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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
2023
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Long-Term Fellowships - LTF
Epigenetics of aging-associated behavioral changes and loss of brain plasticity using the ant model
SOREK Matan (ISRAEL)
4106: CDB - The Trustees of the University of Pennsylvania - Philadelphia - United States
BERGER Shelley (Host supervisor)
Background:Eusocial insects are characterized by a remarkable system of division of labor within the same
colony.The C. floridanus ant has two worker castes that differ in both morphological and behavioral characteristics. Major workers have larger body size and defend the colony, whereas Minor workers provide nursing and foraging.Recently it has been shown that young Majors can be reprogrammed to display increased foraging behavior like the Minor foraging state. Strikingly, this can be done using injection of Trichostatin A (TSA), a histone deacetylase inhibitor.Interestingly, this behavioral plasticity has an optimal time window at 5 days after hatching, and then at 10 days reprogramming efficiency abruptly decreases.In another form of behavioral changes of worker ants, Majors show a natural gradual increase in foraging behavior with age, whereas Minors forage less. Therefore, strict behavioral caste identity is compromised with time.
Aims:We propose to investigate the epigenetic mechanisms that affect the aging-like characteristics of behavioral caste reprogramming in ants and that are altered in separate castes during natural ant aging.
Central hypotheses:Epigenetic mechanisms are the driving force behind the qualitative division into different castes, and caste reprogramming has a limited time window that is determined by early adult-associated decrease in brain plasticity.On the other hand, the process of animal aging is associated with epigenetic alterations and aging-associated behavioral changes in ants are similar to loss of cellular identity during aging.Because of the parallels between the two processes, we hypothesize that the epigenetic mechanisms which underlie the time-limited plasticity of behavioral reprogramming are general mechanisms related also to ant aging, and may be similar in humans.
The experimental system:We will characterize the transcriptional changes that are associated with Major and Minor aging focusing on gain and loss of foraging respectively, as well as the changes in TSA-injected young Major ants between d5 and d10 after hatching, when the reprogramming time window closes. Based on these results, we will find key responsible epigenetic factors that parallel, and then genetically perturb them to alter the aging-related behavioral phenotypes.In particular, we postulate that similar perturbation will extend the reprogramming window in Majors in early adult life, and will extend foraging in Minors during aging.
Conclusions:The molecular mechanisms that will be revealed by this project may shed light on human related processes.These include psychiatric diseases (like depression) that are associated with loss of brain plasticity and which peak around late adolescence (the parallel of Major-induced reprogramming), and human psychological changes and neurological diseases associated with aging (the parallel of behavioral changes during ant aging) and could be cross-correlated with the relevant human GWAS studies.
2023
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Long-Term Fellowships - LTF
Molecular and morphogenetic characterization of early neurogenesis in cephalopods
STOCK Jessica (GERMANY)
Eugene Bell Center - Marine Biological Laboratory - Woods Hole - United States
ALBERTIN Caroline (Host supervisor)
The molecular and genetic mechanisms that underlie the formation of a complex brain with extensive cognitive abilities remains one of the biggest biological mysteries. Decades of research investigating the connection between embryonic development and the adult brain suggest a correlation between advanced cognitive behavior and the complexity of early neurogenesis, as the latter provides greater cell diversity and brain size. While vertebrate models have provided key insights into neurodevelopmental mechanisms, little is known about the development of the largest invertebrate nervous systems: those found in coleoid cephalopods (octopus, squid, and cuttlefish). The astounding intelligence of cephalopods has fascinated researchers for decades, yet modern molecular tools, including high-quality genome assemblies and CRISPR-mediated gene manipulation, have only recently been developed. With brains that rival those found in vertebrates in both size and complexity, cephalopods stand out among invertebrates and provide a unique opportunity to investigate the fundamental principles that build a centralized nervous system remarkably similar, but convergently evolved, to vertebrates.
Here, I will harness newly developed tools to provide a comprehensive molecular, genetic, and morphological description of the key stages in early cephalopod neurogenesis, including the (i) specification of neuroectoderm and neural progenitors, (ii) the early patterning of different brain regions, and (iii) the morphogenetic mechanisms shaping the embryonic brain. To accomplish these aims, I will leverage recently established tools in the longfin inshore squid Doryteuthis pealeii and the bobtail squid Euprymna scolopes, including multicolor fluorescent in situ hybridization, single cell RNA sequencing, and live cell imaging to identify and detail the cellular and molecular events in neural progenitor specification and neuronal patterning. I will also develop new methods for use in cephalopods based on my previous work in zebrafish, such as lineage tracing and cell transplantation, to reveal key mechanisms of neurogenesis. Furthermore, through genetic manipulation using the CRISPR/Cas9 system, I will then identify and functionally characterize specific molecular factors that are essential for different steps of neurodevelopment.
In summary, this project will elucidate the molecular mechanisms underlying early neurogenesis in cephalopods. This work will reveal elements that are either cephalopod-specific, which will provide insights into alternative ways to build a complex brain, or that are similar to mechanisms described in vertebrates, thereby identifying convergent mechanisms that are essential for the development of a complex brain and lay the foundation for enhanced cognitive behaviors.
