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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
2022
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Grant Awardees - Program
Super-resolution multifunctional scanning ion conductance microscopy: tapping the cell's energy grid
MACHESKY Laura (USA)
Migration, invasion and metastasis lab - CRUK Beatson Institute - Glasgow - UK
SASAKI Atsuo (JAPAN)
Department of Internal Medicine / Cancer Energy Metabolism Lab. - University of Cincinnati College of Medicine - Cincinnati - USA
TAKAHASHI Yasufumi (JAPAN)
Graduate School of Engineering Electronics - Nagoya university - Kanazawa - JAPAN
Cells show a remarkable resiliency when energy-starved, maintaining their ability to migrate to a new energy-rich environment, where they can re-purpose their cytoskeleton to take up nutrients via macropinocytosis. ATP and GTP are the major energy currencies of the cell, driving motor activity, cytoskeletal polymer dynamics and signaling. While the cell generally maintains robust global levels of ATP and GTP in nutrient-starved conditions, it is the local concentrations and ratios of ATP/ADP and GTP/GDP that drive motility and signaling. Multiple parameters control ATP/GTP flux, including: -Diffusion -Biosynthesis vs consumption -Shuttling and compartmentation However, how the cell meets energy demand is largely unclear, because we lack tools to measure multiple parameters simultaneously at sub-cellular resolution over time in live cells. Our multidisciplinary team, with expertise in motility (Machesky), metabolism (Sasaki), and Scanning Ion Conductance Microscopy (SICM) (Takahashi) will address this unmet need. SICM offers advantages of measurements without perturbation, correlation with high-resolution confocal imaging and simultaneous measurement of multiple parameters. Our team will thus engineer the first live single-cell multiscale platform, using cellular feedback to guide sampling and stimuli, providing the means to acquire a holistic view of cellular energy flux. We have two main objectives, each with new technology driven by our biological questions. Objective 1. Develop metabolic and protein mapping SICM to discover how cells use membraneless compartmentation to control metabolite supply and demand at the leading edge. We will establish how diffusion, biosynthesis and consumption generate and maintain intracellular nucleotide gradients using subcellular metabolic sampling SICM. We also probe subcellular localization and organization of metabolic enzymes, using femtoliter scale subcellular protein proximity labelling. Objective 2. Develop cell-to-machine feedback loop controlled SICM to determine how a cell decides to walk or to eat Using cell feedback guided SICM, we discover how mechanosensing via plasma membrane tension, integrins and the cytoskeleton, as well as nutrient sensing, allowing the cell to either locomote or use its cytoskeleton to perform nutrient uptake via macropinocytosis.
2022
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Long-Term Fellowships - LTF
Understanding ancient woolly mammoth gene function through multiplex gene editing
MAJEWSKI Dorothy (.)
. - President and Fellows of Harvard College, Harvard Medical School - Boston - United States
CHURCH George (Host supervisor)
The ability to sequence ancient DNA from extinct species is a relatively recent development in evolutionary biology with the potential to provide direct information on evolutionary pressures spanning tens of thousands of years. However, our ability to functionally characterize these genes is limited to predictions based on orthologues in living ancestors. Using multiplex gene editing techniques currently being developed in the Church lab at Harvard University, I will modify Asian elephant cell lines with multiple candidate mutations simultaneously based on the related woolly mammoth genome. Functional characterization of mammoth genes in the context of elephant tissues can provide insight into cold-resistance adaptations selected for by harsh environmental conditions. Several loci of interest from the mammoth genome will be targeted based on sequence comparison with the elephant genome, specifically aiming to find orthologous proteins altered from a common ancestor over the course of speciation. Multiplex gene editing methods will be optimized for the elephant cell lines, both in immortalized somatic cells and eventually induced pluripotent stem cells. Functional analysis will be performed by a combination of cell-based and biochemical approaches. The technology to modify many genes simultaneously will create a foundation for the long term goal of generating Asian elephant – woolly mammoth hybrid embryos, a part of de-extinction efforts to fill lost ecological niches that can be applied to several species in the future.
2022
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Long-Term Fellowships - LTF
Feeding or folding? Untangling the ecology of spatial patterning in microbial consortia
MEACOCK Oliver (.)
