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2019 -
Long-Term Fellowships - LTF

Circuit mechanisms for visual stability

TREMBLAY Robin (CANADA)

- Institute of Molecular and Clinical Ophthalmology - Basel - SWITZERLAND

ROSKA Botond (Host supervisor)

Our eye movements constantly generate motion patterns on our retina, yet our perception of objects in space remains stable. For the brain to recognize self-generated visual motions to construct an image that is spatially invariant of one’s own movement, retinotopic visual information has to be integrated with eye position. Primate studies have shown cortical areas containing neurons responding to different combinations of these two reference frames, and perturbations of these areas suggest a role for space perception. However, little is known about the cellular and circuit mechanisms by which reference frame transformations underlying visual stability occur. I propose to fill that void by bringing this field into mouse research where methods to monitor, perturb and dissect neurons and circuits in much more precise and targeted ways are possible. Using preparations in which visual inputs, eye positions and eye movements are experimentally tracked and controlled will allow me to isolate visual, proprioceptive and motor components. Brain-wide functional ultrasound imaging will reveal areas activated by each component alone or in combination. Calcium imaging will then provide large population responses with single cell resolution. Finally, single-cell-initiated rabies tracing and whole-cell recording will be used to delve into the circuit and synaptic mechanisms underlying the functional properties we find among different neuronal populations. This project will accelerate the field of visual stability, and more generally sensorimotor integration, by providing a new niche where cellular and circuit mechanisms can be thoroughly dissected.

2019 -
Long-Term Fellowships - LTF

A new reversible lesion technique for studying the primate brain in naturalistic environments

TREMBLAY Sebastien (CANADA)

Department of Neuroscience - University of Pennsylvania - Philadelphia - USA

PLATT Michael (Host supervisor)

Understanding how the brain works is the next great frontier in biology. One can choose among many available tools and approaches to undertake this challenge. One approach that has proven successful is to investigate the necessary role of a brain area as a first step before trying to understand the neural mechanisms by which it accomplishes its role. To identify the necessary role of a brain area, one needs to manipulate its activity with causal research methods. Optogenetics is a new causal research method that brought about a revolution in brain research conducted with rodents and small animals. Unfortunately, the same cannot be said about optogenetics when applied to animals more similar to humans, such as non-human primates. The larger primate brain poses new challenges to the success of this powerful research method. In this research project, I will develop a new optogenetic-based reversible lesion technique that addresses these challenges. Moreover, I will do so while freeing non-human primates from the physical restraints imposed on them for the practical purpose of accessing their brain. This original method will put together three new technologies: inhibitory step-function opsins, convection-enhanced delivery of opsins, and chronically implanted LED illuminators that are wirelessly activated. With this tool, it will be possible to study for the first time the causal role of brain areas of monkeys that are behaving in naturalistic environments. I will apply this tool to the study of social cognition in monkeys interacting with their peers, and borrow well-studied behavioural tasks from ethology and primatology to develop the emerging field of neuro-ethology.

2019 -
Cross Disciplinary Fellowships - CDF

Modelling the sequence - structure - function relationship in proteins with machine learning

TUBIANA Jérôme (FRANCE)

Edmond J. Safra Center for Bioinformatics - Tel Aviv University - Tel Aviv - ISRAEL

WOLFSON Haim (Host supervisor)
ZUK Or (Host supervisor)

