Skip to main content
2018 -
Long-Term Fellowships - LTF

Rapid reshaping of nuclear architecture through dynamic patterns of ribosomal DNA cluster-usage


Department of Molecular Biology - Max Planck Institute for Developmental Biology - Tübingen - GERMANY

WEIGEL Detlef (Host supervisor)

It has become increasingly evident that the transcriptional activity of a gene is intrinsically linked to its positioning within the nucleus. A distinctive subnuclear structure is the nucleolus, which is mainly formed upon transcription of ribosomal RNA (rRNA) genes. Hundreds to thousands of rRNA genes are tandemly arrayed in megabase-size rDNA clusters. The model plant Arabidopsis thaliana carries two unlinked rDNA clusters, with natural variation in rDNA cluster-activity, meaning that some strains express only one or the other cluster, and some both. Because large genomic regions adjacent to the actively transcribed rDNA cluster(s) –thus associated with the nucleolus– are expressed at lower levels than the genome average, I expect large-scale variation in gene activity. My goal is to investigate how variation in rDNA cluster-usage and its consequent reshaping of 3D genome architecture impact not only the expression of adjacent protein-coding genes, but also how genome-wide gene regulatory networks (GRNs) can adapt to such large-scale differences in gene expression.
I propose to take full advantage of the diversity of genetic resources available in A. thaliana, including experimental populations, a large catalog of genomes and transcriptomes, as well as its accessibility for genetic engineering to pursue the following aims: (1) investigate the impact of rDNA-cluster usage on GRNs in natural strains, (2) swap rDNA expression patterns using crosses, and assess effects on GRNs, and (3) induce targeted inversions and translocations using CRISPR-Cas9 technology to directly test the functional consequences of gene-positioning with respect to active rDNA clusters.

2018 -
Long-Term Fellowships - LTF

Neural microcircuits underlying prosocial behavior

RAY Saikat (INDIA)

Department of Neurobiology - Weizmann Institute - Rehovot - ISRAEL

ULANOVSKY Nachum (Host supervisor)

A primary feature of highly-social animals, like humans, is the tendency to help one another. These behaviors, where one animal helps another without immediate benefit to itself, are known as prosocial behaviors. While there has been considerable research into how the brain controls social behaviors driven by fear or aggression, there has been almost no investigation of brain mechanisms of prosocial behaviors– when one animal aids another. We will conduct the first mechanistic investigation of the microcircuits underlying prosocial behaviors. To this end, we will utilize the natural food-sharing behaviors of Egyptian fruit bats; where provider-bats feed scrounger-bats; and will conduct wireless single-unit electrophysiological recordings from multiple freely-behaving bats living and interacting together in a colony. We will investigate two brain areas: (i) Medial prefrontal cortex, specifically infralimbic cortex– a brain area linked in humans to prosocial behaviors– where we will investigate neural correlates of prosocial feeding events. (ii) Hippocampus– an area involved in social memory and strongly connected with the prefrontal cortex– where we will investigate how other animals are recognized, a key component of prosocial behaviors. We will further introduce ethological manipulations to the freely-behaving colony to determine how natural variations, such as changes in competition or resource-availability, impacts prosocial behaviors and their neural representations. Finally we will switch a provider bat to a scrounger, by adding weight to create temporary ‘handicap’– and investigate the changes in the underlying neural representations of both oneself and others.

2018 -
Long-Term Fellowships - LTF

Discovering the mechanisms underlying intrinsic repair of muscle cells in wildtype and sarcopenia


Department of Experimental and Health Sciences - Universitat Pompeu Fabra / ICREA - Barcelona - SPAIN

MUÑOZ CÁNOVES Pura (Host supervisor)
BEATO Miguel (Host supervisor)

