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Awardees

2021 -
Long-Term Fellowships - LTF

Dissecting the mechanisms underlying cytoplasmic reorganization and embryo patterning in ascidians

BOLGER-MUNRO Madison (CANADA)

- Institute of Science and Technology Austria - Klosterneuburg - AUSTRIA

HEISENBERG Carl-Philipp (Host supervisor)
The asymmetric distribution of cytoplasmic domains and RNAs is critical for asymmetric cell division and fate determination. Therefore, unraveling the mechanisms that drive the asymmetric distribution of the cytoplasm is essential for understanding animal development. Once fertilized, ascidian eggs undergo a massive cytoplasmic reorganization that precisely localizes maternal determinants to establish the anterior-posterior body axis. Following this reorganization, an invariant cleavage pattern predictably segregates maternal determinants asymmetrically into blastomeres, conferring differential cell fates. Thus, the establishment of polarity in the ascidian egg determines the body plan of the whole animal. Thus, ascidians are a powerful model for studying how cytoplasmic organization and the asymmetric distribution of maternal factors patterns animal development. Despite its vital role in establishing embryonic patterning, remarkably little is known about the mechanisms that orchestrate cytoplasmic reorganization and the distribution of maternal factors. In this project, I will use high-resolution microscopy, force and cell shape manipulations, and proximity biotinylation to address the following fundamental questions: 1) What mechanisms regulate cytoplasmic reorganization and anterior-posterior polarity in the ascidian egg? 2) How is cytoplasmic reorganization translated into the precise positioning of maternal determinants? Significance: This study will shed light on the processes that define the anterior-posterior body axis and pattern of development in ascidians and deepen our understanding of how embryogenesis is conserved and has evolved among chordates.
2021 -
Grant Awardees - Early Career

T cell microvillus as a new signaling organelle

BOTTANELLI Francesca (ITALY)

Institute of Biochemistry - Freie Universität Berlin - Berlin - GERMANY

SU Xiaolei (CHINA, PEOPLE'S REPUBLIC OF)

Department of Cell Biology - Yale School of Medicine - New haven - USA

ZHAO Wenting (HONG KONG, CHINA)

School of Chemical and Biomedical Engineering - Nanyang Technological Unviersity - Singapore - SINGAPORE

The surface of many immune cells is covered with submicron-sized membrane protrusions called microvilli. Microvilli were traditionally considered to be involved in lymphocyte migration and adhesion. Interestingly, recent studies suggest that microvilli enrich the T cell receptor (TCR) in their tips, and those are where T cells form initial contacts with the antigen-presenting cells (APCs). However, beyond those descriptive findings, it remains unknown how the unique architecture of microvilli regulates the nanoscale localization of signaling proteins and lipids, and the associated biochemical reactions that lead to transmembrane signaling and T cell activation. It remains a daunting challenge to tackle these problems because of the nanoscale size and highly dynamic nature of microvilli. To reveal the spatial organization and signaling function of T cell microvilli, we have assembled a team composed of a T cell biologist (SU), a nano-engineering scientist (ZHAO), and a super-resolution microscopy expert (BOTTANELLI). Our central hypothesis is that microvilli spatially segregate and organize proteins and lipids to effectively initiate and transduce TCR signaling. This project will be supported by our complementary technical and biological expertise in T cell signaling and biochemical reconstitution (SU), nanofabrication and membrane biophysics (ZHAO), and live-cell stimulated emission depletion (STED) super-resolution microscopy and membrane trafficking (BOTTANELLI). We aim to establish the microvillus as a new signaling organelle for immune responses. Our contributions are expected to expand the classical 2D textbook models of membrane receptor signaling into a 3D perspective.
2021 -
Cross Disciplinary Fellowships - CDF

Spatiotemporal patterning of polydisperse multispecies microbial communities

BOWAL Kimberly (CANADA)

John A. Paulson School of Engineering and Applied Sciences - Harvard University - Cambridge - USA

MAHADEVAN Lakshminarayanan (Host supervisor)

