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2019 -
Long-Term Fellowships - LTF

The role of neuro-immunological memory in response to enteric infections


Laboratory of Mucosal Immunology - Rockefeller University - New York - USA

MUCIDA Daniel (Host supervisor)

The gastrointestinal (GI) tract is efficiently organized to protect the host from potential dangerous stimuli and to tolerate commensal microbiota and food antigens. It hosts as many neurons as the spinal cord and more immune cells than all other compartments together. The innervation of the digestive tract is involved in determining the patterns of its movements, control of gastric acid secretion, release of gut hormones, modifying nutrient handling and interacting with the gut immune system. Infections of the GI tract can result in neuronal damage and dysregulation of these functions. The host laboratory has recently demonstrated that upon infection, in response to specific neurotransmitters, macrophages – a subset of innate immune cells – can acquire tissue-protective phenotype and minimize neuronal loss. Both immune and nervous systems are equipped with mechanisms allowing to store and recall information on previously encountered events. On this basis, I aim to examine whether GI infections trigger a neuro-immunological memory supporting tissue repair or response to subsequent infections. This is of fundamental and clinical interest, as interactions between immune and neuronal cells are proposed to be part of several disease processes, ranging from multiple sclerosis to irritable bowel syndrome (IBS).

2019 -
Long-Term Fellowships - LTF

The role of tanycytes in temperature and metabolic regulation


Institute of Pharmacology - University of Heidelberg - Heidelberg - GERMANY

SIEMENS Jan (Host supervisor)

Hypothalamic tanycytes are sensory glia-like cells lining the walls of the 3rd ventricle (3V) that were proposed to respond to a variety of metabolic and environmental stimuli. The preoptic area (POA) is a hypothalamic region involved in thermoregulation whose nuclei are distributed around the 3V. The POA receives input from peripheral temperature receptors but also contains neurons that respond to deep-brain thermal changes, although the exact mechanism of this phenomenon is not clear. Due to the privileged position of tanycytes, with their somata directly contacting the cerebrospinal fluid and processes reaching portal blood vessels, we propose that tanycytes are part of the central temperature-sensing circuitry. This hypothesis is supported by the fact that they express two receptors, TRPM5 and TRPM3, which are known to be temperature-sensitive. In this project I will use transgenic mouse lines and employ a combination of electrophysiological, chemogenetic, optogenetic and imaging techniques to explore the sensory roles of tanycytes, mostly focusing on thermodetection. I will start with characterising sensory capabilities of tanycytes including their responsiveness to temperature changes and analysing their functional diversity. Then I will test whether tanycytes communicate with neurons in the POA and if so, I will attempt to identify the phenotype of these neurons. Lastly, I will perform in vivo experiments to test the effect of chemogenetic activation and inhibition of temperature-sensitive tanycytes on thermal effector responses as well as eating behaviour. Overall, I expect my study to shed light on the role tanycytes play in temperature detection and homeostasis.

2019 -
Long-Term Fellowships - LTF

Investigating the role of muscles in morphological plasticity of sea anemone Nematostella vectensis


Developmental Biology Unit - EMBL, Heidelberg - Heidelberg - GERMANY

IKMI Aissam (Host supervisor)

Morphological plasticity is a key adaptive process allowing organisms to cope with changes in their environment. In animals, this process has been described in ephemeral organisms (e.g. flies, worms and mice) that typically experience a specific period in which development will respond to environmental signals producing long-lasting changes in animal body. In contrast, animals with extreme longevity are constantly patterning such that they must continuously adjust their developmental and physiological behaviours with the unpredictable fluctuations of food supply. To decipher the logic of such enhanced morphological plasticity, I am using the sea anemone Nematostella vectensis, a cnidarian laboratory model that exhibits a striking ability to adjust developmental patterns to the nutritional status of the environment while having a long lifespan. Based on preliminary data from the host lab, muscle is emerging as a central tissue that mediates the nutrient-dependent development of Nematostella tentacles. I will define this novel property of muscle cells in response to feeding using transgenic reporter lines. In parallel, I will also establish novel genetic tools to manipulate different muscle types and determine their specific contribution to post-embryonic development. I will also perform single-cell sequencing experiments to characterize the potential metabolic and developmental properties of muscles. Altogether, this proposed work will provide new insight into how morphological plasticity is encoded at the cellular and molecular levels in a long-lived animal.

