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2021 -
Long-Term Fellowships - LTF

The role of metabolism in regulating pathological osteoclastogenesis in arthritis

HASEGAWA Tetsuo (JAPAN)

MRC Laboratory of Molecular Biology - University of Cambridge - Cambridge - UK

PEARCE Edward (Host supervisor)
CLATWORTHY Menna (Host supervisor)
Osteoclasts are macrophage lineage cells with unique bone-destroying capacity, playing key roles in steady-state bone remodelling inside the bone marrow (BM) and pathological joint destruction in patients with rheumatoid arthritis (RA), in which the hypertrophied synovium (called "pannus") invades the outer surface of the articular bone. While osteoclastogenesis is known to involve dynamic metabolic changes, little is known about the metabolic pathways involved in the pathological osteoclastogenesis in the inflammatory synovial tissue setting. I therefore aim to elucidate the extracellular energy microenvironment and metabolic regulation of pathological osteoclasts causing bone destruction in arthritis. I will perform imaging mass spectrometry of the knee joints of arthritic mice to elucidate the metabolic states of osteoclasts in the pannus microenvironment and compare it with physiological BM settings. I will also extract the pannus directly into the metabolite extraction buffer, and analyze the extract through mass spectrometry by comparing healthy and diseased joints. Based on these in situ information, I will elucidate how the energy microenvironment and metabolites enriched in the arthritic joints govern the function and metabolism of osteoclasts through analysing metabolic profiling assays, such as extracellular acidification rate, oxygen consumption rate, and carbon isotype (13C) tracing. Overall, these proposed studies will provide novel insights into the metabolic regulation of pathological osteoclastogenesis, potentially leading to the development of a new strategy for treating bone destruction in RA without interfering with physiological bone remodelling.
2021 -
Long-Term Fellowships - LTF

Role of stress-induced modulation of B cell function in cardiovascular disease

SINGH Sumnima (NEPAL)

- Icahn School of Medicine at Mount Sinai - New York - USA

SWIRSKI Filip (Host supervisor)
Cardiovascular disease (CVD) is the leading cause of global morbidity and mortality. While psychological stress is a known cardiovascular risk factor, the mechanism by which the brain translates stress into CVD is poorly understood. The underlying cause of CVD is a chronic inflammatory disease called atherosclerosis, the progression and exacerbation of which have been strongly associated with the immune system, including B cells. B cells perform many functions including production of antibodies that provide immunity against disease and cytokines that modulate leukocyte function. However, it remains unknown whether B cells mediate the effects of stress on CVD. Recent studies from the host lab show that stress profoundly affects the number and distribution of B cells in the body. This occurs via a mechanism dependent on the activation of the hypothalamic-pituitary-adrenal axis. In this proposal, I will test the hypothesis that stress aggravates atherosclerosis by modulating B cell function. To recapitulate stress, I will employ a combination of optogenetic and chemogenetic approaches available in the host lab to locally activate specific regions in the brain and characterize the subsequent impact on the phenotype and functional diversity of B cells. I will then identify the B cell-specific mechanisms that mediate the effects of stress on the progression of CVD. These studies will not only delineate potential therapeutic targets for immunomodulation of B cells in prevention and treatment of atherosclerotic CVD, but also provide a direct mechanistic link between stress and chronic inflammation, a general concept with implications beyond atherosclerosis.
2021 -
Grant Awardees - Program Grants

Memory – from material to mind

DIAMOND Mathew (ITALY)

Tactile Perception and Learning Lab - International School for Advanced Studies (SISSA) - Trieste - ITALY

KEIM Nathan (USA)

Dept. of Physics - Pennsylvania State University - University Park - USA

BARAK Omri (ISRAEL)

Faculty of Medicine and Network Biology Research Laboratories - Technion - Israeli Institute of Technology - Haifa - ISRAEL

