Available Master Projects SV

Many strains of E. coli are beneficial commensals while others (pathogenic strains) can cause several gastro-intestinal and urinary tract infections (UTIs). The majority of UTIs are caused by uropathogenic E. coli (UPEC), which affects 150 million people worldwide. UTIs are an especially important cause of morbidity and mortality among infants, older people, and women (Flores-Mireles et al., 2015). UPEC infection of the urinary bladder is countered by innate defences of the host, including influx of anti-bacterial neutrophils and epithelial exfoliation at the infected site. UPEC has been known to replicate inside bladder cells in biofilm-like communities within bulging globular structures called “pods”. The formation of intracellular bacterial pods has been shown to protect UPEC from killing mediated by host neutrophils (Justice et al., 2004). In vitro tissue culture models of infection are often too simplistic; typically, they do not capture the diversity of host-pathogen interactions and are unable to recreate the heterogeneous physical niches that pathogens typically encounter. In this project, we have established differentiated mouse organoid cultures for studying the host-pathogen dynamics of UPEC pathogenesis. In the bladder organoid model system, we use microinjection to infect the orgaoids with UPEC in order to study UPEC growth and responses to antibiotic treatment using time-lapse fluorescence microscopy.
Keywords: microbiology, host-pathogen, organoids, time-lapse imaging

Academic and pharmaceutical companies have invested substantial resources in developing predictive models for human physiology and disease states. However, conventional 2D cell culture models in tissue culture flasks are simplistic and do not recapitulate tissue-level architecture and organ microenvironments. More complex in-vitro systems such as trans-well inserts and organoids are more complex. but they also lack tissue-tissue interfaces, immune cells, and microscale environmental cues that are essential for the normal functioning of organ systems. These limitations can be overcome with organ-on-a-chip devices, which are microfluidic cell culture systems that mimic some aspects of tissue-level and organ-level physiology. Organ-on-a-chip technology has been developed for several organs, including: lung, gut, liver, kidney, and blood-brain barrier. We have developed a bioinspired bladder-on-a-chip (BoC) system using a commercially available organ-on-a-chip microfluidic platform. We have established a 3D co-culture of human bladder epithelial cells and human bladder endothelial cells with urine and nutrition perfusion that can be maintained for long-term differentiation and infection experiments.
Keywords: microbiology, host-pathogen, organ-on-a-chip, time-lapse imaging

Objective: design, chemically synthesize and test fluorescent probes specifically targeting centrioles. Approaches: structural analysis, synthetic chemistry, human cell culture, centriole purification, live cell imaging, super-resolution microscopy (STED).
Keywords: centriole, probe, chemical biology

Objective: bisarsenical multiuse affinity probes to conduct super-resolution imaging of endogenously tagged centriolar proteins in human cells. Approaches: human cell culture, CRISPR/Cas9-mediated engineering, synthetic chemistry, live cell imaging, super-resolution microscopy (STORM).
Keywords: centriole, chemical biology, CRISPR/Cas9, super-resolution imaging

Objective: uncover the mechanism of action of the evolutionarily conserved protein Cep135/Bld10p in mediating canonical and de novo centriole assembly. Approaches: cell biology, live cell imaging, centriole purification, monobody analysis, high throughout super-resolution microscopy (STORM), iSIM, cryo-electron microscopy (cryo-EM).
Keywords: centriole, cell free reconstitution, AFM, cryo-EM

Objective: combine experiments and mathematical modeling to investigate how Plk4, STIL and HsSAS-6 proteins collaborate to ensure assembly of a single procentriole next to each parental centriole, once per cell cycle. Approaches: human cell culture, CRISPR/Cas9-mediated engineering, centriole purification, live cell imaging, super-resolution microscopy (STED), mathematical modeling.
Keywords: centriole, number control, length control, computational model

Objective: test whether centrioles can form in human cells with a SAS-6 protein that assembles into a spiral rather than a ring-bearing structure, as well as into structures with altered fold symmetries. Approaches: site directed mutagenesis, protein expression and purification, cryo-electron microscopy, atomic force microscopy (AFM), human cell culture, CRISPR/Cas9-mediated engineering, super-resolution microscopy (STED).
Keywords: centriole, bioengineering, AFM, CRISPR/Cas9

Objective: investigate how centrioles are inherited/formed in embryos generated through asexual reproduction, where oocytes develop without fertilization by sperm. Approaches: live cell imaging of early embryogenesis in the nematode Panagrolaimus, identification of homologues of C. elegans centriolar proteins, protein expression and purification, antibody generation, immufluorescence analysis, confocal imaging.
Keywords: centriole, C. elegans, parthenogenesis, cell biology

Objective: dissect mechanisms of de novo centriole assembly in the water fern Marsilea vestita. Approaches: live cell imaging, cryo-electron tomography, RNAi-based gene silencing, transcriptome analysis, identification of centriolar proteins, protein expression and purification, antibody generation, immufluorescence analysis, confocal imaging.
Keywords: centriole, de novo assembly, fern, RNAi

Objective: conduct an RNAi-based functional genomic screen in the nematode C. elegans to discover genes necessary for centriole elimination, and begin analyzing their mechanism of action. Approaches: functional genomics, microscopy, image analysis.
Keywords: centriole elimination, RNAi-based functional genomics, microscopy

