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2022 -
Cross Disciplinary Fellowships - CDF

Quantum microscopy of neuron electric signals.


- École Normale Supérieure Paris-Saclay (ENS Cachan) - Gif-sur-Yvette - FRANCE

TREUSSART Francois (Host supervisor)
MOTHET Jean-Pierre (Host supervisor)
Electrophysiology is the gold standard to study neuron function at sub-µs resolution, but it lacks spatial resolution and is invasive. Various microscopies have been introduced to overcome these limitations and image a number of neuron signals simultaneously at high spatio-temporal resolutions. Voltage-sensitive dyes are one such technology but despite increasing temporal performance, it still lags behind electrophysiology techniques. Hence a sensor of neuronal electrical activity that would combine the high spatial resolution of optical microscopy and the fast time response of electrophysiology is still missing. Recently, quantum properties of atomic size systems have been harnessed in this field such as the Nitrogen-Vacancy (NV) defect in diamond. The NV has rapidly become a table-top equipment used to probe magnetic properties of novel materials at the nanoscale. Its translation to neuron sensing has been demonstrated [Barry2016], but limited to a giant axon with low spatial resolution. To improve such sensor performance I recently proposed a unique theoretical approach in which I harness NV ability to sense an electric field like in electrophysiology in diamond nano-pillars [Hanlon2020]. I now seek to implement neuron NV-electrometry in a laboratory possessing both NV physics and neuro-biology expertise. LuMIn lab at ENS Paris-Saclay will provide such cross-disciplinary expertise. I will conduct my work under the supervision of Prof. Treussart, with key inputs from Prof. Roch (NV magnetometry expert) and Dr Mothet, neurophysiologist. This expertise would allow me to design the NV neuro sensing experiment and test its efficacy against other sensing mechanisms.
2022 -
Grant Awardees - Program Grants

The evolution of sperm cell shape and motion


Physical Ecology lab., College of Science, School of Life Sciences - Lincoln Institute for Advanced Studies - Lincoln - UK

SNOOK Rhonda (USA)

Dept. of Zoology - Stockholm University - Stockholm - SWEDEN


Dept. of Mathematics - Tulane University - New Orleans - USA

Across the tree of life, sperm show an unrivalled diversity of shapes and sizes greater than any other cell type. The reasons for such diversity remain elusive. Most work has focussed on simple sperm shape found in externally fertilizing invertebrates and internally fertilizing vertebrates, yet most diversity is found in internally fertilizing invertebrates, especially insects. Therefore to truly understand how and why different sperm shapes have evolved, we need to shift away from these historically studied animals and focus on the evolution of insect sperm. In this project we will test how sperm shape and size variation has evolved and more specifically, how it allows sperm to perform their ultimate function – fertilisation. To do so, we will unite researchers from three differing disciplines: biophysics, evolutionary ecology, and mathematics. A biophysics approach will allow us to test how the sperm swim, and determine how the reproductive fluid and reproductive tracts they move in shape these movements. An evolutionary ecology focus will allow us to test how both large- and small-scale evolutionary variation in sperm shape is linked to coevolution with the fertilization environment of the female. The fundamental integration of mathematics across and within our projects will provide synthesis of empirical work and generate new predictions of how the combination of sperm shape and motion, reproductive tract structure, and competition between multiple sperm affect reproductive performance. Only by combining these three disciplines can we truly understand this sperm diversity for the first time. Novel experimental devices, microscale measurements of fluid properties, genetic studies and computational modelling will allow us to chart the evolution of sperm shape, understand how sperm form and female reproductive tracts evolved together, and to link all of these to predict and understand how sperm performance is determined.
2022 -
Grant Awardees - Young Investigator Grants

Biofilm heterogeneity as an evolutionary mechanism for resilience to complex environments


Physics - University of Cambridge - Cambridge - UK


Dept. of Microbiology and Immunology and School of Biomedical Egineering - University of British Columbia - Vancouver - CANADA


Civil, Architectural, and Environmental Engineering - University of Miami - Coral Gables - USA