The brain’s capacity to store and retrieve information is the target of enormous research efforts. Seemingly unrelated research in physics has begun to focus on information storage and retrieval in non-living systems. For instance, a crumpled nickel-titanium wire spontaneously reconfigures into its remembered shape – a paperclip – upon heating. Our proposal posits that the memory dynamics being discovered in non-living systems are less remote from brain memory than might be supposed. Through our experimental neuroscience expertise (DIAMOND), we will train rats in perceptual memory behaviors. To uncover fundamental rules that extend beyond a single paradigm, we will use one stimulus set as the external drive from which the brain generates multiple distinct percepts; furthermore, we will train rats to act upon these percepts in a diverse library of tasks. Through our soft matter physics expertise (KEIM), we will chart out a general framework for memory storage and retrieval aimed at replicating key rat findings, such as the interaction between short-term and longer-term memories. Materials that extract and store information, such as driven suspensions, can be arranged in a flexibly interacting network to serve as a physical model of brain networks. Our computational neural networks expertise (BARAK) will act as the bridge. In a feedback loop within the project, BARAK will characterize materials networks in a language that can be applied to experimental neuroscience. By converting materials network properties into biological mechanisms, such as persistent firing patterns, BARAK will provide DIAMOND with quantitative predictions for the neuronal population states across a network of cortical regions (analogous to the network of materials). Removal of a single module from the materials network might be analogous to optogenetic suppression of a single cortical region; the team, together, will interpret parallel experiments of this sort. While not neglecting what makes the brain qualitatively different from an inanimate material, our identification of common motifs between material and mind engenders a new approach that envisions behavior as the task-dependent configuration of a repertoire of fundamental memory properties.
2021 -
Grant Awardees - Program Grants

Evolution of neural circuit dynamics and brain computations in Astyanax blind cave fish

SUMBRE German (ARGENTINA)

Dept. of Biology - Ecole Normale Superieure - Paris - FRANCE

KEENE Alex (USA)

Department of Biology - Texas A&M University - College Station - USA

GJORGJIEVA Julijana (MACEDONIA)

School of Life Sciences - Technical University of Munich - Freising - GERMANY

Environmental changes often drive drastic evolutionary changes in behavior and brain function. While genetic mapping studies have provided insight into the genetic basis of behavioral evolution, much less is known about the neural circuit dynamics and brain computations that drive this behavioral change. Across phyla, cave ecosystems provide the opportunity to examine how environmental change impacts the evolution of morphology, development and behavior. The Mexican tetra, Astyanax mexicanus is a leading model for studying genetic mechanisms underlying trait evolution. A. mexicanus consists of a surface (river) and several cave populations that independently evolved in largely isolated caves, allowing for comparative approaches to identify genetic and neural variants associated with behavioral evolution. Cave populations of A. mexicanus exhibit prominent changes in sensory systems including loss of vision and expansion of smell, taste, mechanosensation and lateral line. Despite the robust changes in behavior and morphology, the shifts in processing sensory information within the brain has been unexplored. Here, we will apply an interdisciplinary approach that leverages newly developed genetic tools and synergistic interaction between PIs with expertise in behavioral evolution, functional imaging and theoretical modeling to investigate how changes in neural dynamics underlie the evolution of sensory systems to new environments with different sensory constraints. This synergistic collaboration will shed light on general evolutionary principles underlying the repurposing of neural circuit dynamics and computations of sensory systems that could have broad implications for understanding the evolution of brain function, plasticity and intra-species differences in sensory processing.
2020 -
Long-Term Fellowships - LTF

Using visual proteomics to understand membrane dynamics in the malaria parasite P. falciparum

FERREIRA Josie (UK)

Centre for Structural Systems Biology - University of Hamburg - Hamburg - GERMANY

GILBERGER Tim (Host supervisor)
The malaria disease represents a significant global burden. Despite major advances in its treatment and control, rising resistance to front-line therapies makes the demand for innovative solutions more important than ever. To identify possible intervention points, we need a firm grasp on the processes that govern the parasites complex lifecycle. Central to the evolutionary success of the malaria parasite is the rapid invasion of erythrocytes and subsequent replication. During invasion, the parasite utilises intricate machinery coordinated by a sequence of receptor-ligand interactions, allowing the invagination of the erythrocyte membrane. Inside the erythrocyte, transient structures essential for invasion are rapidly disassembled. These include a double membrane structure termed the inner membrane complex. Despite their importance, our understanding of these transient structures is limited. I propose a correlative approach to understand receptor-ligand mediated erythrocyte invasion and subsequent disassembly of the inner membrane complex. I aim to directly visualise and analyse these processes in situ. This will be achieved using super-resolution fluorescence microscopy to guide specimen FIB-milling for electron cryo-tomography and subtomogram averaging. Simultaneously, studying the inner membrane complex over time in combination with mass spectrometry will allow me to identify and target key players in the disassembly process. Finally, using cryo-tomograms, I will generate a series of atlases of protein and organelle positions within the parasite and host cell. These will provide details of the alterations in the molecular landscape during and post invasion.
2020 -
Long-Term Fellowships - LTF