Objective: develop machine learning strategies (e.g. using Tensorflow) for high throughput protein structure prediction. Apply machine learning to identify homologues of the critical centriolar protein SAS-6 across all domains of life and thus help trace its origin. Approaches: computational biology, machine learning, structural prediction. Collaboration between the Gönczy (EPFL, Life Sciences) and Dessimoz (UNIL and SIB) laboratories.
Keywords: centriole, bioinformatics, evolution of protein families

Objective: analyze outcome of a screen performed in the yeast S. cerevisiae to identify genes that are important for determining organismal thermal range, and investigate whether their function is conserved in the nematode C. elegans. Approaches: computational biology, bioinformatics analysis, functional genomics, microscopy.
Keywords: yeast, thermal range, computational biology, functional genomics

Organoids form through poorly understood morphogenetic processes in which initially homogeneous ensembles of stem cells spontaneously self-organize in suspension or within permissive three-dimensional extracellular matrices. Yet, the absence of virtually any predefined patterning influences such as morphogen gradients or mechanical cues results in an extensive heterogeneity. Moreover, the current mismatch in shape, size and lifespan between native organs and their in vitro counterparts hinders their even wider applicability. The goal of this Master project is the development of next-generation gastrointestinal organoids that are assembled by guiding cell-intrinsic self-patterning through engineered stem cell microenvironments. The student will employ advanced biomaterials and/or microtechnology approaches to control the behaviour of organoid-forming stem cells.
Keywords: Organoids, stem cells, self-organization, patterning, hydrogel, microfluidics, biofabrication

The Drosophila antimicrobial response at the time of the Cas9/CRISPR gene targeting revolution The application of Drosophila genetics has generated insights into insect immunity and uncovered general principles of animal host defense. These studies have shown that Drosophila has multiple defense “modules” that can be deployed in a coordinated response against distinct pathogens. Today, Drosophila can be considered as having one of the best-characterized host defense systems among the metazoan. The Cas9/CRISPR revolution offers new opportunities to revisit in a systematic manner Drosophila immunity. At the interface between large-scale genomic studies that lack resolution and individual gene analysis that lack breadth, our laboratory has undertaken a meso-scale ‘skilled’ analysis of immune modules, notably by addressing the individual and overlapping function of large immune gene family. The aim of the master project is to characterize the function of Drosophila immune modules (ex. antimicrobial peptides, phagocytosis,….) using powerful genetic approaches. Methods: Drosophila genetics, molecular biology, genomic, histology, microbiology, bioinformatic.
Keywords: immunology, genetics, drosophila, antimicrobials

The foreign within: Drosophila-Spiroplasma interaction as a model of insect endosymbiosis Virtually every species of insect harbors facultative bacterial endosymbiotic bacterium (endosymbiont) that are transmitted from females to their offspring. Many manipulate host reproduction in order to spread within host populations. Others increase the fitness of their hosts by protecting their hosts against parasites. In spite of growing interest in endosymbionts, very little is known about the molecular mechanisms underlying endosymbiont-insect interactions. To fill this gap, we are dissecting the interaction between Drosophila and its native endosymbiont Spiroplasma poulsonii. The master project will use a broad range of approaches (molecular genetics, histology, microbiology, genomics….) to dissect the molecular mechanisms underlying key features of the symbiosis, including vertical transmission, regulation of symbiont growth, and symbiont-mediated protection against parasites. We believe that the fundamental knowledge generated on the Drosophila-Spiroplasma interaction will serve as a paradigm for other endosymbiont-insect interactions.
Keywords: symbiosis, drosophila, bacteria, genetics

Insects generate complex behaviors with a numerically simple nervous system. The objective of this project is to leverage computer vision and deep learning algorithms to study the leg positions of tethered behaving flies from high-resolution movies. These behavioral sequences can then be linked to simultaneously acquired neuroimaging data. This project at the interface of computer science, and neurobiology will be supervised at the Neuroengineering Laboratory in close interaction with computer science groups on campus.
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To understand the behavior of complex systems it is often necessary to build a model. The goal of this project is to develop a biorealistic 3D simulation of Drosophila. This model will be used to test bioinspired neural networks limb controllers. The project at the interface between robotics, computer science, and neurobiology will be supervised at the Neuroengineering Laboratory in close collaboration with the Biorobotics Laboratory.
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A central goal of neuroscience is to link neural activity and behavior. The objective of this project is to use computer vision and deep learning approaches to extract neural activity patterns during behavior and to make accurate predictions behavioral and internal states. This project at the interface between computer science and neurobiology will be supervised at the Neuroengineering Laboratory in close interaction with computer science and image processing groups on campus.
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Nature has solved numerous challenges associated with autonomous behavioral control. We hope to leverage these solutions in robotics. The goal of this project is to construct an insect-inspired robot and to test bioinspired algorithms of limb control. This project at the interface of robotics and biology will be supervised at the Neuroengineering Laboratory in collaboration with EPFL robotics groups.
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Surgical interventions commonly performed in medicine and research require skill and extensive training. The objective of this project is to democratize and automate microsurgery by developing automated vision-guided robotic systems that dissect and prepare animals for neural recordings. This project at the interface between robotics and neurobiology will be supervised at the Neuroengineering Laboratory in collaboration with the Microrobotics Laboratory.
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Despite the high prevalence of trauma-related disorders and the consequent need to better understand how long-lasting traumatic memories can be attenuated, the brain circuits supporting this process remain largely unknown. We have recently shown – using real-time fiber photometry recordings, bidirectional chemogenetic manipulations and functional circuit mapping in the mouse – that the nucleus reuniens of the thalamus (NRe) mediates remote fear memory extinction. In light of these results, we are now investigating the input-output organization of this NRe-centered brain circuit. To address this question, we are employing a combination of viral retrograde tracers, cFos immunohistochemistry (IHC) and projection-specific chemogenetics. Moreover, we are setting up a pipeline for the molecular profiling by RNAseq of differentially projecting NRe neurons by FACS sorting of retrogradely labeled cells. We are looking for a highly motivated M.Sc. student to 1) map active brain areas active upon remote extinction injected with retrogradely transported viruses into BLA and NRe by confocal microscopy, intraregional correlation matrixes and cell colocalization analysis. 2) chemo- and optogenetically manipulate input regions to the NRe during remote fear memory extinction 3) to fluorescently sort input cells and molecularly analyze (next generation sequencing) input regions to the NRe.
Keywords: Behavioral neuroscience, chemogenetics, optogenetics, fear extinction