2019 -
Career Development Awards

Probing the molecular mechanism of SNARE-complex disassembly by NSF


School of Life Science - University of Science and Technology of China - Hefei - CHINA, PEOPLE'S REPUBLIC OF

Soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) proteins are the essential molecular machinery to catalyze membrane fusion in all the trafficking steps of the secretory pathway. Cognate vesicle SNAREs (v-SNAREs) and target SNAREs (t-SNAREs) progressively zipper together from their N-terminal domains (NTDs) toward their C-terminal domains (CTDs) into a four-helical bundle, which pulls the bilayers together and provides the energy for fusion. Since this helical bundle is inactive for subsequent rounds of fusion, NSF and a-SNAP (alpha-soluble NSF attachment protein) are recruited to disassemble it into individual, reactivated SNAREs, using the energy from ATP hydrolysis. Despite its crucial role in maintaining the fusion competence of the secretory pathway, surprisingly little is known regarding when, where and how NSF disassembles the SNARE complex. In Aim 1, I will examine when the SNARE complex is disassembled by NSF, and address how trans-SNARE complexes, formed in the early stage of membrane fusion, are protected from disassembly by NSF to avoid futile cycling. In Aim 2, I will engineer a new optical sensor to monitor the conformational state of the SNARE complex, thus allowing to visualize where the action of NSF occurs inside living cells. Finally, I will examine how ATP hydrolysis by NSF is converted to disassembly of the SNARE complex using novel reconstitution and single-molecule approaches that afford µsec time solution (Aim 3). Together, the proposed research will reveal unprecedented insights into the molecular mechanism of SNARE-complex disassembly by NSF, and shed new light on fundamental questions in membrane fusion.

2019 -
Long-Term Fellowships - LTF

Cell-cell contacts in tissue patterning and evolution


Scripps Institution of Oceanography - UC San Diego - La Jolla - USA

LYONS Deirdre (Host supervisor)

How cell differentiation and morphogenesis are coordinated during embryonic development is an open question in developmental biology. The accepted theory sees morphogenesis as a consequence of the cell differentiation events initiated by biochemical signals. However, recent evidence shows that embryonic cells can adjust their differentiation program according to the size and duration of their cell-cell contacts, suggesting that the interplay between biochemical signals and mechanical stimuli determines cell fate. Yet, how these stimuli are integrated in the gene regulatory networks of cell differentiation is largely unknown. Here I will pioneer an evolutionary approach to find conserved mechanisms by which cell-cell contacts regulate gene expression, by comparing two echinoderm species, sea urchin and sea star. In both species, mesendoderm differentiation depends on Wnt/ß-catenin signalling. However, they present different patterns of Wnt/ß-catenin activity and different cell-cell adhesion properties, with sea star cells being far less adhesive than sea urchin cells. Using a combination of live imaging, scRNAseq and theoretical modelling, I will determine how cell-cell contacts regulate mesendoderm cell differentiation in the two species and if variation in cell-cell contact formation underlies the divergence of tissue patterns between sea urchin and star embryos. This study will uncover basic principles of cell differentiation and tissue patterning, broadening our understanding of embryonic development and evolution.

2019 -
Career Development Awards

T-lymphocyte exhaustion in the 3D tumor microenvironment

BAVA Felice Alessio (ITALY)

Department of Genotoxic Stress and Cancer - Curie Institute - Paris-Orsay - FRANCE

Tumors are complex tissues in which cancer cells establish a plethora of interactions with the surrounding microenvironment. In certain tumors, some of these interactions lead to the progressive loss of function of T-lymphocyte sub-populations, which become “exhausted” (Tex). Therapies aimed at restoring Tex activity have proved promising, but the molecular mechanisms underlying exhaustion and their relation to the Tumor MicroEnvironment (TME) organization are poorly understood. To date, much progress has been made using single-cell technologies to define populations based on shared gene-expression patterns. But assigning the spatial distribution of distinct cells in intact tissues is still a hurdle. This is crucial to determine the exact niches in which Tex reside and understand the underpinnings of exhaustion. Here we will employ STARmap [1] – a novel 3D intact-tissue in situ transcriptomics method that I helped develop – to determine the spatial distribution of Tex and the transcriptional programs associated with Tex progression towards dysfunctional states (Aim 1). Based on our preliminary results, we will also explore the involvement of the DNA-damage response (DDR) pathway in T-lymphocyte exhaustion (Aim 2). We will then determine the spatial organization of the TME, in which Tex subpopulations reside, and define 3D Tex-niches (Aim 3). Overall, we will link 3D imaging-based molecular information with functional significance, to uncover novel mechanisms involved in T-lymphocyte exhaustion and in tumorigenesis.