2023
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Long-Term Fellowships - LTF
Behavioral functions and microcircuit mechanisms of heading representation in larval zebrafish
TANAKA Ryosuke (JAPAN)
School of Medicine - Technical University of Munich (Technische Universität München, TUM) - Munich - GERMANY
PORTUGUES Ruben (Host supervisor)
To flexibly navigate their environments, animals create internal maps of the world. Such internal maps have been proposed to be crucial not only to spatial navigation, but also to abstract higher order cognitive inferences in humans. Seminal works in rodents have uncovered diverse representations of space in the brain, which likely implement these internal maps. However, the sheer complexity of mammalian brains has hampered our understanding of how microscopic circuits of neurons construct these internal maps. Larval zebrafish, with its small size, optical accessibility, and genetic tractability, is an ideal vertebrate model to study circuit mechanisms underlying neural representations of space. A recent work in larval zebrafish has discovered a group of neurons innervating a highly conserved brain structure called interpeduncular nucleus (IPN) whose population activity keeps track of the animal's heading by integrating its intended turns in an angular coordinate. However, it still remains unclear how this heading representation is used for flexible behaviors, as well as how the circuitry surrounding these compass-like neurons implement angular integration. My postdoctoral project will address these two key questions. First, to explore potential behavioral functions of the compass-like neurons, I will establish novel place learning assays that exploit ethologically relevant, naturalistic behaviors of larval zebrafish, such as positional homeostasis or hiding in the presence of visual threats. Using targeted laser ablation and optogenetic manipulation, I will then aim to demonstrate that the heading representation in the compass-like neurons is involved in such spatial behaviors. Second, I will attempt to identify the sources of turn-related motor signals provided into the compass neuron network. To this end, I will first morphologically identify neuron populations that innervate both the compass neurons and the IPN using light-inducible gene expression systems and/or photoactivatable fluorescent proteins. I will then functionally characterize the activity of these identified neurons with two-photon calcium imaging to see if any of them encode intended turning of fish. In parallel, I will perform electron micrograph reconstruction of IPN-projecting neurons to find circuit motives that can support angular integration. Overall, these experiments will uncover the functions and mechanisms of a conserved circuit that computes heading directions, shedding a new light to how internal maps of the world are constructed in vertebrate brains, including ours.
2023
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Cross Disciplinary Fellowships - CDF
Genetically encoded reporters for brain-wide studies of neuronal function
TIRUKOTI Deva Nishanth (INDIA)
Bio Engineering - Massachusetts Institute of Technology - MIT - Cambridge - United States
JASANOFF Alan P. (Host supervisor)
Determining how mechanistically distinct elements of brain processing combine to perform integrated functions is one of the foremost challenges of neuroscience. A new technology called hemogenetic imaging addresses this need by permitting brain-wide studies of neural signaling by genetically targeted cell populations for the first time in living animals. Hemogenetic imaging is performed using reporter proteins called NOSTICs. These probes are calcium-activated enzymes that produce the gaseous vasodilator NO in stimulated cells; this induces artificial neurovascular signals that can be detected by virtually all noninvasive functional neuroimaging methods, permitting these methods for the first time to monitor resolved elements of neural processing. In initial studies, hemogenetic probes were applied for first-of-their-kind circuit-specific functional magnetic resonance imaging (fMRI) studies in rat brains. Although such studies are already powerful, improvements to the probe technology could produce critical quantitative and qualitative enhancements that I propose to pursue in this project.
Aim 1. Develop second-generation NOSTIC probe for multiplexed hemogentic imaging. Understanding brain mechanisms requires discerning how functionally distinct neural populations in the brain interact. In this aim, I approach this problem by designing new NOSTIC reporters that display differential sensitivity to substrates and inhibitors that will allow functional imaging signals from different reporters to be distinguished from one another and from endogenous activity signatures in the brain. I will validate the reporters by fMRI in rats.
Aim 2. Develop NOSTIC-based probes to study gene regulation events. Existing NOSTIC probes function as probes for intracellular signaling dynamics, but it is of great interest to engineer variants that can monitor other parameters of cellular function in the brain. In this aim, I will generate NOSTICs that are activated by exogenous designer drugs. Because these drug-induced activatable NOSTICs (diaNOSTICs) can be constitutively expressed and are only turned on in the presence of the drug, comparison of image intensities obtained before vs. after diaNOSTIC activation will act as a sensitive basis for resolving reporter expression profiles, potentially repeatedly and in the same animal.
Central hypothesis: I hypothesize that next-generation NOSTIC probes can be effectively engineered using protein chemistry techniques and that these probes will permit multiplexed brain-wide imaging studies of cellular signaling and gene expression in live animals.
Experimental system: My work will be carried out using invitro molecular biology, biochemistry, and cell biology techniques, followed by invivo imaging in rodents.
Conclusion: Collectively, the work I plan will establish revolutionary new technology for studying the brain-wide patterns of activity and gene expression that underlie mammalian brain function in diverse contexts.
2023
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Long-Term Fellowships - LTF
Semantic-motor representation and plasticity for M1
TSAY Jonathan (USA)
MRC CBU - Medical Research Council Cognition & Brain Sciences Unit - Cambridge - United Kingdom
MAKIN Tamar (Host supervisor)
For most of my clinical training in physiotherapy, the sensorimotor system was depicted as a primitive “motor” that moves the body in a reflexive and subconscious manner, separate from the mind. Yet, my recent research has upended this dichotomy, revealing that high-level decisions and low-level action execution jointly enable successful motor control. That is, cognition and action are inseparable.
Here, I aim to push this envelope to a new frontier, asking how sensorimotor representations in the brain are shaped by semantic cognition. Specifically, I will use gestural movements to investigate whether the primary motor cortex (M1) carries semantic meaning. By pairing powerful neuroimaging with representational similarity analyses, I will tackle three fundamental questions in cognitive neuroscience: Year 1: are semantic representations embedded in low-level sensorimotor processing; Year 2: how are M1 representations transformed by semantic-motor experience; and, Year 3: how is semantic information transmitted to M1. In one extreme, semantic and sensorimotor representations may inhabit orthogonal representational subspaces, with comprehension and production requiring distinct representational geometries. Alternatively, the “embodied” nature of gesticulation may have a multiplexed representation, with semantic and sensorimotor information embedded in the same brain regions.