Biofilms are structured communities of bacteria that grow at interfaces and have a remarkable ability to adapt and thrive in a tremendous diversity of hostile environments, including antibiotic-impregnated prosthetic implants. As such, biofilms are the most pervasive life-form on Earth. Our understanding of how biofilms achieve and have evolved this amazing resilience is woefully incomplete, as evidenced by our inability to disrupt detrimental biofilm formation. We hypothesize that phenotypic plasticity and biofilm morphology are coupled and have coevolved to promote optimal adaptation and survival in fluctuating hostile environments. We formulate this hypothesis based on 1) the correlation between biofilm morphology and phenotypic spatial organization 2) the widespread phenotypic heterogeneity among bacterial species, and 3) the multiple mechanisms through which functional and phenotypic diversity may confer advantages to biofilms. While isolated parts of this problem have been investigated, the intrinsic coupling between the mechanics, microbiology and evolution across multiple scales has not yet been explored. Our overall goal is to understand the feedback between cell-to-cell phenotypic heterogeneity, local physico-chemical conditions, and macroscale biofilm morphology, and to elucidate its evolutionary path and role on the amazing resilience of biofilms. Our research plan consists of three aims. First, we will learn the microscopic rules that govern the interplay between mechanical forces and gene expression. Second, we will determine whether and how phenotypic plasticity and associated biofilm morphology in the wildtype confers a fitness advantage to the biofilms. Third and last, we will elucidate how phenotypic heterogeneity could have spontaneously evolved. Our approach consists of a synergistic combination of a bottom-up multiscale modeling framework to map the mechanisms that control the feedback and co-evolution between phenotypic heterogeneity and biofilm morphology, in-vitro microfluidics and top-agar setups to inform and validate the computational models, directed evolution experiments, and in-vivo characterization of gut microbial biofilms to corroborate and revise our in silico understanding of biofilm behavior. The completion of this work will enable an integrated model of the role of heterogeneity in establishing biofilm resilience.
2022 -
Cross Disciplinary Fellowships - CDF

Development of wireless focused ultrasound system for sono-optogenetics in freely behaving animals


- The University of Texas at Austin - Austin - United States

WANG Huiliang (Host supervisor)
Optogenetic techniques have been applied to modulate genetically-targeted neurons and find their wide applications in neuroscience research field to understand the link between brain function and behavior. However, traditional optogenetic methods use optical fibers for light delivery, which could cause brain damages due to the invasive fiber implantation surgery. Recently, my host supervisor Dr. Huiliang Wang has co-developed a technology called Sono-opotogenetics that uses mechanoluminescent nanoparticles to convert focused ultrasound (FUS) to light for optogenetic stimulation. This technology does not require invasive surgery hence it is minimally-invasive to the animals. However, the FUS system used in this work requires head-fixation of the mice. Therefore, it could not be used for neuroscience studies in freely-behaving mice. Through the Human Frontier Science Program, I am aiming to develop a wireless, wearable ultrasound transducers for sono-optogenetic neuromodulation in freely-behaving mice. I will plan to fabricate flexible ultrasound transducers utilizing my micro-fabrication skills. I have gained over my PhD study in Korea and integrate with a wireless communication system. The proposed wearable focused ultrasound system together with sono-optogenetics technology, is expected to allow us to perform non-invasive sono-optogenetic stimulation in freely moving animals. For example, it could be a powerful genetically-targeted neuromodulation tools in cognitive or memory behavioral studies with freely moving animal in complex-structured mazes.
2022 -
Grant Awardees - Program Grants

The social origins of rhythm

KING Stephanie (UK)

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

MADSEN Peter Teglberg (DENMARK)

Dept. Of Biology, Section for Zoophysiology - Aarhus University - Aarhus - DENMARK

COOK Peter (USA)

Psychology - New College of Florida - Sarasota - USA


Department Human Neurosciences - Sapienza University of Rome - Rome - ITALY

The enjoyment of music is ubiquitous across human societies and cultures. Among the (bio)cognitive underpinnings to process and enjoy music, rhythm plays a key role. In humans, musical beat processing intimately links perception and action when we entrain rhythmic movements to musical beats. In social settings, this leads to rhythmic actions within groups of people, such as dancing or marching in unison, but what selective pressures led to rhythmic behaviour to begin with, and why did the social use of rhythm evolve? The search for the origins of social rhythm is complicated because unlike other biological traits, rhythmic processing does not fossilize and humans only constitute one datapoint to build testable hypotheses on rhythm evolution. However, rhythmic processing is not unique to humans, with examples found across the animal kingdom. In this project, we will integrate approaches from field biology, comparative neuroscience, artificial intelligence, and speech sciences to test competing hypotheses on the evolutionary roots of rhythmic abilities. We will study a wide range of marine mammal species, known for their vocal flexibility but subject to differing social pressures, as a test-bench for evolutionary hypotheses on the origins of social rhythm in our own species.
2022 -
Grant Awardees - Young Investigator Grants

The atmosphere: a living breathing ecosystem?