Skeletal muscle has the capacity to regenerate after injury. This process involves an orchestra of cells and factors that sequentially intervene to repair muscle fibers. Muscle regeneration is particularly vital for muscle disorders and aged muscle in which myofibers are constantly degrading.
In contrast to the classical approach in studying muscle regeneration, this project focuses on exploring the intrinsic capacity of damaged myofiber to self-repair. We observed that after local injury, nearby nuclei migrate to the damaged site where they become internalized, re-organize chromatin and begin rotating. This cell response coincides with repair of the injury and has never been previously described. Interestingly this process is impaired in aged myofibers that are incapable of repair post injury.
We therefore propose to study the intrinsic capacity of myofibers to repair. We will first explore the underlying mechanisms driving nuclear migrations to the damaged site after local injury. We will then establish how chromatin is re-organized for myofiber self-repair. Finally, we will investigate the failing mechanisms in aged myofibers.
The difference between intrinsic myofiber repair and regeneration most likely stems from the severity of the injury, with minor damage triggering the intrinsic repair program. The capacity of myofibers to self-repair may be the first line of defense to muscle injury. Exploring the mechanisms of this newly observed process could reveal novel therapeutic strategies to maintain myofiber integrity. This could delay the involvement of the multi-cellular regenerative process, usually overwhelmed or diminished in muscle disorders and old age.

2018 -
Long-Term Fellowships - LTF

Investigating the function of prion domains in transcription factors regulating cell differentiation


Chemical and Systems Biology Department - Stanford University School of Medicine - Stanford - USA

JAROSZ Daniel (Host supervisor)
WYSOCKA Joanna (Host supervisor)

What makes us human? Understanding the evolutionary emergence of human traits is important both for fundamental knowledge and our capacity to treat diverse diseases. In this project I aim to understand molecular mechanisms governing human speech development. FoxP2 is a highly conserved transcription factor, dubbed the ‘speech gene’ because families with mutations in this protein have speech deficits. Two amino acids variants in FoxP2 have been subject to strong selection in our lineage. Introducing them into mice increases vocalization. Yet these mutations do not localize to FoxP2’s DNA-binding domain. Rather, they bracket a long prion-like domain near its N-terminus. Preliminary results show that these variants enhance FoxP2’s capacity to form ‘infectious’ prion-like aggregates. Remarkably, FoxP2 aggregates arise naturally, and in a developmentally regulated manner in the neural crest.
I aim to characterize the physiological function of FoxP2 prion-like aggregation during neural crest differentiation, identify the developmental consequences of the evolutionarily selected mutations in this protein, and ultimately identify molecular mechanism(s) by which FoxP2 regulates cellular differentiation. I will test the importance of FoxP2’s prion domain using a series of powerful genetic and cell biological approaches. Subsequently, I will investigate the regulation of prion formation during development. Finally, as a long-term goal I will test if aggregation alone, or templated propagation of the prion per se, is required for normal differentiation. If fulfilled, the aims of this proposal thus have the potential to transform our understanding of human development and evolution.

2018 -
Long-Term Fellowships - LTF

Active and passive listening channels for auditory scene analysis


Comparative Neural Systems and Behavior Lab, Dept. Psychological and Brain Sciences - Johns Hopkins University - Baltimore - USA

MOSS Cynthia (Host supervisor)

Animals exploit acoustic signals for a wide range of behaviors, from sound communication to predator localization, which require the discrimination and identification of different sound sources in the auditory scene. Echolocating bats, for example, rely not only on sound to navigate the environment, but also to communicate with conspecifics. Therefore, bats must segregate self-generated echoes from other acoustic signals in the environment, including those produced by conspecifics. Past research has yielded a wealth of data on the neural mechanisms of biological sonar in bats, but far less is known about how the bat auditory system differentiates between echolocation and social communication signals. My research aims to address this question by recording and analyzing midbrain inferior colliculus responses to sound stimuli that carry echo information from the environment or social information from conspecifics. Experiment 1 will compare neural activity in bats listening to playbacks of their own echolocation signals, those of conspecifics, and acoustic communication signals. Experiment 2 will investigate the dynamics of neural activity evoked by actively echolocating bats engaged in a target-tracking task. Experiment 3 will employ novel methods to characterize auditory activity evoked by sonar echoes and social communication signals in the free-flying bat as it navigates around objects in its physical environment. Comparative studies are key to identifying specializations and general principles of neural systems, and this project will advance a deeper understanding of auditory processing in animals that rely on sound to guide behavior.