The goal of this project is to organize and link cancer genomics data obtained from different sources and in different formats within a browsable data portal accessible to people in the lab.
Keywords: Big genomic data, data portal, data integration

Oxford nanopore sequencing (ONT) allows identification of RNA and DNA sequences. When subjected to an electric field, pore forming proteins allow for the translocation of polynucleotides between two compartments filled with electrolytic solution. The passage of each different nucleotide inside the pore creates a distinct, measurable alteration in the ionic current, and the controlled threading of a DNA or RNA chain across the pore allows for the sequential identification of each nucleotide. This recent technology already started making a significant impact, allowing for the sequencing of long DNA sequences, and also long polyadenylated RNA. Recently, it has been shown that this technology, combined with novel machine learning algorithms, is able to distinguish modified and unmodified nucleotides since each modification comes with a characteristic alteration of ionic currents. This makes ONT a promising technology in the study of epigenetics, epitranscriptomics and tRNA regulation. In this semester project, the students will apply and further develop the machine learning algorithms needed for base calling (parsing of voltage traces into the RNA alphabet), such as recurrent neural network (RNN) using long short-term memory (LSTM) to identify long nucleotide sequences and their modifications. Test sets and train sets coming from a recent dataset that our lab has produced will be provided. The main challenge will be to find, improve and implement the best state of the art network architecture. The students will be free to use library and language of their choice, although an implementation using PyTorch would be preferred.
Keywords: bioinformatics, computational biology, recurrent neural networks, genomics

We have recently shown the implementation of collinear Hox genes expression in “gastruloids”, a mouse embryonic stem (mES) cells-based organoid that mimic early embryonic spatial and temporal genes expression [1]. The aim of this project is to generate stable deletions and knockin in mES cells in order to study the underlying mechanisms of Hox genes expression in this gastruloids.
Keywords: Gene regulation, chromatin, organoids, CRISPR/cas9

While proliferating, cells need to duplicate not just their DNA but also their cytosolic and membrane components. Cell growth is indeed the outcome of multiple processes, including the de novo synthesis of proteins and lipids. To this purpose, during phases of active cell division, the rate of growth is matched to the availability of nutrients required for the coordinated protein biosynthesis and membrane expansion. How the lipid synthetic system is regulated in response to growth stimuli or nutrients availability and how lipid remodelling influences growth is partially understood. Here we will evaluate changes in lipid metabolism as a consequence of different growth conditions and the impact of lipid synthetic inhibition to cell growth.
Keywords: lipid metabolism, proliferation and cancer, intracellular trafficking

Starting from the 1970s, a number of studies have reported that the plasma membrane composition in terms of sphingolipids is subjected to remodelling during neural development. These changes are accompanied by a reprogramming in the expression of genes encoding the sphingolipid synthetic enzymes. Our preliminary data indicate that post-translational regulation of the sphingolipid synthetic machinery synergizes with transcriptional programs to assist GSL remodelling. Specifically we find that the localization and stability of key enzymes involved in the metabolic rewiring are inversely affected in the course of neural differentiation. Here we want to study the molecular mechanisms accounting for this post-translational regulation.
Keywords: neural tube organoids, neural differentiation, lipid metabolism

Lipids are fundamental constituents of all living beings. They participate in energy metabolism, account for the assembly of biological membranes, act as signalling molecules, and interact with proteins to influence their function and intracellular distribution. Eukaryotic cells produce thousands of different lipids each endowed with peculiar structural features and contributing to specific biological functions. Cellular lipidomes vary among cell types and are reprogrammed in differentiation events. Recent contributions including from our group have shown that lipid composition is subjected to remarkable cell-to-cell variation in syngeneic, homogeneous cell populations suggesting that cell-to-cell lipid heterogeneity contributes to the emergence of multicellular patterns. Lipid biologists have so far addressed lipidomes in bulk cell extracts or selected lipids at the single-cell level. Thus, how lipidomes vary form one cell to another and which cell-to-cell lipid variations have biological meaning remains to be defined. Here, we will develop an integrated pipeline coupling high-resolution mass spectrometry imaging, single-cell multi-omics and lipid probes to attain Single-Cell in situ Lipidomics analysis of cell populations. We will use this approach to interrogate the role of single-cell lipidome variations in the medically relevant case of dermal fibroblast heterogeneity..
Keywords: single cell omics, cell identity, senescence, cancer