. - University of Lausanne - Lausanne - SWITZERLAND
MITRI Sara (Host supervisor)
The ecology of microbial communities is characterised by a rich interplay between metabolic and mechanical processes. In sessile communities, these processes typically play out through changes in the spatial structure of the system, such as the strong intermixing of strains that rely on each other’s secretions, or the buckling of a biofilm due to growth-induced forces. However, as species in naturally-occurring communities can differ widely in both their metabolic and physical properties, it has thus far proven difficult to disentangle the contributions of these two types of process during the emergence of spatial structure in multi-species consortia.
To address this, I propose a three-pronged course of research, using the Mitri group’s recently characterised four species consortium as a testbed. In stream one, I will develop microfluidic techniques to physically separate different species while allowing chemical exchange between them, isolating those spatial patterns driven purely by metabolic mechanisms. In stream two, I will adapt pre-existing ecological theory to uncover the underlying metabolic interactions necessary to explain these patterns, as well as investigate patterning’s importance in enabling the community to perform a user-defined function such as toxin degradation. Finally, in stream three, I will reintroduce the previously excluded mechanical interactions in a controlled manner, engineering the emergent patterns to improve the community’s ability to fulfil its target function. This project will combine my proven analytical capabilities with the ecological insights of my host group to bring a fresh, more predictive perspective to microbial ecology.
2022
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Long-Term Fellowships - LTF
Neural basis of relative aversive value coding in mice
MIRANDA Magdalena (.)
. - Institute for Functional Genomics (Institut de Génomique Fonctionnelle, IGF-CNRS) - Montpellier - FRANCE
TROUCHE Stéphanie (Host supervisor)
Absolute (good or bad), but also relative (better or worse), values can be assigned to an experience to guide appropriate actions (approach or avoidance). While previous work mainly focused on appetitive relative value coding, a detailed understanding of the neural mechanisms allowing animals to compare relative aversive value is at its infancy. Additionally, the extent to which value computed during learning is affected by specific internal states to alter value-based decisions remains elusive. The paraventricular thalamus (PVT) is modulated by hypothalamic inputs and also integrates positive and negative emotional states. Moreover, through its glutamatergic projections to the Nucleus Accumbens (NAc), the PVT is therefore ideally positioned to impact value coding and appropriate behavior selection. In this project I will use a novel behavioral task combined with optogenetics and in vivo physiology to examine the neural mechanisms for absolute versus relative value assignment during learning in mice and how internal state affect value signals. By monitoring and manipulating the neural activity simultaneously with dopamine kinetics from genetically defined neuronal populations in behaving mice, this project will investigate 1) the role of the PVT-NAc pathway, 2) the physiological changes of the DA release in the NAc and 3) the effect of acute changes in internal state (e.g. thirst) during both relative and absolute aversive learning and choice. This project therefore aims to build the first functional circuit model in mice for relative aversive value coding and highlights how internal states integrated in the PVT modulate value coding and value-based decisions.
2022
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Long-Term Fellowships - LTF
Delineating control of translation upon iron starvation
MOLENAARS Marte (.)
. - New York University Grossman School of Medicine - New York - United States
POSSEMATO Richard (Host supervisor)
Iron is the most abundant transition metal in biological systems. Iron and iron-containing cofactors support essential processes like energy metabolism or DNA replication. As with many essential nutrients, cells have mechanisms to sense shortages and alter metabolically intensive processes like translation. My over-arching goal is to gain mechanistic understanding of the translational program dedicated to cope with the iron deprivation. Known mechanisms for iron sensing involve Iron regulatory proteins (IRP) 1 and 2, which have RNA binding domains that bind iron-responsive elements (IRE) upon iron starvation. Known IRP targets are involved in iron metabolism: IRPs bind the 3`UTR of mRNA related to iron uptake or the 5`UTR of mRNAs related to iron storage to stabilize or inhibit translation, respectively. Interestingly, I have found that (1) iron starvation rapidly inhibits mammalian translation globally and (2) novel IRP-bound mRNA species are selectively affected. Here, I will determine how iron sensing pathways regulate translation globally, and delineate which mRNAs are directly regulated by IRPs. Using polysome profiling I will define how mRNA translation rates are affected by iron starvation and determine whether these effects are dependent upon IRPs or other common translational control mechanisms such as mTORC1. I will isolate polysomal RNA and perform RIP-seq of IRP-bound mRNAs upon induction of the iron starvation response pharmacologically or genetically to identify novel transcripts regulated by the IRP system. These findings will have an impact on diseases where iron metabolism is dysregulated, such as Friedrich’s Ataxia, iron storage diseases, or cancer.