2019 -
Long-Term Fellowships - LTF

Exploring the role of the tumor vasculature in brain metastasis


Department of Oncology - University of Lausanne - Lausanne - SWITZERLAND

JOYCE Johanna (Host supervisor)

Brain metastasis (BrM) represents the most common brain malignancy, predominantly arising from non-small cell lung cancer, breast cancer and melanoma. We hypothesize that the tumor microenvironment (TME) plays an essential role in the establishment and progression of BrM. The brain is constituted by a unique TME, which includes tissue-resident cell types such as astrocytes and microglia, and critically, the blood-brain barrier (BBB). Cancer cells are able to exploit the brain vasculature for their own benefit, by forming the blood-tumor barrier. This specialized vasculature is an essential TME compartment, as it may suppress anti-tumor responses by blocking immune cell infiltration, specifically of cytotoxic T cells. Indeed, a new perspective to target the tumor vasculature in combination with immunotherapy has recently emerged from studying other cancers; however, this concept has not been explored in BrM to date. Therefore, in the proposed project, I will investigate the biology of two major cellular components of the BBB: endothelial cells (ECs) and pericytes in BrM arising from distinct primary tumors. For this purpose, I will perform transcriptomic analysis of these cell types in patient BrM samples originating from lung, breast or melanoma primary tumors. I will combine this analysis with different experimental approaches available in the host lab, including immunocompetent mouse BrM models and in vitro and ex vivo cell cultures that have been optimized to model the brain TME. This integrated and complementary experimental strategy will facilitate the identification of innovative therapies for BrM to be used alone or in combination with immunotherapies.

2019 -
Long-Term Fellowships - LTF

Defining how activation of skin and lymph node sensory neurons controls immunity


Microbiology and Immunology - University of California - San Francisco - USA

CYSTER Jason G. (Host supervisor)

Pain sensation, though unpleasant, is considered protective as it provokes aversive behavior from noxious stimuli. Studies show that sensory neurons, which generate the perception of pain and touch, interact with another important protection mechanism, the immune system. Ablation of sensory neurons can alter the skin-resident immune cell response. However, many aspects of this interaction remain uncharacterized.
Cells and antigens from barrier sites, like the skin, are drained and sampled by the lymph nodes (LN). Interestingly, LN are innervated by fibers expressing the sensory neuron derived-peptides Substance P and Calcitonin gene-related peptide. Some of these fibers are found in close proximity to leukocytes. However, their direct impact on immune cell activity is unknown.
This project aims to characterize the effects of sensory neurons in the skin and LN on immune cell behavior. To this aim, we propose to combine chemogenetics to locally activate sensory neurons, with a broad analysis of immune cell responses. Mice expressing Cre under the control of sensory neuronal markers, including the broadly expressed gene Advillin and genes selective for subsets of sensory neurons, will be injected intradermally or in the LN with a viral vector encoding the Cre-dependent expression of the hM3D(Gq) activating receptor. Once validated, this technique will be used to locally activate sensory neurons and characterize subsequent immunological changes using flow cytometry, histological and live imaging techniques. This project can provide new insights into how sensory innervations, which regulate behavior by creating the sensation of touch and pain, shape local immune responses.

2019 -
Long-Term Fellowships - LTF

Synaptic basis of temporal learning


Department of Neuroscience - Institut Pasteur - Paris - FRANCE

DIGREGORIO David (Host supervisor)

A key brain region involved in accurate temporal refinement of motor and also cognitive behaviours is the cerebellum. Cerebellar granule cells (GCs) receive multisensory information from outside the cerebellum via mossy fibres (MF). The prevailing hypothesis is that, in order to learn temporal sequences, the cerebellum requires a rich diversity of GC activity patterns that as a population represent a distributed temporal representation of sensory inputs. But this has never been directly demonstrated. Unpublished network models from the hosting laboratory strongly suggest that their previous findings (input specific diversity of MF-GC synaptic dynamics) are sufficient to generate a diverse GC firing patterns that act as a temporal basis for cerebellar learning. We will use novel high speed two-photon in vivo imaging of GC firing patterns in behaving animals, and examine whether the diversity of GC firing patterns requires functional diversity of MF-GC synapses, and whether this mechanism is specific for different sensory modalities, using optogenetic activation of specific input types. Finally, we will optogenetically inhibit specific MF types to show their influence over specific timescales of eyeblink conditioning, then image the temporal representation in the GC layer before, during and after a temporal learning task. Expected results will included identification of the underlying cellular and circuit mechanism of temporal learning required for fine tuning motor and cognitive processes.