Understanding and exploiting the sequence - structure - function relationship is one of the fundamental goals of bioinformatics. Systematic predictions of protein structure, function and interactions could provide a global understanding of the protein interaction networks that underlie cell’s life. Conversely, being able to design molecules, peptides or proteins with a prescribed fold or function is a promising lead for drug design. Unfortunately, current state-of-the-art remains far away from this goal. Indeed, direct approaches based on physical interactions, such as Ab Initio Molecular Dynamics (MD) or Fragment-based folding are often either too computationally expensive or inaccurate. Recently, important progress were achieved in structure, function and protein-protein interactions prediction by the introduction of coevolution-based approaches such as Direct Coupling Analysis (DCA). Though powerful, such models are strongly limited in practice because they require many sequences from the same family in order to accurately predict structure. One natural explanation is that they lack general knowledge of proteins biochemistry, such as amino-acid similarity and stereotypes of interactions. Here, we propose to leverage recent advances in the fields of transfer learning and deep generative models to design new coevolution models that share knowledge between protein families, and thus would be more efficient than naive DCA. Beyond structure prediction, we also propose new general-purpose architectures that aim at learning directly the sequence - structure - function relationship, and discuss applications to protein function prediction and sequence/fold designs.

2019 -
Long-Term Fellowships - LTF

Role of functional connectivity dynamic changes to cognitive control-mood interplay

VAGHI Matilde (ITALY)

Department of Psychology - Stanford University - Stanford - USA

POLDRACK Russell (Host supervisor)

This project aims at clarifying how brain connectivity fluctuations over time relate to mood changes and its interplay to cognitive control. Three specific aims are defined. 1) I will clarify how aberrant mood responses contribute to cognitive control abilities. 2) I will identify how mood fluctuations over short timescales of days to months impact cognitive control abilities. 3) I will investigate how dynamic changes in brain connectivity relates to mood changes and its interplay with cognitive control.
I will use reinforcement learning algorithms and computational models of mood to describe cognitive control-mood interplay and determine how aberrant mood reactions relate to impaired behavioural adjustment. To this end, I will investigate cognitive control-mood interplay in a large sample of healthy adolescents and adolescents with clinical and subclinical depression as impaired mood reactivity is mostly pronounced in this population. Behavioural data of cognitive control–mood interplay will be used conjointly with functional resting state brain imaging data. Repeated, longitudinal assessment at the behavioural and brain level will elucidate dynamics of network configuration over time and how they impact on mood changes and its interaction with cognitive control. With this project I aim to reach a mechanistic understanding of cognitive control-mood interplay and associated brain networks. The project has also implications for the understanding of symptoms of depression, which is a major, leading cause of disability.

2019 -
Long-Term Fellowships - LTF

Unraveling regulation of mutagenesis by DNA damage and antibiotic stress responses in single cells

VINCENT Maxence (FRANCE)

Department of Biochemistry - University of Oxford - Oxford - UK

UPHOFF Stephan (Host supervisor)

Classical ensemble experiments have been used to characterize DNA damage responses that protect bacterial cells against the toxic and mutagenic effects of DNA damage and stress conditions. More recently, examining the underlying gene regulatory mechanisms at the level of single cells and single molecules revealed unexpected stochastic effects that cause cellular heterogeneity in the damage response. These observations provoke the question whether variations in gene expression modulate DNA repair activities and the rates of mutagenesis of individual cells.

I will address this fundamental question using the E. coli adaptive response to DNA alkylation damage as a model. It has been shown that the regulator protein Ada exhibits extreme variation in gene expression between cells in an isogenic population. Using single-cell expression reporters and single-molecule tracking, I will investigate how this variation affects the expression and DNA repair activities of the genes that are regulated by Ada, namely aidB, alkA and alkB. I will then link phenotypic and genetic variation by whole-genome sequencing of single-cell isolates. This will uncover the impact of DNA repair heterogeneity on mutagenesis at the genome level. Finally, I will investigate the role of the adaptive response in antibiotic-induced mutagenesis.

Because the DNA repair pathways are highly conserved, my findings will also impact our understanding of DNA repair and mutagenesis in eukaryotes.