2022
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Grant Awardees - Program
Mental 3D space-time travel in fission-fusion animal societies
WAHLBERG Magnus (SWEDEN)
Marine Biological Research Center - Dept. of Biology - Kerteminde - DENMARK
MOSS Cynthia (USA)
Dept. of Psychological and Brain Sciences - Johns Hopkins University - Baltimore - USA
PEREMANS Herbert (BELGIUM)
Dept. of Engineering Management - University of Antwerp - Antwerp - BELGIUM
VON BAYERN Auguste (GERMANY)
Dept. of Behavioural Ecology and Evolutionary Genetics - Max-Planck-Institute for Ornithology - Seewiesen - GERMANY
Flying and swimming animals can move freely in three-dimensional space, but their ability to use past information to inform future decisions remains largely unknown. Time flows in one direction, and no living creatures can physically move backwards into the past or forwards into the future. Animals can, however, use memories to adapt their behavior in future events. For humans, it is even possible to mentally travel backwards and forwards in time; we can ‘see’ ourselves in past situations and foresee ourselves in future ones. Mental time-travel is regarded as a fundamental property of human success, enabling us to organize societies and travel to the moon. Here we study to what degree other animals possess mental time travel abilities. We study dolphins, bats and parrots, which all travel and forage in 3-D space and live in large groups where they are constantly engage in social interactions, both cooperation and competition. Any degree of mental time travel abilities would be advantageous for them to anticipate the best solutions in the execution of future tasks. We investigate how our model species perceive time, and any evidence for them making use of episodic memory and perform future planning. By using similar experimental approaches for all model species, we compare mental time travel in animals living in vastly different environments and exposed to a large variety of challenges. By comparing the performance of our model species, we can decipher the underlying evolutionary mechanisms and requirements for mental time travel. We will use the results of our investigations to construct robots that exhibit different degrees of mental time travel functions. By studying the success rate with which robots solve problems, and by manipulating the robots’ abilities to mentally travel in time and collaborate, we will aim to pinpoint which mental time travel traits are most pertinent for solving different types of problems. The robot studies not only inform us about how our model species function, but may also inspire the development of robots that successfully solve difficult problems requiring complex decision-making, such as responding appropriately in emergency situation and executing complex construction operations.
2022
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Long-Term Fellowships - LTF
Neuronal changes following pathogen infection: mechanisms underpinning sickness-related behaviors
MURIA Aurélie (.)
. - University of Bonn (Rheinische Friedrich-Wilhelms-Universität Bonn) - Bonn - GERMANY
GRUNWALD KADOW Ilona (Host supervisor)
When sick, animals undergo adaptive changes related to both infection control and recovery. The molecular and neuronal changes induced by infection, in particular central brain adaptations following pathogen ingestion or injury (peripheral infection), are still poorly understood. The immune system has been proposed to play a crucial role in behavioral adaptations. Characterizing the neuronal changes following activation of peripheral immune signaling would thus permit to better understand how infections impact, in the short and long term, the physiology and function of the brain. The innate immune system of Drosophila is a useful model to assess this question, thanks to its neurogenetic tools. The host lab showed that pathogen ingestion leads to adaptive feeding through immune signaling in neurons and changes in the mushroom bodies. Using in vivo ROS sensing and calcium/voltage whole brain imaging, I will first i) establish a map of neuronal activity and plasticity in flies infected with pathogens (i.e. Ecc15 and Pseudomonas) of various virulence, by oral ingestion or injury (i.e. before, during sickness, after recovery). Through 2-photon imaging and RNAi approaches, I will ii) define the role of the innate immune pathway in the affected brain regions and iii) characterize the immediate and long-lasting impacts of infection on specific neurons and synapses, such as serotoninergic and octopaminergic, in brain regions associated with sickness-related behavioral adaptations, such as feeding. I anticipate that the results of this project will significantly widen our understanding of how immune signaling and infection change the nervous system, in the short- and long-term.
2022
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Long-Term Fellowships - LTF
Exploring the combinatorial space of plant immune receptors and pathogen signals
OFIR Gal (.)
