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2021 -
Cross Disciplinary Fellowships - CDF

Discerning topological defects as hotspots of biological activity in microbial systems

RANI Garima (INDIA)

Department of Physics and Materials Science - University of Luxembourg - Luxembourg - LUXEMBOURG

SENGUPTA Anupam (Host supervisor)
Living matter represents spatially structured soft materials with internal energies far from the thermal equilibrium. The inherent order and fluidity in such systems lead to dynamic, anisotropic properties spanning orders of scales. Spontaneous symmetry breaking in structured matter nucleates local singularities called topological defects. Despite reported evidence of topological defects in living systems, their biological functions have remained grossly unexplored, denying us, to date, a holistic biophysical picture. With a focus on microbial species, I propose to develop the first experimental framework to understand topology-induced microbial physiology, based on a combination of cutting-edge methods including advanced imaging, spectroscopy and machine learning. Specifically, by tracking defect genesis and dynamics in bacterial colonies of species with diverse phenotypes (morphology and motility traits), I will quantify biological activity in the defect vicinity over short to generational timescales. Using fluorescence confocal and electron microscopy (to track molecular transport, exudates and ROS levels), and nanoSIMS technique (to quantify nutrient uptake), I will obtain seminal data linking defects to microbial physiology, and harness this mapping relation to construct machine learning algorithms that will ultimately predict the biological role of defects in multi-species communities. By discerning the biological functions of topological defects, I will be in robust position to pioneer a quantitative approach to this uncharted problem, heralding a unifying framework to predict more complex scenarios, thereby advancing our general understanding of physics of life.
2021 -
Cross Disciplinary Fellowships - CDF

Intestinal organoid-based bioavailability platform: Biovanoids

RECKZEH Elena (GERMANY)

Institute for Developmental Biology and Stem Cell Research - Hubrecht Institute - Utrecht - NETHERLANDS

CLEVERS Hans (Host supervisor)
The small intestine is the major site of nutrient absorption after food intake and malabsorption (impaired nutrient uptake) affects millions of people worldwide. However, there is an unmet need to study malabsorption with physiologically relevant in vitro models. Glucose-galactose malabsorption (GGM) is a genetic disorder that affects the SGLT1 protein, which results in diarrhea and life-threatening dehydration upon glucose and galactose consumption. In my research I aim to establish a physiologically relevant platform to assess nutrient bioavailability employing intestinal organoids (biovanoids) to model GGM. GGM biovanoids will be generated by introducing a disease-associated mutation in SGLT1 (C292Y) using CRISPR/Cas9-mediated base editing. Some aged GGM patients describe an acquired glucose tolerance, which accelerated upon probiotic consumption of certain bacteria. The influence of SGLT1 mutations on host-microbe interactions and possible metabolic adaptation through e.g. age-associated hormonal changes will be studied using GGM biovanoids. This may offer an opportunity to introduce glucose tolerance in young GGM patients. Overall, biovanoids offer a promising platform to generate essential knowledge about malabsorption. To elaborate further applications, biovanoids will be validated for their potential to predict intestinal absorption and gut wall metabolism of drugs. Poor bioavailability contributes to high attrition rates of oral drugs during clinical phases of drug development and currently applied models fail to reliably predict bioavailability in humans. Biovanoids could improve these predictions to eventually increase successful drug approval to the market.
2021 -
Cross Disciplinary Fellowships - CDF

Information flow in the brain at single-neuron resolution

SOITU Cristian (ROMANIA)

Department of Neuroscience - Cold Spring Harbor Laboratory - Cold Spring Harbor - USA