2019 -
Long-Term Fellowships - LTF

Epigenetic normalization through engineering of S-adenosyl methionine metabolism


Cancer Center - MGH Boston - Boston - USA

MOSTOSLAVSKY Raul (Host supervisor)

Pancreatic ductal adenocarcinoma (PDAC) remains an incurable disease with a high death rate. PDACs are exceptionally difficult to treat because of high genetic plasticity and encapsulation by cancer-associated fibroblasts (CAFs). Either are due to an altered epigenetic landscape where PDACs and CAFs show a switch towards global chromatin hypo-methylation, and concomitant hyper-methylation of tumor-suppressor genes. As CAFs do not show any mutagenesis, the molecular cause must be found in the tumor microenvironment.

The nutrient microenvironment represents a novel but important aspects of tumor biology. Nutrients are converted into the basic building blocks that fuel cellular proliferation, but also regulate epigenetic modifications. S-Adenosyl-Methionine (SAM) represents a nodal point in one carbon metabolism and is required for methylation of histones and DNA. We therefore propose that metabolism cannot sustain the high SAM requirement of both PDAC and CAF, thus shunting away carbons from epigenetic maintenance. This project therefore aims to map the link between nutrient availability, one carbon metabolism, availability of SAM, and the methylation profile of chromatin. Furthermore, we will establish a genetic sensor and CRISPR-based screening system to visualize the regulation of SAM compartmentalization, and attempt to normalize the epigenome of PDACs and CAFs through engineering of SAM metabolism (EpiSAMe). These studies will shed new insight into the crosstalk between metabolism and epigenetics in PDAC and provide novel molecular for the treatment of this devastating disease.

2019 -
Long-Term Fellowships - LTF

Dissecting the role of metabolism in cancer genomic instability


Meyer Cancer Center - Weill Cornell Medical College - New York - USA

CANTLEY Lewis (Host supervisor)

Genomic instability is a common feature of cancers and can have an important impact on cancer progression and response to treatment. However, the mechanisms underlying cancer genomic instability are not completely understood. While DNA repair defects are thought to be a major cause of this trait, other factors seem to be involved. In the last decade, metabolism has received a lot of attention within the cancer research community. Most of the work has focused on understanding the metabolic requirements of cancer cells for survival and proliferation. However, metabolism does not only provide building blocks for biosynthesis, but it also generates reactive by-products that can damage cellular components such as DNA. Thus, the metabolic alterations characteristic of cancer cells might not only support cancer development by supporting biosynthesis but also by promoting genomic instability.

The aim of this research proposal is to identify changes in the metabolism of endogenous genotoxins in cancer and to elucidate the role of these alterations, particularly in the context of genomic instability. In addition, the potential exploitation of this aspect of metabolism for cancer therapy will be explored. To achieve these goals a diverse range of techniques and study systems will be used, including transcriptomics, metabolomics, CRISPR-based genetic screens, cancer cell lines and mouse models.

2019 -
Long-Term Fellowships - LTF

Prochlorococcus cyanophage: lysogenic potential and development of a genetic system


Departments of Civil and Environmental Engineering and Biology - MIT - Cambridge - USA

CHISHOLM Sallie W. (Host supervisor)

Prochlorococcus, the smallest photosynthetic organism, has diversified into many ‘ecotypes’ with finely tuned distinct ecological niches. The small and variable genomes of these cyanobacteria encode genes unique to particular habitats. A driving force for gene transfer and evolution in cyanobacteria is phage-mediated. While numerous reports describe lytic cyanophages that infect Prochlorococcus, surprisingly there is only indirect evidence that lysogenic phages – those that spend a portion of their life cycle incorporated into the host genome – exist. The central goals of this proposal are i) to analyze the occurrence of lysogens in wild populations of Prochlorococcus, and ii) to establish a robust protocol for gene editing allowing precise manipulation of the Prochlorococcus genome. The second goal will exploit, but is not dependent upon, advances from the first.
This will be the first study to assess lysogeny across natural Prochlorococcus populations and to develop phage-mediated genetic systems for engineering cyanobacteria. The development of efficient tools for genome editing would be extremely beneficial for understanding Prochlorococcus metabolism. It would allow functional studies for thousands of unannotated genes that influence the relative fitness of different ecotypes in different environments. A unique aspect of my proposal is the employment of a novel synthetic biology strategy to build engineered phages with broad host specificity, and to use them as vehicles for genome editing systems such as CRISPR/Cas9. This technique will be useful for several applications and will further establish Prochlorococcus as a model organism in environmental microbiology.