2019 -
Long-Term Fellowships - LTF

Mechanisms controlling development of aggression

VINOGRAD Amit (ISRAEL)

Division of Biology - Caltech - Pasadena - USA

ANDERSON David (Host supervisor)

Aggression, manifested in violence and brutality, poses major risks to our society. While our understanding of the neural correlates of aggression progressed substantially, how aggression is developed and why, remains an open question. Part of this gap is due to the view of the neural circuitry of aggression as fixed, making aggressive behaviors inevitable. Yet, recent advances in the anatomical and genetic basis reveal that aggression has an experience dependent aspect, holding great promise for unraveling the mechanisms of aggression. Aimed at revealing the mechanisms that control aggressive behaviors, this study leverages experience dependent plasticity in tandem with a fusion of circuit and cellular level approaches.
Using a combination of advanced technologies including 2-photon imaging in head fixed mice, single cell RNA sequencing, a combination of 2-photon imaging with in-situ hybridization and gene editing with CRISPR/CAS9, three questions are addressed: 1. What are the changes in neuronal activity following experience dependent plasticity? 2. What are the genetic changes that are associated with the alterations found in neuronal activity? 3. What links these genetic changes to neuronal activity and aggression?
Joining cellular level and circuit level approaches to examine how aggression is developed by experience dependent plasticity should yield a new understanding on the relationship between genes, neuronal function and aggressive behavior. By discovering these basic features in the mechanism underlying aggression, the knowledge obtained from this study could open the path to a new era in which prevention of pathological aggression will become feasible.

2019 -
Cross Disciplinary Fellowships - CDF

Cellular resolution neuronal activation and recording in freely moving flies and fish

VO Doan Tat Thang (VIETNAM)

Institute of Biology I - University of Freiburg - Freiburg - GERMANY

STRAW Andrew D. (Host supervisor)

Functional imaging and optogenetic activation of neural circuits during behavior of untethered animals would allow detailed investigation into the closed-loop interaction of sensory inputs, brain, and motor outputs of behaviors in naturalistic conditions. Previous work investigating the role of Drosophila central complex in navigation and the optic tectum of larval zebrafish in prey capture have been informative, but tethering the animals in such experiments has limited the extent to which circuit mechanisms for multi-sensory, closed-loop control could be investigated. I propose to achieve cellular resolution neural activation and recording in freely moving Drosophila and larval zebrafish, by developing a system for aiming a fast volumetric two-photon microscope to precisely follow, with minimal latency, a region in the animal’s brain. The “feedback based lock-on module” provides low latency feedback to aim the imaging volume of the microscope. Integrating the lock-on module to a fast two-photon microscope based on Bessel beam optics along with an optogenetic stimulator will enable closed-loop analysis of neural mechanism of animal behaviors. The system will then be used to study neural activities of the Drosophila central complex during idiothetic path integration and optic tectum of larval zebrafish during prey capture after expressing GECIs and optogenetic channels into the various sets of neurons using different binary expression systems like GAL4 and LexA.

2019 -
Long-Term Fellowships - LTF

The coevolution of transposable elements and zinc finger proteins across the vertebrate phylogeny

WELLS Jonathan (UK)

Department of Molecular Biology and Genetics - Cornell University - Ithaca - USA

FESCHOTTE Cédric (Host supervisor)

Transposable elements (TEs) comprise a substantial proportion of all vertebrate genomes, including more than half of our own. They are particularly active in the germ line and during development, and impose an significant evolutionary burden on organisms. As such, numerous mechanisms have evolved to control their spread, including the KRAB zinc finger (KZF) family - the largest and most diverse group of transcription factors in mammals. Strong evidence points to an arms race between TEs and KZFs, and their genome frequencies are highly correlated across diverse vertebrate species. However, KZFs are involved in numerous biological processes beyond TE repression, and we do not yet understand how coevolution with TEs has produced this functional diversity in vertebrates. In addition, whilst the KZFs are mostly limited to tetrapods, other large ZF subfamilies exist outside of this lineage, and the roles of many of these are completely unknown.

Using a comparative and functional genomics approach, I will investigate the dynamics of TE-ZF coevolution, in order to better understand how this phenomenon has shaped the architecture and regulation of vertebrate genomes. Specifically, I will test the hypothesis that TE insertion near ZFs leads to co-regulation of their activity, and furthermore, that this process drives the genomic clustering of ZFs. In parallel, I will use functional techniques and long read re-sequencing to undertake a comprehensive study of of a large, un-described and mysterious family of ZFs in zebrafish. In doing so, I hope to open new lines of research in this essential model organism of embryogenesis and development.

