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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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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.
2022
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Cross Disciplinary Fellowships - CDF
Tumour homing immune cells for cavitation therapy
SMITH Cameron (.)
. - California Institute of Technology - Pasadena - United States
SHAPIRO Mikhail (Host supervisor)
One of the great difficulties in the treatment of cancer is the inaccessibility of the tumour core. Due to poor vascularity, hypoxia, and high interstitial pressure, many conventional cancer therapeutics are unable to treat this significant portion of the target tumour, leading to less successful therapies. In this project we will address these limitations by utilising recent developments in synthetic biology and ultrasound. Our approach will take advantage of the Shapiro laboratory’s work on genetically encoded air-filled proteins called gas vesicles (GVs), which we will express in engineered tumour-infiltrating macrophages and T-cells in response to tumour-specific biomarkers such as VEGF, Her2, or claudin-6. The resulting GVs will act as seeds for highly selective and localised therapy when combined with focused ultrasound. We hypothesise that high energy inertial cavitation – the formation and violent collapse of bubbles – will be seeded by GVs to damage surrounding tumour cells. This would both allow for selective killing of tumour cells as well as the potential release of antigens which would make the tumour more susceptible to attack by the immune system, while additionally having the potential to allow the immune system to recognise and attack metastases. Successful completion of this project will produce a new class of local and targeted anti-tumour therapy and create a scientific and technological foundation for future developments and therapies utilising the combination of engineered cells and ultrasound.
2022
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Long-Term Fellowships - LTF
Enhancing receptor signaling by liquid condensate formation
SONG Daesun (.)
. - The Board of Trustees of the Leland Stanford Junior University - Redwood City - United States
LIN Michael (Host supervisor)
Transmembrane receptors activate intracellular signaling pathways mediating growth, survival, or differentiation. Liquid condensate formation by T cell receptors enhances downstream signaling, but whether condensation can generally enhance receptor function is unknown. I propose to study the ability of condensation to generally enhance receptor function using the epidermal growth factor receptor (EGFR) as a model, with the following aims:
1. Design inducible EGFR condensates. Fusions of cryptochrome 2 (CRY2) and the Fused-in-Sarcoma intrinsically disordered region (IDR) form droplets in response to blue light, while cryptochrome variants CRY2olig and GFP-CRY2high without IDR create visible accumulations of unknown liquidity. I will fuse EGFR-GFP to CRY2-IDR, CRY2olig, or CRY2high and assess liquidity of light-induced accumulations by time-lapse morphology and FRAP.
2. Compare signaling –/+ EGFR condensation. I will activate the above proteins –/+ light –/+ EGF, comparing to EGFR-GFP, while measuring amplitude and kinetics of EGFR/Akt/ERK phosphorylation, Shc-RFP recruitment, and receptor internalization. This will determine if condensation enhances signaling, and if so at what step and in what manner.
3. Determine if any observed signaling enhancement also augments function by assessing proliferation of keratinocytes expressing EGFR-EGFP or the above fusions –/+ light –/+ EGF.
This project will combine my existing expertise with liquid condensates from my Ph.D. training with the expertise of the Lin Lab at Stanford in CRY2 biochemistry and EGFR signaling to obtain insights into the role of condensation in organizing and amplifying biological signals.
2022
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Long-Term Fellowships - LTF
Functional cell atlas of neural crest cell contribution to newt development and regeneration
SUZUKI Miyuki (.)
. - California Institute of Technology - Pasadena - United States
BRONNER Marianne (Host supervisor)
During development, neural crest stem cells arise within the forming central nervous system but then migrate into and throughout the periphery where they differentiate into diverse cell types. In addition to their importance in development, neural crest cells have recently been implicated in organ regeneration (e.g. heart regeneration in adult zebrafish) raising the intriguing possibility that they may be required in multiple regenerating structures. Salamanders have the remarkable regenerative ability and represent an excellent model for exploring the role of neural crest cells in both organogenesis and organ regeneration. To identify neural crest-derived cells that potentially re-express a neural crest gene regulatory program during organ regeneration, I have established Sox10::EGFP and Cre/loxP transgenic newts, Pleurodeles waltl, that genetically label and enable visualization of Sox10-expressing cells in vivo. With this in hand, I will explore two pressing questions: 1. Do neural crest-derived cells contribute to adult limb and heart regeneration in the newt? 2. If so, what are the underlying molecular mechanisms? To address these questions, in Aim 1, I will generate an atlas of cell types formed by neural crest-derived cells using Cre/loxP technique; in Aim 2, I will evaluate the involvement of neural crest-derived cells in organogenesis and organ regeneration using in vivo cell ablation technique. Aim 3 will generate a single-cell RNA-seq transcriptome profile during the regenerative process. This comprehensive atlas of cellular fates and functions of neural crest in newts promises to deepen understanding of development and regeneration in vertebrates.