Deciphering the functions and mechanisms of brain-wide motor representations

LEV Itamar (ISRAEL)

Department for Neurobiology - University of Vienna - Vienna - AUSTRIA

ZIMMER Manuel (Host supervisor)
Brain-wide representations of ongoing behavior were recently observed in neuronal activity patterns measured form various organisms such as worms, flies, and mice. Surprisingly, also primary sensory areas, like the V1 visual cortex in mice, previously thought to exclusively represent sensory information are also strongly modulated by behavioral variables like running speed. While this phenomenon seems to be prevalent, its functions and underlying neuronal mechanisms are elusive. I hypothesize that motor commands are integral components of sensorimotor transformations. Like others have suggested for the V1 area, I propose that this sensorimotor integration allows behavior-dependent sensory gain control, and more speculatively also involves predictive coding, i.e. that perception is tuned to unexpected outcomes of the animal's explorative movements. To address these hypotheses, I will use the tractable model organism C. elegans which is amendable to the cutting-edge whole-brain calcium imaging technology. I will develop new whole-brain imaging assays in freely-moving worms. I will then use these assays to search for gain-control circuits where the sensitivity of sensory neurons is modulated by different behavioral states. I will also look for predictive-coding circuits involving error-coding neurons, sensitive to unexpected stimuli. To study the behavioral relevance of these mechanisms, e.g. during navigation, I will interfere with the neuronal activity of the relevant circuits via optogenetics and other transgenic inhibition tools. Therefore, by combining these different approaches I aim to uncover generalizable functions and mechanisms of brain-wide motor representations.
2020 -
Long-Term Fellowships - LTF

Brain remodeling and deceleration of aging upon caste transition in the ant Harpegnathos saltator

SIERIEBRIENNIKOV Bogdan (UKRAINE)

Department of Biochemistry and Molecular Pharmacology - New York University Langone School of Medicine - New York - USA

REINBERG Danny (Host supervisor)
Identical genomes in social insects generate castes with distinct morphologies and behaviors. The Harpegnathos ants have a remarkable lifestyle, whereby the queen’s death triggers transition of a subset of workers to become her substitutes, called gamergates. This entails minor changes in morphology, yet a pronounced shift in behavior, and remarkably, a fivefold extension of lifespan. This process is reversible if the gamergate is placed in a colony with a real queen. The capability of such a dramatic transition in adult life provides a unique context to study neuronal plasticity and aging. Moreover, social insects challenge major aging theories as their calorie intake and fecundity positively correlate with lifespan, in contrast to most animals. I aim to provide an extensive mechanistic description of the worker-to-gamergate transition in H. saltator, and to characterize the mechanisms of the resultant aging deceleration. I will study the brain as it regulates caste transition and produces hormones implicated in aging, while also being affected by both processes. First, I will perform single-cell RNA-sequencing of the worker and nascent gamergate brains to describe changes in genes controlling synaptic wiring and cellular signaling. Next, I will test whether deceleration of aging in gamergates is accompanied by decreased rates of molecular damage, protein synthesis, transposon activity, and telomere shortening. Finally, I will combine both datasets to link transcriptional changes during the caste transition with aging-related molecular processes. Deciphering the paradoxical aging mechanism in social insects may uncover previously unknown strategies to prolong lifespan.
2020 -
Cross Disciplinary Fellowships - CDF

Data-driven discovery of decentralised control mechanisms of action selection

GOSZTOLAI Adam (HUNGARY)

Neuroengineering Laboratory - Brain Mind Institute and Interfaculty Bioengineering Institute - Lausanne - SWITZERLAND

IJSPEERT Auke (Host supervisor)

In our lives, we are continuously generating a sequence of actions. What are the neural mechanisms that cause the selection of one action above all others? These mechanisms can provide key insights for designing artificial robotic controllers that are as flexible as their neurobiological counterparts. The dominant ‘feedforward’ model for action selection suggests that decisions are made in the brain, upon which a command signal is sent to downstream motor circuits. However, this model ignores the critical role that peripheral mechanosensory feedback signals likely play in action selection. Such a potentially paradigm-shifting ‘feedback-centric’ model of action selection, its dynamical mechanisms, and its neuronal instantiation have yet to be explored. As an HFSP Cross-Disciplinary Fellow in the laboratories of Pavan Ramdya (experimental neuroscience) and Auke Ijspeert (dynamical systems modelling), I will develop such a model through a combination of data-driven dynamical systems theory, optogenetics, and behavioral analysis in Drosophila melanogaster. I aim to discover how a variety of Drosophila limbed behaviors can be generated by a common modelling framework, whereby a set of neural oscillators are coupled through limb-mechanosensory feedback loops and driven by descending neurons. Using these models, I will predict and experimentally test how perturbing sensory feedback pathways affect action selection. Finally, I will cluster the distribution of model feedback topologies that explain different Drosophila behaviors to identify fundamental structure-function relationships and to reveal how one neural network can select and generate a remarkable diversity of actions.