Bacteria play a significant role in human health, the environment and industrial applications. In these environments bacteria are most often found in multispecies communities in which colonies containing different cell shapes interact closely. Recently, time-lapse microscopy has shown that these multispecies interactions can be cooperative or competitive, presenting dynamic and complex behaviours hypothesised to be a consequence of the shape-dependent physical and chemical interactions. However, the role of shape polydispersity in individual and collective dynamics is poorly understood, prompting questions such as: How do different bacterial shapes influence interspecies interactions? How do polydisperse communities engage in competitive or cooperative actions that direct spatiotemporal patterning? I will address these questions using agent-based modelling grounded in experimental data to provide a predictive understanding of multispecies interactions in space and time. This biophysical model will describe physical and chemical interactions between sphere- and rod-shaped individuals and be used to probe the principles governing multispecies bacterial communities considering a variety of factors. This will allow me to map out spatiotemporal patterns related to cooperative and competitive behaviours, highlighting the role of shape polydispersity in partitioning or mixing of dynamic multispecies communities. The theoretical framework generated and interaction principles elucidated will shed light on complex multispecies bacterial systems of great importance and will also have the potential to address other active collectives that feature polydisperse interacting communities.

2021 -
Grant Awardees - Program

How a single cell shapes a shoot

BRADY Siobhan (CANADA)

Department of Plant Biology and Genome Center - University of California, Davis - Davis - USA

SMITH Richard S. (UK)

Dept. of Computational and Systems Biology - John Innes Centre - Norwich - UK

VERNOUX Teva (FRANCE)

Laboratoire Reproduction et Developpement des Plantes - Ecole Normale Supérieure de Lyon - Lyon - FRANCE

ZURBRIGGEN Matias (GERMANY)

Institute of Synthetic Biology - CEPLAS - University of Duesseldorf - Duesseldorf - GERMANY

Phyllotaxis, the regular arrangement of leaves around stems, is one of the most striking natural patterns; it has puzzled biologists, physicists and mathematicians for centuries. Phyllotaxis first evolved in simple plants, like the moss Physcomitrium Patens, but has mostly been studied in plants of recent evolutionary origin, like Arabidopsis. In contrast with the multicellular Arabidopsis shoot apex, successive rotating division planes of a single apical cell directly determine moss phyllotaxis, with each apical cell derivative generating directly a leaf. This provides a system to understand how the geometry of a single apical cell and its daughter cells, their resultant physical forces and biochemical cues self-organize 4D patterns of division orientation and ultimately shape a shoot. To explore the fundamental question of how phyllotaxis emerged, at single cell-resolution, we will use our unique inter-disciplinary expertise to combine developmental genetics, optical and physical imaging, single cell genomics, optogenetics and computational modeling in moss. This will generate key insights into the contribution of cell division orientation to the evolution of phyllotaxis.
2021 -
Long-Term Fellowships - LTF

Identifying metabolic drivers of anti-tumor immunity

BRUNNER Julia Stefanie (AUSTRIA)

Cell Biology Program - Memorial Sloan Kettering Cancer Center - New York - USA

FINLEY Lydia (Host supervisor)
Cytotoxic T lymphocytes (CTLs) are major effectors of the adaptive immune defense against cancer. Local microenvironmental cues induce CTLs to undergo specialization into effector, memory or exhausted programs. CTL fate decisions have dramatic effects on successful cancer clearance, but how these programs are controlled remains ill-defined. Recently, metabolites have emerged as potential regulators of gene expression programs, raising the possibility that local metabolite levels may control cell fate programs. In particular, the universal methyl donor, S-adenosylmethionine (SAM), has been suggested to control chromatin methylation and cell fate decisions, but the degree to which SAM levels fluctuate in physiological contexts and the pathways that respond to changes in SAM levels remain unknown. To date, the lack of tools to probe metabolite levels in defined cell populations has hampered the study of the role of metabolites in cell fate decisions in vivo. Here, using cutting-edge, RNA based SAM biosensors, I will overcome current technical limitations by imaging SAM abundance in real-time on a single cell level. These novel tools will allow me to determine how physiological fluctuations in SAM influence CTL asymmetric divisions, effector functions and tumor cell killing. Leveraging SAM biosensors in the context of tumor cell models will show the impact of metabolite availability on CTLs in the tumor niche. These studies will reveal fundamental principles of immune cell fate commitment and provide a paradigm-shifting approach to study the contribution of intracellular metabolic fluxes to the regulation of cell fate decisions in physiologically relevant microenvironments.
2021 -
Long-Term Fellowships - LTF

Visualizing the cohesin-RNA Polymerase II interaction at nanometer resolution

CACCIANINI Laura (ITALY)