2018 -
Long-Term Fellowships - LTF

Inheritance and transduction of environmental information in asexually reproducing plants


Department of Plant Biology and Forest Genetics - Swedish University of Agricultural Sciences - Uppsala - SWEDEN

KOHLER Claudia (Host supervisor)

It is estimated that about 40% of plant species can reproduce asexually, suggesting that this mode of reproduction is beneficial to allow plant survival under certain environmental conditions. Despite its prevalence, we know very little about how asexual reproduction contributes to the environmental stress response in plants. The central hypothesis of this proposal is that environmental stress induces epigenetic changes that can be stably propagated to the asexual progeny and potentially contribute to plant adaptation. To test this hypothesis, I will analyze the phenotypic, transcriptional and epigenetic changes in response to stress using Arabidopsis lyrata (A. lyrata), a plant species that asexually produces novel ramets from its root. In particular, I will investigate stress memory in novel ramets produced from parental plants that have been exposed to environmental stress (heat, salt, and cold stress). I will generate and analyze epigenetic profiles of ramets propagated over five generations under stress or non-stress conditions to identify stress-induced epimutations. I will furthermore investigate the signal transduction between maternal plants and ramets attached to each other through roots. Transcriptomic and phenotypic analyses will reveal how stress treatment of parental plants affects the attached ramets. Finally, I will test whether induced epimutations have adaptive value by investigating whether clones derived from stress-treated maternal plants are better adapted to stress. The proposed study will not only reveal a potential novel mechanism to adapt to environmental conditions, but also provide the basis for the generation of stress-adapted crops and trees.

2018 -
Long-Term Fellowships - LTF

Quantitative analysis of cell death of E. coli during starvation


Systems Biology Department - Harvard Medical School - Boston - USA

BASAN Markus (Host supervisor)

Despite a century of study, little is known about the mechanisms underlying bacterial cell death and survival during starvation, even for the simple model organism E. coli. In this project, we will address long-standing questions on how starvation results in cell death, i.e. which molecular processes collapse irrevocably and why. Our preliminary data indicates that cell death of E. coli during starvation is due to turgor pressure induced lysis. I will approach this hypothesis with two objectives: 1. Understanding cell wall dynamics during starvation-induced lysis and 2. Elucidating the role of turgor pressure during lysis and its dependence on metabolic state. In objective 1, I will quantify the role of cell wall remodeling in starvation-induced lysis. I will capture rare lysis events using microscopy, genetically titrate key cell wall hydrolases and metabolic enzymes involved in cell wall turnover, as well as investigate the trade-off between optimal starvation survival and swift growth resumption. In objective 2, I will characterize the energy-dependence of osmoregulation (ion pumps and channels) and its effect on cell wall remodeling. Theory and experiments will be combined, eventually resulting in a mathematical model that will be capable of predicting starvation dynamics under diverse environmental and genetic perturbations. The project will also reveal new avenues to fight dormant and recurring infections, as it will identify the essential processes that enable long-term survival, which therefore constitute important drug targets.

2018 -
Long-Term Fellowships - LTF

Neural coding during motor learning in the cerebellar cortex


Department of Neuroscience, Physiology and Pharmacology - University College London - London - UK

SILVER Robin Angus (Host supervisor)

The cerebellum is a particularly attractive model system for studying brain function since it has a relatively simple and well-defined circuit and its computations are directly related to behavior. Key functions of the cerebellum are the fine coordination of movements and motor learning.
Influential early theoretical work predicted how input from mossy fibers is recoded in granule cells in the input layer of the cerebellar cortex to increase the computational performance and to achieve separation of similar patterns. However, due to the limited possibility to simultaneously record inputs and outputs of this granule cell layer the mechanisms employed are still not fully understood. Likewise, it is unknown how mossy fiber inputs or the transformations in the granule cell layer change during motor learning. Finally, whether expectation mismatches, important to the fine coordination of movements and motor learning, are encoded in granule cells is unclear.
Therefore, simultaneous two-photon in vivo imaging of two different calcium indicators in 100-300 mossy fibers and granule cells in awake behaving mice will be employed. A water-droplet-reaching task will be used to assess pattern separation between similar movements, contributions from different precerebellar regions to information processing, and alterations in mossy fiber input and computations during learning. A lever-press task introducing force fields will be used to generate an expectation mismatch.
The proposed study aims to significantly improve the understanding of computations, including learning-related adaptations, in the cerebellar cortex to shed light on the basic processing performed in neuronal circuits.