2019 -
Long-Term Fellowships - LTF

Manipulation of linear plasmids in vivo for enhanced homologous recombination

WILLIS Julian (UK)

Broad Institute of MIT and Harvard - Harvard University - Cambridge - USA

LIU David (Host supervisor)

The genome editing field is currently limited in its control over how double-strand breaks can be selectively repaired by non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways. By providing a donor DNA template, HDR offers potential for corrective therapies targeting a much larger number of genetic diseases which cannot be cured by either single nucleotide substitutions or gene inactivation alone. Yet the efficiency of HDR remains considerably lower than that of NHEJ, hampering its usefulness for therapeutic applications. The use of linear plasmids for enhanced homologous recombination in this proposal directly aims to tackle this challenge and should drive efficient genome editing towards clinical translation.

Unlike circular plasmids which are a ubiquitous tool used throughout modern molecular biology, linear plasmids are an underappreciated biological phenomenon despite being widespread in nature. What constitutes their biological function and what genes they encode is largely unknown. The ability to manipulate linear plasmids in vivo will provide a powerful tool to study and understand their biological significance for the first time. Linear plasmids are double-stranded DNA genetic elements characterised by terminal proteins covalently attached to the 5'-end of each linear DNA strand. In particular, the feature of a terminal protein covalently linked to DNA is a strong prospect for biotechnology applications: I will exploit such linear plasmid systems in mammalian cells for enhanced homologous recombination.

2019 -
Cross Disciplinary Fellowships - CDF

Applying surface chemistry techniques to study electron-transfer in conductive proteins and biofilms

WOOD Mary (UK)

Laboratory of Nanobiotechnology - EPFL - Lausanne - SWITZERLAND

BOGHOSSIAN Ardemis (Host supervisor)

The overall aim of the proposed work is to develop new physical chemistry/bioelectrochemistry techniques in order to better understand the electron-transfer mechanisms of conductive biofilms at the electrode surface. This will have immediate benefits in the development of the promising renewable biophotovoltaic (BPV) technology as well as long-term significance for improvements in understanding the role of key biological electron-transfer species across a broad range of systems.

BPVs use photosynthetic biofilms to harvest solar energy and then convert this into electrical current. They are, however, limited in power output due to unexpectedly slow electron-transfer at the biofilm/electrode interface, and it remains unclear why this is. There is an urgent need to improve fundamental understanding of these electron-transfer mechanisms in order to direct future development of BPVs and remove this bottleneck for their maximum efficiency.

Here, we propose the combination of a number of sophisticated and highly-specialised surface-study techniques in combination with the bioelectrochemistry, synthetic biology and electrode design already in place in the host group, to study the key species (such as the individual redox proteins and complexes) both individually and in situ within model lipid bilayers and finally within the biofilms themselves. Importantly, this will allow us to build up a mechanistic picture of each aspect of these complex buried biointerfaces and hence distinguish between different electron-transfer mechanisms (e.g. via pili aromatic amino acids, outer-membrane redox proteins or diffusional shuttles) that are currently proposed.

2019 -
Long-Term Fellowships - LTF

Elucidating the functional asymmetry of echolocation and communication systems in odontocete brains

WRIGHT Alexandra (USA)

School of Biology - University of St. Andrews - St. Andrews - UK

TYACK Peter Lloyd (Host supervisor)