. - Max Planck Institute for Biology Tübingen - Tübingen - GERMANY
WEIGEL Detlef (Host supervisor)
To defend themselves against pathogens, plants employ an amazing diversity of immune receptors responding to pathogen signatures or to pathogenic manipulation of plant cells. While several major families of immune receptors are known, most of their members respond to unknown signals from unknown pathogens. Better understanding of the immune repertoire against a diverse array of pathogens can shed light on the ecological and evolutionary forces shaping plants’ immune arsenal.
I will establish a high-throughput screening pipeline for immune responses to an array of plant viruses. I will first focus on the well-studied NLR immune receptors. NLR genes of unknown specificities will be bioinformatically identified in fully assembled genomes, and will be co-expressed in plant cells with a library of plant viruses. Immune response activation will be monitored using multiple approaches - transcriptome changes, production of reactive oxygen species and signaling molecules, and programmed cell death.
In a second step, the proposed pipeline will be used for discovery of novel immune-related genes. Candidate genes will be identified using genomic hallmarks of immune genes – excessive diversity and copy number variation within species, sharing of alleles between species, presence/absence between closely related strains, diversification by unequal crossing over and immune-related protein domain signatures. Candidate genes will then be tested experimentally for immune responses using co-expression with a collection of plant viral infectious clones to discover new antiviral mechanisms in plants.
2022
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Long-Term Fellowships - LTF
Spatial and temporal scales of serotonin neuromodulation
ÖZÇETE Özge demet (.)
. - Harvard Medical School - Boston - United States
KAESER Pascal (Host supervisor)
Serotonin controls brain functions including mood, affection and reward, and modulating serotonergic activity is used to treat anxiety, depression and other disorders. While serotonin is thought to act as a volume transmitter, the spatial and temporal scales of serotonin transmission are not well understood. At classical synapses, position, timing and extent of neurotransmitter release are controlled by the active zone, a specialized protein complex. I here propose to dissect the protein machinery for serotonin release. I will use superresolution microscopy to identify secretory protein clusters that embody release hotspots in serotonin axons. To assess the spatiotemporal dynamics of serotonin release, I will employ the recently developed fluorescent serotonin sensors in mouse striatum. I will record serotonin release in striatal brain slices and in vivo using imaging and photometry in combination with chemo- or optogenetic control of serotonergic activity. I will next determine whether proteins that mediate spatial precision and rapid release dynamics at synapses, for example active zone scaffolds, fast calcium sensors, and voltage-gated calcium channels, are needed for serotonin release. My host laboratory has developed a series of conditional mouse mutants for this purpose. In summary, I expect to uncover the key features of serotonin release. Building on my experience with synaptic signalling, I will be able to generate new models on the spatiotemporal organization of serotonin transmission. This work will provide insights into the principles of neuromodulation and may offer new targets for modulating serotonergic activity in disease.
2022
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Grant Awardees - Program
New ways to generate color: light manipulation by crystal-forming pigments
STUART-FOX Devi (AUSTRALIA)
School of Biosciences - The University of Melbourne - Melbourne - AUSTRALIA
TZIKA Athanasia (GREECE)
Department of Genetics and Evolution - University of Geneva - Geneva - SWITZERLAND
PALMER Benjamin (UK)
Department of Chemistry - Ben-Gurion University of the Negev - Rehovot - ISRAEL
Recently discovered organic crystals in the eyes of shrimp exhibit remarkable optical properties, never observed in synthetic materials. Intriguingly, the same crystal-forming pteridine pigments are abundant in the skin of many vertebrates. Pteridines are the dominant class of pigment within the xanthophore pigment cells of reptiles, amphibians and fish; yet the optical properties of crystalline pteridines remain completely unexplored. How do these pigments contribute to vivid skin colors and what is the mechanism of molecular self-assembly? We seek to answer these questions by integrating comparative biology, materials chemistry, optics, molecular evo-devo and transcriptomics, and exploiting opportunities provided by reptilian models. In Aim 1, we will characterize the ultrastructure of pigment cells and the chemical, material and optical properties of crystalline pteridine pigments for multiple dragon lizard species and color forms of the corn snake. We will relate the optical properties of pteridine crystals within xanthophore pigment cells to those of guanine crystals within iridophore pigment cells. Aim 1 will enable us to integrate pigment-structure interactions at different scales of structural organization (cellular ultrastructure and subcellular optics) to produce a comprehensive model of skin color generation in reptiles. By discovering the special optical properties that arise from the crystallinity of certain pigments and their ordered assembly, we will reveal new ways that vertebrates generate vivid colors. In Aim 2, we will elucidate the formation and molecular control of crystalline materials within pigment cells throughout ontogeny in bearded dragons and corn snakes. Currently, we do not know what proteins control crystal nucleation, growth or assembly or which proteins are involved in transport of molecular precursors. Understanding the link between gene and crystal ‘phenotype’ would reveal how organisms exquisitely regulate the formation and properties of molecular crystals. This new and exciting connection between molecular biology and materials science could pave the way for the development of genetic tools to design new synthetic molecular crystals.
