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Funding
Funding
HFSP supports novel, innovative and interdisciplinary basic research focused on the complex mechanisms of living organisms. A clear emphasis is placed on novel collaborations that bring biologists together to focus on problems at the frontier of the life sciences.
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Awardees
Awardees
In this section you find information about the awardees in the HFSP scientific programs. This includes a searchable database of HFSP awardees, information on the HFSP Nakasone Award and other achievements by HFSP awardees.
- News & Impact
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Events
Events
HFSP promotes and participates in several events every year. We are committed to bringing together the scientific community and forging new opportunities to network and have scientific discussions that help to create bridges and partnerships for the future of frontier science.
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About
About
The Human Frontier Science Program is a program of funding for frontier research in the life sciences. It is implemented by the International Human Frontier Science Program Organization (HFSPO) with its office in Strasbourg. Here you can find all you need to know about the HFSPO.
Awardees
2024
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Long-Term Fellowships - LTF
Mapping the interactions between bacteria in the microbiome for targeted strain replacement
STOKAR-AVIHAIL Avigail (ISRAEL)
Genome Biology - European Molecular Biology Laboratory (EMBL-Heidelberg) - Heidelberg - GERMANY
TYPAS Athanasios (Host supervisor)
The importance of the human gut microbiome in health and disease highlights the need for ways to actively modulate it. Although fecal microbiota transplantation is used to profoundly change dysbiotic microbiotas, more targeted and rational ways of modulating the microbiome are currently missing. Replacing a specific strain by another strain of the same species, carrying a desired trait for the community is a strategy that would ensure minimal impact on the community composition as a whole. To be able to do this and overcome the colonization resistance of such stable microbial communities, we need to understand the underlying community dynamics. I propose two of the most abundant and prevalent species in the human gut microbiota, Bacteroides uniformis and Phocaeicola vulgatus, and come up with strategies for strain replacement. Aims: 1. Identify B. uniformis or P. vulgatus strains that kill the resident co-specific strain of 5 characterized human gut microbiotas. 2. Study whether and how the microbiome protects a resident strain from inhibition by the incoming strain. 3. For interactions that persist at the community level, dissect the mechanistic and genetic basis of the interaction. 4. Introduce the killing genetic trait and an additional desired trait, into the resident strain, and use this modified strain for strain replacement. Hypotheses: 1. Different strains of the same species commonly interact via negative interactions. Thus, I expect to identify mainly cases of intraspecies inhibition. I hypothesize that in some cases the identified inhibition interactions will also occur when the strains are in a complex community setting, whereas in other cases the community may protect the resident strain. 2. I hypothesize that for some of the identified interactions, a specific gene or group of genes will be necessary and sufficient for inhibition\protection of a strain from inhibition, and thus can be identified by genetic screens and introduced to other strains if necessary. Experimental Setup: Existing large strain collections of B. uniformis & P. vulgatus will be used to test pairwise interactions within each species. Negative interactions will be checked for their persistence within microbiome communities, using fluorescence tagging or plating on selective plates to monitor the two strains of interest. Mutant libraries and follow up targeted experiments will be used to decipher the genetic basis for these interactions. Personalized human microbiomes for which the individual species/strains have been isolated, will be used to identify community protection mechanisms. Conclusion: This project combines my skills in studying interactions between microorganisms, and the Typas lab's systematic screening and microbiome expertise. This study will lead to new discoveries regarding how bacteria interact in natural communities, and provide important mechanistic understanding to enable successful strain replacement in gut microbiomes.
2024
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Long-Term Fellowships - LTF
Understanding the host-microbe arms race through the TLR5-flagellin axis
TAN Yi Han (SINGAPORE)
Microbiome Science - Max Planck Institute for Biology Tübingen - Tübingen - GERMANY
LEY Ruth (Host supervisor)
Background The host constantly encounters microbes at interfaces such as the gut and respiratory mucosa. Pattern recognition receptors (PRRs) enable the host to rapidly detect conserved pathogen associated molecular patterns and mount immune responses. Toll-like receptor 5 (TLR5) is a PRR which recognises bacterial flagellin and drives inflammatory responses upon activation. TLR5 regulates the microbiome, and TLR5-deficient mice exhibit microbiome-dependent metabolic syndrome. Interestingly, TLR5 deficiency increases susceptibility to infection but protects against inflammatory diseases such as Crohn’s disease and Systemic lupus erythematosus. Recent work by Clasen et al discovered that bacteria have evolved different strategies during engagement of TLR5. Stimulator flagellins strongly bind and activate TLR5, triggering an inflammatory response which benefits certain pathogens. Alternatively, pathogens may possess flagellins which do not bind and evade TLR5 signalling. Some commensals produce silent flagellins which bind TLR5 well but do not activate TLR5, contributing to immunological tolerance. PRRs may engage in co-evolutionary arms races with their microbial ligands at the host-microbe interface. The human TLR5 seems to be undergoing purifying selection. However, the functional TLR5F616L and TLR5N592S variants are maintained at relatively high frequencies. Although TLR5N592S is associated with ulcerative colitis and colorectal cancer and TLR5F616L is associated with Crohn’s disease they may confer some benefits. These variants have only been characterised in the context of stimulatory flagellins. Hypotheses We hypothesise that the F616L and N592S SNPs evolved to fine-tune TLR5 signalling in response to silent or stimulatory flagellins. These TLR5 variants may differ from the dominant allele studied in Clasen et al with respect to their interactions with the two classes of flagellin. TLR5 heterodimers, which comprise monomers of the dominant TLR5 with TLR5 variant (1:1 ratio) may also exhibit altered binding and activation. Aims 1. Examine the interaction of TLR5F616L and TLR5N592S with different flagellin types 2. Determine changes in TLR5 signalling after stimulation with different flagellin types 3. Investigate effects of TLR5 heterodimers on signalling Experimental approaches We will examine the binding of representative silent and stimulatory flagellins to TLR5 variant monomers as well as homo and heterodimers. CRIPR-Cas9 based editing will be used to create homozygote and heterozygote knock-ins of TLR5 variants in human small intestine, colon and lung organoids. Subsequently, RNA-seq and ELISA will be used to determine responses to stimulation of organoids with representative flagellins. Conclusions and significance This study will improve our understanding of the role of TLR5 variants in disease and may yield new insights into PRR evolution. This work could also aid the development of therapeutics targeting TLR5 signalling.