The goal of this project is to digitally reconstruct the axons and dendrites of cortical neurons in the mouse brain. Single neurons labelled with fluorescence will be imaged across the entire mouse brain at high resolution. The axons and dendrites will be traced through semi-automated procedures and quantified in the context of a standard mouse brain atlas.
Keywords: mouse neocortex, axon, dendrite, 3D imaging

The goal of this project is to comprehensively map the locations and numbers of genetically-defined types of inhibitory neurons in the mouse neocortex. Genetically-engineered mice will be used to label specific types of GABAergic neurons with fluorescent proteins, and then the entire mouse brain will be imaged at high resolution. The student will develop image analysis methods to locate each neuron within a standard mouse brain atlas.
Keywords: Mouse neocortex, imaging, image analysis

The goal is to analyse multi-site extracellular recordings of neuronal activity in mice performing a goal-directed behavior learned through reward-based training. The neurophysiological data will be correlated with behavior quantified from high-speed videography. Specifically, we will investigate how neuronal circuits in the mouse brain learn to transform whisker sensory information into goal-directed licking motor output through reward-based learning.
Keywords: sensory processing, sensorimotor transformation, motor control, reward-based learning

The goal of this project is to analyse functional calcium imaging data in behaving mice. We will correlate the dynamic calcium signals with behavior quantified from high-speed video filming. The aim is to investigate how neuronal circuits in the mouse brain learn to transform whisker sensory information into goal-directed licking motor output through reward-based learning.
Keywords: sensory processing, sensorimotor transformation, motor control, reward-based learning

The goal of this project is to image neuronal activity in behaving head-restrained mice. Mice will be trained through reward-based learning to carry out a goal-directed sensorimotor transformation. Two-photon microscopy will be used to image neurons expressing genetically-encoded calcium indicators with cellular resolution. We will correlate neuronal activity with sensory stimuli and behavior quantified from high-speed filming. Students will need to follow Module 1 of the animal experimentation course or equivalent. Minimum project duration 6 months.
Keywords: cellular imaging, sensory processing, motor control, reward-based learning

The human Ceramide Transfer Protein CERT (encoded by the gene COL4A3BP presently referred to as CERT1) is a cytosolic lipid transfer protein responsible for the non-vesicular transport of ceramide from the endoplasmic reticulum (ER) to the Golgi apparatus during sphingolipid biosynthesis. CERT1 activity is mediated by several functional motifs including an N-terminal pleckstrin homology (PH) domain that binds to phosphoinositide phosphatidylinositol-4-phosphate in the trans-Golgi and a C-terminal steroidogenic acute regulatory protein-related lipid transfer (START) domain that serves as a binding domain for ceramide. Genome-wide studies have suggested a putative association between CERT1 and intellectual disability (ID), still validation in a large cohort and dissection of the molecular etiology of the disease are lacking. We searched for human patients with CERT1 mutations and identified 19 individuals with de novo missense variants who suffer an infantile-onset developmental syndrome with severe ID, seizure and autism spectrum disorder. Here we want to address the molecular bases of the disease by studying the effects of patient mutations on CERT lipid transfer activity and on overall lipid metabolism.
Keywords: Inborn errors of lipid metabolism, lipid transfer proteins, Membrane contact sites

Morphogenetic movements are generally believed to be guided by mechanical forces along with morphogen gradients. Likewise, emerging data show that cells respond to various mechanical signals including ECM stiffening due to deposition or remodeling of collagen fibers and compressive stress generated by confined growth. However, the physical mechanism causing such multicellular movements remains unknown. MICROBS Laboratory has been developing small scale soft actuated biomaterials that can transduce electromagnetic energy into mechanical work. We have recently introduced optomechanical microactuators that can apply physiologically relevant forces within a three-dimensional workspace. The objective of this project is the integration of these microactuators within biological models, by embedding into ECM with cells that form higher order structures such as spheroids and organoids. The student is going to work on the surface chemistry of the actuators to optimize the transmission of forces. A time-lapse fluorescence imaging methodology will be established that involves i) finding the excitation parameters (i.e. duration, frequency, amplitude of actuator contraction) that leads to a physiological (or pathological) multi-cellular response ii) development of techniques for high-throughput, multi-agent actuation schemes for the generation of arbitrary stress profiles, and finally iii) investigation of techniques for the mapping of stress throughout the tissue.
Keywords: Bioengineering; mechnaotransduction; cell biology

The benefits of meditation have been explored and described from a behavioral perpective but little is known on how brain function supports transition between normal and meditative states. We propose to explore brain dynamics during metitation using fMRI and EEG data. More precisely, we will compute the dominant dynamic modes in normal and meditative conditions in order to better understand the spatio-temporal properties of brain function in these two states.
Keywords: Human neuroimaging, computational approaches, dynamical models, autoregressive models

Your task will be to analyse a recently acquired dataset including resting-state fMRI data and behavioural measures for 39 preterm children and 27 term-born controls, aged 9–13 years old. The main goal will be to compare the relationship between brain function, behavioural measures, and clinical assessments in the two groups, and interpret the results in view of the existing literature. If you would like to dive deeper into this subject, we also have a second resting-state recording, as well as behavioural data, for the preterm group after 12 weeks of mindfulness meditation training.
Keywords: Human neuroimaging, subspace methods