2022
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Long-Term Fellowships - LTF
Genome-wide profiling and targeted editing of chromatin state at double-strand breaks in cancer
PARNANDI Nishita (.)
. - The Francis Crick Institute Ltd - London - United Kingdom
BOULTON Simon (Host supervisor)
DNA double-strand breaks (DSBs) are toxic lesions that drive cancer, aging and neurological disorders. DSBs are predominantly repaired by two competing repair pathways, classical non-homologous end joining (c-NHEJ) and homologous recombination (HR), and the choice between these two pathways is extensively regulated. Exploiting pathway choice forms the basis for several cancer therapies. Yet, there are no genome-wide tools to accurately predict pathway choice at individual DSBs, which limits the efficacy of chemotherapies.
Induction of DSBs causes dynamic changes in nearby chromatin that influences repair. Key changes that occur in chromatin state are DSB-induced histone post-translational modifications (PTMs), which then recruit specific DSB repair factors to constrain pathway choice. Identifying histone PTMs near DSB sites could serve as a critical “marker” for pathway choice. However, limitations of current tools hamper our understanding of the correlation between chromatin state and pathway choice. To overcome these limitations, I will develop the first genome-wide high-throughput method for joint profiling of histone modifications and DSBs in the same cell population. I will validate the method by comparing measured chromatin state changes against the expected effects of well-characterized processes such as the cell cycle. Based on the improved understanding of the link between chromatin state and DSB repair pathway choice, I will use dCas9-fusion to engineer chromatin state and direct pathway choice to optimize sensitivity to chemotherapeutic drugs, including PARP and POLQ inhibitors. Ultimately, these results can be harnessed to advance chemotherapies in patients.
2022
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Long-Term Fellowships - LTF
Molecular mechanism of ERAD-M by in vitro reconstitution
PFITZNER Anna-katharina (.)
. - President and Fellows of Harvard College, Harvard Medical School - Boston - United States
RAPOPORT Tom (Host supervisor)
ER-associated degradation (ERAD) is a quality control pathway clearing misfolded proteins from the ER by retrotranslocation across the ER membrane and subsequent proteasomal degradation. It is linked to many diseases, e.g., cystic fibrosis. Membrane destabilization by a dedicated channel is thought to facilitate translocation of luminal substrates (ERAD-L). Although in vivo studies have evidenced Dfm1 as channel for misfolded transmembrane (TM) proteins (ERAD-M), the molecular details remain elusive. This project aims to study the mechanism of TM protein extraction from membranes and to explore lipid bilayer destabilization as a general mechanism for retrotranslocation. To this purpose, we will reconstitute ERAD-M translocation in vitro and quantify destabilization of lipid bilayers in ERAD-pathways with diverse substrates. First, we will analyze the Dfm1 complex in vivo, before coreconstituting it with substrate (NBD-labeled) into liposomes (Rhodamine-PE) and follow extraction activity by release of Rhodamine quenching on NBD fluorescence. Contribution of functional domains, known interaction partners and substrate ubiquitination will be tested. Secondly, bilayer destabilization of ERAD-L and ERAD-M channels, reconstituted in liposomes, will be quantified using a fluorescent reporter probe for lipid order (FliptR). Influence of lipid composition (lipid shape, bending rigidity) on bilayer destabilization and translocation activity will be evaluated. Our work will not only provide experimental verification of the role of Dfm1 in ERAD-M, but also help to understand how proteins with diverse energetical requirements overcome the thermodynamical barrier to cross membranes.