2024
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Long-Term Fellowships - LTF
Following dance vibrations on a swarm: the emergent mechanics of honey bee collectives
VIJAYAN Sajesh (INDIA)
Biology - The University of Western Ontario - London - CANADA
MHATRE Natasha (Host supervisor)
When animals form groups, they display emergent properties that can be quite different from those shown by individuals. For example, fire ants self-assemble into dynamic structures to face adverse conditions. This study looks at how a structure composed entirely of interlinked and interacting honeybees can transmit vibrations as part of the waggle dance communication system. When honeybees move nests, they form large, organized combless clusters called swarms. Swarms consist of several layers of bees, and the structural integrity of the swarm is maintained by bees rearranging themselves. Since combs are needed for reproduction, bees need to quickly transition out of the swarm stage by choosing a new nest-site. This decision-making is mediated by waggle dances. A dancer bee attracts followers to itself and communicates information to them via a waggle dance. Substrate vibrations are an important part of dance communication, and previous work has assumed that combs are required to carry these vibrations. Data from one honeybee species (A. dorsata), however, strongly hints that even swarming bees communicate using waggle dance vibrations which must therefore transmit through their interlinked bodies. I propose to study the vibrational characteristics of the dance signal on these two different substrates, and also of the receiver’s vibration detecting sensory system. To study substrate-dependent transmission properties, I will measure the dance vibrations on combs and swarms using a combination of laser Doppler vibrometry and behavioral observations. Next, I will use electrophysiological measurements to test the tuning of the leg mechanosensory organs for dance vibration detection. To test that the cue relevant to dance detection is indeed substrate vibration, I will disrupt the leg mechanosensory organ, and test whether dances can still be detected on either substrate. Lastly, I will use mathematical modeling to understand the physical principles governing vibration transmission on combs and swarms. Biophysical and mechanical explorations of bee swarms have usually focused on the principles that enable individual bees to form these large collectives. This study will be the first to explore honeybee swarms as a material that transmits vibrations and will provide a new direction to explore the honeybee swarm as an active material. The swarm can be considered as a metamaterial whose mechanical properties can differ based on the arrangement and interaction of individual bees. Importantly, we will test how interconnected bees can provide a flexible, yet reliable medium for communication and decision-making. Hence, honeybee swarms will form a template that can be extended to design autonomous systems that can self-organize and communicate. These findings will have implications in fields ranging from animal communication to swarm dynamics and robotics.
2024
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Long-Term Fellowships - LTF
The biophysics of causality – sensing and control of network dynamics by single neurons
VOITOV Ivan (CANADA)
Zuckerman Institute - The Trustees of Columbia University in the City of New York - New York - United States
POLLEUX Franck (Host supervisor)
Each neuron in the central nervous system establishes thousands of synaptic input and output connections, forming networks that generate the brain-wide activity patterns that underlie behavior. However, a fundamental gap remains in our understanding of how neurons, through local plasticity mechanisms, can organize themselves into behaviorally useful circuits - how can a single cell discern its own contribution to these global activity patterns? One radical idea is that neurons form control loops with their networks, using the feedback received following their own action potential firing to gauge their causal influence on network dynamics, and adapting to this feedback in order to drive the network to a specific function. Thus, this project aims to bridge the gap between cellular physiology and network computations by examining the precise role that an individual neuron’s output plays in the control of its inputs, and the interplay of such control with the neuron’s own plasticity mechanisms. I will leverage recent advances in optical imaging and molecular perturbation techniques to study how single hippocampal CA1 pyramidal cells influence and are influenced by their local network during place field formation, a well-characterized and behaviorally relevant form of plasticity. I will use state-of-the-art two-photon 3D acousto-optic deflector microscopy to longitudinally monitor the synaptic inputs and outputs of a single CA1 neuron by co-expressing recently developed high-affinity presynaptic glutamate sensors with red-shifted calcium indicators. After characterizing a neuron’s nominal input and output dynamics during plasticity, I will disrupt glutamate release originating from this single neuron by using precise molecular tools, such as inhibition of presynaptic vesicle fusion or single cell conditional deletion of VGLUT1, sparing all other presynaptic processes. The driving hypothesis is that individual neurons sense their role in network computations by actively regulating their own input through action potential firing. A major objective will therefore be to characterize the effects of output blockade on key physiological properties of CA1 hippocampal neurons, such as dendritic amplification and synaptic stability. In addition, by simultaneously recording the activity of surrounding neurons, I will be able to quantify the role of the single manipulated neuron in the local network, providing first-of-its-kind evidence for several previously hypothesized mechanisms, such as lateral feedback inhibition, in the regulation of hippocampal memory formation. Unraveling the control loops that neurons form with their networks will offer unprecedented insights into the interplay between a neuron's plasticity rules and their role in shaping network function. By defining a novel mechanism for neuronal sensing of their causal network contributions, this project will lead to fertile ground for future development of biological learning algorithms.
2024
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Long-Term Fellowships - LTF
Does the striatum use cerebellar motor state predictions to guide rapid and complex movement?