2018 -
Career Development Awards

Towards a quantitative understanding of the mechanistic coupling of X-inactivation and pluripotency


Otto-Warburg Laboratory - Max Planck Institute for Molecular Genetics - Berlin - GERMANY

During embryonic development a series of gene expression programs are executed in a tightly controlled, quantitative manner. A multitude of developmental processes must progress in a highly coordinated fashion governed by complex gene-regulatory networks. To elucidate the regulatory principles that allow the coordinated execution of multiple developmental processes I propose to investigate the interplay between X-chromosome inactivation and cellular differentiation, which occur during early embryogenesis of mammals and can be recapitulated in female mouse embryonic stem cells in cell culture. X-inactivation is initiated by up-regulation of the long non-coding RNA Xist, which will mediate gene silencing of the entire chromosome in cis. Xist up-regulation is thought to be triggered by down-regulation of pluripotency factors that repress Xist in undifferentiated cells. More recently however I discovered that X-inactivation will also feed back into the differentiation process, suggesting a more complex interplay between these two events. I propose to combine several experimental and theoretical approaches to elucidate the structure and function of the underlying regulatory network. To this end, we will perform CRISPR-based screens to identify key regulators that mediate these interactions and perform quantitative perturbation experiments of the identified factors. We will use these data sets to discriminate between alternative topologies of the underlying regulatory network and to develop a quantitative predictive mathematical model. In this way I hope to gain a quantitative understanding of a complex regulatory network that governs early mammalian development.

2018 -
Long-Term Fellowships - LTF

Deciphering metabolic rewiring of cysteine metabolism for redox control in cancer cells


Cancer Biology and Genetics - Memorial Sloan Kettering Cancer Center - New York - USA

THOMPSON Craig B. (Host supervisor)

Cancer cells undergo metabolic reprograming to sustain proliferation and to enable metastatic outgrowth, but this results in oxidative stress limiting cancer progression. Cancer cells are able to overcome their distorted redox balance, however, mechanisms providing redox tolerance during cancer progression are not well understood. Redox tolerance is largely provided by cysteine-derived glutathione, the major cellular antioxidant. Despite the clear biological relevance of cysteine metabolism, the role of de novo cysteine synthesis (transsulfuration) for cancer progression remains elusive. Our objective is to unravel the contribution of the transsulfuration pathway to redox control in cancer cells. We hypothesize that metastasizing cancer cells circumvent the need for cysteine import by activating the transsulfuration machinery to overcome oxidative stress-induced cell death. In this research program, we will explore whether induction of transsulfuration can sustain redox control in cancer cells under cysteine deprivation, identify factors that drive or limit utilization of the transsulfuration pathway, and define the role of the transsulfuration pathway and its regulating factors for cancer progression. To reach these aims, we will employ cell culture and in vivo models, state-of-the-art metabolomics, CRISPR/Cas9 screening, and test the validity of the findings in human cancer specimen. My approach will create a better understanding of transsulfuration in the context of cancer and elicit novel concepts of redox control mechanisms. As result, this research program will shed light on unprecedented tumour vulnerabilities that could be exploited as anti-cancer therapy.

2018 -
Long-Term Fellowships - LTF

How actin generates force in clathrin-mediated endocytosis – a cryo-electron tomography study


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

DRUBIN David G. (Host supervisor)
DAVIES Karen (Host supervisor)

Clathrin-mediated endocytosis (CME) represents a main pathway that enables cells to take up extracellular and membrane-associated material. Membrane tension represents a major obstacle for vesiculation during CME. In mammalian cells, force provided through actin polymerization is required for formation of deep membrane invaginations and neck constriction for efficient CME under high membrane tension conditions.
The goal of the research described in this proposal is to build a structural model for how actin provides force during CME in mammalian cells. By applying state-of-the-art cryo-electron tomography, I will investigate the three-dimensional architecture of the actin network during CME progression in mammalian cells. Using a previously described cryo-electron tomography compatible protein tag, I aim to create a molecular map for actin interactors that mediate CME. Additionally, I propose that the actin network adapts to plasma membrane tension in CME through changes in filament and associated molecule number as well as filament organization. To test this hypothesis, I will manipulate membrane tension prior to sample preparation for examination by cryo-electron tomography. The data obtained will be used to create a comprehensive prediction model for force generation by actin in CME.