The corpus callosum is the largest white matter pathway connecting homologous structures of the two cerebral hemispheres and crucial for the transfer and integration of information across the brain. Developmental absence (agenesis) of the corpus callosum (AgCC) is a congenital brain malformation resulting from disruption of corpus callosum formation. Evidence suggests the existence of structural and functional neuroplastic response to preserve interhemispheric transfer in AgCC. In a cohort of children with AgCC that is much larger than previously explored samples of this rare clinical condition, we want to apply a newly-developed method for combining structural data from Diffusion Spectrum Imaging (DSI) and the functional data from functional Magnetic Resonance Imaging (fMRI). We integrate the two modalities by using state-of-the-art techniques borrowed from the field of graph signal processing. The aim would be to understand the difference in the existing structure-functional relationships between patients with AgCC versus healthy controls. How do AgCC patients manage to recuperate with the absence of the corpus callossum?
Keywords: MRI; functional and structural connectivity

During embryonic development flat, polarized epithelia sheets morph into complex three-dimensional structures and eventually form specialized compartments and organs. Initial bending and invagination events in epithelia are triggered by cellular contractile forces that lead to local cell shape changes and rearrangements. In principle, one can rationally shape biological tissues by controlling the location and magnitude of these mechanical forces. In this project you will work with engineered epithelial tissues and epithelial-mesenchymal multilayered constructs. First part of the project involves characterization of tissue composition and morphology using wide-field, confocal and light-sheet microscopy. In the second part, you will perturb cell mechanics by applying state-of-the-art manipulation technology and investigate local tissue architecture. Gained knowledge will be used to design and sculpt engineered 3D bodies. An in-house computational model will aid the exploration of the design space.
Keywords: tissue engineering, microscopy, microtechnology, optogenetics

The role of the motor cortex in locomotion is not yet fully understood. In order to study the role of corticolumbar neurons in leg motor control in the healthy rat and during recovery after a sever spinal cord contusion, longitudinal calcium imaging recordings have been performed. We suggest 3 possible sub-projects consisting in the analysis of these gathered neuronal data: - investigation of the dynamics of this specific population of neurons during a fine motor control task as opposed to natural walking in the intact animal. - assessment of the stability of representation of locomotion in the corticolumbar population in the intact animal and throughout recovery. - analysis of the dynamics of corticolumbar neurons during recovery of voluntary leg motor control after SCI in trained and control untrained animals.
Keywords: spinal cord injury; motor cortex; calcium imaging; neural decoding

The genomes of hosts and pathogens are partially shaped by co-evolution. For example, positive selection forces are applied on both pathogen genetic variations, which evade the host immune system, and on host genetic variants, which decrease susceptibility to infections. Leveraging paired host-pathogen genome sequencing data, the student will utilize computational methods to explore the imprints of the co-evolution process on both genomes. Moreover, the student will also develop statistical methods to disentangle the complex interplay between host and pathogen genetics and to model the joint effects which contribute to the inter-individual heterogeneity in clinical outcome. The project will contribute to a deeper understanding of the co-evolution process, and shed light on the genetic underpinnings of infection severity and treatment responses.
Keywords: genomics, bioinformatics, statistics, infectious diseases

The TGFβ-related prohormone Activin-A is frequently upregulated in solid tumors and mediates tumor-induced muscle wasting as well as oncogenic or tumor-suppressive functions, depending on the context. The goal of this project is to validate binding of Activin-A to specific proteins that we found in an interactome screen for factors that preferentially bind mature Activin-A or precursor processing intermediates, respectively, and to analyze their functions in regulating the bioavailability and local signaling of Activin-A in the tumor microenvironment to promote tumor immune evasion, or endocrine Activin-A signals that mediate muscle wasting.
Keywords: TGFβ signaling; tumor immune evasion; proteomics; protein trafficking; proteases

A robust immune response is required for clearance of viral respiratory infections. To uncover susceptibility to severe disease, we will investigate genomic variation in 120 children requiring intensive care support upon infection by a respiratory virus. The effect of both structural and functional genetic variation will be examined by (i) quantifying large deletions and copy number variants and (ii) gene burden testing for pathogenic variants from affected cases compared to healthy controls. Methods: exome sequencing and genotyping datasets have been prepared for 400 cases and controls. Command line bioinformatic tools will be used to process data. Methods will include the use of GATK command line tools for exome analysis [1], R data analysis for association testing [2] and Plink for genotyping data analysis [3]. Visualization will be used to interpret statistically relevant findings.
Keywords: bioinformatics, immunity, visualization, statistics

Astrocytes are known to provide various essential complex functions including structural and trophic support, primary roles in synaptic transmission, and maintenance of ionic homeostasis that allow efficient information processing by neuronal circuits (Nedergaard et al., 2003; Sofroniew and Vinters, 2010). Although alpha-synuclein (α-syn) is expressed at very low levels in astrocytes, α-syn inclusions are found in astrocytes under pathological conditions in the postmortem Parkinson’s disease brain (Wakabayashi et al., 2000; Song et al., 2009). As of today, there are no cellular or animal models that truly recapitulates astrocytic α-syn pathology as seen in postmortem PD brain. In the presence of α-syn overexpression, abundant α-syn aggregations could be detected (Lee et al., 2010; Sacino et al, 2014; Sorrentino et al., 2018) but the biochemical and ultrastructural properties of these aggregates and their relation to α-syn astrocytic pathology remains poorly understood. Since α-syn is expressed by human astrocytes and its protein level is a key determinant of aggregation, pathology formation and predisposition to developing PD, we plan to investigate conditions that could potentially induce changes in α-syn expression and its protein levels in primary astrocytes, with a greater emphasis on natural mechanisms rather than α-syn overexpression.
Keywords: Astrocyte, Parkinson’s disease, Synuclein, Inclusion