WEGLAGE Moritz (GERMANY)
Department of Organismic and Evolutionary Biology - President & Fellows of Harvard College - Cambridge - United States
ÖLVECZKY Bence (Host supervisor)
The brain’s ability to control fast, yet complex and tightly-coordinated movements, like guitar solos, is remarkable. Any sensory feedback ostensibly guiding such rapid movements is necessarily delayed, as it takes time for nerve impulses to travel to-and-fro, between brain and fingertips. This begs the question: How does the brain mitigate sensory delays (and noise) when generating rapid, yet complex movements? One possibility is that such movements are guided by near instant, “0-lag” estimates of the current state of the body, rather than by slow “actual” sensory feedback. A brain region commonly believed to compute model-based motor state estimates is the cerebellum [1]. Here, I hypothesize that fast, yet complex movement sequences generated by the dorsolateral “sensorimotor” striatum (DLS) are guided by 0-lag body state estimates computed by the cerebellum (CB) and relayed to DLS via the intralaminar thalamic nuclei (ILN). To verify this hypothesis, I will attempt to (Aim 1) demonstrate that the signal transmitted via the CB-ILN-DLS pathway [2] is congruent with model-based body state predictions; and (Aim 2) confirm that the pathway is critical to coordinate and control fast, complex, and DLS-dependent movement sequences with precision. To achieve these aims, I propose to record (using electrophysiology and optotagging) the activity of DLS-projecting ILN neurons, as well as to reversibly inactivate (using chemogenetics) the CB input to ILN-DLS “relay neurons”, in freely-moving rats executing fast, complex, and confirmed DLS-dependent movements [3]. If the hypothesis is true, the activity of the ILN-DLS neurons should accurately reflect current body state in detail and with little-to-no temporal lag – until unpredictable deviations are introduced to the sensorimotor state, or the neurons’ CB input is blocked. Once the CB input to ILN is blocked, rats should further misjudge the position of their limbs in space, and mistime, over- or undershoot their movements – in particular when moving fast. CB and DLS are critically implicated in motor control in health and disease, but are thought to principally interact through the cerebral cortex [4,5]. The cortex-DLS loop has been linked to efficient model-free action selection driven by state-dependent action policies, whereas the cortex-CB loop is believed to facilitate flexible model-based online control of ongoing movements [4]. This study aims to reveal a yet unexplored mechanism by which model-based CB predictions may be integrated into model-free DLS policies, without cortical involvement. The exploration of suchlike subcortical CB-DLS interactions is potentially paradigm-shifting and may pave the way towards the discovery of novel causes, mechanisms, and treatment options with regard to the many movement disorders associated with CB and DLS dysfunction.
2024
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Long-Term Fellowships - LTF
Exploring novel riboswitches in plants: uncovering new regulatory mechanisms for plant metabolism
XU Jin (CHINA, PEOPLE'S REPUBLIC OF)
Cell and Developmental Biology - John Innes Centre, Norwich, UK - Norwich - United Kingdom
DING Yiliang (Host supervisor)
Background Riboswitches are regulatory RNAs with specific structures that detect metabolites/ions to regulate RNA processes rapidly and precisely, and they serve as regulatory modules in multiple metabolic pathways of bacteria. However, identifying riboswitches in plant is challenging due to limitations in identification methods and incomplete UTR annotation. Tomato is an ideal model for studying plant metabolism due to the presence of major metabolite classes and my previous research has demonstrated that RNA structure plays a critical role in tomato. This research proposes to explore novel riboswitches in tomato and identify previously unknown plant metabolite riboswitches. This research will have a broad range of routes to impact noting the role of metabolic pathways in determining nutritional, resilience and pharmacological qualities in plants. Aims 1) Generating in vivo RNA structurome landscapes for different developmental stages in tomato I will generate RNA structurome landscapes using in vivo RNA structure profiling methods developed in my host lab and further determine RNA structure alterations across developmental stages. 2) Deep mining novel riboswitches in transcriptome-wide structural comparisons I will develop cutting-edge predictive models based on deep learning to explore systematically non-trivial relationship between RNA structural alterations and RNA processing changes. 3) Validating and optimizing riboswitches identified from tomato I will mutate RNA structures and validate identified riboswitches. By working with biophysicists in Prof. Zoe Waller’s group at UCL, a long-term collaborator of my host lab, we will assess the binding of identified riboswitches with metabolites. I will then optimize the RNA structure to achieve either metabolite hypo/hyper-sensitive plants. Hypotheses 1) Riboswitches play a crucial role in regulating animal and bacterial metabolism. I hypothesize that they are also globally present in plants. 2) Traditional metabolic regulation is challenged by the redundancy of functional genes, and overexpression may lead to gene silencing due to feedback. I plan to identify specific riboswitches, paving the way for new regulatory mechanisms to control plant metabolites. 3) Novel AI-based methods will allow us to identify riboswitch with high efficiency and accuracy at the high-throughput manner. Approach 1)In vivo RNA structure profiling in tomato using chemical structure profiling methods. 2)Deep mining novel riboswitches in plants via AI approaches. 3)Validation of riboswitches with plant transgenics, biophysics, and metabolism. Conclusions 1)Novel transcriptome-wide RNA structural comparative analysis for identifying novel RNA riboswitches. 2)Identifying plant-specific riboswitches and paving the way for new metabolic regulatory mechanisms. 3)Novel AI methods for identifying functional RNA structure motifs. 4)New frameworks for identifying riboswitches in eukaryotes at the genome-wide.
2024
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Long-Term Fellowships - LTF
A nucleus-driven paradigm of mechanotransduction and morphogenesis
YOSHIDA Mari (JAPAN)
Genetics and Developmental Biology - Institut Curie - PARIS - FRANCE
BELLAÏCHE Yohanns (Host supervisor)
Nucleus states such as shape and stiffness regulate gene expression and the nucleus has emerged as a key mechanotransduction organelle. However, we lack an understanding of the role of nucleus states and mechanotransduction during tissue development in vivo. Previous studies on mechanotransduction have established that the nucleus senses mechanical forces applied to the cell to modulate gene expression. Doing so, these former studies have assumed that such response is ‘passive’ as they did not fully consider the initial state of the nucleus prior to force transmission. However, based on accumulating works and my own research on the nucleus, the nucleus is a dynamic organelle that constantly moves, deforms, and changes its mechanical properties or subnuclear organization. As nuclear force transmission and gene expression depends on nucleus states, I hypothesize that the initial states of the nucleus (e.g. shape, position, stiffness) and subnuclear organization play a key role in modulating nuclear mechanotransduction and consequently any processes linked to mechanotransduction, such as tissue morphogenesis. To address this outstanding hypothesis, I chose the Drosophila epithelial tissue of the pupal dorsal thorax as a model. This tissue is composed of more than 10,000 cells whose various dynamics regulated by gene expression and mechanical forces have been characterized. In addition, it is amenable to physical manipulation, spatialomics and optogenetics. Building on these resources, I propose the following research plan: 1) I will determine nucleus states at tissue scale during development by lattice light-sheet microscopy. I will then alter nucleus states (position, movement, shape, size) within the tissue at defined time points by optogenetic loss/gain of function of known regulators of nucleus states. 2) I will compare the spatial transcriptome of tissues with/without alteration of nucleus states to determine whether the expression of the genes involved in transcription or mechanotransduction is changed. Then, the mechanisms controlling such transcriptional changes will be studied by determining gene loci localization and epigenetic modifications. 3) Next, I will apply mechanical forces to the tissue with/without alteration of nucleus states, using physical and optogenetic tools. Then I will compare the spatial transcriptome to determine whether the initial nucleus states modulate mechanotransduction. 4) Last, I will assess cell and tissue morphogenesis with altered nucleus states to uncover the impact of nucleus states on tissue morphogenesis. The Bellaïche lab has developed state-of-the-art techniques required for this research. Hence, I expect the combination of my expertise (nuclear dynamics, live cell imaging), the model system, and the host lab's know-how will greatly synergize to define novel concepts that broaden the horizons of mechanotransduction and morphogenesis.