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


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


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


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

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 -
Cross Disciplinary Fellowships - CDF

An Extreme Approach to Biomineralization: Biomineral Selection by Extremophiles

KNOLL Pamela (USA)

- University of Edinburgh - Edinburgh - United Kingdom

COCKELL Charles (Host supervisor)
CARTWRIGHT Julyan (Host supervisor)
In biomineralization, organisms actively build structures (e.g., bones) or initiate a reaction from the secretion of precipitation-inducing chemicals (e.g., stromatolites). Even within extreme temperature and pH environments, bacteria-induced mineral precipitation uses enzyme-mediated reactions and/or controls the surrounding metal redox state to create dense mats of mineral filaments. While inorganic reactions are capable of mimicking these morphologies, such as laboratory grown chemical gardens, biominerals are often composed of mineral phases that are seldom selected in inorganic precipitation. Complicating the understanding of mineral selection in extremophiles versus similar inorganic counterparts is the large variation between their environmental conditions during precipitation. Using temperature/pressure vessels, I will investigate biominerals formed by thermoacidophiles and thermoalkaliphiles and compare their crystal products to those of chemical gardens formed under the same conditions. The goal is to understand the distinction between precipitation in living versus nonliving systems including the modification of crystal structure and habit within the silica-rich environments where both structures are found as well as the effect of metabolic processes on existing inorganic and biomineral structures. Tackling knowledge gaps in extremophiles will provide insights into the mechanisms for biomineralization and survival of these organisms in mineral-rich environments (at toxic levels for most organisms). This work can also pave the way to understanding how life could withstand the harsh conditions of early Earth and current conditions on other planetary bodies.
2022 -
Grant Awardees - Program Grants

Multi-omic reconstruction of flow across the distributed metabolism of early-branching Dracula ants


Department of Biology - University of Fribourg - Fribourg - SWITZERLAND

FISHER Brian Lee (USA)

Entomology - California Academy of Sciences - San Francisco - USA


Amsterdam Institute of Molecular and Life Science (AIMMS) - VU University Amsterdam - Amsterdam - NETHERLANDS

Many successes in life are based on collaboration – this extends to the molecular level, where life is fueled by the chemical processes collectively called metabolism. Microorganisms exchange nutrients through cross-feeding, and multicellular organisms are made up of tissues with different metabolic roles and needs. Social insects, where the notion of self is distributed over multiple individuals, take this collaboration still further: Many ant colonies engage in social exchanges of experimentally accessible fluids that contain both exogenously sourced and endogenously produced materials. Larvae of many social insects have been purported to be a ‘digestive caste.’ They are fed exogenously sourced food by adults and return a nutritious fluid whose metabolic functions remain unestablished. The mode of transmission from larvae to adults varies across ant species: In some, larvae voluntarily secrete fluids, while in early-branching ‘Dracula’ ants, adults non-destructively drink larval hemolymph. Such socially exchanged fluids can be analysed to monitor the fluxes of distributed metabolism, making ant colonies apt model systems to study the molecular mechanisms of inter-system communication and division of metabolic labor. We address three key questions (i) what is being exchanged? (ii) what are the functional implications of these exchanges? and (iii) how did these modes of exchange evolve? We combine behavior observations with detailed molecular analyses of four species representing different social feeding modes and evolutionary lineages. We perform proteomics and metabolomics on each colony-tissue and exchanged fluid. Based on genomes and gene expression, we reconstruct metabolic networks for advanced multi-omic data integration to identify active pathways. Novel community-scale metabolic modeling will be used to probe colony-level functionality of social exchange. Critical pathways will be validated with fluorescent metabolite probes in an automated colony- and transmission-tracking system and by genetic or feeding perturbations. This project offers new ways to view social behavior, evolutionary biology, metabolism and the physics of collective behavior. Ultimately, this work will innovate by elucidating the functional role of distributed metabolism, probing its evolution, and providing new tools to study community-level metabolic interactions.
2022 -
Grant Awardees - Young Investigator Grants

