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Awardees

2023 -
Long-Term Fellowships - LTF

Phytoplankton translational regulation: From models to communities

WIENER David (.)

. - University of Washington - Seattle - United States

E. VIRGINIA Armbrust (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 -
Long-Term Fellowships - LTF

Discovery of new cyclic nucleotide immune receptors in human innate immunity

YAMAGUCHI Sonomi (.)

. - Dana-Farber Cancer Institute - Boston - United States

PHILIP Kranzusch (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 -
Cross Disciplinary Fellowships - CDF

Mechanotransduction of T cell antigen recognition examined with 3D super-resolution imaging

ZAZA Cecilia (.)

. - University College London - London - United Kingdom

SABRINA Simoncelli (Host supervisor)
SERGI Padilla-Parra (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 -
Long-Term Fellowships - LTF

Mechanistic Investigations of the Circuits Driving Spontaneous Neuropathic Pain

ZENG Xiangsunze (.)

. - Boston Children's Hospital - Boston - United States

CLIFFORD Woolf (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 -
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 -
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 -
Grant Awardees - Program

Spatial and deep neurolipidomics to reveal synapse diversity

AHRENDS Robert (GERMANY)

Analytical Chemistry - University Vienna - Vienna - AUSTRIA

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

VERHELST Steven (NETHERLANDS)

Department of Cellular and Molecular Medicine - KU Leuven -University of Leuven - Leuven - BELGIUM

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 -
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 -
Grant Awardees - Program

Unravelling the mechanisms of brain and behavioral elaboration in ecologically diverse butterflies

BACQUET Caroline (CHILE)

Life Sciences - Universidad Regional Amazónica Ikiam - Tena - ECUADOR

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

MONTGOMERY Stephen (UK)

School of Biological Sciences - University of Bristol - Bristol - UK

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 -
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 -
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

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

OBERST Sebastian (AUSTRALIA)

Faculty of Engineering and IT, Centre for Audio, Acoustics and Vibration - University of Technology Sydney - Sydney - AUSTRALIA

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 -
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 -
Grant Awardees - Program

Dynamics of multilayer epithelial structures: Integrative mechanical characterization of epidermis

BI Dapeng (USA)

Physics - Northeastern University - Boston - USA

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

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.
2022 -
Long-Term Fellowships - LTF

Regulation of phagosome dynamics in antigen cross-presentation by dendritic cells

BIRAM Adi (.)

. - The Francis Crick Institute Ltd - London - United Kingdom

REIS E SOUSA Caetano (Host supervisor)

Type 1 conventional dendritic (cDC1) cells play a major role in orchestrating anti-viral and antitumor immunity by cross-presenting antigens on major histocompatibility complex class I (MHCI) molecules to CD8+ T cells. cDC1 cells in both mice and human express dendritic cell natural killer lectin group receptor-1 (DNGR-1, encoded by Clec9a), which detects dead cells and supports cross-presentation of dead cell-associated antigens. Recent studies have shown that DNGR-1 favors cross-presentation by promoting phagosomal rupture upon ligand engagement, allowing the escape of phagosomal contents into the cytosol, where they access the MHC class I antigen processing pathway. Although DNGR-1 was shown to destabilize the phagosomal membrane, it is unclear how phagosomal rupture is regulated downstream of DNGR-1 signaling. Here, we will employ a genome wide high throughput screening approach to identify novel regulators of phagosomal rupture and integrity and examine their role in antigen cross-presentation and antitumor immunity. We will utilize multiple cellular assays to mechanistically evaluate the contribution

of potential regulators, followed by generation of in vivo mouse models to study their function. Using a multidisciplinary approach that combines cell biology and functional immunology, we aim to uncover important players in DNGR-1-mediated phagosomal rupture and study their roles in various cancer models. Our approach will provide new insights into the basics of antigen crosspresentation and open new avenues in the development of therapeutic strategies manipulating cross-presentation in cancer.