2023
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Long-Term Fellowships - LTF
Deciphering the Role of Outer Radial Glia in Autism
AHMED Mai (EGYPT)
Yun Li Lab - The Hospital for Sick Children - Toronto - CANADA
LI Yun (Host supervisor)
Autism Spectrum Disorder (ASD) is a devastating neurodevelopmental disorder that causes deficits in social interaction and behavior. To date, 1031 genes are linked to ASD, suggesting its strong genetic background. However, how perturbations in these genes contribute to ASD pathology at the cellular and molecular levels remains largely elusive. Outer radial glia (oRG) are a recently identified population of neural stem cells that is highly enriched in the brains of humans and higher primates. oRG generate the majority of human cortical neurons and contribute to cortical expansion and folding. In this project, we hypothesize that oRG are involved in the pathology of ASD based on several observations. The brains of ASD patients during early development show altered growth and folding, which suggests possible defects in oRG proliferation or differentiation. In addition, a study published by the Li lab found that a mutation in a known ASD gene led to increased proliferation of oRG. Here, I aim to employ CRISPR-based knockout screens to investigate the role of oRG in ASD pathology using human pluripotent stem cell (hPSC)-derived oRG in 2D neural cultures and 3D brain organoids. To realize my aim, I will perform CRISPR screens in arrayed and pooled formats to determine which ASD gene knockouts perturb oRG at both the functional and transcriptomic levels. Based on the results of the screens, I will select high-potential ASD genes that induced significant changes in oRG. Then, I will generate 3D cortical organoids from stable CRISPR knockout hPSC lines and examine in detail how ASD gene disruption affects oRG dynamic behavior, oRG-derived neuronal populations, and organoid development. By leveraging human stem cell models, together with the recent advances in CRISPR screens and single-cell transcriptomics, the proposed study provides a targeted large-scale approach to fill a current gap in our knowledge on the role of oRG in ASD pathology. On a global scale, my study will shed light on the different gene networks that converge within oRG for ASD pathology, which is expected to pave the road for potential biomarkers and therapeutic targets that can improve disease outcomes in ASD patients.
2023
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Long-Term Fellowships - LTF
Profiling tumor proteolysis with genetically-encoded signaling integrators
ALGOV Itay (ISRAEL)
Cancer biology - Dana-Farber Cancer Institute - Boston - United States
ZHOU Xin (Host supervisor)
Elevated extracellular protease activity is a hallmark of cancer, known to play an important role in shedding and activating receptors and remodeling the extracellular matrix. Technologies that allow us to understand the complexity, dynamics, and heterogeneity of extracellular proteolysis would significantly advance our understanding of how proteases impact tumor growth and metastasis, and inform how we could harness elevated proteolysis to design safer cancer drugs.
It remains difficult to characterize tumor microenvironment protease activities with current molecular tools. RNAseq can determine intracellular transcript levels but doesn’t report protease activities or extracellular proteolysis. Protease sensors, such as genetically encoded reporters or small molecule probes, only allow testing of one substrate sequence at a time, which prevents us from a systematic understanding of the proteolysis landscape.
To break the technology barrier for a deeper understanding of the protease activities in the tumor microenvironment, I propose to develop proteolysis signaling integrators (PSIs) that can transform a proteolysis event into a transcriptional event within a defined time window. I have designed two systems for the PSIs. The first is based on leucine zippers, alpha-helical dimerization motifs found in transcription factors. The second one is based on Protease-Activated Receptors (PARs), G protein-coupled receptors activated by proteases. In both systems, I have designed to couple a proteolysis event of a substrate sequence to release a Gal4 transcription factor (TF). The design of PSIs is modular so that a large library of substrates can be encoded and tested simultaneously. A small-molecule controllable destabilizing domain (ddDomain) will be incorporated into a PSI to control the time of expression. Tumor cells engineered to express the library of PSIs will be implanted in mice and activated for expression after the tumor grows to a specific size. If a proteolysis event happens, the Gal4 TF will drive transcription of an enhanced green fluorescent protein (EGFP), resulting in a quantitative signal of the proteolytic events. Following isolation of the tumor, cells with low, medium, and high EGFP signals will be separated and sequenced to determine the propensity of proteolysis for different substrate sequences. The development of PSIs has the potential to transform how we characterize extracellular protease activities, and the gained knowledge will inform the development of a new generation of protease-based prodrugs.
2023
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Grant Awardees - Program Grants
Bacterial targeting of the host epitranscriptome
HARTLAND Elizabeth (AUSTRALIA)
- Monash University - Clayton - AUSTRALIA
ALLAIN Frédéric (FRANCE)
- Eidgenoessische Technische Hochschule Zuerich (ETH Zürich) - Zurich - SWITZERLAND
HELM Mark (GERMANY)
- Johannes Gutenberg University of Mainz - Mainz - GERMANY
The post-transcriptional processing and modification of cellular RNA provides an additional level of gene regulation that is known as the epitranscriptome. However, despite current knowledge of RNA modifications, the functional significance of many epitranscriptomic changes within the cell is unknown. Here we will explore the impact of bacterial infection on the host epitranscriptome using methods to identify the direct and specific modification of host RNA by bacterial pathogens. Many host-interacting bacteria use specialised protein secretion systems to inject “effector” proteins into eukaryotic cells that target various cellular processes to promote bacterial survival. Although many bacterial effector proteins are known to mediate post-translational modifications of host proteins, effectors that directly modify host RNA and alter the epitranscriptome have not been described. We hypothesise that host-interacting bacteria harbour undiscovered RNA-binding effector proteins that post-transcriptionally target eukaryotic RNA with novel modifications. Such RNA modifying effectors would offer the potential to investigate the significance of RNA modifications in host cell responses and functional biology.