2020 -
Grant Awardees - Program Grants

Developing a method for rapid disassembly of neurodegenerative biomolecular condensates

INOUE Takanari (JAPAN)

Dept. of Cell Biology/ Center for Cell Dynamics - Johns Hopkins University - Baltimore - USA

PERLSON Eran (ISRAEL)

Dept. of Physiology and Pharmacology - Tel Aviv University - Tel Aviv - ISRAEL

SYKES Cécile (FRANCE)

Département de Physique - Ecole Normale Supérieure - Paris - FRANCE

Uncontrolled loss of neurons is a hallmark of neurodegenerative diseases (NDs) such as Alzheimer’s disease and amyotrophic lateral sclerosis (ALS). In NDs, an abnormal assembly of proteins and mRNAs known as a biomolecular condensate (BC) is believed to contribute to neurotoxicity and ensuing neuronal death. Despite high mortality and poor quality of patients’ lives, as well as the enormous socio-economic burden of patient care, the exact molecular and cellular mechanisms underlying ND pathogenesis remain largely unknown. This roadblock in ND studies primarily originates from mutual dependency between “molecular assembly” of general ND proteins and “functionality” of individual ND proteins. Molecular assembly is a dynamic process that can take place locally, and changes actively in its physical property by transitioning among soluble phase, liquid-like droplets, hydrogels and insoluble aggregates. To our knowledge, there is currently no technique to disassemble ND-related BCs to distinguish these physical and biochemical characteristics, especially in a physiologically relevant context. By integrating expertise in neurophysiology, chemical biology, and soft-matter biophysics, we propose to develop a conceptually unique methodology termed “dePOLYMER”. Here, light illumination or chemical administration actuates a genetically-encoded molecular probe designed to polymerize actin to generate constrictive force against an intended object such as BCs in living cells. When force density exceeds the surface tension of target BCs, dePOLYMER is expected to trigger their dispersion. We will specifically target stress granules as a model for non-pathogenic BCs, as well as pathogenic ALS-related BCs. Using a model for ALS, we will next aim to demonstrate dispersion of BCs consisting of ALS proteins in a manner specific for constituent proteins and cell types. In summary, the goal of our study is to offer a novel technique to efficiently disperse BCs in a rapidly inducible manner. Implementation of dePOLYMER in ALS model systems may enable future identification of the molecular and cellular foundation of neurotoxicity, thus a potentially new treatment strategy for NDs. Due to the inherently modular design of dePOLYMER probes, the technique should be generalizable to virtually all BCs whose molecular components are known, let alone other ND-related BCs.
2020 -
Grant Awardees - Young Investigator Grants

Hormone delivery in plants: mechanisms and physiological roles of gibberellic acid transporters - RENEWAL APP

NOUR-ELDIN Hussam Hassan (DENMARK)

Dept. of Dynamic Molecular Interactions - Institute of Plant and Environmental Sciences - Frederiksberg - DENMARK

SHANI Eilon (ISRAEL)

School of Plant Sciences and Food Security - Tel Aviv University - Tel Aviv - ISRAEL

KAWATE Toshimitsu (JAPAN)

Dept. of Molecular Medicine - Cornell University - Ithaca - USA

BAND Leah (UK)

Div. of Plant and Crop Science, School of Biosciences, - University of Nottingham - Loughborough - UK