Most odontocete cetaceans (toothed whales, dolphins, and porpoises) produce echolocation and communication sounds using bilateral pairs of sound-generating phonic lips. The production of high-frequency echolocation clicks and analysis of the returning echoes allow foraging odontocetes to detect, localize, and capture prey. Communication between odontocete conspecifics is mediated by family-specific sounds, with dolphins producing low-frequency whistles and porpoises emitting high-frequency social clicks. Previous research on the lateralization of sound production in dolphins suggested a left hemisphere bias for echolocation and a right hemisphere bias for conspecific communication; however, similar to other behavioral studies of cetacean lateralization, hemispheric specialization was inferred, rather than measured. Here, I aim to perform the first assessment of hemispheric specialization for the production and perception of echolocation and communication sounds in the bottlenose dolphin (Tursiops truncatus) and harbor porpoise (Phocoena phocoena). Using bioacoustics approaches, novel species-customized electroencephalography-functional near-infrared spectroscopy (EEG-fNIRS) arrays, and functional magnetic resonance imaging (fMRI), I will directly and indirectly measure neural activity underlying motor control and auditory sensation in these odontocetes. In addition to providing unprecedented insights into cetacean brain function, this project has the potential to redefine the limits of neuroscience and animal behavior research through the introduction of portable, non-invasive, and customizable EEG-fNIRS equipment that can be adapted for taxonomically diverse species.

2019 -
Long-Term Fellowships - LTF

Designing a new class of protein ligands to control cell surface receptor signaling

YANG Aerin (KOREA, REPUBLIC OF (SOUTH KOREA))

Department of Molecular and Cellular Physiology - Stanford University - Stanford - USA

GARCIA K. Christopher (Host supervisor)

Cytokines act as essential regulators of immunity by eliciting signaling outputs from cell surface receptors. There have been extensive efforts to use cytokines for a wide range of immune disease, including cancer, but their functional pleiotropy has limited their clinical utility. Precedent studies in the Garcia lab, demonstrated that surrogate cytokine ligands can alter signaling output by modifying receptor dimer geometry. For more precise topological control of receptor-ligand interactions and signaling, we hope to create a new class of modular binding scaffold proteins which are applicable to diverse receptor targets. The new scaffolds will be computationally designed and engineered to have three major characteristics: (i) high binding specificity to a target receptor, (ii) self-assembly to form dimers or trimers, (iii) drug-like properties including minimal immunogenicity. These scaffolds will be used for manipulating the geometry of cell surface receptors to fine-tune of signaling outputs. These novel scaffolds can also be utilized to drive the formation of non-natural receptor pairings to elicit completely new functional outputs. Proof-of-concept experiments from Garcia lab have shown that non-natural receptor dimers of receptor tyrosine kinases (RTK) can induce different signaling outputs from each of their parental receptors. We believe that the new scaffolds can efficiently combine any cytokine receptor and RTK to form diverse combinations of dimeric or trimeric receptor pairs. In this way, it will help us to broaden our knowledge on kinase-linked receptor signaling and also have a chance of finding new agonistic and therapeutically meaningful protein ligands.

2019 -
Long-Term Fellowships - LTF

Single-cell DNA methylation dynamics of stem cell differentiation across intestinal crypts

YEUNG Jake (CANADA)

Laboratory of Quantitative Biology - Hubrecht Institute - Utrecht - NETHERLANDS

VAN OUDENAARDEN Alexander (Host supervisor)

Intestinal stem cells, which reside in crypts, fuel self-renewal, maintenance, and repair of the epithelial lining of the gut. The regulatory mechanisms that govern maintenance and differentiation of intestinal stem cells, as well as structural and functional differences along regions of the intestine are poorly understood. DNA methylation (DNAme) holds potential in deciphering these mechanisms by revealing gene regulation and clonal structure of cell populations.

The goal is to investigate the dynamics, diversity, and function of DNAme patterns regulating intestinal epithelial homeostasis at single-cell resolution. This proposal will survey single-cell DNAme of intestinal crypts at three anatomical scales: dynamics within individual crypts, diversity between neighboring crypts, and region-specific diversity from proximal to distal sections of the small intestine. Our hypothesis, which builds on preliminary data, is that DNAme patterns of intestinal cells are largely determined by the clonal history of these cells and therefore hold promise as an endogenous lineage tracing tool. To test this hypothesis, I will use a range of single-cell sequencing techniques and develop computational methods to pursue three specific aims:

Aim 1: Determine the single-cell DNAme dynamics within intestinal crypts.