Department of Biology - Massachusetts Institute of Technology - Boston - USA

VOS Seychelle (Host supervisor)
Throughout a cell’s life, DNA must be accessed to express genes, copied and equally partitioned when the cell divides, and simultaneously this 2 meter long fiber is compacted in a micron-scale space. Chromatin architecture is highly regulated and is linked to gene expression. DNA looping is a preferential mechanism of DNA-related compaction in mammals. These loops are generated by cohesin, a complex known to keep sister chromatids together and that extrudes DNA loops in a ATP-dependent manner. Disruption of loop-based structures or perturbations of cohesin pathway can have dramatic effects on transcription. Despite the growing evidence of a cohesin-RNA Polymerase (Pol) II interaction, little is known about its structural details. My goal is to establish how these two complexes contact each other by means of correlative light electron microscopy (CLEM). Recent evidence indicates that cohesin is necessary to retain Pol II at centromeres and to ensure proper silencing of chromosome arms. Mitotic transcription offers the advantage of being localized in space and time. To understand how cohesin can maintain Pol II at centromeres in mitosis I will perform: (i) two-color STORM to assess cohesin-Pol II spatial distribution; (ii) in-situ cryo electron tomography (cryo-ET) on Xenopus laevis egg extracts; (iii) in-situ cryo-ET in FIB-milled mitotic cells, exploiting the physical alignment of metaphase plate and fluorescently labelled centromeres to identify the plane of interest. The latter two steps are related but independent. This study will provide the structural information needed to understand the interplay between genome folding and transcription.
2021 -
Grant Awardees - Program

The role of bone cellular and sub-cellular porosity network connectomics on calcium homeostasis

CARRIERO Alessandra (ITALY)

Dept. of Biomedical Engineering - The City College of New York - New York - USA

GOURRIER Aurélien (FRANCE)

Lab. for Interdisciplinary Physics - LIPHY - CNRS - St Martin d'Heres - FRANCE

GRANDFIELD Kathryn (CANADA)

Dept. of Materials Science and Engineering - McMaster University - Hamilton - CANADA

Bones serve as a mineral reservoir in vertebrates to achieve calcium and phosphate homeostasis. However, the precise cellular regulation of this process is not fully understood. Osteocytes (Oy), the most abundant bone cells, form an interconnected dendritic network embedded in the bone tissue through a pore system called the lacuna-canalicular network (LCN). Oy are believed to orchestrate mineral release and uptake either indirectly, by triggering remodeling via bone resorbing/forming cells, or directly, through a localized process, known as osteocytic osteolysis (OO). Although postulated in the 1960-70s, the relative importance of OO for mineral homeostasis is unclear and its mechanisms still poorly described. Most studies on calcium transport focus on the LCN, although there is growing evidence that a complex sub-cellular mineralization pathway exists. In this proposal, we challenge the classical view that the LCN alone determines calcium transport and hypothesize the existence of an intermediate level of mesoscale porosity that plays a central role in calcium exchange. Our scientific approach uses interdisciplinary expertise in materials science, physics and biomedical engineering, and integrates a series of multiscale and multimodal imaging platforms connected through deep-learning and the application of connectomics. Here, we will: i) decipher the mesoscale porosity and mineral heterogeneity at the LCN, ii) determine the spatial distribution of OO, and iii) produce a connectomics analysis of fluid transport and calcium exchange in bone. We will use lactating and weaning C57BL6 mice that exhibit large reversible mineral depletion/remineralization. We will acquire bone ultrastructure visualization in 3D using an emerging plasma focused ion beam scanning electron microscope. This will be combined with confocal and two-photon excitation fluorescence microscopy using an original deep-learning super-resolution correlative imaging approach. Finally, multiscale network connectivity will be analyzed using connectomic approaches based on graph theory and experimental data will be used to perform numerical simulations of fluid transport. This research will reveal the structural mechanisms and extent of OO demineralization/remineralization at the cellular and sub-cellular scale and identify key parameters affecting fluid transport during OO.
2021 -
Cross Disciplinary Fellowships - CDF

Birth, life and death of marine snow: real-time observations and biophysics of a sinking eco-system

CHAJWA Rahul (INDIA)

Department of Bioengineering - Stanford University - Stanford - USA

PRAKASH Manu (Host supervisor)