Plants are sessile organisms whose growth and development rely on finely-tuned signaling mediated by plant hormones (phytohormones). One of the pivotal phytohormones, gibberellic acid (GA), promotes a wide range of developmental processes in plants, such as seed germination, root and shoot elongation, fiber and cambium development, flowering time and fruit patterning. It is therefore crucial for plants to tightly regulate the distribution of GA throughout their lifespan. Our original HFSP team, in parallel to colleagues in the field, demonstrated that a class of nitrate/peptide transporters (NPFs) actively transport GA and play major roles in GA delivery and response. However, we still do not know the mechanism by which the GA transporters select and move their substrates. One of the major impediments is the lack of high-resolution structures. Also, functional redundancy severely hampers genetic studies to investigate the contribution of each transporter in plant growth. To understand the mechanisms of active GA transport in plants, our team will address the following three objectives: 1) Uncover the molecular mechanisms of key novel NPF GA transporters using a combination of structural and functional studies; 2) Investigate the physiological functions of active GA transport in root development and fiber formation using genetic, cellular, and systems biology approaches; and 3) Identify novel GA transporters, beyond the NPF family. These objectives will require innovative techniques, for instance, we will overcome functional redundancy using our unique multi-targeted forward-genetic cell-type-specific transportome-scale screening. Our comprehensive studies on GA delivery at multiple levels—from the molecular and cellular mechanisms of individual transporters to the GA-trafficking protein network in the plant body—will greatly facilitate the design of GA-transporter specific modulators and deliver crucial knowledge on the mechanisms of active GA transport in plants. As genetic manipulation of GA biosynthesis and perception drove the first Green Revolution in world agriculture, controlling GA delivery through manipulation of GA transporters has the potential to generate a second Green revolution to improve agricultural traits.
2020 -
Long-Term Fellowships - LTF

Relevance of lipid droplet-mitochondria contact sites for brown adipose tissue function

FISCHER Alexander (GERMANY)

Department of Genetics and Complex Diseases - Harvard Medical School - Boston - USA

FARESE Robert (Host supervisor)
Brown adipose tissue (BAT) thermogenesis is essential for survival in cold temperatures. To meet the energetic demands of this process, BAT relies on efficient energy supply from the circulation as well as from intracellular triglyceride stores in lipid droplets. The fatty acids stored in triglycerides can be liberated by lipolysis and serve as fuel for mitochondrial thermogenesis. However, high intracellular levels of free fatty acids are detrimental for cellular survival, demanding for efficient transfer processes. Microscopical analyses indicate a tight interaction between mitochondria and lipid droplets, yet even the fundamental triggers leading to the initiation of contact site formation as well as their physiological role remain elusive. In this proposal, I therefore want to examine the hypothesis that molecular complexes mediating interactions between mitochondria and lipid droplets are formed in activated BAT, and that these contact sites are critical for BAT function. To achieve these goals, microscopical interaction studies will be employed to shed light on the conditions triggering contact site formation. The molecular machinery mediating the interaction will be identified using an APEX-proximity labelling approach. Genetic manipulation will be employed to examine the role of the proteins identified in this screen for initiation and maintenance of contact sites. The relevance of these proteins for BAT function will then be analyzed using CRISPR-Cas9 technology in primary adipocytes and mice. Conclusively, the proposed approaches will not only help understanding the mechanisms involved in organelle contact site formation but also define their physiological role.
2020 -
Long-Term Fellowships - LTF

The ontogeny of behavior

LEVY Dana Rubi (ISRAEL)

Department of Neurobiology - Harvard Medical School - Boston - USA

DATTA Sandeep Robert (Host supervisor)
Naturalistic behaviors are refined and stabilized throughout an animal’s life. Their formation is dependent upon multiple internal and external cues, giving rise to both stereotypical intraspecific responses and individually-unique behavioral patterns. The striatum has been widely implicated in controlling voluntary action and encoding behavioral modules and sequences in adulthood. However, how striatal dynamics might support and structure the evolution of behavior throughout development remains surprisingly unexplored. Here, I propose to incorporate longitudinal, unsupervised behavioral phenotyping with high-throughput in-vivo neuronal recordings in freely-behaving mice in order to characterize the evolution of naturalistic behavioral modules and their neural correlates from weaning to adulthood. To explore the interplay between external cues, circuit dynamics and behavioral plasticity, I will confound environmental features during development and study how behavioral adaptation is reflected in the underlying single-cell and population striatal codes. Finally, I will utilize this large-scale dataset to investigate the emergence of behavioral variation and to identify the neural correlates of individuality.
2020 -
Long-Term Fellowships - LTF

A chemical biology approach to unravel phosphatidylethanolamine transport and metabolism

SIMON Clémence (FRANCE)