How fishes use historical hydrodynamic motion cues in search and navigation tasks


Department of Zoology - University of Cambridge - Cambridge - UK


Dept. of Sustainable and Environmental Engineering - Westlake University - Hangzhou - CHINA, PEOPLE'S REPUBLIC OF



Just as boats leave a wake as they travel over the surface of the water, underwater animals also leave a trail of water disturbance as they move through their environment. These trails, termed ‘hydrodynamic motion cues’, hold information about the size of the animal that was travelling through that location in the past, what type of animal it was, and how that animal was moving. In effect, these hydrodynamic motion cues represent a ‘liquid fingerprint’, holding information about the animal itself and and how it was travelling through that location in the past. Many species of fishes are able to detect the hydrodynamic pressure of these liquid fingerprint, however, we know little about how the hydrodynamic information detected by animals is used in their behavioural decision-making. In this project, we will test whether fishes that sense the hydrodynamic cues generated from the past movements of other animals use this information in different behavioural tasks. For example, some prey fishes may use these cues to find other group members, while other predatory species may use these cues to track their prey. Using a combination of behavioural experiments, modern sensing technology, and machine learning techniques, this project aims to understand how hydrodynamic motion cues are used by fishes in search and navigation tasks. This work will not only allow us to understand some of the extraordinary sensory and behavioral adaptations that animals have evolved in underwater environments, but will also be informative for engineering applications, including the design of autonomous sensing vehicles.
2022 -
Cross Disciplinary Fellowships - CDF

Understanding and controlling the sub-motors of bacterial rotary nanomachines.


- University of Oxford - Oxford - United Kingdom

BERRY Richard (Host supervisor)
The bacterial flagellar motor (BFM) consists of hundreds of proteins that assemble into a transmembrane rotary nanomachine. It propels the flagella that drive bacterial swimming. New structural studies suggest that the motor is itself powered by smaller rotary motors. The latter, called stator complexes, are now thought to be autonomous rotary machines, powered by transmembrane ion flux, that drive the rest of the BFM. They share the structural motif of a pentamer surrounding a dimer (5:2), but it is not yet known whether these complexes really are rotary machines, and if so how rotation drives their functions. Here, we will deliver the stators into Droplets on Hydrogel Bilayers, which will allow single-molecule fluorescence imaging and membrane energization. Coupled to FRET and precise sodiometry based on organic sensors, this will allow us to determine the relation between the ion flux, the conformation and the rotation of the units. Finally, we will decipher their interaction with the whole BFM by fast measurements of their discrete dynamics: attaching gold nanorods to the BFM and following rotation in vivo by polarization microscopy, with angular resolution of a few degrees at sub-microsecond timescales. This project will be the first to characterize the molecular mechanisms behind the activation and the dynamics of the sub-motors of the BFM, using advanced techniques from bilayer biochemistry and single-molecule fluorescence, and will bring a new understanding of large rotary machines. It will also open avenues for synthetic biology, making important steps towards the synthesis of artificial cells endowed with the ability to self-propel.
2022 -
Grant Awardees - Program Grants

Unravelling the code of mitochondrial-nuclear communication


Department of Molecular Medicine - University of Pavia - Pavia - ITALY


Interdisciplinary Nanoscience Center (iNANO) - Aarhus University - Aarhus - DENMARK


NeuroGenomics & Translational Bioinformatics Laboratory - McLean Hospital/ Harvard Medical School - Belmont - USA