Ecosystems on our planet are driven out of equilibrium with energy input from the sun resulting in a flux of matter across food chains, joining the carbon cycle. This flux is remarkably vivid in the biological pump of our oceans, with gravity driving the downward flux of carbon in the form of marine snow, and the microbes inhabiting and decaying it, thus regulating global climate. The hydrodynamic, biotic and non-equilibrium character of this sinking microbial ecosystem, warrants an active matter physics framework, in an atypical setting. We propose a unique approach to understanding marine snow as a novel class of sedimenting active matter, using a newly invented “hydrodynamic treadmill” capable of direct micro-scale observations of particles sedimenting virtually forever. This would allow us to observe both short and long term dynamics of marine snow sinking in an ambient microbiome, thus achieving an ecologically relevant setting on a tabletop. Through a controlled physical simulation of oceanic conditions we would offer novel insights into birth, life and decay of marine snow aggregates with the following aims- Aim 1: study the formation and dynamics of marine snow aggregate from microscopic density fluctuations of sinking phytoplankton cells, which can now be observed for the first time. Aim 2: make quantitative the efficiency at which ambient microbes can find and populate sinking particles via hydrodynamic and chemical cues, highlighting the role of marine microbes on the global climate. Aim 3: study the long-time dynamics and decomposition of this self-organized active matter as an open microbial ecosystem made of microbes sinking with “islands” of marine snow.

2021 -
Grant Awardees - Early Career

Coupling movement and metabolism in plant stomatal cells: a multiscale and multiphysics approach

CHEUNG Lily (USA)

Dept. of Chemical and Biomolecular Engineering - Georgia Institute of Technology - Atlanta - USA

RAISSIG Michael (SWITZERLAND)

Centre for Organismal Studies - Heidelberg University - Heidelberg - GERMANY

ROUTIER-KIERZKOWSKA Anne-Lise (FRANCE)

IRBV, Departement of Biological Sciences - University of Montreal - Montreal - CANADA

Grasses like rice, maize, and wheat are vital for human nutrition and provide half of all calories consumed by humans. The agricultural success of grasses is partially credited to the superior dynamics of their leaf “breathing” valves called stomata, which open to facilitate carbon dioxide absorption for photosynthesis and close to minimize water loss via transpiration. Unlike most plants, grass stomata consist of two dumbbell-shaped guard cells (GCs) surrounding the aperture; each flanked laterally by a subsidiary cell (SC). This four-celled complex allows for faster response to fluctuating light and humidity. Yet, the exact function of SCs in stomatal dynamics was unclear until recently, when the first SC-specific gene involved in coordinating the movement of GCs and SCs was identified in maize. This gene is a sugar transporter of the SWEET family, suggesting that SCs function through a complex mechanism involving the interplay between cell deformation and metabolism. In this project, we will develop a mechano-metabolic modeling framework to integrate the role of sugars with cell morphology and mechanics in stomatal dynamics—a goal impossible to reach with genetics, biochemistry or physics alone. Our model will be informed by mutant analysis in the newly adopted model grass Brachypodium distachyon, 3D cell shape reconstructions, and in vivo measurements of transporter activity, sugar concentration, cell wall elasticity, and turgor pressure. We will use this model to test a proposed feedback mechanism involving cell deformation, water flow, osmotic pressure, and energy metabolism to predict stomatal dynamics. By elucidating the relevance of sugar transport in a cell-type-specific manner, as well as the role of mechanical anisotropy and cell geometry, our modeling framework will explain why grass stomata present very fast opening and closing dynamics. It could also help predict physiological and cellular characteristics that can be targeted by bioengineering to make faster stomata and, ultimately, increase water-use efficiency in crops to help them withstand the drought and heatwaves associated with climate change.
2021 -
Grant Awardees - Early Career

Unraveling the fundamental mechanisms of neuromodulation by focused ultrasound

COSTA Tiago (PORTUGAL)

Dept. of Microelectronics/Bioelectronics - Delft University of Technology - Delft - NETHERLANDS

HARTEL Andreas (GERMANY)

Bioelectronic Systesm Lab - Columbia University - New York - USA

KOPEC Wojciech (POLAND)

Dept. of Theoretical and Computational Biophysics - Max Planck Institute for Biophysical Chemistry - Goettingen - GERMANY