2019 -
Long-Term Fellowships - LTF

Structural and functional characterization of P-Rex 1/2 in cell signaling and cancer


Biozentrum - University of Basel - Basel - SWITZERLAND

MAIER Timm (Host supervisor)

Phosphatidyl-inositol 3,4,5 triphosphoshate-dependent Rac exchanger (P-Rex) are a group of proteins involved in the activation of the small GTPase Rac, by acting as a guanidine exchange factor (GEF). Both Rac and P-Rex proteins are known to be overexpressed and altered in several cancers, consistent with their role in both cell mobility and their numerous interactions with both the mTOR axis and the PI3K/PTEN pathway. P-Rex1/2 specifically, are known to interact with mTOR and PTEN, among others, placing them at the nexus of regulatory pathways for cell metabolism, proliferation and mobility.
Despite their central role in cell signaling, very little is known about the interplay between such interactions. No structural information is available for the full-length P-Rex proteins and how different interaction partners affect its structure and function. I will therefore set out to better characterize the emerging properties of the multidomain P-Rex proteins by purifying both P-Rex1/2 and determining their structure using cryo-EM and orthogonal biophysical characterization methods. I then aim to define the interaction between P-Rex proteins and its regulatory partners, PTEN and the mTOR complexes 1 and 2. I will define their domains of interactions and determine the structure of the complexes, using a combination of cryo-EM and cross-linking and mass-spectrometry.
I expect to provide new insights into the functions of P-Rex proteins and their crosstalk with core cellular signaling pathways. Structures of full-lengths P-Rex alone or in complex with its interaction partners will serve as a platform for drug discovery, thereby providing new cancer therapeutic avenues.

2019 -
Long-Term Fellowships - LTF

Astroglial bioenergetic control of positive and negative reinforcement


Neurocentre Magendie, INSERM - University of Bordeaux - Bordeaux - FRANCE

MARSICANO Giovanni (Host supervisor)

The endocannabinoid system (ECS) is involved in a variety of brain functions, including reward and aversion, mainly through type-1 cannabinoid receptors (CB1). The Nucleus Accumbens (NAc) is a key brain region in the control of positive and negative reinforcement. ECS impairments in the NAc lead to negative emotional states. By responding to neurotransmitters with intracellular Ca2+ increases and releasing gliotransmitters that modulate synaptic transmission and animal behavior, astrocytes play active roles in neural information processing. While CB1-mediated astrocyte-neuron communication has been shown in several brain regions, it is unknown whether this communication exists in in the NAc. Mitochondrial CB1 receptors (mtCB1) directly regulate mitochondrial energetic activity, synaptic transmission and behavior, but the role of astroglial mtCB1 in these processes is unknown. Combining electrophysiology, subcellular-specific live Ca2+ imaging and behavior, this proposal aims at defining the contribution of astrocytic CB1 (plasmatic and/or mitochondrial) to synaptic plasticity in the NAc and their behavioral impact. The specific goals of this proposal are to define 1) whether astrocytes in the NAc express functional CB1; 2) how astrocytic CB1 regulate synaptic transmission and plasticity in the NAc; 3) how astrocytic CB1 impact reward and aversion and 4) how astrocytic mtCB1 influence astrocyte activity, synaptic plasticity in the NAc and behavior. The expected results will shed light onto the involvement of astrocytes in brain motivational systems through the ECS, and would reveal astrocytes as potential targets for treatment of motivational disorders.

2019 -
Career Development Awards

Protein surfactants - a general principle for cellular organization?