Aim 2: Analyze the diversity of DNAme patterns between crypts along different regions of the intestine.

Aim 3: Disentangle the contribution of cell-type and clonal history in DNAme patterns.

This proposal combines computational with experimental approaches, and leverages existing collaborations between the van Oudenaarden and Clevers labs at the Hubrecht Institute.

2019 -
Long-Term Fellowships - LTF

Unwrapping myelin plasticity in health and disease

YEUNG WONG Maggie Sui Yan (SWEDEN)

Department of Neurology - UC San Francisco - San Francisco - USA

CHAN Jonah R. (Host supervisor)

The brain has a remarkable capacity for combining long-term memory with exquisite plasticity allowing for adaptation to the environment. A growing aspect of neural plasticity is modulation of myelination. How can myelination be altered? Myelination can be altered by the generation of new myelinating oligodendrocytes or alternatively by mature myelinating oligodendrocytes rendering their existing myelin. The current dogma is that continuous generation of oligodendrocytes underlies myelin remodeling—even though the contribution of mature oligodendrocytes remains poorly understood. Here I propose a multidisciplinary approach, combining my expertise in human cell biology with Dr. Chan’s extensive proficiency in oligodendrocyte biology to study the cellular and molecular mechanisms underlying myelin alterations upon induced neuronal activity and after injury. I plan to explore the myelinogenic potential of mature oligodendrocytes and their contribution to myelin remodeling. This strategy combines genetic fate-mapping and manipulation of oligodendrocyte lineage cells, in vivo pharmacogenetic neuronal stimulation (DREADDs) with single cell, temporal-resolved gene expression analysis and behavioral assessment. More specifically, genetically altered progenitors unable to generate new oligodendrocytes and mature oligodendrocytes will be labeled and profiled using single cell RNA-seq. This will allow for the longitudinal assessment of genes involved in activity-dependent myelination and the consequence of this manipulation. Knowledge of myelin plasticity is essential for the development of new treatments for demyelinating disease such as multiple sclerosis.

2019 -
Career Development Awards

A molecular approach to brain sexual dimorphism: cell types and circuits in the medial amygdala

ZEISEL Amit (ISRAEL)

Faculty of Biotechnology and Food Engineering - Technion - Israel Institute of Technology - Haifa - ISRAEL

Neurons are the most diverse class of nervous system cell types, based on thorough characterization of single cells into molecular taxonomies. Individually neurons are fascinating and complicated, but at the core of computation are their interactions. The unique arrangement of circuits between specialized neuronal types results in a wide range of sophisticated functions and complex behaviors. While female and male brains largely perform the same sophisticated functions, the neurobiological basis for gender differences in some behaviors has fascinated researchers over decades. Sexual dimorphism in the amygdala (specifically the posterodorsal medial amygdala, MePD) shapes gender differences in reproductive behavior, aggression or social recognition, with well-established contribution of gonadal steroid hormones. At the core of this dimorphism are neuroanatomical differences of the MePD, such as regional and cell volume, cell number and cell circuitry. While the phenomenon is well established using relatively simple methods, a more global, systematic characterization of differences in circuits in the context of cell types and gene expression has not been technically possible. To this end, I propose to develop and apply an integrated approach for simultaneous connectomics and transcriptomics measurements of the medial amygdala at single cell resolution. This study will reveal the contribution of circuits, cell types and gene expression to gender-based amygdala dimorphism. Further, the proposed framework to understanding circuit implementations in the context of cell types will advance other studies of nervous system function and behavioral neuroscience.