The energetic status of mitochondria often defines the outcomes of complex cellular responses. However, the modalities through which mitochondria-derived signals (retrograde signalling) are perceived by the nucleus and translated into specific transcriptional responses are poorly understood. A major roadblock in studying the crosstalk between these two organelles is our inability to isolate the messages they exchange from the background signalling events constantly taking place within the cell. We propose to overcome this issue with a bottom-up approach in which we will attempt to develop a synthetic, matrix-sustained two-organelle unit and use it as a platform to address a number of questions fundamental to mitochondrial and nuclear biology. By incorporating biosensors for small compounds that participate in mitochondria-nucleus crosstalk both, in the matrix and organelles, we will be able to identify the signalling molecules employed by these organelles under specific conditions (from nutrient availability to mitochondrial DNA damage). Similarly, by employing next generation single nucleus RNA sequencing we plan to identify the specific transcriptional signatures triggered by distinct mitochondrial changes in nuclei of the same background. We designed a collaborative research plan that builds across all three fields of expertise and combines cutting-edge techniques with conceptual perspectives. Städler, a materials chemistry expert, will develop the inter-organelle communication matrixes (IOCMs) and optimize the encapsulation of mitochondria and nuclei. Lefkimmiatis, a cell physiologist, will develop the biosensors, validate their functional incorporation in the support matrix and organelles, and will perform the imaging experiments for the identification of organelle-derived signals. Finally, Daskalakis, an expert in transcriptomics, will employ single nucleus RNA sequencing and bioinformatic analysis for recognizing the transcriptional signatures coupled to specific mitochondrial conditions. By working together, we will paint a comprehensive picture of how mitochondria and nuclei communicate as well as provide the scientific community with a platform that offers a controlled environment optimal for investigating complex communication pathways in the absence of background “signalling noise”.
2022 -
Grant Awardees - Young Investigator Grants

Crossing the barrier: horizontal gene transfer in synergistic protocells


Department of Chemistry - University of Guelph - Guelph - CANADA


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


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 -
Cross Disciplinary Fellowships - CDF

Tumour homing immune cells for cavitation therapy

SMITH Cameron (UK)

- California Institute of Technology - Pasadena - United States

SHAPIRO Mikhail (Host supervisor)
One of the great difficulties in the treatment of cancer is the inaccessibility of the tumour core. Due to poor vascularity, hypoxia, and high interstitial pressure, many conventional cancer therapeutics are unable to treat this significant portion of the target tumour, leading to less successful therapies. In this project we will address these limitations by utilising recent developments in synthetic biology and ultrasound. Our approach will take advantage of the Shapiro laboratory’s work on genetically encoded air-filled proteins called gas vesicles (GVs), which we will express in engineered tumour-infiltrating macrophages and T-cells in response to tumour-specific biomarkers such as VEGF, Her2, or claudin-6. The resulting GVs will act as seeds for highly selective and localised therapy when combined with focused ultrasound. We hypothesise that high energy inertial cavitation – the formation and violent collapse of bubbles – will be seeded by GVs to damage surrounding tumour cells. This would both allow for selective killing of tumour cells as well as the potential release of antigens which would make the tumour more susceptible to attack by the immune system, while additionally having the potential to allow the immune system to recognise and attack metastases. Successful completion of this project will produce a new class of local and targeted anti-tumour therapy and create a scientific and technological foundation for future developments and therapies utilising the combination of engineered cells and ultrasound.
2022 -
Grant Awardees - Program Grants

Regulation of neuronal physiology by the electromechanical effects of the action potential


biology and biological engineering - california institute of technology - Pasadena - USA


SciLifeLab - Karolinska Institute - Stockholm - SWEDEN

ROYLE Stephen (UK)