2022
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Long-Term Fellowships - LTF
Investigating the regulomic basis of major evolutionary transitions
TAYLOR Benjamin (.)
. - Purdue University - West Lafayette - United States
HARPUR Brock (Host supervisor)
The evolution of life on Earth has been extensively shaped by major transitions in biological complexity. The evolution of insect eusociality is one such transition and has occurred multiple times independently in recent evolutionary history. Unfortunately, the mechanistic basis of this transition is poorly understood. One major hypothesis proposes that eusociality is associated with substantial increases in gene regulatory complexity, but no study to date has provided a robust empirical test of this possibility. I propose to provide such a test. Using a novel meta-analytic machine learning approach, I will integrate new and existing multi-omic datasets from eusocial, subsocial, and solitary hymenopteran species to identify phylogenetically-robust signatures of the transition to eusociality. I predict that eusocial species will exhibit substantial expansions in regulatory complexity compared to related solitary taxa, in the form of increases in the proportion of the genome that is subject to alternative splicing or epigenetic regulation. Additionally, I will combine population genomic data and lab-based transgenic experiments to validate the functional role of regulatory loci, thereby corroborating the causal role of the regulome in generating complex social phenotypes. This project will integrate my experience in machine learning and gene expression analysis with expertise in alternative splicing and functional genomics provided by Dr Harpur’s group. Doing so will allow us to greatly advance our understanding of how social life evolves and diversifies by answering a fundamental biological question: how can biological complexity evolve without increases in gene content?
2022
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Long-Term Fellowships - LTF
Templated polypeptide synthesis inside a nanopore cavity
TOPARLAK Omer duhan (.)
. - University of Oxford - Oxford - United Kingdom
BAYLEY Hagan (Host supervisor)
Genetically-coded protein synthesis is the universal hallmark of cellular life, where the ribosome is the central figure, linking nucleic acids to protein catalysts. Yet, our understanding of templated polypeptide synthesis is restricted to the extant ribosome and its engineered derivatives, with its limited chemistry. In order to facilitate the design of artificial ribosomes by simplifying the complex nature of the task, we propose to study peptide bond formation and the DNA-templated polymerization of amino acids within a nanotube cavity. Recent developments in nanopore technologies have unlocked the potential of single molecule chemistry with angstrom-level precision. To this end, we will utilize phi29 DNA packaging motor nanopores, which will allow the base pairing between template DNA and aminoacylated polynucleotides as activated substrates. Inspired by non-ribosomal peptide synthesis and prebiotic reactions on the early Earth, we will explore thiol-thioester, thiol-disulfide and S-to-N acyl transfer reactions. We will make use of thioester-activated (e.g. acetyl-CoA) and aminoacylated trinucleotides as transfer RNA mimics to drive polymerization. Modified or unnatural amino acid side chains on the nanopore wall can enable otherwise uphill condensation reactions. The newly synthesized polymers will not be restricted to the inclusion of natural amino acid side chains or conventional polypeptide backbones. The synthesis will take place continuously, at a useful rate and without the need for an external fuel. The ultimate chemistry we propose will enable (bio)chemists to produce efficient protein synthesis devices that will serve as a foundation for synthetic cells.
2022
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Cross Disciplinary Fellowships - CDF
A multi-scale all-optical platform for the investigation of membrane potential dynamics
TORTAROLO Giorgio (.)
. - Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne, (EPFL)) - Lausanne - SWITZERLAND
MANLEY Suliana (Host supervisor)
Membrane potential is a ubiquitous cellular feature, underlying important functions including the release of neurotransmitters upon arrival of an action potential, and calcium signaling related to cell proliferation control. Voltage imaging is becoming the standard to investigate membrane potentials, offering significant advantages over electrophysiology: it is less invasive, scalable, and suited to examine intracellular organelles. Although recent imaging implementations capture fast action potentials, they rely on averaging multiple events over a reduced field of view and are limited in temporal resolution. Hence, they can detect the single action potential but miss its propagation dynamics and, significantly, its modulation of synaptic transmission. Furthermore, intracellular propagation of membrane potentials remains unstudied. To overcome these limitations, I propose an all-optical optogenetic approach that leverages “smart” controlling architectures and state-of-the-art detectors to realize a paradigm change: from voltage imaging to on-demand voltage tracking. Upon further developing hardware in the host laboratory, I will investigate the propagation of organellar and plasma membrane potential signals, spontaneous or evoked, in non-excitable cells and neurons. I anticipate that this approach will uncover unprecedented insights into the intra- and inter-cellular signaling mechanisms and their modulation during activity. Indeed, these signatures are hypothesized to be altered by multiple sclerosis and other neurodegenerative diseases, and have so far proved elusive to measure.