2019 -
Long-Term Fellowships - LTF

Investigating heterochromatin dynamics underlying early development and reprogramming

ZHANG Jingchao (CHINA, PEOPLE'S REPUBLIC OF)

Department of Cell and Developmental Biology - University of Pennsylvania - Philadelphia - USA

ZARET Kenneth S. (Host supervisor)

The goal of this proposal is to understand how heterochromatin functions impose major roadblocks to cell fate changes in development and iPS cell reprogramming. Reprogramming somatic cells into pluripotency by the Yamanaka factors has enormous potential in the regenerative field, although the efficiency remains low. Heterochromatin functions as a major epigenetic barrier to cell fate changes and the Zaret lab showed that its erasure on pluripotent genes at the late stage of reprogramming is a rate-limiting step. However, so far little is known about how heterochromatin domains are established, maintained and reset during development and reprogramming. To fill in this gap, we propose to map the dynamics of heterochromatin formation during mouse peri-implantation, when heterochromatin domains are first established, and to map heterochromatin dynamic resetting in reprogramming intermediates. Taking both natural and reprogramming contexts together, we will construct lineage relationships of heterochromatin dynamics at pluripotency genes as they related to transcription. Finally, to gain temporal and mechanistic insights into heterochromatin regulations of pluripotent genes, we will use a live imaging system to assess directly the consequences of systematic knockdown heterochromatin-associated proteins on the transitions between chromatin topologies and transcriptional activation of pluripotent genes and reprogramming efficiency. Our novel approach of combining datasets and analysis of early development and late reprogramming will contribute to designing robust reprogramming strategies with higher efficiencies and realizing full the potential of iPS cells.

2018 -
Cross Disciplinary Fellowships - CDF

Self-organization of bacterial biofilms as active matter

ALERT Ricard (SPAIN)

Lewis-Sigler Institute for Integrative Genomics - Princeton University - Princeton - USA

WINGREEN Ned S. (Host supervisor)

Biofilms are surface-adhered communities of bacterial cells embedded in a polymeric matrix, and they constitute a major form of bacterial life. Biofilms originate in one of two ways: by clonal proliferation from a single founder cell, or by aggregation of many migrating cells. What are the respective benefits and challenges of these two modes of biofilm growth? To answer this question, we need to understand the physical principles that underlie both modes of biofilm formation. Specifically, for clonal proliferation, it is unclear how cell-level processes, such as directional growth and division, cell adhesion, and heterogeneous matrix secretion, give rise to the evolving macroscopic organization and properties of the mature biofilm. For aggregation, the mechanics of how collective cell migration leads to a biofilm remains controversial. Here, under Prof. N. Wingreen’s supervision, I propose an interdisciplinary approach that will address biofilm formation in two such contrasting systems. Collaborating with Prof. B. Bassler, I will develop an active liquid crystal model to understand the growth and internal ordering of Vibrio cholerae biofilms. Working with Prof. J. Shaevitz, I will investigate whether the aggregation of Myxococcus xanthus constitutes a phase separation or a dewetting transition. Their research programs, respectively, provide single-cell resolution of developing biofilms and traction-force maps of collective cell migration. These data call for active matter models — first to elucidate general principles of self-organization that apply broadly across species, and second to understand the evolutionary selection of species-specific modes of biofilm growth.

2018 -
Long-Term Fellowships - LTF

Development of a microtubule nucleation biosensor

ALI Aamir (INDIA)

Department of Cell and Developmental Biology - Institute for Research in Biomedicine - Barcelona - SPAIN

LUDERS Jens (Host supervisor)