The specific aims are to: 1. Discover bacterial effector proteins that bind eukaryotic host RNA during infection using Legionella species as model intracellular bacteria by performing RNA-interactome capture (RIC) from host cell RNA. Epitope tagged RNA-binding effector proteins will then be used for cross-linking RNA immunoprecipitation (CLIP) of host RNA to identify RNA modifications using liquid-chromatography and mass spectrometry (LC-MS). 2. Define the host RNA targets of bacterial effectors and explore the structural basis of effector mediated RNA modifications using epitranscriptomics. Large-scale expression and purification of bacterial RNA-binding effectors with identified consensus RNA-modification motifs will be used for structural analysis of RNA-protein complexes. 3. Investigate the impact of effector-mediated host RNA modifications on the cellular response to infection by assessing bacterial mutant strains for intracellular replication defects and changes in host transcriptional responses to infection. The biodynamics of RNA-binding effectors and their modified host RNAs will be explored in vitro using novel liquid-liquid phase separation (LLPS).
2023
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Long-Term Fellowships - LTF
Investigating the cell-matrix mechano-chemical feedback loops as determinants of tissue fate
ALLANKI Srinivas (INDIA)
Tumor Cell Biol. Lab - The Francis Crick Institute Ltd - London - United Kingdom
SAHAI Erik (Host supervisor)
Emergent tissue architecture is orchestrated by the mechano-chemical feedback interactions among the cellular and extracellular components, across scales. While the biochemical principles of tissue organization have been well studied, the mechanical and biophysical aspects remain less well understood. In a homeostatic tissue, the constituent cells both deposit and maintain the extracellular matrix (ECM), thereby determining tissue mechanics, and are responsive to the mechanical properties of the ECM. An imbalance in these processes can lead to pathologies such as fibrosis and cancer. Hence, remodeling the spatial and biochemical interactions of cells and the ECM can decide the tissue fate in between health and disease. Moreover, physiological aging is associated with changes in tissue structure and mechanics, which may relate to the development of pathologies. However, a holistic view on the in vivo principles governing tissue fate as a function of the complex feedback loops among cell types, cell states, ECM, and tissue mechanics is yet to be defined.
I hypothesize that mechanical heterogeneity within the homeostatic tissue leads to the formation of stiffness-dependent cell states, which prime the cells in stiff regions to disease. Hence, the aims are – 1) to characterize the in vivo spatial arrangement of various cell types and their respective transcriptional states as a function of the surrounding ECM and tissue mechanics, and 2) to identify specific cell-matrix feedback loops that define the tissue fate.
Using the homeostatic and fibrotic murine skin as models of health and disease, I will spatio-temporally map their mechano-chemical properties by combining mechanical mapping (nano-indentation) with high-resolution spatial matrisomics (imaging mass cytometry) and transcriptomics (Stereo-seq). With these data, I will uncover the spatio-temporal correlations among tissue mechanics, topology, and biochemical properties, including cellular composition, arrangement, and their transcriptomes, as well as the ECM alignment and stiffness. Next, to determine the causality of these correlations, I will manipulate the cell-matrix loops in silico using agent-based modelling and in vitro using co-cultures with stiff vs. soft matrix-generating fibroblasts. I will then systematically test these theories by using 4D live imaging coupled with nano-indentation in tissue explants. The shortlisted feedback loops will be manipulated in vivo in the homeostatic tissue using mosaic expression systems and gene-level perturbations (Perturb-seq) and assayed for the tissue fate. Finally, I will test whether these cell-matrix loops are conserved in human pathologies, including skin cancer/fibrosis.
Altogether, this project will provide a comprehensive understanding of disease emergence and how local mechano-chemical feedback loops orchestrate the macroscopic tissue fate in space and time, and opens new avenues for generating preventive therapeutics.
2023
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Grant Awardees - Early Career
Encoding motion in an interface: the shape-morphing armored skin of pufferfish
AMINI Shahrouz (IRAN)
- Max Planck Institute of Colloids and Interfaces (Max-Planck-Institut für Kolloid- und Grenzflächenforschung) - Potsdam - GERMANY
CAMP Ariel (United States)
- University of Liverpool - Liverpool - United Kingdom
RAFSANJANI Ahmad (IRAN)
- University of Southern Denmark (Syddansk Universitet, SDU) - Odense M - DENMARK
Spiny pufferfishes, e.g., porcupinefish, defend themselves by transforming from a streamlined torpedo to a large, prickly sphere. This dramatic yet reversible shape morphing is achieved by highly mineralized hard spines anchored to a very extensible soft skin that stretches up to 40% as the body inflates. The armored skin is activated by body inflation: as the skin stretches, the sharp spines rotate into an erect position, rigidly pointing outward as a visual warning and mechanical defense. Interfacing between hard and soft tissues is ubiquitous in nature like bone and tendon, but it is very unusual for such an interface to embrace extensive, lifelong distortions while maintaining the material integrity. Remarkably, the skin-spine interface of pufferfish does exactly this function, dramatically morphing both skin and spines with every inflation-deflation cycle and using this transformation as a defense mechanism. How do puffers assemble this unlikely combination of extensible and rigid materials into a repeatedly stretched interface—without tearing themselves apart? How does the drastic skin extension drive and guide spine rotation? How do properties of soft skin and hard spine reciprocally shape dynamic movements? In this project, we integrate our expertise in mechanics, biology, and robotics to provide unprecedented insights into the multi-scale architecture and complex function of the porcupinefish’s armored skin. We will systematically investigate the dynamics of the body expansion, skin stretching, and spine erection and adapt the deployed structural and architectural strategies to create bio-inspired functional interfaces. The micromechanical experiments will reveal the secret to the integrity and performance of the interface of materials with contrasting properties. The musculoskeletal measurements, both on live animals and fresh tissues, shed light on the kinematics and functional morphology of the armored skin of pufferfish. The soft robotics model presents a cyber-physical twin for pufferfish capable of reproducing reactive behaviors consistent with its morphing behavior to verify and generate biological hypotheses. Our collaborative project unravels how the interfacial morphology of pufferfish skin encodes complex shape-morphing functions transferable to adaptive architectures for biomedical, surveillance, and environmental monitoring application.