2018 -
Long-Term Fellowships - LTF

Extracellular vesicles and their role in immune homeostasis


Department of Pathology - University of California - San Francisco - USA

KRUMMEL Matthew F. (Host supervisor)

The ability to tolerate an evolving definition of ‘self’, is crucial for every living being, however, its origin and complexity is barely understood. Recently, extracellular vesicles (EVs) have been shown to promote tolerance in cancer. Additionally, antigen-presenting cells (APCs) can transport tumor- and self-derived EVs to lymph nodes where immune responses can be generated. As tumors rarely invent pathways but rather use available tools I hypothesize that EV transfer is a yet unrecognized, major mechanism in immune homeostasis. Here, I will assess the impact of self-antigen transfer during immune homeostasis. I will perturb the system with viral infections to discriminate the role of tolerogenic EV-transfer from the transfer during an immune response.
I will use mice expressing ZsGreen in alveolar epithelium and infect them with dsRed-labelled influenza to label ‘self’ and ‘foreign’. APCs in draining lymph nodes will be assessed for EV transfer through marker expression. I will visualize transferred EVs with lattice light sheet microscopy, and with large antibodies panels that delineate vesicular pathways, to discriminate handling and fate of EVs associated with influenza from tissue-derived EVs. Both EV types and APCs bearing them will be tested for their potential to elicit an immune response. Furthermore, EVs will be subjected to quantitative proteomics to understand how ‘self’ is encoded. Finally, an in vitro CRISPR screen followed by functional assessment in mice will identify regulators of EV release and uptake. Assessment of EV fate, content and origin in immune homeostasis will lay the foundation for future therapeutics in autoimmunity and cancer treatment.

2018 -
Long-Term Fellowships - LTF

How dinosaurs lost their tails: unveiling the developmental origins of a major evolutionary shift


Department of Pathology - Brigham and Women's Hospital - Boston - USA

POURQUIE Olivier (Host supervisor)

The evolution of birds from dinosaur ancestors was accompanied by numerous changes in morphology. Of these, the near-complete loss of the tail was arguably the most significant single anatomical modification. While the fossil record has demonstrated the progressive loss of this main appendage, the underlying mechanisms that caused this remain unknown. Our project aims at understanding the developmental pathways that changed over the course of dinosaur to bird evolution giving rise to the modern avian tail. Since this change in morphology occurred quite fast in evolutionary terms, we hypothesize that discrete changes in gene expression potentially had an organ-wide effect on adult morphology, effectively stunting tail formation as a whole. Because non-avian dinosaurs no longer exist, this project will instead use American alligators, as they are the closest living relatives to birds, and will compare their embryonic development and genetics to the domestic chicken. We will focus on differences that exist at an anatomical level, and relate them to tissue and cell dynamics by performing a detailed characterization of posterior axis formation between species, using techniques such as in situ hybridization, immunofluorescence and cell-fate analysis. We will also create for the first time a full transcriptome of tail development in both alligators and chickens. We will use this information to then perform cutting-edge functional studies combining in vivo electroporation, alligator-chicken xenotransplantations and avian germ-line transgenesis, in order to precisely find the genes and cell behaviors that changed in tail development over the course of bird evolution.

2018 -
Long-Term Fellowships - LTF

Modulation of single cell volume and mass growth dynamics by intrinsic and extrinsic factors


Laboratory of Subcellular Structure and Cellular Dynamics - Institut Curie - Paris - FRANCE

PIEL Matthieu (Host supervisor)

Cells that make up the same tissue or organ tend to have a stereotypic physical size, while variability in cell size is a marker of abnormal cell growth. Cell size homeostasis depends on a coordination between growth and cell division cycle. How size homeostasis is achieved in mammalian cells is still debated and contributions remain scarce due to the difficulty in measuring cell size parameters accurately.
In this project, I propose to combine two independent and precise methods for cell size measurement: quantitative phase microscopy to measure cell dry mass and fluorescence exclusion, developed in host lab, to measure cell volume. Furthermore, I will introduce well-controlled perturbations in the cell environment, in culture medium and physical environment of cells, such as depletion of nutrient and growth factors, modulation of cell adhesion and spreading, as well as cell confinement. This will provide a general picture of the dynamics of single cell mass and volume as a function of environmental parameters.
Specifically, I will:1) record and study fluctuations in mass and volume growth across the cell division cycle and 2) Study mechanisms that couple mass and volume thus modulating cell density.
Additionally, physiological relevance will be studied using activation of primary naïve T-cell differentiation in culture, where a drastic increase in cell size precedes asymmetric divisions in size and fate.
This work will provide a fundamental understanding of how normal and cancer cells grow and regulate their size. It will also elucidate functional consequences of modifications in mechanisms of mass/volume coupling during the development of specific immune functions.