ZADOR Anthony (Host supervisor)
The flow of information between different regions of the brain during decision making is a largely unknown process. This is mainly because there are no tools available to disentangle the complex interaction of myriad cell types in the brain, governed by gene expression, connectivity, spatial organization, and other properties. This proposal aims to investigate the anatomical substrate of inter-regional communication at single neuron level. We hypothesize that a specific group of neurons that project directly between brain areas provide the “scaffolding” for the correlation between structural and functional connectivity. Tools developed in the proposed host group, as well as their previous work on the topic, make this question accessible for investigation. We aim to identify this privileged subpopulation of neurons by combining two-photon imaging of activity in single neurons with anatomical projections extracted using Barcoded Anatomy Resolved by Sequencing (BARseq). Successful completion of this project would generate unprecedented datasets that bridge information at all levels–anatomical, genetic, physiological and behavioural. Gaining knowledge of the flow of information in the brain would push the frontiers of what it is one of the grand challenges of our time–to understand how behaviour arises from neural circuits.
2021 -
Cross Disciplinary Fellowships - CDF

Molecular insights into RNA-directed integration by transposon-encoded CRISPR–Cas systems

THOMAS GEORGE Jerrin (INDIA)

Department of Biochemistry and Molecular Biophysics - Columbia University - New York - USA

GONZALEZ Ruben Jr (Host supervisor)
Over the past decade, programmable gene editing has been transformed by the discovery and development of prokaryotic adaptive immune systems known as CRISPR-Cas. These systems, which evolved to eliminate foreign genetic elements such as plasmid and phage via RNA-guided nucleic acid degradation, have been powerfully redeployed for many gene editing applications. Recently, these systems have been expanded with the discovery of nuclease-deficient CRISPR-Cas systems that direct RNA-guided transposition. Transposon-encoded CRISPR–Cas systems can insert large genetic payloads into bacterial genomes without relying on DNA double-strand breaks or host repair factors, eliminating the major limitations of current integration approaches that rely on CRISPR-Cas9. Nonetheless, the molecular mechanisms of key steps in this newly discovered RNA-guided transposition pathway remain uncharacterized, restricting the applications of this potentially powerful technology. Specifically, the mechanisms through which the transposase machinery is recruited following DNA targeting, the integration orientation of donor DNA is selected, and the megadalton protein-DNA transpososome complex is disassembled, are yet to be elucidated. To determine these mechanisms, I propose to employ a powerful combination of genetic, biochemical, and single-molecule biophysical approaches that is made uniquely possible by integrating the expertise in the Sternberg and Gonzalez laboratories. The results of my studies will transform RNA-guided transposition into a highly tractable, precise, and efficient RNA-guided DNA integration tool for next-generation genome engineering.
2021 -
Cross Disciplinary Fellowships - CDF

Recording neural activity over long time periods using a novel chemi-genetic integrator

TSAO Kelvin (CANADA)

Department of Chemistry - The University of Tokyo - Tokyo - JAPAN

CAMPBELL Robert E. (Host supervisor)
Neurons can be studied by monitoring intracellular calcium ion levels using fluorogenic calcium ion sensors. However, current sensors produce transient signals, potentially missing integral neuron activity and making it challenging to measure accumulated neuron activity over time. Alternatively, genetically encoded calcium ion signal integrators accumulate and integrate neuron activity over a defined time. However, these signal integrators are dependent on a light-assisted photoconversion process and only integrate neuron activity over a short time period. Furthermore, imaging cannot take place during irradiation and even irradiation must be ensured. We propose a calcium ion signal integrator that functions independently of photoconversion for monitoring neuron activity that has accumulated over extended time periods to address these issues. This novel tool consists of a genetically encoded protein sensor (GEPS) that undergoes a conformational change from an opened state to a closed state upon binding to calcium ions. After binding to calcium ions and adopting its closed conformation, the GEPS brings together two cysteines, which both react with a complementary and fluorogenic di-acrylamide probe. Labelling the closed GEPS with this fluorogenic probe slowly produces an irreversible and accumulating fluorescent signal independent of photoconversion but depends on calcium ion concentration. The integrated signal can be later imaged by fluorescence microscopy to identify activated neurons and their relative activity. This novel calcium ion signal integrator will greatly contribute to the future understanding of neuron development and diseases such as stroke.
2021 -
Cross Disciplinary Fellowships - CDF