Cellular communication is mediated by voltage-gated, ligand-gated and mechanosensitive ion channels. Tools for modulating neuronal communication based on focused ultrasound (FUS) were developed to overcome fundamental limitations in optogenetics, combining non-invasive approaches and high spatial resolution without the need for genetic modification of neurons. Yet, little is known about the fundamental mechanisms of how focused ultrasound waves influence the finely tuned interplay of ion channels and lipid bilayers. How does the frequency and intensity of the ultrasound wave affects the lipid bilayer and different types of ion channels? What is the physical mechanism that governs the triggering of ion channel activity? These questions remain unanswered, with existing hypothesis limited by the spatio-temporal resolution of traditional optical, electrophysiology and ultrasound tools, which prohibit observations at the single ion channel level. To answer these questions we hypothesize that, if there would be a way to monitor effects of the FUS on the lipid bilayer and single ion channels with high temporal resolution, one should be able to monitor ultrasound-evoked oscillating current responses informing on ultrasound neuromodulation mechanisms. Hence, the aim of this proposal is to develop a concurrent experimental and computational approach, where state-of-the-art ultrasound and current read-out devices enabling high-bandwidth electrophysiology are matched with computational electrophysiology simulations. This will allow us for the first time to match the frequency of the focused ultrasound with the bandwidth of single ion channel recordings and the length of the computer-based simulations. We will focus our efforts in three aims, where Aim1 will establish the recording systems and simulations using model membranes alone and a mechanosensitive model channel. In Aim2 we will develop a recording platform integrating US stimulation and high bandwidth recordings in complementary metal-oxide semiconductor (CMOS) technology, extending our efforts on non-mechanosensitive channels. In Aim3, we will combine the gained knowledge from Aims 1 and 2 to focus on mechanosensitive channel that are hypothesized to be involved in neuromodulation.
2021 -
Grant Awardees - Program

Transcriptional program of Golgi biogenesis

DE BOER Jan (NETHERLANDS)

Dept. of Biomedical Engineering - Eindhoven University of Technology - Eindhoven - NETHERLANDS

KHODJAKOV Alexey (USA)

Lab. of Cellular and Molecular Basis of Diseases - Wadsworth Center - Albany - USA

POLISHCHUK Roman (RUSSIA)

Cell Biology and Disease Mechanism Program - Telethon Institute of Genetics and Medicine (TIGEM) - Pozzuoli - ITALY

The main objective of our proposal is to reveal the transcriptional program that governs Golgi biogenesis. Synthesis of new Golgi components is required in a large cohort of physiological processes ranging from cell growth to tissue biogenesis. However, how transcription contributes to Golgi biogenesis has yet to be sufficiently understood. Although several mechanisms regulating expression of Golgi genes have been described, their specificity for Golgi biogenesis remains controversial because they emerged from studying pleotropic responses to drugs, toxins, and ER stress that occur in the presence of resident Golgi (or at least its main constituents). HERE WE PROPOSE TO ANALYZE HOW THE CELL REGULATES TRANSCRIPTION TO BUILD THE GOLGI FROM SCRATCH AFTER PHYSICAL REMOVAL OF THIS ORGANELLE. To achieve this challenging objective, the Golgi-containing portion of the cytoplasm will be severed by a laser from the rest of the cell, shaped by microfabricated patterns to be amenable for such Golgi nanosurgery. This procedure triggers a massive de novo assembly of the Golgi in the remaining part of the cell (karyoplast) that contains the nucleus. Golgi biogenesis in the karyoplast occurs in the absence of a preexisting Golgi organelle enabling a straightforward analysis of the transcriptional mechanisms required to build a new Golgi. This analysis will be done by collecting karyoplasts at different stages of Golgi recovery for single cell RNA-seq. A key to the success of our strategy is the international team of investigators with interdisciplinary expertise in laser nanosurgery, transcriptomics, microfabrication and high content screening of bioengineered materials. Analysis of the transcriptome during the de novo assembly of the Golgi will unveil (i) how transcription of various genes correlates with various stages of Golgi regeneration, (ii) which signaling mechanisms are involved in this process, and (iii) which transcription factors drive Golgi biogenesis. We will establish how this transcriptional program operates in processes that require active Golgi biogenesis, specifically cell growth during preparation for division, accelerated secretion, and cell differentiation. Finally, using microfabricated scaffolds and growth patterns we will explore how this Golgi-specific transcriptional program could be controlled to promote engineering of bone and muscle tissue.
2021 -
Grant Awardees - Program

How do malaria mosquitoes swarm and mate? The functional biology of mating swarms

DIABATE Abdoulaye (BURKINA FASO)

Laboratoire de Parasitologie Entomologie - Institut de Recherche en Sciences de la Santé DRO - Bobo Dioulasso - BURKINA FASO

MUELLER Ruth (GERMANY)

Unit Entomology - Institute of Tropical Medicine Antwerp - Antwerp - BELGIUM

MUIJRES Florian (NETHERLANDS)

