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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
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.
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.