2022
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Long-Term Fellowships - LTF
The cellular and developmental genetic mechanisms underlying germline response to climate change
RAJAKUMAR Arjuna (.)
. - Whitehead Institute for Biomedical Research - Cambridge - United States
LEHMANN Ruth (Host supervisor)
Fertility is declining globally for a range of animals including insects, fish, and mammals. Rising temperatures due to climate change are expected to worsen this problem because temperature is known to influence key biological processes including immunity and cellular physiology, and abnormal temperature levels can elicit a maladaptive response. While organisms have evolved the capacity to respond to fluctuating environments in a constant and predictable way, a capacity known as canalization, previous work indicates that the germline is temperature sensitive, where high temperatures induce sterility. We propose to use Drosophila melanogaster as a model to understand the mechanistic basis of temperature-induced sterility through the following aims: 1) Combining developmental genetics with super-resolution microscopy, we will test how temperature affects germplasm assembly and whether intrinsic disordered domains, characteristic of germ granule proteins, are involved in temperature sensing. 2) Using hybrid dysgenesis, a system that generates sterile progeny and is exacerbated by high temperatures, we will test whether piRNA pathway control and transposable element activity change across a temperature gradient. 3) Using Drosophilid populations adapted to high temperatures, we will test if mitochondria purifying selection within the germline is temperature-optimized and whether mitochondria transplantation from adapted to non-adapted individuals can modulate temperature-induced sterility. Altogether this work will further our understanding of the cellular and molecular mechanisms underlying the germline response to temperature and how this may be impacted by climate change.
2022
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Cross Disciplinary Fellowships - CDF
Understanding and controlling the sub-motors of bacterial rotary nanomachines
RIEU Martin (.)
. - University of Oxford - Oxford - United Kingdom
BERRY Richard (Host supervisor)
The bacterial flagellar motor (BFM) consists of hundreds of proteins that assemble into a transmembrane rotary nanomachine. It propels the flagella that drive bacterial swimming. New structural studies suggest that the motor is itself powered by smaller rotary motors. The latter, called stator complexes, are now thought to be autonomous rotary machines, powered by transmembrane ion flux, that drive the rest of the BFM. They share the structural motif of a pentamer surrounding a dimer (5:2), but it is not yet known whether these complexes really are rotary machines, and if so how rotation drives their functions.
Here, we will deliver the stators into Droplets on Hydrogel Bilayers, which will allow single-molecule fluorescence imaging and membrane energization. Coupled to FRET and precise sodiometry based on organic sensors, this will allow us to determine the relation between the ion flux, the conformation and the rotation of the units. Finally, we will decipher their interaction with the whole BFM by fast measurements of their discrete dynamics: attaching gold nanorods to the BFM and following rotation in vivo by polarization microscopy, with angular resolution of a few degrees at sub-microsecond timescales.
This project will be the first to characterize the molecular mechanisms behind the activation and the dynamics of the sub-motors of the BFM, using advanced techniques from bilayer biochemistry and single-molecule fluorescence, and will bring a new understanding of large rotary machines. It will also open avenues for synthetic biology, making important steps towards the synthesis of artificial cells endowed with the ability to self-propel.
2022
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Long-Term Fellowships - LTF
Revealing the control of epithelial mechanics during wound healing using in vivo force manipulation
ROGALLA Svana (.)
. - Instituto Biofisika, Basque Centre for Biophysics (UPV/EHU, CSIC) - Leioa - SPAIN
SOLON Jerome (Host supervisor)
Wound healing is a dynamic process in which a living organism replaces lost or damaged tissue based on molecular, hormonal and cellular responses. Understanding the mechanics behind the cellular responses during wound healing processes is a key question in biology and biomedicine, however, the contribution of tissue mechanics (setting tissue deformation upon forces) to wound healing in live animals remains poorly understood. In this project, I will use live Drosophila melanogaster embryos as a model system to reveal how changes in epithelial mechanics are controlled during wound repair. Combining Drosophila genetics with laser dissection, and a novel procedure allowing the application of controlled forces on a single magnetic particle embedded within the tissue in vivo, I will measure the changes in epithelial mechanics within the wounded tissue and link these to specific wound healing regulatory signals. The project will comprise three consecutive stages: 1) I will measure changes in mechanical forces during the different phases of wound healing and correlate them with activation of biochemical signals, such as Hippo and JnK pathways. 2) Based on these measurements and in collaboration with theoretical physicists, I will create a biophysical model of wound healing processes. 3) I will investigate the effect of ectopic forces on the kinetics of wound healing and on cell response, particularly focusing on potential modulation in gene activity by mechanical perturbation. Altogether, these experiments will allow to reveal the control of wound healing in vivo encompassing mechanical and biochemical signals and the resulting changes in epithelial mechanics and cellular forces.