2018 -
Long-Term Fellowships - LTF

Neuronal networks of salience and spatial detection in the murine superior colliculus


Department of Neuroethology - Institute of Science and Technology Austria - Klosterneuburg - AUSTRIA

JOESCH Maximilian (Host supervisor)

Though the central task of the brain is to detect important sensory stimuli to shape appropriate behaviors, our mechanistic understanding of the underlying neural processing is scarce. Here I propose a research plan that will explore the neuronal operations that transform visual information into behavior in the superior colliculus (SC). The SC has been assigned a role in extracting visual saliency, processing spatial attention and instructing goal-directed behaviors across species. Technical and methodological limitations, however, have restricted a detailed mechanistic understanding these critical neuronal computations. Here I aim to overcome these barriers by taking advantage of the modern neurogenetic tool-box and adapt the mouse as a model organism to study visual spatial and salience processing in the SC. Head-fixed mice will be trained to report the presence and location of a differing, salient stimulus among a row of identical stimuli in a sensorimotor two-alternative forced choice detection task. Simultaneous optical recording of the activity of thousands of genetically defined SC neurons, in combination with optogenetic manipulations and intracellular electrophysiology, will allow matching neural transformations to the animal’s performance. The proposed design permits testing and comparing neuronal responses to a wide range of stimulus features, the analysis of context dependent neural coding principles (e.g. salience), attention, as well as the interrelationship of neural and psychophysical discrimination capabilities. Together, this multidisciplinary approach will determine how neural circuits encode and transform sensory signals to guide directed behavior.

2018 -
Long-Term Fellowships - LTF

Understanding the molecular mechanism for biased signaling in G protein-coupled receptors


Department of Computer Science, Department of Molecular and Cellular Physiology - Stanford University - Stanford - USA

DROR Ron (Host supervisor)

G protein-coupled receptors (GPCRs) comprise the largest class of human membrane proteins and are targeted by a third of all existing drugs. Remarkably, in a process called biased signaling, different extracellular ligands binding to the same GPCR can trigger distinct intracellular signaling pathways by favoring either G protein or arrestin activation. Despite dramatic progress in the structural biology of GPCRs and their intracellular binding partners, little is understood about arrestin activation and how biased signaling is achieved. In this work, I will use extensive atomistic molecular dynamics simulations to elucidate GPCR-mediated arrestin activation and how it differs from G protein activation. I will closely collaborate with experimental scientists and design complementary experiments that validate and guide the simulations. The research will identify GPCR conformations and phosphorylation patterns that preferentially couple to either G proteins or to arrestins, providing a foundation for the rational design of biased ligands that selectively induce specific signaling profiles. Uncovering how biased signaling occurs at the molecular level is essential not only for a deeper understanding of biological signaling, but also for the development of safer and more efficient drugs, such as superior antipsychotics, medications for heart and pulmonary disease, and powerful pain medications that lack the dangerous side effects of current opiates.

2018 -
Long-Term Fellowships - LTF

Revealing the biophysical mechanisms for transparency and near infrared reflectance in animals


Department of Biology - Duke University - Durham - USA

JOHNSEN Sönke (Host supervisor)

Transparency and enhanced near-infrared (NIR) reflectance are two fascinating and widespread characteristics found in a broad array of animals. However, despite some functional and ecological claims, the biophysical bases for their occurrence in nature are largely unknown. Since the physics of light scattering is well understood, theoretical models have suggested different routes for achieving each phenomenon by modification of variables like refractive index, size, shape and stacking parameters of cellular and extracellular scatterers. The proposed project aims to provide a deep empirical and transdisciplinary analysis of the predicted ultrastructural, physical and chemical properties of transparent and NIR reflecting tissues. To accomplish this objective I propose to use glass frogs (Centrolenidae) as an ideal study system in which both optical phenomena coexist. First, I will design a set up for correct measurements of diffuse and direct transmittance spectra of frogs’ tissues to objectively quantify transparency. Ultrastructure analysis will be performed by TEM, SEM and FIB-SEM to identify main intra and extracellular scatterers and accurately measure their size and distribution. Based on this ultrastructure information I will use Monte Carlo methods, finite element analysis, finite difference time domain, and discrete dipole approximations to model light propagation in order to explain how transparency and NIR reflectance are attained.