A cross-disciplinary approach will be necessary to answer these questions: Together with my host Prof. Tamar Makin, and collaborators Profs. Mairead Macsweeney and Matt Lambon Ralph, (Directors of UCL’s Deafness, Cognition and Language Research Centre, and the MRC Cognition and Brain Unit, respectively), I will design novel paradigms to elicit a range of semantic processes, quantify gestural production with markerless tracking, unveil geometric features of brain representation using advanced neuroimaging methods with high temporal and spatial resolution (MEG/fMRI). To examine the effect of neuroplasticity, I will compare how representations differ before and after semantic-motor training, and between patient groups with semantic cognition and sensorimotor control deficits. The training enabled by this proposal will position me at the forefront of a new intersection between semantic cognition and sensorimotor control.
Together, this research offers a paradigmatic shift in human cognitive neuroscience – from a traditional view in which semantic and sensorimotor representations operate in isolation, to one where semantic content may prove vital for successful sensorimotor control, and vice versa. Not only will this work offer a more holistic view on these two essential abilities, but it may also improve the capability of brain-computer interfaces to harness semantic and sensorimotor content, and thus augment rehabilitation for patients with language and speech deficits.
2023
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Long-Term Fellowships - LTF
Understanding tumor-immune interactions in cancer initiation and progression
VEGA-PÉREZ Adrian (SPAIN)
Medicine - Weill Medical College of Cornell University - New York - United States
DOW Lukas (Host supervisor)
• Background
The aim of cancer immunotherapy is to engage the immune system against tumor cells but spare normal tissues. Tumor-specific ‘neoantigens’ generated by mutations present only in cancer cells, make an ideal target for immune-mediated tumor control, yet how the immune system engages directly with nascent cancers expressing neoantigens is poorly understood. Understanding the dynamics of immune cell engagement with tumor cells as they become ‘visible’ to the immune system may help define new ways to improve immune-based cancer treatments. Genetically modified mice (GEMM) are key model systems for understanding immune-cancer interactions, particularly at the early stages of tumor development; However, the lack of neoantigens produced during murine tumor development limits their utility. My proposal aims to use new in vivo base editing tools to allow temporal control of antigen production in early and evolving pancreatic tumors, in vivo.
• The aims of the proposed research project and central hypotheses
To improve upon existing pre-clinical immunogenic mouse models, we will use CRISPR base editing technologies to induce and generate neoantigens at defined times during tumor development. This will allow us to explore early interactions between tumor cells and the immune system and antigen-specific T cell immune responses.
• The experimental system
We will use a novel mouse model, developed by the Dow lab, that carries an inducible and regulated optimized cytosine base editor (iBE) that enables temporal regulation of a base editor in murine tissues. The inducible and transient expression of the BE can drive high base editing efficiencies in multiple mouse tissues and can be used to build in vivo models that harbor specific cancer-associated single nucleotide variants.
The model allows us to generate highly multicomplex mutational profiles using organoids which can be studied ex vivo and then transplant into immunocompetent mice. In addition, we can drive tumor growth in vivo using established Cre-based cancer models and induce the expression of neoantigen via base editing at defined stages throughout tumor expansion.
Specifically, we will use a BE-dependent reporter (GO) (Katti et al) to initiate expression of neoantigens. As a proof of concept, I will use the ovalbumin peptide SIINFEKL which expression will be selectively induced when the BE is activated. In addition, and in contrast to other inducible antigen systems that contain a limited number of antigens, this system has the capacity to generate multiple endogenous neoantigens derived from single nucleotide variants. This will be important to interrogate the impact of intratumoral heterogeneity of neoantigens.
• Conclusions
Our model will offer the possibility of spatial-temporal regulation of inducible neoantigens expression in vivo in immunocompetent mice enable to study a physiologic response by endogenous T cells during the initiation and evolution of cancer.
2023
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Long-Term Fellowships - LTF
Mapping the functional connectome for conscious perception
WESTERBERG Jacob (USA)
Vision and Cognition - Netherlands Institute for Neuroscience-KNAW - Amsterdam - NETHERLANDS
ROELFSEMA Pieter (Host supervisor)
Conscious perception is a core quality of human cognition. However, a comprehensive empirical account for consciousness remains one of the greatest challenges in modern neuroscience. Theoretical descriptions put forward mechanisms, but their realization in neural tissue is scarcely tested. One gap in knowledge preventing progress is in knowing where exactly to investigate. That is, the understanding of which brain areas are necessary for conscious perception remains elusive. Are there specific brain areas always engaged for conscious awareness and do any contribute more than others? Our objective is to map the functional connectome for stimuli entering and being maintained in conscious awareness. We hypothesize there is a core set of brain areas necessary for the conscious awareness of perceivable stimuli. To test this hypothesis, we will employ electromicrostimulation with functional magnetic resonance imaging (EM-fMRI) in behaving monkeys. Subjects will receive state-of-the-art cranial implants for unprecedented whole-brain access for neural stimulation. This method allows us to (1) probe a vast array of brain areas to determine their role in conscious perception and (2) identify the minimum configuration of brain areas that activate when a stimulus is perceived. Notably, where human fMRI falls short in causal experimental control and monkey electrophysiology in the spatial scope of measurement, the unique combination of EM-fMRI allows for comprehensive evaluation of neural circuitry for conscious perception. Crucially, we design the study to (3) dissociate circuitry for consciousness from that for attention, oft tightly coupled but rarely experimentally distinguished, and (4) test predictions of theoretical accounts for conscious awareness. The task designs orthogonalize attention and conscious access through multimodal electrical and sensory stimulation at the threshold for awareness. Moreover, the results will be explored within theoretical frameworks, including the Global Neuronal Workspace Theory and the Integrated Information Theory and the data can be used to test other theories, because we will publish them open access. The project is highly feasible, given the experience of the Roelfsema Group in probing neural mechanisms of consciousness (e.g., van Vugt et al., 2018, Science) and EM-fMRI (Ekstrom et al., 2008, Science). Beyond local institutional support, Profs. Stanislas Dehaene (Neurospin, FR) and Wim Vanduffel (KU Leuven, BE) are active collaborators whose expertise in consciousness and EM-fMRI will enhance the project and enhance my training. My experience in monkey cognitive neurophysiology has prepared me to pursue these objectives, yet the project affords substantial scientific growth in the form of methodological and conceptual training. Altogether, this project is designed to yield impactful findings that will propel the field of consciousness research forward and prepare me for a career as an independent investigator.