Cell Biology and Biophysics Unit - EMBL - Heidelberg - GERMANY

Compartmentalization into functional units is the key principle of cellular life. In addition to conventional membrane-bound organelles, cells utilize membrane-less biomolecular condensates to locally concentrate proteins and nucleic acids. Prominent examples of such condensates are nucleoli, P granules or centrosomes, which play central roles in diverse cellular functions. Recent studies have demonstrated that membrane-less condensates assemble by liquid-liquid phase separation of proteins that are characterized by multi-valency, intrinsic disorder and low complexity sequences. The molecular mechanisms that control assembly and disassembly, shape and size of such membrane-less organelles remain key unanswered questions of modern cell biology.
To address this fundamental gap in our knowledge, I propose an interdisciplinary research programme that combines powerful in vitro reconstitution with systematic screening technologies. Based on my discovery that the chromosome surface protein Ki-67 acts as a surface-active agent (surfactant) for one of the largest membrane-less assemblies, the mitotic chromosome, I will explore the radically new concept of surfactants for the global regulation of other membrane-less organelles. Starting from defining the molecular properties, mechanisms and regulatory basis for the action of Ki-67, I will systematically identify and characterize the surfactants of other membrane-less organelles in human cells. This ambitious research programme has the potential to provide novel paradigms of spatial and temporal control of membrane-less cellular assemblies and thereby substantially advance our understanding of cellular organization.

2019 -
Long-Term Fellowships - LTF

Saturating mutagenesis of the mitochondrial genome in search for critical cis-regulatory elements


Department of Genetics - Harvard Medical School - Boston - USA

CHURCHMAN L. Stirling (Host supervisor)

A plausible explanation for why mitochondria have their own DNA (mtDNA) is to ensure colocalization of redox-genes and redox-regulation to the same membrane-bound organelle. While this distributed control system seems logical, very little is known about how such autonomous regulation takes place. A variety of methods that are widely applicable to study genomes fail to work on mtDNA, and sequence-to-function mapping of the mitochondrial genome is missing. I plan to create a modified, hypermutating DNA polymerase gamma (polG), the designated mtDNA replicase. polG is encoded in the nuclear genome and can therefore be easily manipulated. Hypermutator polG will be integrated into the nuclear genome of S. cerevisiae, which will introduce mutations in mtDNA without altering the nuclear genome. I will then use selection assays followed by next generation sequencing to study the ability of mtDNA yeast variants to adapt to respiratory conditions. Such experiment will highlight regulatory hotspots in mtDNA that will be mechanistically evaluated using genome-wide methods like native elongating transcript sequencing (NET-seq) and mitochondrial ribosome profiling that are the ‘bread and butter’ of the Churchman lab. Clear view of the fitness landscape associated with mtDNA will inform research into many deep questions in mitochondrial biology, ranging from ‘how selection shapes mitochondrial genomes?’ to ‘why do certain mtDNA mutations cause cancer?’.

2019 -
Long-Term Fellowships - LTF

Elucidation of Trypanosoma brucei dynamics and biophysical properties in the host adipose tissue


Department of Parasitology - Instituto de Medicina Molecular Joao Lobo Antunes - Lisbon - PORTUGAL

MIRANDA-FIGUEIREDO Luisa (Host supervisor)

Trypanosoma brucei is the causative agent of sleeping sickness. In the mammalian host, parasites exist in two major niches: the blood, and the brain. Recently, Dr. Figueiredo’s lab found a previously undiscovered third reservoir of parasites in the adipose tissue which were transcriptionally distinct from blood stream forms, and the genes upregulated included various markers relevant to parasite metabolism. My proposed work in Dr. Figueiredo’s lab is to implement in vivo imaging methods to a) investigate the parasite’s mechanisms of homing and crossing of the vascular endothelium into the adipose tissue, and to carefully define the adipose tissue niche that acts as reservoir for the parasites; and b) to elucidate host vasculature, and parasite factors involved in allowing such unique phenomenon, including generating parasite mutants deficient in adenylate cyclises, flagellar proteins, and mechano-sensing proteins among others. Using in vivo techniques and biophysical and molecular methods, I aim to investigate the biological significance of parasite residence in the adipose tissue – a location which could be clinically relevant for interventions in human and veterinary medicine.

