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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
Uncovering the nuclear dynamics of telomeres upon replication stress
GONZALEZ MANJON Anna (.)
. - The University of Sydney - Sydney - AUSTRALIA
CESARE Tony (Host supervisor)
Regulated spatiotemporal nuclear organization is critical for genome function. During my PhD I demonstrated that disrupted chromatin organization at the nuclear lamina can mediate chemotherapy resistance through altered gene expression. As a post-doc, I will explore how dynamic alteration of nuclear spatiotemporal organization promotes genome stability during the replication stress response (RSR). The Cesare lab identified that nuclear actin forces potentiate movement of replication-stressed chromatin, including telomeres, towards the nuclear periphery to facilitate homology directed repair. Telomeres are an exceptional model for this study because straightforward methods exist to induce telomere-specific replication stress and determine telomere interatomic networks. Telomeres are also suitable to live imaging and interact with nuclear domains/condensates during replication stress through unknown mechanisms. Using this telomere model, I will examine the following aims that explore open questions on nuclear dynamics. i) Identify the regulators of RSR-dependent telomere movement using time resolved APEX2 interatomics profiled by mass spectrometry. ii) Characterize how telomere dynamics during replication stress alters both local and global chromatin organization through ChIP, Hi-C/4C, and ATAC-seq methods. iii) Study the consequences of perturbed telomere localization following experimentally directed telomere movement to nuclear domains/condensates. Each aim will include functional interrogation of the revealed pathway/consequences. This study will enhance our understanding of RSR-dependent chromatin dynamics and revel the impact of these processes on genome stability.
2022
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Long-Term Fellowships - LTF
Mapping the neuromodulatory heterogeneity in decision making
HAGIHARA Kenta m. (.)
. - Allen Institute for Brain Science - Seattle - United States
SVOBODA Karel (Host supervisor)
Small groups of neuromodulatory (NM) neurons send brain-wide projections and influence diverse brain functions. Failures of NMs are associated with debilitating neurological and psychiatric disorders. Although NM systems are often thought of as diffuse, there is a complex tapestry of heterogeneity within each system. An outstanding question is how NM systems exert specific effects on circuit subsystems during behavior.
Systematic interrogation of this question requires dissecting the diversity of NM cell types and their connectivity to identified target neurons and their NM receptors at multiple spatial scales. In my post-doctoral program, I will take a multi-faceted approach to examine the influence of serotonergic (5HT) neuron types on their postsynaptic targets and on neural ensemble dynamics in frontal cortex.
My research will first define sub-types of 5HT neurons in the dorsal raphe projecting to the frontal cortex by combined analysis of transcriptome and whole-brain anatomical reconstruction. I will gain genetic access to these types using enhancer adeno associated viruses. Next, using expansion microscopy and multiplexed immunostaining, I will examine synapse-resolution connectivity of 5HT neuron types by characterizing their post-synaptic receptor subtype distribution in target neurons. Finally, by simultaneously measuring activities of 5HT subtypes and their targets in mice engaged in foraging behavior, I will examine how such heterogeneous 5HT modulation influences population coding underlying economic decision-making. Our approach will provide a blueprint for mapping the NM heterogeneity in general and may reveal new targets for clinical intervention.
2022
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Long-Term Fellowships - LTF
Understanding the neural mechanism underlying affiliative social behavior
HAYAT Hanna (.)
. - The Regents of the University of California, Los Angeles - Los Angeles - United States
HONG Weizhe (Host supervisor)
Social interactions between individuals are a hallmark of human society and involve two or more individuals engaging with one another. Whereas neural correlates of behaviors such aggression and mating have been studied extensively, little is known about the brain circuits that promote affiliative social interactions, which are crucial to maintain social cohesiveness and to the physical and emotional well-being of social species including humans. One of the most common affiliative behaviors observed across a large range of species is allogrooming, but the neural mechanisms underlying this behavior remain largely unknown. Here I propose to use high-density Neuropixels probe to record simultaneously hundreds of neurons from several brain regions during allogrooming (e.g. one probe can record activity from the medial amygdala, the hippocampus and thalamus simultaneously). Neuropixels enables recordings from local populations of neurons in one region as well as several populations across many regions, an essential step toward better understanding of global activity coordination during behavior. It will give me the opportunity to identify brain regions involved in social grooming, to decipher neuronal activity patterns involved in allogrooming from sensory input to motor output and to understand the inter-play and correlated activity between those regions. Using computational tools, I will build predictive models of behavior based on the brain activity. Investigation of the neural circuitry that controls affiliative social contact may help us understand the deficits of social behavior observed in neuropsychiatric conditions such as autism.