Organizing microtubules (MTs) into arrays is fundamental for many cellular functions and critically depends on MT nucleation by the gamma-Tubulin Ring Complex (gammaTuRC). MT Nucleation occurs from the centrosome as well as from dispersed non-centrosomal sites and is temporally regulated. Although the role of gammaTuRC in MT nucleation is widely accepted, the tools for measuring this activity are severely limited. Current methods rely on indirect readouts using MT plus end tracking proteins, based on the rationale that nucleation generates growing MT plus ends. However, polymerization of MT ends generated by severing enzymes or MT rescue can also result in growing plus ends and may be mis-interpreted as nucleation. To address this, I propose to develop a biosensor for the specific detection of gammaTuRC-dependent nucleation within the cells. I will explore several alternative approaches designed to detect interaction between gamma-tubulin molecules in the gammaTuRC and alpha-beta-tubulin oligomers, as it occurs during nucleation. I will use tagged gamma-tubulin in combination with chemical or protein-based probes to generate a fluorescence signal upon formation of the gammaTuRC/MT interface. The signal will be based on FRET, SPLIT-GFP fluorescence complementation, or aggregation-induced emission by a “turn on” chemical probe. I will then use the biosensor to characterize MT nucleation in cycling cells and in post-mitotic neurons differentiating in vitro. This work will provide unprecedented insights into gammaTuRC-dependent nucleation and its regulation in space and time, and will significantly advance our understanding of how cells assemble and remodel MT arrays.

2018 -
Long-Term Fellowships - LTF

Dissecting the role of dopamine to supervise limbic neural ensembles during emotional learning

AMADEI Elizabeth (USA)

Institute of Neuroinformatics - ETH Zurich - Zurich - SWITZERLAND

GREWE Benjamin F. (Host supervisor)

The ability to associate sensory stimuli with appropriate emotional meaning while computing an optimal behavioral response is essential for survival. One key regulator of this emotional learning is the neurochemical dopamine (DA) acting in multiple brain areas such as the medial prefrontal cortex (mPFC) and basolateral amygdala (BLA). DA’s modulation of neural plasticity during emotional learning has traditionally been studied using electrophysiology in individual neurons, but how it occurs on the level of large neuronal networks (ensembles) remains unknown. To address this gap, I will investigate DA’s influence on dynamic ensemble activity within the mPFC and BLA during pavlovian fear conditioning, a classic model of emotional learning. Using in vivo calcium imaging and optogenetic control of DA release in mice, I will test DA’s role in establishing ensemble representations of conditioned stimuli. The long-term goals of this project are to (1) reveal key principles by which DA modulates neuronal ensemble coding and (2) lay the groundwork for future studies investigating how abnormal changes in ensemble coding relate to DA-sensitive anxiety disorders such as post-traumatic stress disorder.

2018 -
Long-Term Fellowships - LTF

The origin of thoughts: neural mechanisms of spontaneous thought generation in wakefulness and sleep

ANDRILLON Thomas (FRANCE)

Monash Institute of Cognitive and Clinical Neuroscience - Monash University - Clayton - AUSTRALIA

PEARSON Joel (Host supervisor)
TSUCHIYA Naotsugu (Host supervisor)

The brain is a ceaseless worker, endlessly integrating the information it receives into a continuous stream of conscious thoughts. Interestingly, even falling asleep does not completely suppress conscious thoughts, as exemplified by dreams. This is all the more surprising since wakefulness and sleep differ so greatly in terms of neural activity and phenomenology. What is then the core neural substrate enabling the generation of conscious thoughts?
I will focus here on spontaneous thought generation across wakefulness and sleep. Spontaneous thoughts will be here defined as conscious representations that are not triggered by a specific external event (e.g. an image, a word). Mind-wandering is a classical example of spontaneous thoughts during wakefulness, and dreams during sleep.
My goal will be to identify the neural correlates of spontaneous thought generation, i.e. the minimal set of brain regions that are jointly sufficient to spontaneously produce conscious representations even in the absence of sensory stimulation. I will use both correlational and interventional approaches. By directly stimulating the human brain, I will seek to understand how brain activations constrain the content of thoughts.
Comparing the neuronal correlates of spontaneous thoughts in wakefulness and sleep will be quite powerful because spontaneous thoughts arise without external stimuli, removing confounds due to sensory stimulations. Furthermore, the resulting neural correlates of spontaneous thoughts will, by construct, generalize across different conscious states, allowing us to isolate purer neural correlates of consciousness than previously proposed.