2022 -
Grant Awardees - Early Career

Crossing the barrier: horizontal gene transfer in synergistic protocells

BONFIO Claudia (ITALY)

Laboratory of Supramolecular Biochemistry - Supramolecular Science and Engineering Institute (ISIS) - Strasbourg - FRANCE

O'FLAHERTY Derek (CANADA)

Department of Chemistry - University of Guelph - Guelph - CANADA

SPRUIJT Evan (NETHERLANDS)

Physical Organic Chemistry - Radboud University Nijmegen, Institute for Molecules and Materials - Nijmegen - NETHERLANDS

Replication is a key property of living systems and must have played a central role in the origin of life. However, current models of protocells do not support an autonomous cycle of replication: membraneless organelles (coacervates) can sequester nucleic acids, but lack stability and impede proper base pairing important to RNA biochemistry, while membrane-bound structures (liposomes) can host prebiotic RNA biochemistry without being able to take in the required substrates. Our team suggests that the advent of life resulted from the emergence of a prebiotic ecosystem of synergistically interactive protocells rather than individual self-sustaining systems. Whereas RNA-based coacervates and liposomes have been studied separately, we innovatively propose that cooperative interactions between protocells might overcome major obstacles for replication in minimal cells. Inspired by symbiosis in biology, we envision that protocell synergy helped overcome this issue by enabling the primitive horizontal gene transfer (pHGT) between protocells, in order to unlock critical processes important to life. In living cells, liposomes and coacervates coexist, while performing different tasks. Similarly, their primitive versions might have had different, yet synergistic, roles in supporting RNA-based biochemistry, leading to a prebiotic scenario of increased complexity (introducing new functionalities) and diversity (improving fitness and efficiency). By elucidating the conditions required for coexistence, interaction and transfer between coacervates and liposomes, we will establish symbiosis as a novel factor in the origin of life, and at the same time gain a better understanding of the interactions between membraneless organelles and membranes in modern biology. The investigation of these three-way interactions between RNA, liposomes and coacervates constitutes a key innovative element, and will allow us to answer several questions fundamental to biology. We will illuminate i) how protocell recognition/interaction occur and ii) how genetic material is stored by and transferred between protocells, to build co-operative systems capable of pHGT. This unique opportunity will capitalize on each member’s set of expertise (Bonfio – membranes, O’Flaherty – nucleic acids, Spruijt – coacervates), that would otherwise be impractical without each member’s key contributions.
2022 -
Grant Awardees - Program

Transition and reconstruction of Central Nervous System due to aging and disease

BOURNE James (AUSTRALIA)

Cellular and Cognitive Neurodevelopment - National institute for mental health - Bethesda - USA

FUJIYAMA Fumino (JAPAN)

Laboratory of Histology and Cytology, Faculty of Medicine and Graduate School of Medicine - Hokkaido University - Sapporo - JAPAN

HJERLING-LEFFLER Jens (SWEDEN)

Dept. Medical Biochemistry and Biophysics - Karolinska Institutet - STOCKHOLM - SWEDEN

ZOU Yimin (USA)