2023
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Grant Awardees - Early Career
Decoding the sulfation codes in the glycocalyx
MILLER Rebecca (United Kingdom)
- Københavns Universitet (University of Copenhagen, UCPH) - Copenhagen - DENMARK
ANGGARA Kelvin (INDONESIA)
- Max Planck Institute for Solid State Research (Max-Planck-Institut für Festkörperforschung) - Stuttgart - GERMANY
Large polysaccharides are widely found in nature. Arguably one of the most complex and biologically diverse groups of polysaccharides are the glycosaminoglycans (GAGs) that despite a relatively simple disaccharide repeating backbone attain enormous structural variation through decoration by sulfate groups. While many important and diverse bioactivities assigned to GAGs are believed to be directed by distinct patterns of sulfation along the large GAG chains, direct structural identification of these motifs remains largely unexplored due to analytic barriers. Therefore, our aim is to marry emerging technology advances to make a quantum leap in glycosciences with atomic-level sequencing and structural determination of polysaccharides at the single-molecule level. We hypothesize that precise genetic engineering of glycosylation in cells (RLM’s team at UCPH) will enable us to produce sufficiently homogeneous GAG chains for direct sequencing analysis by single-molecule imaging using electrospray ion-beam deposition and scanning tunneling microscopy (KA’s team at MPI). We focus on GAGs that through complex sulfation patterns orchestrated by 30 distinct sulfotransferases produce recognition landing paths - sulfation codes - for a myriad of GAG-binding proteins that serve essential functions in all metazoans. We will produce these GAGs from the library of cells, and they will be structurally characterized by imaging them one-molecule-at-a-time using scanning tunnelling microscopy to provide the visual form and shape. The images corroborated by ab initio calculations at the level of Density Functional Theory (DFT) will reveal structural GAG motifs that give rise to distinct bioactivities. We believe this interdisciplinary strategy will enable us to dissect the bioactive cues embedded in the long GAG chains. Moreover, we believe that the strategy of combining genetic glycoengineering to reduce the complexity and heterogeneity of GAGs combined with single-molecule imaging will lead to a major breakthrough in glycosciences, which will more generally open up opportunities for direct analysis of other types of polysaccharides, including bacterial lipopolysaccharides, plant polysaccharides such as chitosan, as well as more complex glycoconjugates such as proteoglycans and glycoproteins.
2023
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Grant Awardees - Program Grants
Understanding fundamental mechanisms governing insect cell membrane deformability
GEROLD Gisa (GERMANY)
- Innsbruck Medical University - Innsbruck - AUSTRIA
ARIOTTI Nicholas (AUSTRALIA)
- Institute for Molecular Bioscience - Brisbane - AUSTRALIA
PERRIMON Norbert (United States)
- Harvard Medical School - Boston - United States
Insect cell membranes differ from mammalian membranes by deformability, lipid content, lipid distribution in microdomains and membrane leaflet asymmetry. Enveloped insect-borne viruses require intimate interactions with cellular membranes to enter cells, replicate their genomes in cells and bud from cells. Despite fundamental biophysical differences between insect and mammalian membranes, insect-borne viruses can productively infect cells from both phyla. Decades of studies on insect-borne viruses have not addressed the machinery of insect membrane deformation and its exploitation by viruses.
Here we hypothesize that insect-borne viruses have evolved to biophysically manipulate membranes from both phyla and/or hijack physiological membrane properties from both phyla. Whether genes involved in membrane dynamics or deformation are genetically similar in insects and mammals or whether insects and mammals achieve similar outcomes using distinct sets of genes remains elusive to date. Therefore, our objectives are to bundle the knowledge from three disciplines to unravel fundamental membrane processes in insect cells and compare these to mammalian cells.
Working at the interface of insect genetics, membrane biophysics and virology our newly formed team has assembled innovative technologies to break through this barrier in the field. Through the combined expertise of the PIs, we will: 1. Employ gene editing libraries in insect cells to identify host factors steering virus – membrane interactions; 2. Visualize membrane deformation at high-resolution upon genetic manipulation in uninfected and virus-infected insect cells using time-lapse imaging, high resolution imaging and biophysical probes; 3. Assess the impact of membrane deformation on permissiveness to insect-borne viruses by infection assays and sophisticated virological assays probing virus entry, genome replication at plasma membrane microdomains and virus budding from insect cells. 4. Compare the membrane deformation mechanisms in insect cells to those in mammalian cells.
These studies will provide insight into mechanisms driving insect versus mammalian membrane shape and function. Thereby, they will revolutionize our understanding of virus adaptation across fundamentally different species.
2023
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Grant Awardees - Program Grants
Uncovering the real paleo diet: Novel isotope analytics of amino acids from fossil hominin teeth
NEUBAUER Cajetan (GERMANY)
- University of Colorado Boulder - Boulder - United States
BAKKOUR Rani (Syria)
- Technical University of Munich (Technische Universität München, TUM) - Garching - GERMANY
LÜDECKE Tina (GERMANY)
- Max Planck Insitute for Chemistry - Mainz - GERMANY
Accumulating evidence suggests that fossil tooth enamel is remarkably efficient in preserving amino acids (AAs). Intact AAs in fossils have the potential to reveal paleodietary isotopic proxies that may enable unique insights into the lives of even our most ancient human ancestors. While isotope studies have been a great aid for examining how diet has shaped the evolution of key human traits (e.g., brain expansion, bipedalism), current isotope ratio mass spectrometry (IRMS) is fundamentally restricted to gases. However, improved sensitivity and the ability to measure intact biomolecules would permit access to the full spectrum of paleodietary information that is encoded in organic compounds preserved in enamel. While the application of classic IRMS methods for AA analysis of bone collagen have proven valuable for food web reconstruction in ecology and archaeology, the approach is limited to relatively recent (100kya) human prehistory. This project aims to employ a new analytical paradigm based on electrospray-Orbitrap MS to access ancient biomolecules. It will measure comprehensive (compound- and site-specific) isotopic information simultaneously in biomolecules with unprecedented sensitivities. Sensitivity of the electrospray-Orbitrap for isotopes is >10,000-fold higher than isotopic NMR and at least 10 to 100-fold better than the most sensitive IRMS today. This step change makes it conceivable to attempt measuring isotopes directly within intact fossilized polar molecules, including the minute quantities of AAs preserved in hominin enamel. Our team proposes a new analytical frontier: the quantification of paleodietary signatures encoded in intact molecules (“isotopocules”) that are millions of years old. Our US group has developed initial AA isotopocule measurements. Together with fossil preparation and affinity isolation methods pioneered by our two groups in Germany, this novel technique will be validated in a modern African ecosystem (Gorongosa National Park, Mozambique), then refined and applied to hominin fossils (>1Mya). This project will establish a framework to test hypotheses and ask more nuanced mechanistic questions about early hominin food acquisition and habits. The approach we propose has significant potential to be more broadly applied in paleontology, as well as environmental and health research.