Engineered collagen fibrils through controlled microfluidics and DNA directed processes

ARNON Zohar (ISRAEL)

Department of Chemical Engineering and of Applied Physics and Materials Science - Columbia University - New York - USA

GANG Oleg (Host supervisor)
Collagen plays a major structural role in various connective tissues, such as tendons, skin, bones, hair and more. Due to the diverse natural utilization of collagen fibers in the different tissues, synthetic and recombinant collagens are used for numerous applications, specifically, in the fields of biomaterials science and medicine. Yet, the ability to fabricate and assemble continuous collagen fibrils across length scales is still an unmet need. Here, we aim to establish a methodology for the fabrication of designed collagen organization, with control on multiple scales, which cannot be attained by current fabrication methods. Designed DNA nano-vessels can be coordinated into a guided 3D pattern. Molecular recognition sites within the nano-vessels will induce collagen formation with precise spatial specifications. Microfluidic techniques will allow the rapid and immediate adjustment of the assembly environment, enabling investigation of various parameters and their effect on the formation process. We intend to study the relationship between collagen architectures and their mechanical properties, in order to rationally design desired end-product attributes. We believe that the Gang group exceptional expertise with DNA nanotechnology together with my own experience with microfluidic techniques and self- and co-assembly mechanisms will produce a fertile conceptual ground for a fruitful study. Elucidating key elements in the relationship between the structure and mechanical properties will enable the regular use of collagen-based biomimetic materials for numerous applications, including drug delivery systems, tissue regeneration platforms, reinforcement scaffolds and more.
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 -
Cross Disciplinary Fellowships - CDF

Geo-electrochemical synthesis of organosulfur compounds as the hub of proto-metabolism

CAMPRUBI Eloi (SPAIN)

Earth-Life Science Institute - Tokyo Institute of Technology - Tokyo - JAPAN

NAKAMURA Ryuhei (Host supervisor)
Understanding how life emerged in the early Earth and how this process occurs elsewhere is one of our greatest problems in biology. Organosulfur compounds such as thioesters play a central and conserved role in the metabolism of all life, and it is likely they performed foundational roles during its emergence. Specifically, thioesters permit coupling between energy-releasing and energy-consuming processes and promote polymerization reactions. Thus, they are at the core of energy harvesting and biosynthetic processes. Although non-enzymatic synthesis of such molecules has been demonstrated, the associated extreme conditions are problematic for subsequent biochemistry. I will use a newly developed high-pressure microfluidics reactor which separates charge across a membrane and mimics the conditions of a hydrothermal vent in its pressure characteristics, together with a series of catalytically-active Fe-rich minerals, to promote the synthesis of thioesters and related organosulfur species under mild conditions relevant to the early Earth and other planetary bodies (e.g. Enceladus). Through this process, promotion of polymerisation reactions such as to fatty acids and isoprenoids or to peptides via the synthesis of amino acid thioester intermediates will be targeted. I will use electrochemistry and advanced isotopic analysis as new tools to unravel the molecular mechanisms of prebiotic thioester synthesis and their relevance to modern biological pathways. My results will provide a greater understanding of chemical energy coupling in relationship to self-organization and will have a significant impact on our understanding of the nature and distribution of life in the Universe.
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 -
Cross Disciplinary Fellowships - CDF

Cell migration in complex environments as a crucial step in the immune response

JAKUSZEIT Theresa (GERMANY)