2022
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Long-Term Fellowships - LTF
Biochemical and structural characterisation of the mycobacterial T4SS-like/T7SS conjugation system
HENNELL JAMES Rory (.)
. - University Medical Center Hamburg-Eppendorf - Hamburg - GERMANY
MARLOVITS Thomas (Host supervisor)
Bacterial conjugation allows the transfer of genetic material between bacterial strains and is associated with the spread of antibiotic resistance and virulence factors. Recent work has discovered a conjugable plasmid (pRAW) in Mycobacterium marinum and related plasmids that are present in up to 50% of natural Mycobacterium isolates, including the Non-Tuberculosis Mycobacteria which often cause infections in immune-compromised patients. Most bacterial conjugation systems use the Type IV Secretion System (T4SS). pRAW encodes a T4SS-like system and a Type VII Secretion System (T7SS) termed ESX-P1. The T4SS-like gene cluster lacks key genes and transposon mutagenesis experiments showed that both the T4SS-like genes and T7SS genes were required for successful conjugation, suggesting that they function together in conjugation.
In this project I will structurally and biochemically characterise the components of these T4SS-like and T7SS secretion systems through three main approaches: cryo-electron tomography of secretion systems in native cells, purification of secretion complexes from native cells for biochemical and cryoEM analysis, purification of recombinant secretion complexes from Mycobacterium smegmatis. This work will be carried out in the Marlovits laboratory, where there is expertise in structural biology in collaboration with the Bitter laboratory, where there is expertise in genetics of mycobacteria. Structural and biochemical studies of this complex will enhance our understanding of a fundamental biological process which may contribute to the spread of antibiotic resistance and virulence factors in bacteria that cause a significant disease burden worldwide.
2022
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Long-Term Fellowships - LTF
Cell-specific functional connectivity of cerebellar outputs for locomotor learning
HERENT Coralie (.)
. - Champalimaud Foundation (Fundação D. Anna de Sommer Champalimaud e Dr. Carlos Montez Champalimaud) - Lisbon - PORTUGAL
CAREY Megan (Host supervisor)
We constantly navigate a complex world filled with uneven terrains that alter our walking pattern. Learning to correct for predictable errors in a changing environment is crucial for smooth and coordinated locomotion. A striking example is the adaptability of locomotor patterns upon exposure to a split-belt treadmill, where opposite limbs move at different speeds. The host laboratory previously showed that mouse, like human, locomotor learning depends critically on the cerebellum and specifically, on neurons projecting to the cerebellar interposed nucleus (IP). Importantly, spatial and temporal components of learning (location and timing of paw placement) proceeded independently, suggesting that they might be dissociable at the circuit level. This proposal aims to identify and characterize the functional connectivity of cerebellar output circuits conveying corrective calibration signals that modify ongoing locomotor movements in space and time. Specifically, we will: 1) Use cutting-edge viral tools to map output circuits downstream of the IP and identify key candidates for spatiotemporal calibration signals; 2) Use high-resolution quantitative behavioral analysis and circuit manipulation to test specific functional roles of projection-defined subsets of IP neurons in locomotor learning; 3) Use optogenetically-guided multi-probe recordings of projection-specific IP neurons during learning to understand how the cerebellum transforms locomotor errors into spatiotemporal calibration of locomotor movements. Overall, this work will reveal unprecedented insights into neural circuits ensuring the adaptability of motor commands, directly relevant for human rehabilitative therapy.
2022
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Long-Term Fellowships - LTF
Evolutionary, expression, and functional characterization of ancient putative chemosensors
HIMMEL Nathaniel (.)