2018 -
Long-Term Fellowships - LTF

How mechanical stress determines the direction of cell division plane in plants


The Plant Reproduction and Development Laboratory - ENS Lyon - Lyon - FRANCE

HAMANT Olivier (Host supervisor)

Cell geometry, hormones and mechanical stress have all been involved in Cell division plane orientation (CDPO), yet the corresponding molecular mechanisms remain unknown notably because 1- CDPOs are more variable than initially anticipated, 2- the relation between microtubule dynamics and CDPO robustness has not been analyzed, 3- the mechanotransduction pathways controlling CDPO are unknown. Using 4D live imaging, quantitative image analysis and biomechanics, I will analyze how microtubule dynamics is used, or filtered out, to generate robust cell division planes, and in turn how tissue tension feed back on microtubule dynamics to control CDPO. Using the Arabidopsis shoot apical meristem as an experimental system, I will draw a correlation map between microtubule dynamics, cell shape and growth, cell cycle, and CDPO and identify the spatio-temporal scales at which these correlations exist. I will then test the corresponding causalities using mutants affected in microtubule functions and CDPO robustness (TTP complex), mechanosensing (e.g. FER, DEK1), and micromechanics (compression, ablation, inducible lines and mosaics with cell wall defects). I will thus challenge the robustness of cell divisions and characterize the mechanotransduction pathways controlling CDPO.

2018 -
Long-Term Fellowships - LTF

The complexed interactions of mAtg9 membrane protein in the regulation of autophagy


Biological Chemistry and Physiology - University of California, Los Angeles - Los Angeles - USA

GONEN Tamir (Host supervisor)

Autophagy is a vital cellular process in all eukaryotes in which cytoplasmic organelles, proteins, and pathogens are inexplicably engulfed in a double membrane and transported to the lysosome for degradation and recycling. While the biochemistry is still poorly understood, defects in autophagy are known to result in different pathologies including inflammatory, neurodegenerative, and neoplastic diseases.
More than 30 proteins orchestrate autophagy, including the single membrane protein Atg9 which participates in different complexes that regulate the initiation and trafficking of the autophagosome. Although protein partners and molecular mechanisms are relatively known for Atg9 in yeast, not much is known for the mammalian counterpart. Elucidation of the atomic structures of Atg9 and its complexes from yeast and human would provide important mechanistic insights, and may guide the detection of additional partners for the mammalian homolog, and the development of new pharmaceuticals.

I propose to use leading methods in cryogenic electron-microscopy (CryoEM) to determine the structures of both the yeast and human Atg9 proteins alone, and in various functionally important complexes. Specifically, I would focus on electron micro-diffraction (MicroED), electron crystallography, and single particle reconstructions (SP). Overall I aim to join the Gonen laboratory to gain new expertise in membrane protein structural biology, as well as in the aforementioned cryoEM methods, and to encounter new biological systems by exploring the otherwise inaccessible membrane protein complexes involved in autophagy, a crucial yet poorly understood process.

2018 -
Career Development Awards

Dissecting pediatric high-grade glioma by single cell expression profiling


Department of Molecular Cell Biology - Weizmann Institute of Science - Rehovot - ISRAEL

Pediatric high-grade gliomas (pHGG) are the number one cause of cancer-related death in children. Intra-tumor heterogeneity is widely accepted as a major bottleneck for successful cancer treatments and has not been characterized in pHGG. Heterogeneity in clinical tumor samples is governed by cancer cells genetics, their differentiation lineages, cancer stem cell programs and the tumor micro-environment (TME). We recently established the application of single cell RNA sequencing (scRNA-seq) to adult gliomas, demonstrating the ability to identify diverse tumor subclones, redefine cancer stem cell programs and characterize their TME. Here, we propose to extend these approaches to pHGG in order to: (i) Characterize the cellular states within pHGG patient samples, and to identify putative cancer stem cells and differentiation programs; (ii) Evaluate the capacity to model pHGG through analysis of patient-derived cellular and mice models; (iii) Compare the cellular states of distinct pediatric and adult glioma subclasses, leveraging datasets from multiple projects towards an integrated view of glioma classification and biology; (iv) Use the emerging collection of cellular states in adult and pediatric gliomas to deconvolute the compendiums of bulk glioma samples, and model each tumor as a combination of distinct cellular states. This will extend our work to hundreds of glioma samples measured in bulk, and would facilitate the association between tumor composition and clinical features. Through these studies we expect to fundamentally change the understanding of pediatric glioma and provide guidance for new therapeutic approaches.