2023
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Grant Awardees - Program Grants
When the going gets tough: Trans-kingdom spore dormancy and revival mechanisms across scales
BALASUBRAMANIAN Mohan (United Kingdom)
- University of Warwick - Coventry - United Kingdom
BEN YEHUDA Sigal (ISRAEL)
- The Hebrew University of Jerusalem, Jerusalem - Jerusalem - ISRAEL
JANSHOFF Andreas (GERMANY)
- University of Göttingen (Georg-August-Universität Gottingen) - Goettingen - GERMANY
O'SHAUGHNESSY Ben (United Kingdom)
- Columbia University in the City of New York, New York, NY - new york - United States
In response to adverse conditions, organisms across the tree of life retreat into remarkable dormant states as spores. Spores of bacteria, fungi, and plants are the most resilient cell types known, and can revive following prolonged dormancy, enabling long distance organismal dispersal with significant environmental impact. Yet, the dormant state and the rapid revival remain a cell biological and physical mystery. How are cellular organization and revivability preserved without energy from nutrients? What is the biophysical nature of the dormant cytosol and its role in dormancy? What metabolic processes are required for survival? What are the mechanisms of awakening? What role is played by the spore outer layers, and how do their mechanical properties evolve during germination? What factors govern long term spore fitness? How do environmental niches impact spore physical properties? Do common principles govern spore fitness across kingdoms? To deliver a full mechanistic picture, we will combine advanced microscopy, spectroscopy, machine learning, biophysical modelling, and molecular/cell biological studies of bacterial and yeast spores, comparing dormant and nutrient-fed germinating spores. Using machine learning to analyse motions of fluorescently labelled endogenous molecules/complexes and exogenous tracer particles, we will quantify the scale-dependent relaxation kinetics of the dormant cytosol, characterize its material properties which are likely glassy as for other quiescent states, and measure entropy production to quantify metabolic activity. We will measure the cytosol-fluidizing effects of this metabolic activity using ATP uncaging, and test if this can trigger revival. Impedance spectroscopy will measure cytosol water content, a determinant of glassiness, and indentation-relaxation will probe mechanical stiffness of spore outer layers. We will encapsulate spore extracts in confined geometries (e.g. giant unilamellar vesicles) for convenient measurement and manipulation. Data from these studies will be used to develop a biophysical mathematical model of the dormant state, which will be experimentally tested. We will test the impact of diverse natural environments on our model organism spores, test if model spores and those isolated from the environment obey the same principles, and identify the parameters crucial for spore fitness.
2023
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Grant Awardees - Program Grants
Mapping structural and functional connectivity of the distributed sensory system in chiton armor
LI Ling (CHINA)
- The Trustees of the University of Pennsylvania - Philadelphia - United States
BAUM Daniel (GERMANY)
- Zuse Institute Berlin (ZIB) - Berlin - GERMANY
SPEISER Daniel (United States)
- University of South Carolina - USC - Columbia - United States
Many organisms utilize a small number of sensory organs and a centralized nervous system (e.g., the paired eyes and complex brains of vertebrates) to acquire and process information. In contrast, other species have evolved distributed sensory networks (DSNs) consisting of dispersed but interconnected sensory elements to sense and respond to external stimuli. Here, we will explore a new research frontier on nature’s strategies for designing efficient and resilient DSNs by investigating a unique model system, i.e., chitons, via a synergistic interdisciplinary collaboration. Chitons are the only extant mollusks with living tissue embedded within their biomineralized protective shell plates. This innervated tissue (aesthetes) forms a complex three-dimensional (3D) interconnected network that fills thousands of long, narrow channels. These microchannels run through the shell plates and finally extend to the shell surface. It has been shown that the aesthetes perform several sensory functions, particularly photoreception. In addition, the aesthetes of certain chiton species include visual elements with different degree of complexities, ranging from simple photoreceptive organs to eyespots that contribute to spatial vision to image-forming eyes with mineralized lenses! Thousands of these visual sensory organs are distributed across the shell plates, making the system a unique ‘hard-wired’ (embedded in mineralized shells) DSN, through which the organisms collect and process visual information and finally respond. Current knowledge of chiton DSNs is primarily focused on overall behavioral responses of animals and the fine structures of individual sensory elements. We have very limited knowledge regarding the structure and function of the chiton DSNs on the system level. How are chiton DSNs wired up? How do they function? How resilient are chiton DSNs to damage? Our international, interdisciplinary team of material scientists, biologists, and applied mathematicians will address these three fundamental questions by establishing the complete ‘connectome’ of chiton DSNs and investigating its working mechanisms and system resilience. The knowledge gained from this research will transform our current understanding of natural DSNs, which may have significant impact on a number of areas, such as distributed sensing structures, living materials, resilient swarm systems, etc.
2023
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Grant Awardees - Program Grants
SELFCURE: Evolutionary and cognitive processes underlying self-medication of immune-challenged bats
BECKER Daniel (United States)
- The Board of Regents of the University of Oklahoma (University of Oklahoma) - Norman - United States
PAGE Rachel (United States)
- Smithsonian Tropical Research Institute, Washington, DC - Ancón - PANAMA
SIMON Ralph (GERMANY)
- Nuremberg Zoo, Behavioral Ecology and Conservation Lab - Nuremberg - GERMANY
Plant medicinal properties are used by a diverse range of animal taxa. Chimpanzees consume hairy Aspilia leaves when suffering from intestinal parasites, Kodiak bears use Ligustium roots against ectoparasites, and monarch butterflies prevent infection in their offspring by laying their eggs on milkweed, a plant toxic to protozoans. Self-medication behaviors provide an effective mechanism to minimize infection load. But despite its eco-evolutionary importance, we lack clear understanding of how behaviors associated with self-medication evolve. Importantly, animals may possess either an innate mechanism to search for medicinal food items, or they may learn individually or through others to associate specific foods with specific cures. Bats are a especially relevant group to study the mechanisms underlying self-medication. They harbor diverse parasites, feed on a wide variety of foods and, due to their cognitive capacities and extraordinary longevity, have high potential to learn to associate specific food resources with curative properties. Phyllostomid fruit bats in particular are ideal for investigation given the wide variety of plants that they have access to in the Neotropical rainforest.