Centre for Mechanochemical Cell Biology - Warwick Medical School - Coventry - UK

Cell signaling has traditionally been thought to exclusively depend on biochemical processes, but in recent years we have begun to appreciate how physical forces can control cell-cell communication. Mechanical forces generated by cells regulate many physiological processes, including selection of optimal antibodies by lymphocytes, sorting of chromosomes and organelles within the cell, and blood clotting in response to turbulence. Among all cells, neurons and muscle cells have special features because they have excitable membranes capable of generating large voltage fluctuations (~100 mV) known as action potentials. Over the past decades, researchers have accumulated evidence that action potentials generate membrane movements up to 100 angstroms. However, it remains unknown what are the biological consequences of this neuronal electromechanical force. The central hypothesis of this proposal is that the membrane motions associated with action potentials generate mechanical forces that regulate the intercellular communication between neurons and intracellular signaling events within individual neurons. To investigate how the mechanical force of action potentials regulates intercellular communication we will focus on the activation of the mechanoreceptor Notch, a key molecule involved in cell-cell interactions. To explore the effects of the neuronal electromechanical forces on intracellular signalling, we will focus on the regulation of membrane trafficking processes, including endocytosis and sorting of intracellular vesicles. To investigate these issues we have assembled a team with expertise on different aspects of cellular signalling including membrane biophysics, single-particle imaging in living cells, and neurophysiology. A central goal of the proposal is to take advantage of new technologies that can be used to investigate the regulation of cell physiology at several scales of biological complexity, spanning individual molecules, living cells, and transgenic animals. We anticipate that this research will provide unanticipated insights about how mechanical forces control intercellular and intracellular signaling events in neurons.
2022 -
Grant Awardees - Young Investigator Grants

How do ecological network dynamics mediate the response of organisms to novel environments?


Department of Life Sciences - Ben Gurion University of the Negev - Beer-Sheva - ISRAEL


Dept. of Physics and Astronomy Galileo Galilei - University of Padua - Padova - ITALY

HALL James (UK)

Department of Evolution, Ecology and Behaviour - Institute of Infection, Veterinary and Ecological Sciences - Liverpool - UK

In a world fraught with human impact, predicting the response of organisms to environmental changes is a fundamental challenge. A dominant approach is to investigate how demographic and genetic factors determine the adaptability of a single taxon. However, organisms do not live in isolation. Hence, community ecologists investigate how the structure of species interaction networks affects community stability. While the interplay between species-level processes and community-level structures governs the response to environmental change, these two approaches have been disconnected. Moreover, how specific kinds of environmental heterogeneity and perturbations modulate this interplay is understudied. We propose to address these gaps by integrating theory and experiments using bacteria as a model organism. Bacteria are a dominant life form, colonizing almost every environment. In addition, genetic change in bacteria is partly driven by horizontal gene transfer (HGT)--a community-level process whose interplay with other interactions (e.g., competition) has not been studied at a community level. We will develop a theoretical framework to explore how species-level factors interact with the environment, affecting competitive ability and emerging community structures. We will use bacteria to experimentally test communities' responses to multiple kinds of environmental change, testing our theory. Our work will establish a framework for a mechanistic understanding of the interplay between species-level processes, community-level structures, and the environment. While targeted at bacteria, insights from this work will have broad implications for other organisms. This work is only achievable through a unique international collaboration that bridges ecology and evolution, microbiology, and statistical physics.
2022 -
Cross Disciplinary Fellowships - CDF

A Multi-Scale All-Optical Platform for the Investigation of Membrane Potential Dynamics


- École Polytechnique Fédérale de Lausanne EPFL - Lausanne - SWITZERLAND

MANLEY Suliana (Host supervisor)
Membrane potential is a ubiquitous cellular feature, underlying important functions including the release of neurotransmitters upon arrival of an action potential, and calcium signaling related to cell proliferation control. Voltage imaging is becoming the standard to investigate membrane potentials, offering significant advantages over electrophysiology: it is less invasive, scalable, and suited to examine intracellular organelles. Although recent imaging implementations capture fast action potentials, they rely on averaging multiple events over a reduced field of view and are limited in temporal resolution. Hence, they can detect the single action potential but miss its propagation dynamics and, significantly, its modulation of synaptic transmission. Furthermore, intracellular propagation of membrane potentials remains unstudied. To overcome these limitations, I propose an all-optical optogenetic approach that leverages “smart” controlling architectures and state-of-the-art detectors to realize a paradigm change: from voltage imaging to on-demand voltage tracking. Upon further developing hardware in the host laboratory, I will investigate the propagation of organellar and plasma membrane potential signals, spontaneous or evoked, in non-excitable cells and neurons. I anticipate that this approach will uncover unprecedented insights into the intra- and inter-cellular signaling mechanisms and their modulation during activity. Indeed, these signatures are hypothesized to be altered by multiple sclerosis and other neurodegenerative diseases, and have so far proved elusive to measure.
2022 -
Grant Awardees - Program Grants

Super-resolution multifunctional scanning ion conductance microscopy: tapping the cell's energy grid