Experimental Zoology Group - Wageningen University - Wageningen - NETHERLANDS

RIFFELL Jeffrey (USA)

Dept. of Biology - University of Washington - Seattle - USA

Malaria mosquitoes are world’s deadliest creatures. Despite our intensive vector-control efforts they still cause >400,000 human deaths each year. However, we know surprisingly little about the mechanisms that underlie their fecundity. Mosquitoes mate in-flight in complex 3D swarms of up to thousands of individuals of multiple sympatric species. It is thought that to avoid hybridization in such swarms, male and female conspecifics perform a mating dance by synchronizing their wingbeats. But interactions between freely-flying mosquitoes within a swarm have never been quantified. Here, we propose to study the complex dynamics of mating swarms using an interdisciplinary approach by combining expertise from neuroscience, bio(fluid)mechanics, machine vision, behavioral ecology and medical entomology, from laboratories across three continents (Africa, Europe and N. America). Together, we aim to collaboratively study swarming behavior in lab, semi-field and field conditions. For this, we will develop two main research methodologies: A. Dedicated machine-vision-based videography systems for tracking up to 300 mosquitoes flying in a swarm. These systems will be used to study the biomechanics and behavior of multi-species swarms in lab, semi-field and field conditions. B. Novel tethered-flight electrophysiological assays to record the neural responses to approaching conspecifics and allospecifics. By placing this system within a swarm, we will study the neural bases of mate-swarming behavior. By using these systems with a collaborative, multidisciplinary research approach, we aim to jointly answer our four main research questions: Q1. How do mating-swarms form and keep their integrity? Q2. How do individual swarming mosquitoes recognize potential mates? Q3. How do swarming mosquitoes mate in-flight? Q4. How does mosquito swarm dynamics affect mating success and hybridization? This study will generate a new understanding of the functional neuro-mechanics of mating swarms, and provide crucial knowledge about the mechanisms that underlie the fecundity of malaria-vectors. We use the malaria mosquito as our model organism because its fecundity is particularly depending on swarming dynamics, and malaria is the deadliest mosquito-borne disease. Therefore, the project outcomes will directly support the development of malaria-vector control strategies/methods, such as gene-drive, acoustic lures, and monitoring. Swarming is currently an important topic in aerial robotics research; our study will provide novel bio-inspiration for flight control strategies, systems and algorithms of such swarming robots.
2021 -
Long-Term Fellowships - LTF

Predicting enhancer function from sequence through in silico evolution and high-throughput screening

FALO SANJUAN Julia (SPAIN)

Department of Molecular and Cell Biology - University of California - Berkeley - USA

EISEN Michael B. (Host supervisor)
Understanding the DNA sequence rules that govern gene expression remains a major unsolved challenge in biology. Regulatory sequences, termed enhancers, are composed of binding sites for transcription factors, whose number, affinity, spacing and orientation dictate gene expression. Although the roles of some of these parameters are well established, the rules by which binding site arrangement dictate gene expression programs remain poorly understood. We could predict enhancer function if we could test all functional and non-functional enhancer sequences (the ‘enhancer space’). A viable approximation to this approach would be to investigate naturally occurring enhancers. However, not all functional combinations exist in nature, and evolution has mainly maintained functional ones. I propose to cover as much of the enhancer space as possible by: (1) Generating in silico a library of enhancers that could have appeared during evolution, starting from functional but highly divergent enhancers. (2) Testing the activity of this library in a high-throughput manner in cell culture and Drosophila embryos to discover sequence features conferring enhancer functionality, and (3) learn rules of input integration from enhancers' expression patterns. Overall, this proposal aims to discover rules of enhancer function and obtain predictive understanding of function from sequence, providing a landmark step toward decoding gene regulation in development, homeostasis and disease.
2021 -
Long-Term Fellowships - LTF

Investigating neurodevelopment in cortical organoids using voltage and neurotransmitter imaging

GANAPATHY Srividya (USA)

Department of Pediatrics, Cellular and Molecular Medicine - University of California - San Diego - USA