Biochemistry Department - University of Geneva - Geneva - SWITZERLAND

RIEZMAN Howard (Host supervisor)
Glycerophospholipids are one of the major lipid species in cellular membranes of eukaryotic cells. Among glycerophospholipids, phosphatidylethanolamine (PE) is a highly conserved lipid, found in all organelles but mainly synthesized in the endoplasmic reticulum (ER) and in mitochondria. If it has been shown to play essential roles in membrane protein structure and function, its distribution and metabolism have not been fully elucidated. Indeed, little is known about lipid transport in terms of quantitative and qualitative contribution of each pathway, because methods to measure lipid transport between organelles in cells are lacking. Unlike proteins which are relatively easily manipulated by genetic techniques, individual lipid species cannot be readily modified in vivo. Here, I propose to develop and use chemical tools to study PE transport and metabolism in living cells with high spatiotemporal resolution. I will synthesize photocaged PE which can be localized with precision to mitochondria (or ER) within cells and then released with irradiation of light. Using isotope-labelling, I will trace their transport and quantify the metabolites inside living cells by lipidomics and mass spectrometry approaches. Moreover, mass spectrometry imaging could allow visualizing the de novo labeled phospholipids. This interdisciplinary approach will give us the spatiotemporal resolution that is needed to create for the first time a 4D map of PE metabolism in cells. It will allow us to elucidate its metabolism related to its dependence on intracellular localization and prove that PE can or cannot be transported, for instance, bidirectionally between ER and mitochondria.
2020 -
Cross Disciplinary Fellowships - CDF

Miniaturized two-photon microscope capable of deep brain imaging in freely behaving animals

JEONG Seungwon (KOREA, REPUBLIC OF (SOUTH KOREA))

Department of Neuroscience - Johns Hopkins University - Baltimore - USA

KWON Hyungbae (Host supervisor)

One of the ultimate goals in neuroscience is to understand neural correlates of perception, sensation and behaviors. For the past several decades, a number of studies have successfully imaged neuronal activities in behaving animals and further showed the behavioral causality of specific neural circuits by using various optogenetic techniques. More recently, additional significant efforts have made in order to minimize the size of optical system, such that real-time imaging can be done even in freely moving animals. However, high-resolution imaging of deep brain structure in behaving animals still remains challenging. This limitation has hampered our understanding of neural mechanisms in subcortical areas at the resolution of individual cells or synapses. Here I propose to develop a new design of miniaturized microscope by implementing my expertise with optical coherence detection into two-photon (2P) microscopy. This system will allow us to image deep brain areas with synapse resolution in freely behaving animals. Furthermore, both aberration correction and holographic excitation will be implemented with wavefront shaping, which will enables simultaneous imaging and holographic optogenetic control of neural circuits. Using this newly developed microscope, I would like to define neural activities in Nucleus Accumbens (NAc) (4 mm deep from the surface) that are associated with goal-directed behaviors. I will further test direct behavioral causality by selectively activating behaviorally-relevant neuronal populations. In summary, the proposed study will provide new optical approaches that will uncover various neural mechanisms underlying animal’s behaviors or cognition.

2020 -
Grant Awardees - Program Grants

Biological protein springs as allosteric modulators

ITZHAKI Laura (UK)

Dept. of Pharmacology - University of Cambridge - Cambridge - UK

BAHAR Ivet (USA)

Dept. of Computational & Systems Biology - University of Pittsburgh School of Medicine - Pittsburgh - USA

GORDON Reuven (CANADA)

Dept. of Electrical and Computer Engineering - University of Victoria - Victoria - CANADA

YANG Shang-Hua (CHINA, REPUBLIC OF (TAIWAN))

Dept. of Electrical Engineering - National Tsing Hua University - Hsinchu - CHINA, REPUBLIC OF (TAIWAN)