Neurobiology - University of California, San Diego - La Jolla - USA

What is aging? Getting old is not always bad, but it can be difficult both mentally and physically. Brain aging is a universal phenomenon in all mammalian species and continues to be a fundamental biological question. Although there has been much effort to understand brain aging and its many manifestations, including shrinkage and cognitive decline, it largely remains a mystery. With the increased life span of humans and neurodegenerative disorders on the rise, understanding normal aging will have a tremendous societal impact. Contrary to aging, much more is known about brain development. In the past several decades, tremendous progress has been made in deciphering the molecular program responsible for the development and maturation of neurons. Recent advances in genome science have led us to speculate that the very same factors that control fundamental developmental events are repurposed in adulthood to control synapse biology. It is known that the characteristic EEG rhythm decreases as aging. Therefore, we study the potential function of key factors and signalling molecules, which plays a pivotal role in developing the brain, on the formation, maintenance and function of the synapses formed by specific cortical neurons, which are essential for rhythm generation. We postulate that deregulation of these vital developmental factors might have a fundamental role in not only synaptic loss but also synaptic function when the cognitive decline starts in the aging brain. We will take a comparative approach to identify common mechanisms between the non-human primate model and a rodent model and test the functions of the aging program. This proposal relies on multilateral collaborations from distinct expertise in broad areas of neuroscience. Collaborations have made this proposal highly innovative as these questions are otherwise not accessible to researchers from each of the areas these investigators represent. When the issue of "what is aging" is clarified by our multidisciplinary team, it will be a great light not only for the mechanism of aging in healthy humans but also for the treatment and rehabilitation of diseases.
2022 -
Grant Awardees - Program

Modeling electric fields at the heart of enzyme catalysis and function

BOXER Steven (USA)

Dept. of Chemistry - Stanford University - Stanford - USA

WUTTKE Stefan (GERMANY)

Basque Center for Materials, Applications and Nanostructures - Ikerbasque Foundation - Leioa - SPAIN

The synthesis and degradation of nearly all components of living systems are controlled by enzymes. Enzymes can accelerate the rate of biosynthetic processes to a remarkable degree while retaining a high level of specificity. We aim to understand the origin(s) of this rate enhancement by creating synthetic enzyme mimics. Our underlying hypothesis is that the active site elements of enzymes are organized to create large electric fields that interact non-covalently with the substrate bonds undergoing charge displacement during catalysis. If the field is large and oriented correctly, this interaction can make a substantial contribution to lowering the transition state free energy and accelerating the reaction. This concept is called electrostatic catalysis, and while some computational and experimental evidence exists to support this hypothesis, the non-covalent interactions at the heart of this concept have not been recapitulated or their fields measured in synthetic systems. This is a grand challenge at the interface of biology and chemistry. This proposal brings together a group that is expert in the synthesis of molecularly defined porous materials with a more biological group that has developed methods to measure electric fields within organized systems, specifically naturally occurring enzymes, and to connect those fields to the lowering of the activation free energy. By using metal-organic frameworks (MOFs) to precisely install the key functional groups of molecules in apposition to each other, the electric fields created by their non-covalent interactions will be measured for the first time. The synthetic scaffold offers a tremendous diversity of chemical functionality; specific MOF structures that mimic a wide range of enzyme active site geometries that lead to diverse function are proposed. While motivated by enzyme catalysis, electrostatic interactions due to non-covalent interactions are an essential feature of the assembly of living systems on all length-scales, so we expect this work to have both fundamental and applied impact in diverse fields. We build on this fundamental information to create enzyme-like architectures that should, if our hypothesis is correct, be capable of accelerating the rate of chemical transformations as is found in living systems.
2022 -
Grant Awardees - Early Career

The atmosphere: a living breathing ecosystem?

BRADLEY James (UK)

School of Geography - Queen Mary University of London - London - UK

GOORDIAL Jacqueline (CANADA)

School of Environmental Sciences - University of Guelph - Guelph - CANADA

GREENING Chris (AUSTRALIA)

Biomedicine Discovery Institute - Monash University - Clayton, Melbourne - AUSTRALIA

TREMBATH-REICHERT Elizabeth (USA)