Copy number variation (CNV) is an important form of genetic variation that has been suggested as potentially responsible for a significant proportion of the yet unexplained human phenotypic variability. For this project, you will investigate the contribution of CNVs as additional molecular markers to single nucleotide polymorphisms (SNPs) to cardiovascular disease. Using samples and data collected in the context of the CoLaus study, a large cohort of over 5’000 individuals from the general population of Lausanne, you will first harness the power of large-scale genomics and bioinformatics tools to call CNVs from SNP genotyping arrays. The called CNVs are then used for genome-wide association analyses of multiple cardiovascular traits. All together, these analyses have the potential to elucidate the pathogenesis of cardiovascular diseases, and outcomes of this project could include better prediction models and innovative targets for diagnostic or therapeutic development.
Keywords: Bioinformatics; human genomics; copy number variation; cardiovascular diseases

A master student’s project is available in the Laboratory of Molecular and Chemical Biology of Neurodegeneration at the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland (www.epfl.ch). The selected candidates will work on a project at the Laboratory of Molecular and Chemical Biology of Neurodegeneration (http://lashuel-lab.epfl.ch/) aimed to evaluate the expression patterns of alpha synuclein and its pathological forms in different brain areas and their role in the pathogenesis of Parkinson’s disease. To achieve this goal, the applicant will perform cutting-edge techniques such as iDISCO, that permits whole-mount immunolabeling with volume imaging of large cleared samples ranging from perinatal mouse embryos to adult organs, such as brains or kidneys. The desired applicant must be highly motivated to work as members of an interdisciplinary group working at the interface of chemistry and biology in collaboration with world-renowned research groups at the frontiers of neuroscience and brain research. The qualified candidate will benefit from working with very dynamic and multidisciplinary groups in a highly collaborative and stimulating environment and access to state-of-the-art laboratories and core-facilities. For more information about our groups, please visit our website and review our recent publications at http://www.ncbi.nlm.nih.gov/pubmed/?term=Lashuel.
Keywords: parkinson's disease, idisco, alpha-synuclein

Normal development and function of the gut and other internal organs such as our lungs and the heart depend on asymmetric activation of the Nodal cascade. In most deuterostomes, this process is governed by a directional flow of extracellular fluid that stimulates specific ion channels in primary cilia to repress translation of the secreted Nodal antagonist Dand5 specifically on the prospective left side. However, the mechanism that uncouples the regulation of mRNA translation from mechanosensory cilia in patients with laterality defects and other ciliopathies is unknown. The goal of this project is to elucidate how primary cilia activate the RNA-binding protein Bicc1 to repress Dand5 mRNA translation.
Keywords: mechanosensation, cilia, translational regulation,

A tandem repeat of three RNA-binding K homology domains in Bicc1 can bind specific target mRNAs that are implicated in polycystic kidney diseases (PKD) and other ciliopathies. However, until recently, a consensus RNA sequence mediating these interactions and its role in Bicc1-mediated translational repression have remained unknown. This project will validate the importance of novel 4-nucleotide consensus motifs that emerged from an unbiased screen for Bicc1-interacting sequences in mediating the binding of reporter RNAs to recombinant KH domains, and in enabling Bicc1-mediated mRNA localization and translational repression in cell-free assays and in cultured cell lines.
Keywords: translational regulation, RNA binding, reporter assays

Translational repression of specific target mRNAs by Bicc1 critically depends on its Sterile Alpha Motif (SAM) that mediates head-to-tail self-association of structurally well-defined protein surfaces in helical polymers. The goal of this project is to test whether the helical organisation is necessary for polymers to translationally repress Bicc1-associated mRNAs (e.g. by enabling Bicc1 to control RNA folding), and whether it can be engineered to regulate polymerisation at will, or whether the essential contribution of the SAM domain to mRNA silencing can be mimicked by alternative means of inducible self-aggregation other than SAM-mediated liquid-liquid phase transitions.
Keywords: protein engineering, cell biology

Huntington’s Disease (HD) is a genetic and progressive neurodegenerative disorder characterized by motor, cognitive and psychiatric symptoms. Despite the fact that the gene responsible of HD is known, the underlying mechanisms leading to huntingtin (HTT) aggregation, link to neurodegeneration and death is still not clear. Different neurodegenerative disease causing proteins are known to have prion like property. Using seeding property of recombinant alpha-Synuclein proteins, our lab was able to generate a neuronal model of PD and study process of Lewy formation in details (Anne-Laure et al. Biorxv, 2019). The objective of the project is to investigate the seeding property of mutant HTT proteins and the generation of a neuronal model of HD. For this, we will use either Pre Formed HTT Fibrils (PFF) or purified HTT inclusions from primary neurons (native seeds) and add them into primary neuronal culture to assess their ability to be uptaken and to seed the aggregation of endogenous HTT in neurons. The aggregation will need to be characterized by Immunocytochemistry (ICC) and biochemistry depending on different conditions: 1) Use of different HTT protein fragments; 2) Use of different polyglutamines repeats within the Htt protein; 3) Use of HTT protein with and without the Nt17 domain; and 4) The influence of PTMs on HTT protein.
Keywords: Huntington’s disease, Primary neurons, aggregates, seeding