2019 -
Cross Disciplinary Fellowships - CDF

The microscale biophysics of toxin dispersion during harmful algal blooms

DHAR Jayabrata (INDIA)

Physics and Materials Science Research Unit - University of Luxembourg - Luxembourg - LUXEMBOURG

SENGUPTA Anupam (Host supervisor)

Harmful algal blooms (HABs) have been long studied in marine and fresh water environments, yet most research to date has focused at the bulk scale. Despite the well-documented toxic ramifications of HABs on vertebrates and mammals, including humans, we still lack a biophysical understanding of the mechanisms by which toxins disperse during a bloom event. Using a combination of experiments and modelling, in this project I will explore the physico-chemical interplay underlying the release and transport of toxins at the scale of the microorganism. Towards this I will develop micro- and millifluidic experiments to generate ‘bloom-in-lab’ and visualize the dispersion of targeted toxins under three ecologically relevant cues: fluid flow, temperature and salinity. Specifically, I will study red-tide forming Heterosigma akashiwo, a globally distributed marine raphidophyte, known to release a range of toxins, including reactive oxygen-nitrogen species (RONS) during bloom conditions. Original data from high-speed and time-lapse microscopy on fluorescently labelled ‘target’ molecules will put forward first experimental quantifications of toxin release and transport under different micro-environmental cues, thereby informing a new mathematical model that will capture, at microscales, dispersion and auto-feedback dynamics during bloom events. Analysing the coupling between microbial biophysics, transport phenomena and biochemistry, this project will bring about a fundamental, mechanistic understanding of toxin transmission, and help develop accurate and comprehensive algorithms for predicting HAB formation, especially during the rapidly warming climate we encounter today.

2019 -
Career Development Awards

Elucidating the biological impact of precise genome editing in hematopoietic stem cells

DI MICCO Raffaella (ITALY)

San Raffaele Telethon Institute for Gene Therapy - Fondazione Centro San Raffaele - Milan - ITALY

Human medicine is on the verge of a new era where we face the possibility to precisely rewrite the genome to prevent, ameliorate and cure a wide range of immune-hematological diseases. Hematopoietic stem and progenitor cells (HSPC) have long been a preferred source for ex-vivo gene therapy, as gene correction in multipotent progenitors ensures a life-long supply of corrected progeny and polyclonal reconstitution of the bone marrow. Recently, programmable nucleases brought the possibility of genome editing (GE) within the reach of gene therapy by allowing locus-specific gene correction without the risk of aberrant transgene expression. However functional studies that accurately assess possible acute and long-lasting consequences of GE procedures in HSPC are needed to harness GE therapeutic potential. Indeed, despite recent advances in the generation of corrected HSPC by GE, the efficiency of the targeting process and the ability of edited cells to stably reconstitute the hematopoietic system upon transplantation remain limited, pointing to a loss of repopulating capacity of HSPC upon targeting. The goal of this project is to investigate the role of DNA damage response (DDR) pathways in GE strategies and uncover novel molecular players that could be exploited to increase the yield of long-term engrafting gene-edited HSPC. Our findings could be easily applied to gene correction strategies for a variety of inherited pathologies affecting the human immune-hematopoietic system and provide a foundation for more efficient modalities of editing HSPC at genomic sites of interest for both basic and translational research.

2019 -
Long-Term Fellowships - LTF

State-dependent routing of sensorimotor signals across areas of visual cortex


Department of Bioengineering - Stanford University - Stanford - USA

DEISSEROTH Karl (Host supervisor)

Areas of visual cortex integrate signals representing sensory input, ongoing motor actions, and internal states. While neurons in primary visual cortex (V1) were classically interpreted as feature detectors that signal the presence of a specific visual stimulus, recent evidence suggest that V1 circuits participate in the specific, topographical integration of sensorimotor signals. How sensory and sensorimotor computations are implemented in the circuitry of V1 and higher visual areas, and how these computations depend on the behavioral context, is unknown. I will combine novel circuit dissection tools, wide-field-of-view holographic stimulation, and virtual reality environments to approach these questions. I will selectively activate V1 ensembles with distinct functional properties during sensorimotor behavior using holographic stimulation and monitor the effects on the surrounding populations in V1 and higher visual areas. Furthermore, I will analyze the effects of holographic stimulation as a function of different behavioral parameters and during optogenetically induced variations in internal state. Finally, I will explore methods to target the expression of genetically encoded tools to distinct V1 ensembles, each with specific function during sensorimotor behavior, which will allow me to study if different ensembles are selectively connected to circuits throughout the brain, as well as to determine their selective impact on brain-wide dynamics. This project will shed new light onto the function of V1 during sensorimotor behavior, and yield fundamental insights into the mechanisms by which cortex can adapt its processing machinery to varying behavioral demands.