Cell Biology and Cancer Department - Institut Curie - Paris - FRANCE

PIEL Matthieu (Host supervisor)
Cell migration has a crucial function in a variety of processes in the human body, e.g. dendritic cells explore tissues in search of pathogens, while cancer metastasis significantly decreases survival chances. Research over the last decade has shown that different migratory modes may be adaptations to changing extracellular conditions as experienced by immune cells migrating between tissues with different physicochemical properties. However, it remains unclear how cells integrate potentially competing physical and chemical cues to choose a path in complex environments such as dense tissue. To identify key cellular and extracellular factors that limit migration, we need to understand the underlying physical principles of migration under defined physical and chemical conditions. To this end, I will study dendritic cell migration in microfluidic channels with a high control over the microenvironment such as its porosity or gradients of chemokine. Collaborating with Prof. Voituriez, I will develop a mechanical understanding of the cytoskeleton dynamics in complex environments using active hydrodynamic models to study the interaction of cells with physical barriers. I will combine this cellular level of understanding with random walk models to analyse the large-scale dynamics of cell migration. To elucidate the physiological relevance, I will apply the theoretical framework to cells with migratory defects that display a primary immune deficiency. Thus, the interplay of experiment and theory will develop a quantitative understanding of how immune cells integrate physical and chemical cues to navigate complex environments, which is essential for an effective immune response.
2021 -
Cross Disciplinary Fellowships - CDF

Dynamics of active matter in complex and heterogeneous habitats

MARTÍNEZ CALVO Alejandro (SPAIN)

Department of Chemical and Biological Engineering - Princeton University - Princeton - USA

DATTA Sujit (Host supervisor)
Bacteria can self-organize into a myriad of morphologies and thrive in diverse ecosystems by developing survival strategies that protect the community from external threats. It has been recently proposed that understanding the collective mechanisms of prokaryotic cells could pave the way to fathoming the strategies developed by eukaryotic communities, yet this connection remains unclear. Both systems grow in heterogeneous habitats, namely organs or tissues. In this project, through experiments and mathematical modeling I aim to unravel the collective behavior and cooperativeness that bacteria and eukaryotic cells have in common in complex environments. To this end, several bacterial species, as Escherichia coli and Pseudomonas aeruginosa, and MDCK eukaryotic cells, will be cultivated in different 2D and 3D media mimicking realistic conditions, exposing them also to different external stimuli and heterogeneities, namely chemical and thermal gradients, shear flows, or mechanical forcing. From the theory side, I will employ and derive continuum nematic models, and active vertex models in the case of eukaryotic systems. The interplay between experiments, theory and simulations will be essential to understand the underlying cooperative mechanisms and the collective response of active matter in competitive and heterogeneous habitats, a research direction that remains almost virgin to date. Natural outcomes stemming from this proposal are a better understanding of cancer pathogenesis and antibiotic resistance, or the production of living and synthetic meta-materials at our whim by controlling the morphogenic response of active systems.
2021 -
Cross Disciplinary Fellowships - CDF

Compaction and organization of macroH2A containing heterochromatin in therapy-induced senescence

OU Arnold (AUSTRALIA)

Laboratory of Genome Architecture and Dynamics - Rockefeller University - New York - USA

RISCA Viviana (Host supervisor)
Chemotherapy-induced senescence (TIS) is an alternative form of senescence, which is triggered by inhibiting the cell-cycle (senescence after growth arrest or SAGA) with CDK4/6 inhibitors, such as palbociclib. MacroH2As (a non-canonical histone variant of H2A) are enriched in during senescence and is believed to maintain heterochromatin and repression of cell cycle genes. The nucleosome-nucleosome interactions of macroH2A, which influence compaction and transcription, remains largely unknown. This is mainly due to the limitation of current techniques and the challenges which heterochromatin pose. However, the structural mechanisms of macroH2A and its subtypes (1.1, 1.2, and 2) play to maintain stable gene repression during senescence is largely unknown. Using a TIS model liposarcoma cell line and by developing chromatin targeted probes to induce spatially correlated breaks to infer structural information on the nanoscale (tri-nucleosome) level, I will investigate the structural-function relationship in heterochromatin and macroH2A in SAGA induced liposarcoma cells. The findings of this work will provide a better insight into this novel mode of senescence (TIS) by understanding how chromatin reorganization and cell growth genes are repressed and maintained by macroH2A.
2021 -
Cross Disciplinary Fellowships - CDF