Using state-of-the-art tracking techniques, AI-based individual recognition, and targeted and -omics approaches for characterizing immunity and parasites, we propose to investigate the mechanisms underlying self-medication in phyllostomid bats. First, we will determine the immune state, parasite diversity, and nutritional diversity of wild bat populations and investigate potential links between immunity, infection, and certain food plants. Next, by testing immune-challenged and control-treated individual bats on natural and artificially-created medicinal food preferences, we will shed light on the role of learning vs innate mechanisms in self-medication. By tracking groups of bats through a rainforest site that has been studied long-term with fully mapped fruiting tree species, we have the unique opportunity to assess whether immune-challenged individuals switch to a diet with medicinal compounds. Finally, by tracking experimentally immune-challenged and experimentally cured bats trained on artificial sonar beacons indicating the presence of medicinal foods in the wild, we will assess how information regarding self-medication can spread through a bat social network.
2023
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Grant Awardees - Program Grants
Evolution at the plant apex: identifying steps enabling a major organismal radiation.
HARRISON Jill (United Kingdom)
- University of Bristol - Bristol - United Kingdom
BEECKMAN Tom (BELGIUM)
- Vlaams Instituut voor Biotechnologie (Flanders Institute for Biotechnology, VIB) - Gent - BELGIUM
FUJINAMI Rieko (JAPAN)
- KYOTO UNIVERSITY OF EDUCATION - Kyoto - JAPAN
HETHERINGTON Alexander (United Kingdom)
- University of Edinburgh - Edinburgh - United Kingdom
The origin and rise to dominance of vascular plants massively impacted the Earth System and led to an explosive radiation in biodiversity, but how vascular plants originated and diversified to form lycophytes, ferns and seed plants with complex shoot and root systems is unknown. Answers to these questions hinge on apical growth, a key innovation enabling persistent stem cell activity in plants’ growing tips. Like living mosses, the earliest land plants lacked apical growth, and were short lived with tiny stems terminating in the development of spore-producing sporangia. We hypothesise that the origin of apical growth involved the relocation of sporangia from terminal to lateral positions, and the juxtaposition of stem cell and proliferative regions, as seen in the apices of living vascular plants. However, mosses and vascular plants are distantly related with widely divergent forms, and ancestral patterns of apical growth shown by ancient pro-vascular and vascular plant fossils are unknown. Moreover, living vascular plants have diverse patterns of apical growth, and the changes enabling shoot and root evolution are unknown. To test our hypothesis, we propose an innovative research plan that combines morphological data from fossils and living plants at either side of the origin of apical growth with developmental and genetic data from mosses, lycophytes, ferns, and seed plants through four interlinked work packages.
WP1 will use a forward genetic screen in a moss and establish functional reverse genetic analysis in a lycophyte to identify genes involved in the origin of apical growth.
WP2 will determine structure of fossil apices preserved during the emergence of vascular plants to identify ancestral patterns of apical growth.
WP3 will evaluate cell proliferation patterns in a moss and a range of vascular plants and compare apical organizations between living plants and fossils to identify stepwise changes during the evolution of apical growth.
WP4 will use transcriptomic and reverse genetic methods to identify conservation and divergence in the genetic networks for apical growth.
As an integrated whole, the research will lead to a step change in our understanding of apical growth, a key innovation enabling the radiation of today’s dominant vascular plant flora.
2023
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Long-Term Fellowships - LTF
Transcriptional adaptation during vertebrate development at the single-cell level
BELLEC Maelle (FRANCE)
Dept. III - Max Planck Institute for Heart and Lung Research - Bad Nauheim - GERMANY
STAINIER Didier (Host supervisor)
The development of a multicellular organism requires the precise control of gene expression in space and time so that cells adopt their correct identity. However, genetic mutations can alter this complex process. Recently, a transcriptional adaptation (TA) has been uncovered as one of the mechanisms underlying genetic compensation in zebrafish, mouse cells in culture, and C. elegans1,2. TA refers to the phenomenon by which mutated genes (with mRNA-destabilizing mutations) trigger the transcriptional up-regulation of other genes, called adapting genes. Mutant mRNA degradation, e.g., via Nonsense-Mediated Decay (NMD), has been shown to be required for TA3,4. However, little is known about the spatial and temporal characteristics of adapting gene regulation. Yet, TA would be required to be fast and regulated at all the different steps of gene expression in order for the embryo to develop correctly. Recent technological advances have made it possible to access the dynamics of transcription but only a few have been implemented in vertebrates thus far. This project aims to decipher when and where the TA occurs in the context of the developing zebrafish embryo. Aim 1 will test the hypothesis that TA is initiated during the zygotic genome activation and that there are several possible modes of transcriptional upregulation of the adapting genes. To test this hypothesis, I will use mutant alleles of early expressed genes that have been shown to exhibit TA including vcla, aldh2 and alcama. These genes and their corresponding adapting genes will be tagged with different live reporter arrays (e.g. MS2, PP7 loops) using standard genome editing tools in order to monitor transcription in live embryos with high-end microscopy followed by quantitative image analysis. This approach will allow us to determine the time-scale at which TA occurs and also help us understand the different modes of transcriptional upregulation of the adapting genes. Aim 2 will test the hypothesis that mutant mRNA degradation occurs in specialized organelles that are critical for TA. To test this hypothesis, I will use high resolution microscopy to look at the localization of NMD components as well as membrane-less organelles, such as P-bodies granules, together with the mutated and the wild-type mRNA. To test the importance of these granules, I will use mutants defective in P-granule formation and look at the effects on TA in terms of transcriptional output. Until now, TA has been mostly investigated on pooled populations of cells, therefore we lack the understanding of this phenomenon at a cellular level. This project will be important to fill this gap and get a better understanding of the spacio-temporal characteristics of genetic compensation which help the robustness of vertebrate development. 1. Rossi, A. et al. Nature 524, 230–233 (2015). 2. Ma, Z. et al. Nature 568, 259–263 (2019). 3. El-Brolosy, M. A. et al. Nature 568, 193–197(2019). 4. Serobyan, V. et al. Elife 9, e50014(2020).