2023
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Long-Term Fellowships - LTF
Phytoplankton translational regulation: From models to communities
WIENER David (ISRAEL)
Oceanography - University of Washington - Seattle - United States
ARMBRUST E. Virginia (Host supervisor)
Phytoplankton species account for half of the worldwide CO2 fixation and determine several biogeochemical cycles. Characterizing these organisms' gene expression control mechanisms is critical to understanding their ecological role. Importantly, ocean microbial communities are synchronized by the effect of light fluctuations during the day:night cycle. Environmental and laboratory-based studies have shown different phytoplankton components such as RNA levels, metabolites, and lipids, cycle following diel patterns. Interestingly, the diel pattern also dictates metabolic interactions between single-cell eukaryotes and heterotrophic bacteria. Notably, phytoplankton was shown to have mutualistic and antagonistic interactions with bacteria. However, it is unclear if these interactions are diel regulated and how gene expression is controlled depending on the community composition and the light status. While the application of RNA-seq based protocols has allowed quantifying phytoplankton response at the mRNA level, the translational regulatory layer remains unexplored. Studies in several eukaryotes have shown that mRNAs get translated at specific rates, allowing fine-tuning gene expression, but its role in phytoplankton biology is unknown.
In this work, I aim to characterize the phytoplankton translational regulatory landscape focusing on the impact of two key factors, the diel cycle, and bacterial interactions. I plan to use the centric diatom Thalassiosira pseudonana and the pennate diatom Phaeodactylum tricornutum as models, representing two subdivisions of an ecologically relevant phytoplanktonic group (Diatoms). I will measure translation efficiency using ribosome profiling in a culture experiment simulating the day:night light changes and in co-cultures with Ruegeria pomeroyi, a mutualistic bacteria, or Croceibacter atlanticus, an antagonistic bacteria. However, because laboratory models do not represent most species, it is also required to study natural populations directly. Yet, we lack a protocol to measure translational efficiency in them. To solve this constraint, I will develop a new method termed Meta-Riboseq inspired by the principles of ribosome profiling and metatranscriptomic protocols to quantify translational efficiency in natural phytoplankton populations. This combined approach will quantify the extent of translational regulation present in single-celled marine eukaryotes in a controlled experiment and in their environment. Specifically, this setup will allow identifying dynamically translated genes across the diel cycle and specific profiles triggered by mutualistic or antagonistic bacteria-algae interactions. Comparing the two different diatoms models and the diversity within natural populations will allow inferring evolutionary trends in this regulatory layer. In addition, this work will provide a new method and a relevant dataset contributing to further exploration and generation of new hypotheses in the field.
2023
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Long-Term Fellowships - LTF
Discovery of new cyclic nucleotide immune receptors in human innate immunity
YAMAGUCHI Sonomi (JAPAN)
Cancer Immunology - Dana-Farber Cancer Institute - Boston - United States
KRANZUSCH Philip (Host supervisor)
Cyclic nucleotides stimulate the immune response to pathogens and disease by acting as second messengers. In human cells, the enzyme cyclic GMP-AMP synthase (cGAS) recognizes double-stranded DNA from pathogens or tumor cells and produces 2'–5'/3'–5'-cyclic GMP-AMP (2'3'-cGAMP). 2'3'-cGAMP controls antiviral and anti-tumor responses by activating the receptor stimulator of interferon genes (STING) (Sun et al., Science 2012; Ablasser et al., Nature, 2013). Surprisingly, recent studies reveal that prokaryotic and eukaryotic genomes encode various cGAS-like nucleotidyltransferases named cGAS-like Receptors (cGLRs) (Whiteley et al., Nature 2019; Slavik et al., Nature 2021). Animal genomes each encode several cGLRs, and four cGLRs in human cells have no known function. These uncharacterized cGLRs suggest fundamental gaps in our understanding of nucleotide second messenger signaling. I hypothesize that cGLR enzymes in human and animal cells produce diverse nucleotide second messenger signals and control novel immune signaling pathways.