The morphogenesis of vertebrate embryos is well-studied in terms of genetics and biochemical signaling. However, the role of mechanics is not well understood, primarily due to lack of tools and methods to apply forces at relevant spatiotemporal scales. To have a better understanding of the role of mechanics, we have recently developed an ex-vivo assay. Objective of this project is to perturb and probe samples with various micromanipulation systems. The systems will enable application of physiologically relevant stresses on the explants and quantify the results on somitogenesis and morphing. Optimizing the platforms, development of proper imaging tools for recording oscillatory gene signals, and post processing the data for quantification are the main elements of this project.
Keywords: mechanobiolgy, somitogenesis, zebrafish, microengineering, robotics`

Genetically encoded calcium indicators (GECIs) are powerful tools for monitoring intracellular calcium concentration and thus, indirectly, neuronal spiking activity. The family of GCaMP6 GECIs has become instrumental in neuroscience, particularly in in-vivo recordings. However, it is often disregarded that GECIs, like other Ca2+-indicators, are calcium buffers, usually of high affinity, which in typical experiment are strongly overexpressed in every cellular compartment. The presence of a strong buffer is likely to affect naturally occurring calcium-dependent plasticity mechanisms. Our laboratory is setting up an in-vivo calcium imaging approach using a microendoscope to study population dynamics in the insula cortex and amygdala during fear learning. It is therefore important to know if/how GCaMP6 expression influences the function of studied neurons in memory-related tasks. The project will first focus on estimating the added calcium buffering capacity in neurons of lateral amygdala (LA) expressing GCaMP6m using fluorescent calcium imaging and patch-clamp in brain slices. Second, the long-term plasticity of synaptic inputs from the insula cortex will be investigated in the LA neurons expressing GCaMP6m using patch-clamp electrophysiology. These experiments will allow the MA student to investigate quantitative aspects of GCaMP6m overexpression and to study how this affects neuronal plasticity.
Keywords: synaptic plasticity, calcium imaging, patch-clamp electrophysiology, brain slices

In our laboratory, we study the neural networks involved in associative learning of threat in auditory fear conditioning. One of approaches studies the distribution of neurons in the brain that undergo increase in activity upon specific sensory experience. This is achieved using a fluorescent reporter mouse line combined with timed expression of Cre-recombinase downstream of an immediate early response gene cFos. A typical outcome is a set of hundreds of images of histological sections of the mouse brain, in which the distribution of “activity-labeled” neurons needs to be quantified. This is an extremely workload-demanding task in case of manual analysis. There have been multiple recent attempts to automate the detection of single cells and registration of the images onto a reference atlas using advanced image analysis and deep learning. However, there is no single comprehensive pipeline accepting an image stack at its input and producing the cell density table at its output with minimal human input. The project is devoted to a design of such a workflow based on further development of interfaces between some of the published routines. The resulting toolbox will be very instrumental for our lab in particular, and for neuroscience community in general.
Keywords: image analysis, object detection, image registration, automation

Objective: Sleep is essential for learning new skills at any age and for relearning functional capacities (such as motor skills) after a brain lesion (stroke). In the context of an ongoing project aiming at investigating the effects of non-invasive brain stimulation during sleep to enhance learning, the master student will analyse a resting-state fMRI dataset of healthy older / stroke patients. The project will consist in acquisition of data and analyses of structural and functional MRI data. Furthermore, the analysis will include electric field modelling of the applied brain stimulation to gain insight on the stimulation effect and topography.
Keywords: Resting-state fMRI, Noninvasive brain stimulation, Electric field simulation, Multimodal study

The brain is never at rest. Whatever action we may undertake, the brain is processing sensory information to act on the environment. Particularly, it was discovered in recent years that even by being at rest specific areas in the brain are active within a default mode network (DMN) comprising of the posterior cingulate cortex (PCC) or the ventral Anterior Cingulate Cortex (vACC), thought to play a role in different brain functions, as self-reference, social evaluation or episodic memory. However, the relationship of the DMN with different pathological clinical states after stroke is not well defined. After a stroke, lesions may cause damages at different cognitive levels: motor, language, attention etc. In a longitudinal study after stroke, multimodal data are collected from patients suffering from upper limb deficit after stroke. During 4 time points from 1 week to 1 year patients well be characterized with MRI scans for structural and functional MRI analyses. The goal of the study is to evaluate the correlation of the DMN activity with stroke outcome and functional reorganization informed by the structural connectome of each individual patient.
Keywords: stroke, fMRI, brain imaging, default mode network

Stroke injury leads to disability up to 75% of stroke survivors. The understanding of the processes underlying recovery of stroke and the plastic correlates in the brain are not sufficiently understood. Electroencephalography (EEG) provides excellent information about brain connectivity with a high temporal resolution and will add to the understanding of the brain correlates of recovery from stroke. Advanced analytical techniques based on graph analysis will be used to investigate brain activity at rest. To this end, in a longitudinal study multimodal data are collected from stroke patients suffering from upper limb deficit. Patients will be evaluated from the acute (1 week) to the chronic stage (1 year) at 4 time points, brain activity is recorded by means of EEG. The goal of the study is to characterize the changes of the functional connectome during the process of recovery
Keywords: stroke, EEG, graph analysis, longitudinal study