. - University of Lausanne - Lausanne - SWITZERLAND
BENTON Richard (Host supervisor)
Ligand-gated ion channels (e.g. TRPs, IRs/iGluRs) are critical in animal sensory systems to link recognition of external and internal cues to changes in physiology and behavior. Growing evidence indicates that many of these channel families have origins in the last common eukaryotic ancestor (~2 billion years ago), but their functions outside of Metazoa are poorly understood. Recently, homologs of insect chemosensory receptors (“Gustatory Receptor-like”, GRL) were identified by the host lab in several unicellular species, including chytrid fungi, protists, and alga, many of which are motile and are capable of chemotaxis, leading us to hypothesize that these putative channels function in external stimulus-guided behavioral or physiological responses. I propose to characterize ligand-gated ion channels in these understudied taxa, via three aims: (1) Bioinformatically identify and phylogenetically assess all animal ligand-gated ion channel family homologs across unicellular Eukaryota; (2) Determine channel expression and localization (starting with GRLs) across life stages of select unicellular taxa through RNA-sequencing and immunofluorescence; (3) Determine protein biochemical and functional properties both in vitro (through heterologous cell expression) and in vivo, starting with the chytrid Spizellomyces punctatus GRL1, capitalizing on new genetic tools for this species. My studies will expand our understanding of channel evolution and function across taxa, and potentially reveal molecular mechanisms of sensory-guided behavior and physiology in unicellular eukaryotes, offering insights into the early evolution of chemosensation.
2022
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Long-Term Fellowships - LTF
Characterizing how pioneer transcription factors and chromatin structure regulate genome activation
HOPPE Caroline (.)
. - Yale University - New Haven - United States
GIRALDEZ Antonio (Host supervisor)
Zygotic genome activation (ZGA) is a universal step in animal development that involves massive chromatin remodeling and results in priming of cis-regulatory regions and transcriptional activation. In a function conserved across species, pioneer transcription factors (TFs) bind nucleosomal DNA to facilitate opening of regulatory regions to other TFs. In zebrafish, it relies on Nanog, Pou5f3 and SoxB1, yet the specific roles of pioneer TFs and the causal relationship between chromatin architecture and genome activation remain unknown. Further, we lack a holistic understanding of how global chromatin structure is spatially organized and remodeled during genome activation. We will integrate cutting-edge imaging and genomic approaches, including super-resolution, and expansion microscopy to study global chromatin architecture at unprecedented resolution and address these questions at single-cell resolution in zebrafish embryos. We will investigate spatiotemporal behavior of pioneer TF hubs during ZGA, determine interactions of pioneer factors at single molecule resolution and elucidate how promoter-enhancer interactions are modulated in response to pioneer activity.
This is a significant shift in both discipline and methodology from my previous research; I will use a new model organism and develop genomic and chromatin probing techniques while leveraging my microscopy expertise, which is a new dimension for the lab. We expect to elucidate the structure/function relationship of chromatin and pioneer factor dynamics, uncover fundamental mechanisms and provide a framework for dynamic chromatin interactions that will be relevant in other contexts.
2022
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Long-Term Fellowships - LTF
NAMUH -- A human genomic perspective on the evolution of chromosomal inversions
JAY Paul (.)
. - Københavns Universitet (University of Copenhagen, UCPH) - Copenhagen - DENMARK
NIELSEN Rasmus (Host supervisor)
Chromosomal inversions are ubiquitous in genomes. In many species, they are associated with complex traits, such as sexual dimorphism and social organization, but also with detrimental effects and genetic diseases. I have previously shown that inversions could tend to be involved in complex polymorphisms because they capture deleterious mutations. However, despite their well-documented biological importance, our understanding of the evolution of inversions is limited because of the difficulty of detecting them. I propose to take advantage of the abundance of recently sequenced present-day and ancient human genomes to dissect the evolution of chromosomal inversions. I will use cutting-edge methods, based on the detection of specific patterns of genetic diversity, to localize inversions in thousands of humans from periods back to 10kya. Using large-scale biomedical databases, I will test the association between these inversions and many evolutionary relevant characters, such as mortality or genetic diseases. I will test predictions regarding the evolution of inversions by following their frequency over time and by contrasting with other types of mutations. By comparing the genetic diversity in many inverted and non-inverted segments, I will untangle the selective forces acting on inversions, shedding new light on why they arise and how they evolve upon formation. Besides the insights into the consequences of inversions in humans, these in-depth analyses of the evolution of chromosomal inversions may yield groundbreaking fundamental results that will benefit many fields of biology, such as evolution, ecology, medicine and conservation genetics.
2022
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Long-Term Fellowships - LTF
Metabolism as an integrator that coordinates morphogenesis in the developing mammalian embryo
JUNYENT ESPINOSA Sergi (.)