MUOTRI Alysson (Host supervisor)
It is estimated that 1 in 160 children are impacted by neurodevelopmental disorders such as Autism Spectrum Disorder (ASD). In order to develop novel and more effective neurotherapeutic medication to treat ASD, we need a deeper understanding of how specific genetic mutations impact the synaptic properties of the developing brain. In this research, I will assess the synaptic properties of cortical organoids derived from patients with a genetic predisposition for ASD using state-of-the-art genetically encoded fluorescent sensors. Cortical organoids are three-dimensional simplified model systems which recapitulate features of neurodevelopment. I will utilize voltage imaging, which is a revolutionary approach to directly read out the electrical dynamics of neurons in organoids. This method allows access to both spatial and temporal (millisecond) scales hitherto inaccessible to traditional neuroscientific methodology. I will use a fast and sensitive red-light activable voltage sensor along with a reporter for inhibitory (GABA) neurotransmission. Red-light two-photon fluorescence imaging of these voltage and GABA sensors will be used in combination with blue-light stimulation of optogenetic actuators. This method is termed all-optical-electrophysiology and will be used to investigate the impact of an ASD mutation on the intrinsic excitability of neurons and GABAergic neurotransmission. This research facilitates an exciting collaborative effort between biotechnological tool development and its application in a physiologically relevant model system.
2021 -
Grant Awardees - Program

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

GJORGJIEVA Julijana (MACEDONIA)

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

KEENE Alex (USA)

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

SUMBRE German (ARGENTINA)

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

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.
2021 -
Long-Term Fellowships - LTF

How host cell post-transcriptional regulatory adaptations impact chronic coxsackievirus B3 infection

GRIFFITHS Cameron (CANADA)

Department of Biomedical Engineering - University of Virginia - Charlottesville - USA

JANES Kevin (Host supervisor)
This project studies chronic coxsackievirus B3 (CVB3) infection from a systems biology perspective. CVB3 is a positive sense RNA virus that prefers to infect the heart. Although most CVB3 infections are cleared by the immune system, some infections shift to a long-term chronic state for enigmatic reasons. The chronic infection damages the heart, leading to a disease called dilated cardiomyopathy (DCM), which is characterized by a large weakened heart. The only treatment for DCM is heart transplant. During acute CVB3 infection, the positive sense genome is much more abundant than the antisense genome, which is a replication intermediate used as a template to create new sense genomes. However, during chronic infection the sense/antisense ratio is close to 1. My project will test the hypothesis that a shift in the host post-transcriptional regulatory system causes this altered sense/antisense ratio. I will test this hypothesis in a cell culture model of chronic CVB3 infection by interfering with regulatory proteins that can bind to and degrade the CVB3 sense genome. I will also examine how chronically infected cells respond to inflammatory stimuli and how these stimulations impact the CVB3 sense/antisense ratio. In parallel, I will use a computational model of CVB3 infection to identify cellular states that cause an altered sense/antisense ratio and are conducive chronic infection. Finally, I will examine the post-transcriptional regulation and CVB3 sense/antisense ratio in a clinical dataset of gene expression, collected from the hearts of 149 patients with DCM. This project uses an innovative systems-level approach to enhance our understanding of chronic CVB3 infection.
2021 -
Grant Awardees - Program

Friends with benefits? A holistic approach to diffuse mutualism in plant-pollinator interactions

GROZINGER Christina (USA)

Department of Entomology - Center for Pollinator Research - University Park - USA

RISSE Benjamin (GERMANY)

Computer Vision and Machine Learning Systems Group - Faculty of Mathematics and Computer Science - Münster - GERMANY

SICARD Adrien (FRANCE)

Plant Biology department - Swedish University of Agricultural Sciences - Uppsala - SWEDEN

Most flowering plant species benefit from the pollination services of animals, where the animal helps transport pollen between flowers and individual plants, thereby supporting seed and fruit production. In turn, plants provide nutritional resources to pollinators, include nectar (which serves as a source of carbohydrates) and pollen (which serves as a source of protein and fat). This plant-pollinator mutualism is essential to supporting terrestrial ecosystems and is also vital for human agricultural production. Declines in pollinator populations due to anthropogenic change (including habitat loss) endangers these ecosystems and threatens food security. Generalist pollination systems in which flowering plant species uses a broad spectrum of pollinators for pollination services, and pollinator species visit diverse plant species to meet their nutritional needs, can create robust and resilient plant-pollinator communities. Designing and restoring habitats with these generalist systems can serve to reduce or reverse pollinator decline, since multiple pollinator species will be supported. Yet, how such generalist and diffuse mutualisms are formed in an ecological community remains a mystery - primarily due to the lack of tools supporting high throughput monitoring of pollinator visitation patterns and the lack of plant systems where pollinator-attractive traits can be precisely genetically controlled. This interdisciplinary project combines computer vision with plant genetics and pollinator behavioral ecology to identify the mechanisms mediating plant-pollinator interaction networks in generalist pollination systems. In addition to generating novel, broadly accessible monitoring tools and experimental plant systems, this study will provide the first comprehensive characterisation of the plant traits that attract and reward different pollinator species and the pollinator behavioral strategies which optimise pollinator nutrient acquisition in ecological communities. By linking plant genetics, pollinator health and quantitative behavioral data, this project will generate novel concepts and approaches to mitigate pollinator decline in agricultural, urban and natural ecosystems.
2021 -
Long-Term Fellowships - LTF