Over the last decade, humans have made extraordinary advances in our ability to synthetically adapt biology. We are in the midst of developing the tools that can reverse genetic disease by altering DNA, and we are creating proteins that do not exist in nature to perform new functions. Yet our understanding of the basic function of proteins and how this is influenced by design is extremely primitive. Even the basic understanding of binding-based signal transduction in proteins, allostery, is arguably far from complete: we are still a long way from being able to mimic nature’s sophistication in creating functional proteins and engineering allosteric functions into proteins – the difference between a mere description and a true understanding. Our mechanistic understanding of allostery has been hindered by a lack of experimental techniques that can probe single proteins within an ensemble and the gap between experimentally observed and computationally predicted quantities. We will tackle this problem by adopting new single molecule tools, in conjunction with protein design and multiscale theoretical modelling. To understand how protein design impacts allostery, we will use and further develop a combination of theoretical (based on Ising formalism, elastic network models (ENMs), and sequence coevolution analyses) and experimental (nanoplasmonic tweezers, extraordinary acoustic Raman (EAR) spectroscopy, and molecular characterization of folding/binding/function) methods. We choose as model system tandem-repeat proteins because of their simplicity and modularity, structural malleability and adaptability to new functions allosterically driven by alterations in interfacial interactions and assembly state. Using both natural and designed TR proteins (and their mutants), we seek to close the gaps between design, theory/computations and function. The goal is a deeper understanding of the biophysics of allostery that will inform our traverse into synthetic biology while also having a specific impact on TR proteins and their essential roles in cellular pathways. Notably, an important interdisciplinary impact of this work will be to quantify the interaction of electromagnetic waves with proteins in the >10 GHz frequency range, precisely where new 5G cellular phone standards are being developed and proteins are susceptible to disruption due to their elastic resonances.
2020 -
Grant Awardees - Young Investigator Grants

Ménage a trois: balancing predator-prey interactions in a host-microbiome-phageome ecosystem

PERSAT Alexandre (FRANCE)

School of Life Sciences - EPFL - Lausanne - SWITZERLAND

NADELL Carey (USA)

Dept. of Biological Sciences - Dartmouth College - Hanover - USA

The intestinal microbiome is a species-rich, spatially heterogeneous ecosystem and core determinant of overall host health. An explosion of metagenomic studies interrogating the functions of microbiome composition in health and disease has revolutionized our view of intestinal microbial communities, but many important gaps remain in our understanding of these ecosystems. Chief among these are the combined contributions of viruses - particularly bacteriophages - to microbiome homeostasis, and of the spatial and temporal structure of the microbiome. Spatially structured communities, or biofilms, are the norm rather than the exception among microbes in the wild, including the intestinal tract, qualitatively altering their ecological and evolutionary dynamics across species but also with their host or predators. Here, we propose to fill these gaps by performing a mechanistic characterization of the physical and ecological forces driving host-microbiome-phageome ecosystem stability and dynamics. To achieve this, we will use an interdisciplinary approach combining tools and concepts form ecology, physics and engineering. First, we will develop a novel experimental framework built around the miniGut, a tube-shaped organoid that recapitulates critical biological and physical features of the intestine, including mucus secretion. We will use miniGuts to identify and quantify the critical factors governing the steady states and stability of a model microbiome, including the presence of a lysogenic phage engineered to allow us to track bacteria-phage-intestinal spatial dynamics in live samples at single-cell resolution. Underlying all aims will be the development of a dynamical systems perspective on the two- and three-way interactions where we will record ecosystem equilibrium points and trajectories in phase diagrams. Finally, using this knowledge, we will engineer lambda phage to manipulate ecosystem steady-states within miniGuts. To do so, we will transmit new functions to host microbial species via lysogeny, for example altering the bacterium’s ability to adhere to mucus, to tolerate antibiotics, and to either cooperate or antagonize other members of the model microbiome. Altogether, our interdisciplinary study will set the stage for mechanistic explorations of the role of phage and microbiome spatial structure in host physiology.
2020 -
Long-Term Fellowships - LTF

From social networks to neural networks: imaging social memory in the bat hippocampus

FORLI Angelo (ITALY)

Department of Bioengineering and the Helen Wills Neuroscience Institute - UC Berkeley - Berkeley - USA

YARTSEV Michael (Host supervisor)
From invertebrates to mammals, social behavior plays a fundamental role in the survival of species throughout the animal kingdom. In order to take advantage of past interactions with conspecifics, the brain has to encode, consolidate and recall social memories. Recent findings suggest that the hippocampal region CA2 is essential for social memory, but the nature and the stability of information stored in this circuit remains enigmatic. I will utilize the Egyptian fruit bat, a highly social mammal which develops long-term social networks within the colony, to ask how the long-term and dynamic representation of social information is encoded in CA2. I will adopt advanced behavioral measurements combined with machine learning methods to monitor and characterize social interactions and their associated vocalizations within a natural colony of bats over long periods. To investigate the existence and properties of social coding in CA2, I will take advantage of chronic wireless calcium-imaging in freely behaving and flying bats during behaviorally relevant social interactions as well as during sleep. By combining an ethological approach with cutting edge technologies for detailed measurements of long-term behavioral and neural dynamics, I will aim to uncover fundamental properties of social cognition in the mammalian brain.
2020 -
Long-Term Fellowships - LTF