My proposed research will combine biochemistry and structural biology approaches with an unbiased cell-based screen to elucidate how uncharacterized animal cGLRs recognize distinct ligands and to discover how cellular receptors respond to distinct nucleotide signals. First, I will use X-ray crystallography and cryo-EM to determine the structures of uncharacterized human cGLRs and a Drosophila enzyme named cGLR1 known to respond to double-stranded RNA. These structural and biochemical analyses will define how animal cGLRs evolved a conserved ligand-binding groove to recognize the various ligands, including viral nucleic acid and pathogen-derived metabolites. Second, I will conduct a cellular activation screen using nucleotide signals produced by prokaryotic cGAS-like enzymes to identify novel protein receptors stabilized in the presence of nucleotide signals. Given that human STING recognizes both prokaryotic cyclic dinucleotides and the endogenous cGAS product 2'3'-cGAMP, I predict that prokaryotic nucleotide signals including pyrimidine-containing cyclic dinucleotides and larger cyclic trinucleotide signals will enable me to discover new nucleotide signal receptors in animal cells. Supporting this notion, we have completed a pilot screen in human macrophages revealing new candidate receptors specifically stabilized in the presence of nucleotide second messenger signals.
Analogs of 2'3'-cGAMP are rapidly developing as promising new therapeutic drugs, suggesting the importance of understanding nucleotide second messenger signals in cells. My results will reveal novel signals and nucleotide receptors that control the innate immune response and provide the molecular mechanism of how animal cells respond to viral infection.
2023
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Cross Disciplinary Fellowships - CDF
Mechanotransduction of T cell antigen recognition examined with 3D super-resolution imaging
ZAZA Cecilia (ITALY)
LCN - University College London - London - United Kingdom
SIMONCELLI Sabrina (Host supervisor)
PADILLA-PARRA Sergi (Host supervisor)
T cell activation starts with the engagement of the transmembrane T cell receptors (TCRs) with foreign antigen peptides loaded in the major histocompatibility complexes (pMHC) on antigen-presenting cells (APCs). Accumulating evidence in the literature indicates that the TCR acts as a mechanoreceptor, but it remains unclear how pMCH engagement generates forces that are converted to intracellular signalling. One possible hypothesis is that mechanical forces acting on engaged TCRs causes conformational changes within the TCR complex, leading to dissociation of its cytoplasmic zeta-chains from the inner leaflet of the plasma membrane and making them accessible for Scr kinases phosphorylation. However, to date, there are no experimental data that can directly depict this process due to technological three dimensional (3D) imaging limitations in the nanoscale.
The overall goal of this project is to develop and implement new DNA- and plasmonic-based technology to quantify the threshold force required for TCR-complex conformational changes and T cell activation upon antigen binding.
DNA molecular force sensors (MFS), developed to detect single molecule forces on the piconewton scale, have been recently adapted to be compatible with DNA-PAINT, a super-resolution fluorescence imaging technique capable of achieving sub-10 nm spatial resolution in 2D. This new technology, named tension-PAINT, has so far been only used to map integrin receptor pN mechanical events with 25 nm resolution. To examine the effect of mechanical forces on TCR conformational changes, in this project I will combine tension-PAINT with a new 3D super-resolution method based on metal-induced energy transfer (MIET) capable of achieving sub-10 nm axial resolution. MIET makes use of the distance-dependent coupling of a fluorescent emitter's evanescent field to surface plasmons in a thin metallic layer. Like FRET this coupling shows strong distance dependence with a larger dynamic range (of around 150 nm). This phenomenon can be exploited to obtain the axial position of single molecules with nanometre precision through fluorescence lifetime experiments using a wide-field TCSPC camera.
The project has the following scientific aims:
1) Transduce the fluorescence lifetime of single fluorophores to their axial position via MIET using wide-field fluorescence lifetime imaging microscopy. DNA-PAINT compatible 3D nanostructured samples (i.e. DNA-origamis) will be used for calibration.
2) Combine tension-PAINT with MIET to simultaneously map pN mechanical events and molecular positions in 3D with sub-10 nm spatial resolution. Initial demonstrations will be performed using Jurkat T cells and pMCH decorated lipid bilayers to mimic artificial T cell synapse.
3) Use the developed technology to evaluate the impact of receptor-peptide binding affinity and ligand density on the required force to (i) provoke a conformational change within the TCR complex and (ii) to mount proper T-cell activation.
2023
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Long-Term Fellowships - LTF
Mechanistic Investigations of the Circuits Driving Spontaneous Neuropathic Pain
ZENG Xiangsunze (CHINA, PEOPLE'S REPUBLIC OF)
Neurobiology - Boston Children's Hospital - Boston - United States
WOOLF Clifford (Host supervisor)
Pain is a multidimensional sensory experience produced by complex activity in the nervous system triggered from the periphery through the spinal cord and on to the brain. Under healthy conditions, pain is essential for protecting us from harm, however, in the context of injury or disease of the nervous system, pain loses its defensive role and instead produces persistent suffering and disability, constituting a pathological disease state termed neuropathic pain that affects ~10% of the population worldwide (van Hecke et al., Pain, 2014).
Neuropathic pain is categorized by both stimulus-evoked pain and spontaneous pain which possess distinct pathophysiological mechanisms. Of note, the majority of patients complain more of spontaneous pain than evoked pain (Bouhassira et al., Pain, 2005). However, to date preclinical studies are sharply geared only towards studying evoked pain. This is because while an evoked behavioral pain readout can be readily correlated with a stimulus, spontaneous neuropathic pain (SNeuP) arises without an external stimulus and possesses complex dynamics, rendering quantitative study very difficult, and in consequence the fundamental neurobiological mechanisms are essentially unknown (Mogil, Nat. Rev. Neurosci., 2009).