School of Earth and Space Exploration - Arizona State University - Tempe - USA

The atmosphere is the Earth’s largest potential habitat, yet the least understood. Microscopic organisms (microbes) are transported between land and water through the atmosphere in a process that shapes global biodiversity and influences disease transmission. Yet little is known about the nature or activities of these microbes. Are airborne microbes simply passively blown through the atmosphere? Or is the atmosphere a ‘true’ ecosystem, with active microbes utilizing atmospheric gases for energy? Through this collaborative study, we will resolve these questions by systematically studying the composition, capabilities, and activities of atmospheric microorganisms. We will carry out a global genetic survey of microbial composition and traits, thus establishing whether the atmosphere hosts structured and adapted microbial communities. In parallel, we will conduct highly sensitive activity assays to determine whether airborne communities and single cells can metabolise atmospheric substrates. In addition, we will integrate empirical data with theoretical modelling to determine whether the energy available in the atmosphere through trace gases and other sources is sufficient to sustain life. Achieving this ambitious program depends on integrating multiple advances developed by our research team, including cutting-edge techniques (e.g., single-cell tagging and NanoSIMS measurements), theoretical approaches (e.g., bio-energetic single-cell and planetary-scale modelling), and recent major discoveries (e.g., that bacteria can live on atmospheric energy sources). The proposed research directly applies to the HSFP mandate to understand the fundamental mechanisms of life. If the atmosphere is found to be ecologically structured and metabolically active, it would result in the discovery of the largest active biosphere on Earth, and could broaden how (and where) we may search for life on other planets.
2022 -
Long-Term Fellowships - LTF

The Molecular Machinery behind the Wiring Specificity of Serotonin Axonal Projections

CHAN Chui kuen (.)

. - MRC Laboratory of Molecular Biology - Cambridge - United Kingdom

REN Jing (Host supervisor)
The serotonin system is the most widely used pharmacological target for treating depression and anxiety. Despite its fundamental importance, the assembly of serotonin system during development and disrupted consequences remain unknown. Recent studies, leading by my postdoc supervisor Dr. Jing Ren, show that individual subpopulation of raphe nuclei serotonergic axonal fibres innervate specific brain regions, suggesting the significance of serotonin neuron subpopulations behind wiring specificity. These organized serotonin axonal projections modulate neuronal activities in innervated regions and their functions, but how are these projection patterns determined during development? With my strong background in molecular biology and super-resolution microscopy, I am pursuing the answer to this question, how do the synaptic wiring proteins, serotonin receptors and surrounding microenvironment interact to specify serotonin axonal projections? Firstly, I have profiled protein networks of serotonin terminals at different brain areas by proximity biotinylation-facilitated quantitative proteomics. Functions of protein candidates shall be verified in 3D culture and conditional knock-out models. Secondly, I shall investigate mechanical signals from the microenvironment on axon projection specificity, by manipulating substratum stiffness. Finally, serotonin circuitry conduction shall be studied by employing GFP knock-in 5HTR2A mice-derived culture via super-resolution imaging. This study will significantly advance our understanding of the developmental assembly of the serotonin circuitry, providing insights into the relationship between neurodevelopment and mental disorders.
2022 -
Grant Awardees - Program

A bottom-up approach to understand how enzyme structural fluctuations accelerate multistep reactions

CHICA Roberto (CANADA)

Department of Chemistry and Biomolecular Sciences - University of Ottawa - Ottawa - CANADA

GREEN Anthony P. (UK)

Department of Chemistry - Manchester Institute of Biotechnology - Manchester - UK

THOMPSON Michael (USA)

Department of Chemistry and Biochemistry - University of California, Merced - MERCED - USA

Enzymes are a type of protein found within all living cells. Often called biocatalysts, enzymes speed up the rate of biochemical reactions to help support life. Their unique structure imparts certain characteristics and makes them reactive to specific substrates, analogous to a lock and key model. The structure of enzymes is amenable to change, however it is not clear how structural changes in enzymes affect their efficiency (speed of reaction). Our team of interdisciplinary experts is proposing a unique approach to study the effect of structural changes in enzymes on their behavior by using a combination of state-of-the-art time-resolved X-ray crystallography and substrate engineering. This study will allow us to evaluate the link between structural changes and the catalytic efficiency of enzymes for various complex and multistep chemical reactions. The knowledge accrued through these experiments will enable us to predict the role of structural fluctuations in enzyme catalysis, and set the stage for the rational design of efficient artificial enzymes for applications in medicine and industry.