Interdependence of transport and gene regulation during dormancy and growth in axillary buds

PELLETIER James (USA)

Department of Systems Biology - National Centre for Biotechnology / CSIC - Madrid - SPAIN

ARES Saúl (Host supervisor)
Shoot branching in plants integrates a wide range of developmental and environmental cues. During shoot branching, axillary buds transition from dormancy to growth, regulated by signaling factors such as hormones and nutrients, which are produced, transported, and consumed in different ways across the plant. In many species, the highly conserved transcription factor BRANCHED1 (BRC1) maintains axillary buds in a dormant state. The hormone strigolactone (SL) increases BRC1 activity and promotes bud dormancy, and sucrose decreases BRC1 activity and releases bud dormancy, but their relative contributions remain unclear. To clarify mutual dependence of transport and gene regulation during shoot branching, I will determine: (1) how BRC1 activity and axillary bud dormancy depend on transport of SL, sucrose, and other signaling factors, and (2) whether transport of signaling factors into/out of axillary buds depends on plasmodesmata (PD) constituents and aquaporins regulated by BRC1. I will develop a new microfabricated device to enable dynamic buffer control, while live confocal imaging axillary bud activity and growth. I will image fluorescent reporters in existing and new Arabidopsis lines, and I will develop mathematical models integrating transport and gene regulation, to describe and predict dormancy-to-growth transitions in isolated and interacting axillary buds. Few models of plant development have integrated transport mechanics and gene regulation in this way, so this work will have more general implications for plant development.
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 -
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

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

Molecular determinants of selective viral RNA recognition by MDA5

HERRERO DEL VALLE Alba (SPAIN)

Department of Medicine - University of Cambridge - Cambridge - UK

MODIS Yorgo (Host supervisor)
Mammalian cells can recognize the presence of a viral infection by sensing the viral nucleic acids in the cytosol. Viral RNAs activate a specific set of pattern-recognition receptors called RIG-I-like receptors (RLRs). Among these, melanoma-differentiation associated gene 5 (MDA5) selectively recognizes long dsRNAs. Upon recognition of the viral genetic material, RLRs activate an inflammatory type I interferon response. This response needs to be sensitive and specific as its aberrant activation has been linked to autoimmune and autoinflammatory diseases. In the case of MDA5, single nucleotide polymorphisms in IFIH1, the gene encoding MDA5, have been associated with autoimmune diseases including Aicardi-Goutières syndrome, Singleton-Merten syndrome and other interferonopathies where interferon is chronically produced. However, how these mutations lead to the aberrant expression of interferon is still unknown. Besides, it is still poorly understood how MDA5 distinguishes between cellular and viral RNA and how naturally occurring RNA modifications affect the selectivity of MDA5. This work will focus on how MDA5 recognizes viral RNA in the normal and disease-associated contexts. Different variants of MDA5 will be assessed and their dsRNA-activated interferon signaling activities will be compared. The cryo-EM structures of MDA5 filaments will be determined with the aim of understanding at the atomic level how RNA modifications and mutations in MDA5 alter its recognition of dsRNA. This project will provide invaluable insights into viral RNA recognition in health and disease, and will suggest new immunomodulatory strategies.
2021 -
Long-Term Fellowships - LTF

Molecular dynamics of size sensing at the single cell level

KAPADIA Nitin (CANADA)