I now aim to mechanistically interrogate the cellular circuits responsible for SNeuP in a rodent model of neuropathic pain developed in my host lab (Decosterd and Woolf, Pain, 2000). Importantly, we will leverage a novel behavioral readout in mice: brief awakenings from sleep, which is causally linked to, and a biomarker of SNeuP (unpublished data). We hypothesize that there are specific cortical areas whose neural activity are associated with brief awakenings and SNeuP. To test this, we will combine brain-wide functional imaging with miniaturized microscope-based neuronal calcium imaging in freely behaving mice to determine which cortical activity pattern is associated with brief awakenings. We will also examine whether this pattern is present only in specific cortical areas or occurs globally. Based on the spatiotemporal features of cortical activation, we will further classify the activity patterns in fully awake mice using support-vector machine algorithm, and determine which activation patterns are similar to those occurring during SNeuP-evoked brief awakenings in sleeping mice. Next, we will employ a spinal window to chronically image ascending neural pathways emanating from spinal cord nociceptive output circuitry that drive cortical activation. Electrophysiological alterations in the pathways will be studied to identify the source of the ectopic neural activity associated with SNeuP. Our goal is to link this neural activity to spontaneous pain behaviors, using optogenetics and machine learning-based behavioral analyses.
In conclusion, this project aims, for the first time, to tease out the precise circuits underlying SNeuP, which will pave the way for exploration of novel therapeutic interventions.
2022
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Long-Term Fellowships - LTF
Experimental control over sleep cognition via transcranial focused ultrasound
ADELHOEFER Nico (.)
. - Stichting Katholieke Universiteit, Radboudumc - nijmegen - NETHERLANDS
VERHAGEN Lennart (Host supervisor)
Dreams during sleep are a case of cognition unconstrained by concurrent environmental information. Despite the unique potential regarding psychological diagnostics and theories of human experience, the cognitive neuroscience of sleep makes only slow progress of low reliability. One of the main reasons is that experimental stimulus control is prohibited by global sensory inhibition during sleep. I aim to circumvent this shortcoming via experimentally controlling the neurophysiology of sleep cognition via high-resolution, 3-dimensional neuromodulation. This possibility has been established recently with transcranial focused ultrasound (tFUS), which is based on mechanical effects of reversible displacements of neuronal membrane molecules by acoustic vibrations, in turn lead to the opening of ion channels, the influx of calcium ions and thus to the negativization of the membrane potential. The application of tFUS to human sleep is a novel approach. I propose to modulate two key brain structures during REM sleep as a high-yield starting point: (1) the amygdala as a subcortical structure, and (2) the frontopolar cortex. Empirical data on lucid dreaming suggest that triggering both areas in sequence might result in state insight during sleep, leading to volitional control over non-paralyzed muscle groups such as eye movement muscles. If successful, applying tFUS during sleep could solve the two main issues hindering robust progress in studying sleep cognition, namely the lack of stimulus control and missing behavioral measures. This would have far-reaching consequences for scientific dream research, therapies and our understanding of human experience.
2022
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Grant Awardees - Program
Mapping gut-to-brain transmission of prion protein
AGUZZI Adriano (ITALY)
Institute of Neuropathology - University of Zurich - ZURICH - SWITZERLAND
THAISS Christoph (GERMANY)
Dept. of Microbiology - University of Pennsylvania - Philadelphia - USA
Prion diseases are incurable neurodegenerative conditions. They are caused by PrPSc, an infectious form of the cellular prion protein PrPC. Upon ingestion, PrPSc causes misfolding of PrPC and successively propagates to the brain, where it causes a universally fatal spongiform encephalopathy. Inhibition of gut-to-brain transmission should theoretically prevent disease, but the detailed circuit by which PrPSc reaches the brain remains incompletely defined. We have recently used polysynaptic tracing in combination with single-nucleus RNA-sequencing to comprehensively map neuronal gut-brain pathways from the intestinal epithelium to the brain. We made the surprising discovery that a single such pathway, leading from enteroendocrine cells to the brainstem via the enteric nervous system, is characterized by expression of the endogenous prion gene Prnp in each component of the circuit. In this project, we aim at (I) determining the physiological function of PrP in this gut-brain circuit, as well as (II) elucidating if this pathway transmits PrPSc from the intestine to the brain and whether its inhibition can prevent prion disease. To achieve these goals, we will join forces between a lab that has pioneered the study of prion transmission (Aguzzi) and a lab that specializes in the investigation of gut-brain communication (Thaiss).
2022
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Grant Awardees - Program
Spatial and deep neurolipidomics to reveal synapse diversity
AHRENDS Robert (GERMANY)
Analytical Chemistry - University Vienna - Vienna - AUSTRIA
VERHELST Steven (NETHERLANDS)
Department of Cellular and Molecular Medicine - KU Leuven -University of Leuven - Leuven - BELGIUM
ELLIS Shane (AUSTRALIA)
Molecular Horizons and School of Chemistry and Molecular Bioscience - University of Wollongong - Wollongong - AUSTRALIA
KREUTZ Michael (GERMANY)
Center for Molecular Neurobiology - University Medical Center Hamburg-Eppendorf - Hamburg - GERMANY
The astonishing capacity of the brain to process and store information crucially relies on properly functioning synapses. They provide the connecting entities within neural circuits and they properties define circuit function. The molecular composition of synapses can be very different, which has not been appreciated yet to the extent that would allow deeper insights into the molecular underpinnings of information processing in different circuits. While the role of proteins, as core components of the synaptic cell membrane and synaptic transmission has been addressed in certain detail it is unclear to what extent the molecular diversity of lipids can influence synaptic function. Based on new technologies allowing for the first time lipidomic studies at the level of different synapse types, the project aims at unveiling the molecular interactions between lipids and proteins. Newly developed analysis strategies as well as innovative lipid tagging and imaging approaches will enable us to determine the membrane composition of specific synapses with high resolution. This spatial lipidomics workflow will pave the way to studies on how aging and neurological diseases influence synaptic lipid composition with the prospect of therapeutic interventions.