Migration, invasion and metastasis lab - CRUK Beatson Institute - Glasgow - UK


Department of Internal Medicine / Cancer Energy Metabolism Lab. - University of Cincinnati College of Medicine - Cincinnati - USA


Graduate School of Engineering Electronics - Nagoya university - Kanazawa - JAPAN

Cells show a remarkable resiliency when energy-starved, maintaining their ability to migrate to a new energy-rich environment, where they can re-purpose their cytoskeleton to take up nutrients via macropinocytosis. ATP and GTP are the major energy currencies of the cell, driving motor activity, cytoskeletal polymer dynamics and signaling. While the cell generally maintains robust global levels of ATP and GTP in nutrient-starved conditions, it is the local concentrations and ratios of ATP/ADP and GTP/GDP that drive motility and signaling. Multiple parameters control ATP/GTP flux, including: -Diffusion -Biosynthesis vs consumption -Shuttling and compartmentation However, how the cell meets energy demand is largely unclear, because we lack tools to measure multiple parameters simultaneously at sub-cellular resolution over time in live cells. Our multidisciplinary team, with expertise in motility (Machesky), metabolism (Sasaki), and Scanning Ion Conductance Microscopy (SICM) (Takahashi) will address this unmet need. SICM offers advantages of measurements without perturbation, correlation with high-resolution confocal imaging and simultaneous measurement of multiple parameters. Our team will thus engineer the first live single-cell multiscale platform, using cellular feedback to guide sampling and stimuli, providing the means to acquire a holistic view of cellular energy flux. We have two main objectives, each with new technology driven by our biological questions. Objective 1. Develop metabolic and protein mapping SICM to discover how cells use membraneless compartmentation to control metabolite supply and demand at the leading edge. We will establish how diffusion, biosynthesis and consumption generate and maintain intracellular nucleotide gradients using subcellular metabolic sampling SICM. We also probe subcellular localization and organization of metabolic enzymes, using femtoliter scale subcellular protein proximity labelling. Objective 2. Develop cell-to-machine feedback loop controlled SICM to determine how a cell decides to walk or to eat Using cell feedback guided SICM, we discover how mechanosensing via plasma membrane tension, integrins and the cytoskeleton, as well as nutrient sensing, allowing the cell to either locomote or use its cytoskeleton to perform nutrient uptake via macropinocytosis.
2022 -
Grant Awardees - Program Grants

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


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


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

GREEN Anthony P. (UK)

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

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.
2022 -
Cross Disciplinary Fellowships - CDF

Targeted protein degradation and electrophysiology to study the function of the proteasome


- University of Groningen - Groningen - NETHERLANDS

MAGLIA Giovanni (Host supervisor)
TYCH Katarzyna (Host supervisor)
The proteasome, a large protein complex capable of proteolysis, is the primary means by which misfolded or unnecessary proteins are degraded in eukaryotes and archaea. Due to its size and complexity, the mechanisms underlying its function, including the way in which it processes substrates with different primary and secondary structure content, are poorly understood. Accordingly, experimental methods must be used that enable the spatio-temporal measurement of these functions. Biological nanopores are created when a transmembrane protein forms a nanometre-scale hole in a membrane. Building on their effective use in a broad range of applications, planned developments using nanopores include their integration into biosensors for the detection of analytes from blood. Recently, the group of Prof. Maglia developed a proteasome nanopore, paving the way to protein sequencing using nanopores. This significant development also provides an excellent platform for this proposed fundamental study into the function of the proteasome. In this work, PROTACs (proteolysis-targeting chimeras) will be used to target proteins with different primary and secondary structure content for polyubiquitination by the E3 ubiquitin ligase. Electrochemical measurements will be used to observe the impact of physico-chemical properties and structure on unfolding and degradation by the proteasome in real time. PROTACs enable selected proteins to be targeted for degradation from mixtures or biological samples. This project is expected to have a significant impact on our understanding of the function of the proteasome, as well as in the areas of peptide sequencing and biosensors for tailored medicine.
2022 -
Grant Awardees - Program Grants

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


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


Department of Behavioral Physiology & Sociobiology - University of Wuerzburg - Wuerzburg - GERMANY


Department of Biological Sciences - The George Washington University - Washington - USA


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.