Protein correlation profiling analysis of the Nipah virus-host interface

HARRISON Angela (AUSTRALIA)

Centre for Gene Regulation and Expression - University of Dundee - Dundee - UK

LAMOND Angus (Host supervisor)
Nipah virus (NIV) is a highly lethal henipavirus with pandemic potential. Outbreaks of NIV occur almost annually in Asia and there are no approved treatments or vaccines, highlighting the need for research into NIV biology. NIV proteins V and M are highly multifunctional; NIV V disables multiple arms of the type I interferon response to potently suppress antiviral immunity, while NIV M has roles in immune evasion, virus assembly/budding, and modulating cell biology, including ribosomal RNA biogenesis. These many functions are mediated through an array of protein-protein interactions. However, how these viral proteins coordinate so many interactions/functions is currently unclear, as is their impact on endogenous cellular multiprotein complexes more globally, including the translational machinery. The proposed project therefore aims to systematically analyse the molecular composition of distinct complexes formed and altered by NIV V and M proteins using state-of-the-art proteomics strategies. Specifically, the project will use highly innovative fractionation technologies, including ‘full-spectrum’ and ‘Ribo-Mega’ size exclusion chromatography, combined with protein correlation profiling and mass spectrometry, to investigate how NIV V and M proteins exploit and remodel the intracellular host environment to benefit infection. The project is expected to provide unparalleled insight into the NIV:host interface and mechanisms of infection, and be of significant value for accelerating therapeutic/vaccine development. The project will also establish these highly advanced proteomics approaches as valuable tools to study other important viruses.
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 -
Grant Awardees - Program

Assembling and recombining the Arabidopsis centromeres

HENDERSON Ian (UK)

Department of Plant Sciences - University of Cambridge - Cambridge - UK

KAKUTANI Tetsuji (JAPAN)

Dept. of Biological Sciences - The University of Tokyo - Tokyo - JAPAN

SCHATZ Michael (USA)

Departments of Computer Science and Biology - Johns Hopkins University - Baltimore - USA

Centromeres are essential to attach chromosomes to spindle microtubules during cell division. Despite this deeply conserved role, the DNA sequences underlying centromeres are extremely fast evolving, which is termed the ‘centromere paradox’. Many centromeres consist of highly repetitive satellite repeats, where individual repeats are often ~170-200 bp in length and occur in massive tandem arrays. Intriguingly, satellites show concerted evolution within and between chromosomes, indicating mechanisms of sequence exchange between the repeats. However, the recombination pathways that change satellite arrays, and their influence on centromere function, remain poorly understood. In this project, we will investigate genetic and epigenetic factors that control satellite dynamics and centromere function, using Arabidopsis thaliana. Accurate analysis of the Arabidopsis centromeres via short-read sequencing has been impossible, due to the high degree of satellite repetition. Long-read technology has created new opportunities to sequence and assemble the centromeres for the first time. We aim to harness nanopore technology to assemble the Arabidopsis centromeres and dissect the roles of meiotic recombination and epigenetic information. Our success requires interdisciplinary innovation via a combination of genetics, epigenetics and computer science. The Henderson and Kakutani groups will generate Arabidopsis nanopore data. Analysis of long-read sequencing data and repeat regions requires significant computational expertise, which is provided by the Schatz laboratory. They will perform new computer science research into the fundamental algorithms and data structures for the assembly, alignment and analysis of highly repetitive texts, including centromere sequences. The Henderson group will test the role of meiotic recombination on centromere stability, while the Kakutani group will test the role of epigenetic information. The Schatz group are using cutting-edge computational methods to map DNA methylation in nanopore data, which will synergize with our experiments testing the role of this epigenetic mark within the centromeres. The team’s combined computational and biological expertise is strongly complementary and synergistic. Our strategic aim is to provide fundamental insights into the genetic and epigenetic mechanisms that control centromere dynamics in eukaryotes.