2022
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Long-Term Fellowships - LTF
An adaptive role of mammalian cortex in shaping innate visual behavior
ATLAN Gal (.)
. - The Regents of the University of California, San Francisco - San Francisco - United States
SCANZIANI Massimo (Host supervisor)
Classical work by Sperry showed that rotating the eyes of frogs by 180° led to a matching offset in prey capture behavior, which the frogs could not adapt to. In striking contrast, seminal experiments by Erismann and Kohler, in which human subjects wear goggles that invert the field of view, show that behavior adapts completely to the new contingencies within a few days. The long-standing hypothesis for the ability of mammals to adapt to these new contingencies as compared to amphibians, is the presence of the neocortex, and of its corticofugal projections to evolutionary ancient subcortical structures involved in innate behavior.
In this proposal I wish to uncover the role of corticofugal projections from visual cortex to the superior colliculus (SC), an ancestral structure that receives input from the retina and is involved in orienting behavior. Using mice, I will test the hypothesis that when the visual field of the animal is reversibly shifted by custom wearable lenses, cortical input to the SC is necessary in order for the mouse to adapt its innate visually-guided behavior to the new contingencies. For this I will track mice in several ethological assays, from simple orienting, to complex predatory and maternal behavior. By recording and manipulating activity in both SC and in corticofugal neurons in visual cortex, I aim to uncover the neural circuits allowing mice to adapt their behavior to the shifted visual field.
Revealing how neocortex mediates adaptation, elevating innate behavior beyond base instinct, will provide a framework for understanding the evolutionary advantage gained by this structure, and why it is considered a pinnacle of brain evolution.
2022
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Grant Awardees - Program
Unravelling the mechanisms of brain and behavioral elaboration in ecologically diverse butterflies
MONTGOMERY Stephen (UK)
School of Biological Sciences - University of Bristol - Bristol - UK
EL JUNDI Basil (GERMANY)
Department of Behavioral Physiology & Sociobiology - University of Wuerzburg - Wuerzburg - GERMANY
MARTIN Arnaud (FRANCE)
Department of Biological Sciences - The George Washington University - Washington - USA
BACQUET Caroline (CHILE)
Life Sciences - Universidad Regional Amazónica Ikiam - Tena - ECUADOR
How does the brain encode adaptive behavior? And how do neural systems facilitate behavioral elaboration? Answering these questions requires integrating evolutionary perspectives of ecology and neurobiology in taxa that display behavioral diversity and innovation. To do so, we need new investigative tools that allow us to look deeper into the brain, and to experimentally manipulate brain development and function. Developing new tools for specific groups of organisms is a major investment, and careful consideration should be given to which species to target. We present Heliconiini butterflies as a system where investment is clearly justified. The rich ecological diversity of Heliconiini has been studied for 150 years, but only recently has the extent of neuroanatomical variation been revealed, with some brain regions varying in size by over 25X. Our rich understanding of these taxa, combined with their experimental tractability presents new opportunities for an integrative understanding of neural variation. However, the current lack of established investigative tools inhibits our ability to understand this neural diversity. To address this, we will: 1) visualise and quantify neural diversity; 2) link neural activity to behavior in a nature-based virtual reality setup; 3) optimise genetic tools to manipulate brains and behavior; and 4) identify molecular controls of behavioral maturation. Developing this toolkit will unlock the potential of this system as a model for understanding brain and behavioral elaboration.
2022
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Long-Term Fellowships - LTF
Assembly, dynamics, and plasticity of plastid translocon biogenesis
BAG Pushan (.)
. - University of Oxford - Oxford - UK
JARVIS Paul (Host supervisor)
Endosymbiotic organelles, like plastids and mitochondria, have a very small genome and rely heavily on import of cytosol-synthesised proteins (>95% of the proteome). During evolution, these organelles have evolved unique transmembrane protein complexes, named translocons, capable of recognising and importing precursor proteins in an efficient and selective way. In plastids, two translocons, TOC (Outer membrane) and TIC (Inner membrane), function in series to transport proteins across both membranes. Past research has identified many of the components and some mechanistic information in mature organelles. Yet, the synthesis/assembly of these multi-subunit complexes during development remains elusive, as does the mechanistic detail of their operation. Plastid biogenesis is a critical first step during rapid greening upon seed germination or leaf re-emergence in spring. To understand this, I am proposing a combination of 1. proteomics characterisation, to study the expression and assembly of translocon subunits, and 2. super-resolution imaging (cryo EM), to provide structural information on translocon biogenesis during different plastid developmental stages, in a higher plant, Arabidopsis thaliana, and an early-diverging land plant, Physcometrium patens. The results will elucidate structural heterogeneity and the intrinsic plasticity of TIC-TOC complexes in different types of translocons that transports both photosynthetic and non-photosynthetic pre-proteins. This research will broaden our understanding of organelle development and open new ways to engineer and enhance the targeting of proteins to plastids in different cell types.
2022
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Grant Awardees - Program
Good vibes: how do plants recognise and respond to pollinator vibroacoustic signals?
