ROS or repair their damage. While the nucleus is a metabolically active organelle engaged in DNA replication, transcription, and gene regulation, it is also susceptible to ROS generation due to the activity of two enzyme families involved in demethylation and hydroxylation reactions, both of which require O2. However, it is unknown whether the nucleus has dedicated antioxidant systems to protect against ROS toxicity and maintain nuclear functionality. I hypothesize that cells have developed mechanisms to inhibit nuclear ROS and preserve the integrity of DNA and the nuclear envelope. Existing approaches lack the temporal and spatial resolution required to test this hypothesis. Therefore, I aim to develop molecular tools that will enable the systematic discovery of nuclear antioxidant systems and their significance in human physiology. Aim 1: Investigate the mechanisms involved in dissipating nuclear ROS. To explore nuclear antioxidant pathways, we will employ an optogenetic approach to induce high levels of ROS using a flavoprotein localized to the nucleus. This will allow us to assess canonical cell survival mechanisms and perform genetic screens using a nuclear-focused library. Aim 2: Discover redox-sensitive nodes in the nucleus. Given that both enzyme families involved in nuclear ROS generation are fueled by alpha-ketoglutarate and inhibited by succinate, we will manipulate ROS production by supplementing cells with permeable forms of these. I will develop a rapid nuclei immunopurification system and couple it to mass spectrometry analysis. This approach will identify ROS-sensitive alterations in proteins and lipids. Aim 3: Investigate the connection between nuclear ROS and DNA leakage. I hypothesize that ROS may compromise nuclear envelope integrity, leading to DNA leakage, a type of stress sensed by cGAS, which ultimately triggers cell intrinsic and extrinsic immunity. Using the aforementioned tools, we will modulate nuclear ROS, evaluate cGAS activation, and analyze the tumor response to immune-mediated growth arrest and checkpoint therapy. Overall, this project aims to develop innovative technologies to uncover the unexplored role of ROS in the nucleus and its potential association with disease states related to DNA stress.