. - California Institute of Technology - Pasadena - United States
ZERNICKA-GOETZ Magdalena (Host supervisor)
During embryo implantation, the pluripotent epiblast (source of all adult tissues) must coordinate growth, cell fate transitions and the emergence of embryo shape. However, the programs that integrate these processes remain undetermined. Metabolic networks, acting as hubs of all cellular activity, hold the potential to be key. In vitro, metabolic networks enable proliferation and correct cell fate acquisition of pluripotent embryonic cells. Yet, longstanding limitations for studying embryos during implantation have meant that the role of metabolism in embryo morphogenesis, and its precise regulation in space and time, remain unknown. The host lab has recently developed cutting-edge in vitro culture platforms that allow the investigation of the peri-implantation morphogenetic process in natural embryos, and its reconstruction using stem cell-based embryo models. I propose to combine these state-of-the-art embryological tools with time-resolved metabolic analysis using biosensors and single-cell metabolomic approaches; to determine how dynamic metabolic flux coordinates embryo growth and morphogenesis; and to map and model the dynamics of glycolytic flow and key intermediary metabolites during precise stages of epiblast remodelling. Together this will allow me to uncover mechanistic links between metabolic rewiring and cell fate transitions in the developing epiblast. I will then assess how these processes adapt during normal regulation of embryo size, and with maternal malnutrition, where nutrients powering metabolism are drastically reduced. This project will be first to resolve how metabolism and morphogenesis are coordinated in the development of a mammalian embryo.
2022
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Long-Term Fellowships - LTF
Neuronal heme sensing in metabolic adaptation to infection
KITOKO Jamil (.)
. - Fundacao Calouste Gulbenkian - Lisboa - PORTUGAL
SOARES Miguel (Host supervisor)
Sickness behavior is an evolutionarily conserved response to infection, whereby anorexia promotes a protective hypometabolic state. Presumably, this neurometabolic response evolved to restrict pathogens from accessing vital nutrients, such as iron. In mammals, iron is predominantly found within heme, the vast majority of which constitutes the prosthetic groups of hemoglobin, within red blood cells (RBCs). Multiple pathogens evolved to damage RBCs as a strategy to access host iron. This is associated however, with the generation of extracellular labile heme, which can act as a proinflammatory alarmin. Recent data from the host laboratory shows that labile heme elicits sickness behavior and the development of a hypometabolic state, similar to induced by infection with different classes of pathogens. Here I hypothesize that neurons sense labile heme, either directly or indirectly (i.e., via its proinflammatory effects on macrophages), eliciting sickness behavior and the associated organismal hypometabolic state. While intracellular heme can be sensed directly by neurons in the brain, via the Rev-erba/ß family of nuclear receptors, whether this is also the case for extracellular labile heme or whether this occurs indirectly via macrophages is not known and shall be established. I propose to: 1) Characterize brain neuronal activity upon heme administration to mice, using cutting-edge whole-brain clearing, mapping techniques and molecular profiling; 2) Determine critical components of heme-induced neuronal activation using pharmacological approaches to regulate sickness behavior and organismal metabolism, as monitored by state-of-the-art metabolic phenotyping systems.
2022
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Long-Term Fellowships - LTF
Systematic characterization of SNPs in CREs associated with congenital heart disease
LINDENHOFER Dominik (.)
. - European Molecular Biology Laboratory (EMBL-Heidelberg) - Heidelberg - GERMANY
STEINMETZ Lars (Host supervisor)
Genome wide association studies (GWAS) produced a wealth of information on associations between distinct genetic loci and human diseases. Over 90 percent of predicted variants for common diseases are located in the non-coding genome mainly affecting cis-regulatory elements (CREs) like enhancers. Single nucleotide polymorphisms (SNPs) in enhancers can affect gene expression and contribute to disease mechanisms, but for the majority of SNPs their functional contribution to disease is not understood. Current high-throughput methods to study enhancers use CRISPRi to perturb them entirely. This neglects the differential influence of individual SNPs at CREs on disease-relevant gene expression. I aim to establish a method to modify SNPs in CREs in high-throughput using precision genome editing with a targeted scDNA-scRNAseq readout to link variable genomic editing outcomes with disease-relevant gene expression. Screening at this scale will require to advance methods for precision genome editing in mammalian cells, while the single-cell multiomic readout is crucial to precisely link genotype with gene expression profiles due to differential editing efficiencies at distinct loci.
I will use this method to systematically test SNPs in CREs associated with congenital heart disease (CHD), a disorder resulting in structural heart abnormalities at birth. CHD is highly heritable and GWAS identified hundreds of CHD-associated SNPs at risk loci in non-coding regions with their function remaining elusive. Screening for these SNPs in human heart organoids will allow us to determine associated gene expression changes systematically and how they contribute to the disease mechanism of CHD.
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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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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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.