BARBERO Francesca (ITALY)
Life Sciences and Systems Biology - Turin University - Turin - ITALY
OBERST Sebastian (AUSTRALIA)
Faculty of Engineering and IT, Centre for Audio, Acoustics and Vibration - University of Technology Sydney - Sydney - AUSTRALIA
MATUS Tomás (CHILE)
Program for Systems Biology of Molecular Interactions and Regulation/Group of 'Transcriptional Orchestration of Metabolism' - Institute for Integrative Systems Biology (I2SYSBIO), Joint Centre University of Valencia (UV), Spanish Research Council (CSIC) - Paterna, Valencia - SPAIN
A finely-tuned communication is crucial for maintaining plant-pollinator interactions. So far, this complex association has been investigated primarily by focusing on visual and olfactory cues. Recent studies have suggested vibroacoustic (VA) signals as an additional communication channel eliciting plant responses, however, the extent and ultimate roles of VAs in plant interactions are largely unexplored. In the context of plant-pollinator associations, VA signalling has only been scantily addressed, mainly in buzz-pollinated species, neglecting airborne components and without delving into the underlying molecular mechanisms involved. Our project aims at dissecting the molecular and physiological mechanisms of plant responses to distinct VAs emitted by approaching insects, using snapdragon as a model. Since Antirrhinum flower visitors have unequal efficiency as pollinators and emit characteristic VAs, we hypothesise that plants are able to recognise effective pollinators by sensing their specific VA signatures. We also postulate that VA-elicited snapdragon responses affect pollinator behaviours, with effects on pollen transfer, and consequently on plant reproductive fitness. Our project will test these hypotheses by a multidisciplinary approach combining ethology, plant molecular biology, and physics-informed data science. VAs of legitimate and illegitimate flower visitors will be recorded and engineered signals will be played back to test plant early and late electrophysiological, metabolic and transcriptomic responses. We will generate flower-shape and receptor-sensing mutants by CRISPR-Cas gene editing to analyse VA-sensing processes and structural features potentially evolved to enhance plant VA transmission. Behavioural assays will test flower visitors’ preferences to assess if plant responses triggered by VAs can be considered adaptive in the context of pollination. Multidisciplinary data will be interwoven in an evidence-based mathematical model tracing a roadmap to help understanding the origins of phyto-vibroacoustics: why vibroacoustic communication has evolved in plants. By tackling complex dynamics in plant-pollinator systems from a totally new angle, we endeavour to revolutionise our understanding of how plants interact with the biotic and abiotic components of the environment.
2022
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Long-Term Fellowships - LTF
Identifying genes contributing to trait variations throughout vertebrate evolution and development
BARUA Agneesh (.)
. - University of Lausanne - Lausanne - SWITZERLAND
ROBINSON-RECHAVI Marc (Host supervisor)
Genetic novelty begets the emergence of new forms and functions. However, animals can also undergo transitions in form and function within their lifetime by regulating a single genetic framework. Genes involved in such transitions have large phenotypic effects and thus can also be responsible for phenotypic variation between species. To test this, I will identify genes involved in one of the most drastic transitions in vertebrates, metamorphosis. In teleost fish, metamorphosis can turn a transparent, soft-bodied, freshwater larva into a colourful, bony, marine adult. This diversity in form and function makes fish ideal for studying the divergent and conserved molecular mechanisms of vertebrate metamorphosis. I will construct gene regulatory networks using RNA-seq from metamorphic stages of fish with different life histories and traits to identify conserved genes. Using these candidates, I will associate changes in expression with variations in different traits like pigmentation or fin shape. I will then use phylogenetic comparative methods to identify adaptive changes in gene expression and protein sequences. With this approach, I aim to short-list genes contributing the most to trait variations throughout both ontogeny and phylogeny. Lastly, I will functionally validate the effect of these genes in fish models, allowing me to establish a robust genotype-phenotype relationship. This project will increase the repertoire of genes with known phenotypic effects and identify new genes implicated in the origin of form and function, providing new directions for studying vertebrate development and evolution.
2022
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Grant Awardees - Program
Dynamics of multilayer epithelial structures: Integrative mechanical characterization of epidermis
DAS Tamal (INDIA)
TCIS, Collective Cellular Dynamics Lab - Tata Institute for Fundamental Research Hyderabad - Hyderabad - INDIA
SERWANE Friedhelm (GERMANY)
Department of Physics - LMU Munich - Munich - GERMANY
BI Dapeng (USA)
Physics - Northeastern University - Boston - USA
How single layer tissues transform into multilayer systems to become building blocks of organs and organisms is one of the unresolved riddles in biology. An intriguing example of this process is the formation of the most important barrier layer, the skin epidermis, which protects our body from the external environment and withstands large external stresses. During its development, the epidermis starts as a single layer of cells, which proliferate, move outward, and stack-up to build the multilayered epithelium. Understanding epidermal development is critical for understanding, preventing, and curing numerous skin defects, painful blistering, and skin cancers. To this end, skin epidermis development has traditionally been tackled via 3D imaging of fixed tissue, collected mainly from mouse embryos. With this scheme, however, the dynamics of epidermal development cannot be revealed. Besides, progress in research using animal models are limited by the time required to induce genetic perturbations and ethical considerations. Even where it is possible to pinpoint few molecular players using an animal model, the dynamic biophysical mechanism that dictates cell movements in a developing skin dermis remains unexplored. Funded by the HSFP, we will overcome these limitations by developing a stem cell-derived skin model, termed skin organoid. Furthermore, we will introduce a mechano-biological platform to measure tissue mechanics in 3D, and build a predictive 3D model of epidermis. In essence, our strategy is to build a bottom-up system that grants simple access to experimental parameters via biophysical measurements, genetic perturbations, and mathematical modeling, while retaining the physiological relevance. Taken together, owing to the interdisciplinary nature of our team, we plan to use a unique combination of disciplines and technologies, which will enable us to take a radically different approach for tackling the question of how a single layer epithelium transform into a multilayer tissue.