Cell Cycle Laboratory - The Francis Crick Institute - London - UK

NURSE Paul (Host supervisor)
Cells have strict control over their size to ensure proper cell physiology. They also have ways to correct for deviations, referred to as cell-size homeostasis, leading to a very narrow distribution in cell size at division. Although some of the genes involved in this process have been identified, the underlying molecular mechanism has remained elusive. One possibility is that the cell can “sense” its size through a protein whose concentrations are related to cell-size - known as the sizer model. However, this would not completely explain the fact that diploid cells are approximately twice the size of haploids, suggesting that ploidy also plays a role - something that has not garnered a lot of attention in the field. Live-cell fluorescence microscopy is well-suited to address these issues because we can directly visualize the dynamics and localization patterns of sizers, along with cell-size, and quantify these characteristics. I propose to develop a live single-cell fluorescence microscopy approach using a microfluidics device that allows mother cell lineages to be tracked across multiple generations, for use with haploid and diploid strains of the unicellular eukaryotic organism, Schizosaccharomyces pombe. This will allow me to measure protein levels of sizer candidates and their localization, along with cell length, across single lineages. This information could reveal long-term dynamics and correlations between sizer candidates and cell-size, and provide insight into the molecular mechanisms governing cell-size homeostasis and the role that ploidy plays in governing cell-size control within eukaryotes.
2021 -
Long-Term Fellowships - LTF

Pex ex machina: the cell biological mechanics of locally-controlled peroxisome biogenesis

AMEN Triana (RUSSIA)

Global Health Institute - EPFL - Lausanne - SWITZERLAND

D'ANGELO Giovanni (Host supervisor)
The peroxisome is a widely underappreciated regulator of cellular metabolism. It is often credited solely with being a metabolic detoxifier of reactive oxygen species. Peroxisomes, however, are much more than antioxidant filters. Among their multiple capabilities, peroxisomes provide intermediates for gluconeogenesis and amino acid synthesis, enable cells to synthesize complex molecules like penicillin, degrade fatty acids, and synthesize lipids essential for brain development. Peroxisomes are unique organelles in that their many functions are governed primarily by ad hoc local biogenesis. Within the accepted model peroxisomes form by fission of pre-existing organelles or de novo, from the cellular endo-membranes. However, although de novo peroxisome biogenesis explains the formation of peroxisomal membranes, we do not know how peroxisomes expand their membranes during division. Additionally, little is known about the different molecular factors that trigger peroxisome biogenesis. This proposal will examine the molecular mechanisms of peroxisome biogenesis. My goal is to gain mechanistic understanding of the early events of peroxisome formation driven by diverse conditions and identify the autonomous regulation of the partitioning of the peroxisomal membranes. That will allow us to design targeted therapies for a range of peroxisome biogenesis disorders.
2021 -
Long-Term Fellowships - LTF

Elucidating key neuroinflammation pathway(s) involved in the brain of Drosophila

KHAN Anzer (INDIA)

Global Health Institute - École Polytechnique Fédérale de Lausanne - Lausanne - SWITZERLAND

LEMAITRE Bruno (Host supervisor)
Neurodegenerative disorders are primarily defined by neuronal loss within the central nervous system. Traditionally, research on neurodegeneration has focused on neurons, but recently a prominent role for the innate immune system has been proposed. Chronic inflammation, a feature observed in many neurodegenerative contexts, is now suspected to drive disease progression. The study of neurodegenerative disease is made complex by the late onset of neurodegenerative symptoms and difficulties in accessing the brain, amongst other challenges. In recent years, Drosophila has emerged as a powerful model to study neurodegeneration, and several models mimicking human diseases including Alzheimer’s and Parkinson’s have been developed. Here, I intend to elucidate how the innate immune system contributes to neurodegeneration in Drosophila. My first objective will be to provide a broad description of the head immune responses and decipher whether the Drosophila brain possesses a dedicated immune system with its own peculiarities. My second objective will be to characterize the immune response in the brain during neurodegeneration. Antimicrobial peptides (AMPs) have recently been implicated in neurodegeneration in flies. My third objective will be to decipher the contribution of of AMPs to disease progression, using newly generated AMP mutants Collectively, my study will provide a foundation for how neuroimflammatory pathways regulate the health of neurons and their role in neurodegenerative diseases, and it will also help us to understand whether inflammation is a driver of or a response to neurodegeneration.