2022
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Long-Term Fellowships - LTF
Deciphering the nature of genomic conflict using locus-specific chromatin perturbation and capture
RUDNIZKY Sergei (.)
. - Johns Hopkins University School of Medicine - Baltimore - United States
HA Taekjip (Host supervisor)
Chromatin modulates DNA accessibility and hence serves as a fundamental layer in the complex regulation of gene expression and DNA integrity. However, the role of chromatin organization in resolving a genomic conflict between two seemingly competing processes – transcription and DNA damage response (DDR) is not clear. This stems from the dynamic nature of chromatin that is transcribed and repaired in an asynchronous and position-dependent manner. Moreover, locus-specific purification of mammalian chromatin, usually found with only two copies per cell, presents a major challenge regarding the necessary assay specificity and sensitivity. To overcome these limitations, I will develop a single-molecule (SM) pulldown approach based on multi-step enrichment with CRISPR Cas9 and Cas12a, followed by Oligopaint to capture and dissect any chromatin locus of interest. Using light-activated vfCRISPR, I will introduce lesions at transcriptionally active or silent regions to induce DDR with high spatiotemporal control. Captured chromatin will be characterized by SM and super-resolution imaging regarding its composition and organization and will be used as a native substrate to access the dynamics of transcription and DNA repair factors in real-time. Coordination between transcription, DDR, and local chromatin will be examined by guiding vfCRISPR to the promoter and gene body of the heat-shock induced Hsp70 model gene. The developed method can be expanded to mouse models and can be broadly applied to genomic regions of high relevance to health and disease, providing an exciting opportunity for understanding the fundamentals of transcription and DDR in vivo at unprecedented resolution.
2022
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Long-Term Fellowships - LTF
Are endothelial cells regulated differently during limb regeneration than during development?
SAVAGE Aaron (.)
. - President & Fellows of Harvard College - Cambridge - United States
WHITED Jessica (Host supervisor)
Biological question
My question is: how is vascular regrowth regulated during limb regeneration? I aim to understand— at a precise molecular, genetic, and cellular level— how vascular regeneration is regulated in axolotls; whether by angiogenesis or novel mechanisms remains unclear.
Scientific content
This multi-disciplinary project spans developmental biology, genomics, and regenerative medicine, combining cutting-edge transcriptomic, imaging, and molecular biology practices analyze vascular regeneration in axolotl limbs.
Specific aims: 1) Generate the first axolotl vasculature map, using CRISPR knockin-generated transgenics, contrasting native vascular limb patterning to post-regeneration limb patterning; 2) Analyze regenerating vascular cells transcriptionally to elucidate key genes/pathways, using single cell RNA sequencing; 3) Perform in vitro and in vivo assays (morpholino/CRISPRi knockdown; mutagenesis, etc.) to characterize how interplay between key genes/pathways regulates how blood vessels and other tissues, such as fibroblasts interact, informing limb regeneration.
Novel transgenics will express both vascular-specific fluorescent proteins and the TVA receptor, enabling visualization of expression and spatiotemporal delivery of molecular modulators, for precise control of gene expression.
Significance
To understand limb regrowth, it is essential to understand complex interactions between different cell types during regeneration. This project will pioneer characterization of regenerating vessels, informing both wider understanding of limb regeneration and how vessels can be reactivated, generally, to expand in response to injury and disease.
2022
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Long-Term Fellowships - LTF
The ecological role of bacterial specialized metabolites in bacteria-microalgae interactions
SCHLEYER Guy (.)
. - Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI) - Jena - GERMANY
HERTWECK Christian (Host supervisor)
Phytoplankton are marine photosynthetic microorganisms that thrive in the photic zones of the oceans. They form the basis of marine food-webs and greatly influence global biogeochemical cycles and the climate. Many studies highlighted the importance of microbial interactions in shaping community composition, especially bacteria-phytoplankton interactions. Over the past decade, chemical communication was found to be a key aspect in mediating these interactions, such as mutualism and pathogenicity. Although bacteria are prolific producers of specialized metabolites, also known as natural products, the involvement of such metabolites in bacteria-phytoplankton interactions has been largely overlooked. Moreover, these metabolites have been studied mostly for pharmaceutical purposes rather than for their role in nature.
This research is aimed at studying bacterial specialized metabolites and their involvement in mediating bacteria-phytoplankton interactions. To achieve this, I will study ecologically-relevant bacteria-phytoplankton systems, both mutualistic and pathogenic, mediated by chemical communication. The systems will be developed in collaboration with the Pohnert group, which has been studying numerous systems of bacteria-algae interactions. I will identify bacterial specialized metabolites that mediate these interactions using analytical chemistry tools and will further characterize their biosynthetic pathways and their cellular targets using diverse biochemical techniques. These findings will shed light on the role of specialized metabolites in governing bacteria-microalgae interactions and allow us to better understand their ecological role in nature.
2022
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Long-Term Fellowships - LTF
Using computational models to link dynamics of brain plasticity with behavioral changes over time
SCHURR Roey (.)
. - President & Fellows of Harvard College - Cambridge - United States
GERSHMAN Samuel (Host supervisor)
The ultimate goal of neuroscience is to provide a mechanistic explanation of the cognitive processes that drive human behavior. I propose to study the link between changes in one’s brain connectivity and structure and one’s behavioral changes, by integrating computational models, behavior and neuroimaging. Specifically, I will study the dynamical changes of behavioral and neuroimaging measurements to uncover the computational infrastructure of core cognitive processes.
Computational model of behavioral yield subject-specific parameters. These parameters provide a mechanistic explanation to the cognitive process and to inter-subject variability. However, no large-scale longitudinal study has approached the source of observed changes in the estimated parameters over time. Is it measurement noise or true variability in the cognitive process?
I will collect longitudinal data of behavior and neuroimaging from subjects who will perform seven behavioral tasks with established computational models. By studying the covariance of computational parameters over time, I will identify latent factors that may represent core cognitive process (e.g. working memory). I will explore the hypothesis that these latent factors reflect shared neural circuitry across tasks. In particular, I will test whether the dynamical changes in the computational phenotype are associated with functional and structural changes in specific brain networks. Finding such a link between model-based parameters and neuroimaging measurements will be a major step towards a mechanistic understanding of the computational and anatomical infrastructures that underlie core cognitive processes in the human brain.
2022
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Long-Term Fellowships - LTF
Unravelling the mechanisms of bis(monoacylglycero)phosphate synthesis and function in endolysosomes
SINGH Shubham (.)
. - Sloan Kettering Institute for Cancer Research - New York - United States
FARESE Robert (Host supervisor)
Bis(monoglycero)phosphates (BMP) are a structurally unique orphan lipids exclusively localized at endolysosomal systems in the cells. Studies suggests that BMP might play a crucial role in the endolysosomal system by regulating lysosomal hydrolase activity, cholesterol transport and budding of lysosomal intralumenal vesicles. Interestingly, BMP levels are deregulated in various neuropathological conditions characterized by defective endolysosomal system like Niemann-Pick Disease Type C, Gaucher’s disease, Fabry disease, and dementia, etc. Though BMP were discovered five decades back and studies suggest their indispensable role in the endolysosomal physiology, nothing is known about their exact function, metabolism and how their deregulated levels associate with the neurodegenerative diseases. In this proposal, I aim to identify the enzymes that synthesize and degrade BMP in mammalian cells, and exhaustively characterize their role in the endolysosomal systems. I will use chemical genetic and siRNA strategies in conjunction with lipidomics to identify the enzymes that regulate BMP levels. Using in vitro reconstitution, I will determine the function of candidate enzymes and regulators in BMP metabolism. I will use genetic manipulations targeting enzymes to selectively modulate BMP levels in the cells/rodents, and examine their role in the endolysosomal physiology especially in the neurons. Overall, the results of the proposed studies will not only help in mapping BMP metabolism in cells but will also aid in understanding of the role of BMP in the endolysosomal physiology.