Recording and programming human retina cell fates

LIN Hsiu-Chuan (CHINA, REPUBLIC OF (TAIWAN))

Human Retina and Organoid Development Group - Institute of Molecular and Clinical Ophthalmology Basel - Basel - SWITZERLAND

CAMP Gray (Host supervisor)
It is a longstanding goal to decipher cell fate decisions during human development. Stem cell-based culture systems, combined with single-cell sequencing and CRISPR-Cas technologies, offer exciting possibilities to track human cell identities at unprecedented resolution and to engineer specific cell types with high precision. In this proposal, I will develop novel methods to record cell histories, trace lineages, and program human cell fates, with a focus on the human retina. In the first aim, I will develop a fate recording system in induced pluripotent stem cells (iPSCs) that unites evolvable barcodes with molecular memory recorders (Cas1/2) that capture expressed RNA into DNA. This will be used to simultaneously record real transcriptome and lineage histories along the path of cell fate acquisition. In the second aim, I will adopt the CRISPR-Cas12a(Cpf1) system that enables multiplexed gene activation to engineer cell fates based on predictions learned from single-cell transcriptome dissection of organ development. I will focus my project on human retina development where we have a well-characterized three-dimensional organoid culture system, and extensive data analyzing cell fates that emerge in these organoids. This focus will provide insights into the molecular mechanisms controlling human retinogenesis, and at the same time identify methods to engineer specific retinal cell types for therapeutic screening. The strategies and technologies developed in this project are applicable beyond the retina and will contribute to our understanding of general cell fate decisions in humans and guide cell type engineering with clinical potential.
2020 -
Long-Term Fellowships - LTF

Force generation and sensation in rapid plant movement

SLEBODA David (USA)

Department of Physiology - McGill University - Montreal - CANADA

SHARIF NAEINI Reza (Host supervisor)
Touch the sensitive plant Mimosa pudica and it rapidly changes shape, folding its leaves to deter herbivory and dislodge pests. This and other feats of rapid plant motion have fascinated scientists for centuries, but the physiological mechanisms underlying them remain poorly understood. I propose a collaborative, interdisciplinary project to elucidate two key aspects of rapid plant motion: sensation of mechanical stimuli and rapid generation of force. I hypothesize that knowledge of the sensory and motor strategies of motile animals can inform our approach to the study of rapid plant motion, and outline a novel experimental approach that draws tools and theory from the fields of biomechanics, neurophysiology, and materials science to explore rapid motion in Mimosa pudica, a model system for the study of rapid plant movement. I have identified an ideal host laboratory in which to carry out this work situated at a nexus of expertise in mechanotransduction, plant physiology, and mechanical modeling. To this environment I will bring expertise in skeletal muscle physiology and the biomechanics of force production. The proposed work forges a connection between seemingly disparate areas of physiological research, will provide unique training that increases my technical and theoretical breadth, and has great potential to elucidate basic principles underlying sensory and motor strategies in biological systems.
2020 -
Cross Disciplinary Fellowships - CDF

Investigating mechanotransduction at a single molecule level

KASHCHUK Anatolii (UKRAINE)

Department of Physics and Astronomy - University of Florence - Florence - ITALY

CAPITANIO Marco (Host supervisor)

Cells respond to physical force-induced signals by converting the mechanical stimulus into a biochemical response. This process, termed mechanotransduction, is an integral part of cellular physiology and has a profound impact on many biological processes including cell development and differentiation. The project goal is to provide a better understanding of the molecular mechanisms of the initiating 'mechanosensing' and its connection to variations in gene expression by studying the dynamic features of this mechanism at a single molecule level. Force transmission is a highly dynamic process and its investigation requires single molecule techniques with high temporal resolution. Therefore, the immediate aim will be to take advantage of and improve a unique ultra-fast optical trap, recently developed by the supervisor's group at the University of Florence that will allow the investigation of protein-protein interactions in vitro. In particular, the researcher will study the interactions between actin and putative mechanosensitive proteins, under various conditions of mechanical load. In a parallel research line, the researcher will develop an experimental setup and a methodology to apply mechanical stimuli on living cells and monitor the changes in gene expression profiles, with sensitivity down to the single molecule. The aim will be to correlate external mechanical stimuli on specific membrane receptors to intracellular signaling pathways and gene expression profiles, thus creating a powerful tool to enhance our current understanding of the molecular mechanisms of mechanotransduction in vivo.