How strong is embryonic selection in humans? What are the targets of this selection? The best way to address these questions is to compare parental genomes with genomes of their offspring. Using polygenic scores, which provide integral genomic predisposition to different phenotypes, it is possible to analyse the transmission of multiple alleles from parents to offspring. A deviation of the observed score in the offspring from the expected one (mid-parent score) means over- or under- inheritance of the specific set of alleles. This deviation, if statistically robust, means embryonic selection. Here, using genotyped human trios with healthy or affected offspring, we plan to uncover the strength and direction of the human embryonic selection.
Keywords: transmission disequilibrium test, polygenic score, selection

The goal of this interdisciplinary joint lab project is to automate Drosophila genetics and mutant selection through a combination of robotics with new genetic tools designed for machine rather than human manipulation. Studies of the fruit fly Drosophila melanogaster have made foundational contributions to the understanding of development, neuroscience and human disease. Existing proof-of-concept robotic systems can anesthetize, transfer and manipulate individual Drosophila. The student will build and adapt such a system to develop a new generation of ‘smart’ robots with sensors, which together with new genetic tools, will allow for robotic selection of animals of the desired genotype or mutation. This combination of novel genetic tools designed specifically for machine utility with robotics should facilitate an exponential increase in the throughput of genetic manipulation of this important model organism.
Keywords: genetics, robotics, machine vision, genome engineering

Loss of synaptic connections and disruption of neuronal circuits is thought to be an early consequence of neurodegenerative disorders such as Alzheimer’s disease. However, assaying these early aspects of neurodegeneration is difficult and currently cannot be achieved in vivo. In this project, the student will use genome engineering methods to construct new genetic tools for the model organism Drosophila melanogaster designed to measure neural circuit integrity non-invasively from outside the animal. They will then deploy these tools in a humanised model of Alzheimer’s disease to assay the progressive disruption of neuronal circuits as neurodegeneration advances.
Keywords: genome engineering, neurodegeneration, disease, Drosophila

Background An ambitious goal of single-cell analyses is describing dynamical biological processes and shedding light on gene regulation mechanisms. However, because of the destructive nature of single-cell measurements, they can only provide a static snapshot of the cell at a given point of embryonic development. To overcome this fundamental limit, I recently developed a novel method, named “RNA velocity” as it estimates the first derivative of gene expression for each gene in a cell (RNA velocity of single cells, Nature 2018). Measuring the abundance of both unspliced and spliced RNA in the same cell, we can estimate the rate of change of gene expression and predict the future expression levels of a single cell. Activities This project will start by introducing a series of improvements to the current RNA velocity algorithm and software and it will proceed towards an extension of the model to a more general framework. (1) The student will implement in our software velocyto with the dynamical model proposed recently by Fabian Theis lab. (2) The student will analyze situations where the original assumptions of the method are not met and remediate fitting an alternative model (3) The student will use a latent variable model to decompose the velocity vector in interpretable components (e.g. cell cycle, maturation, and response to signals).
Keywords: machine learning, developmental biology, single-cell RNAseq

Background The scientific community is generating a great volume of datasets that record many features from single cells. These datasets survey the same population but each dataset is measuring different features: transcript, chromatin accessibility, DNA-methylation, surface protein concentration. These measurements are disjoint and do not come from the same cell. However, since the datasets are collected from the same organ/tissue/process it should be possible to align this data to obtain a more complete description of the molecular state of each cell. This kind of approach has proved to be possible through a series of multivariate statistics/machine learning procedures (Stuart et al. 2019). Activities The project is divided into two parts an implementation and a method extension part. In the first part, the student will individuate in the literature methods for multimodal data integration and batch correction and reimplement the best of them in python. In the second part, the student will identify common and different procedures in those methods and attempt to combine different them so as to propose a new improved version. Finally, the different methods including the improved one will be benchmarked using different reference datasets.
Keywords: single-cell transcriptomics, bioinformatics, data analysis

Background Single-cell RNA-sequencing (scRNAseq) yields high-quality transcriptomic data from a single cell suspension, but it needs to sacrifice information on cell localization. Conversely, multiplexed single-molecule FISH (osmFISH) has only medium-throughput but allows measurements in situ. Usually, after scRNAseq has been used to define and discover cell types, one would like to map back this knowledge to the tissue using osmFISH. In doing so, it is important to be able to optimally select a gene set that maximizes the information obtainable experimentally. For example, choosing 30 highly specific markers to detect 30 cell types might not be the best option, because, without redundancy, the failure of a probe could mean completely missing a population. We want to design a method that automatically chooses a subset of features that can be highly informative while robust to this kind of experimental uncertainty. Activities The student will (1) Build a model that predicts dense low-throughput measurements from sparse high-throughput data using machine learning and statistical modeling. (2) Design a strategy that optimally selects a set of features to measure by a low-throughput method. (3) Evaluate performances of the method considering uncertainties (4) Incorporate experimenter knowledge in the selection in the form of statistical priors. (5) integrating the procedure in a command-line tool.
Keywords: machine learning, statistical modeling, algorithms

Background It is becoming increasingly evident that radial glia-like cells, the stem cells of the nervous system, are not a homogeneous population. In particular, using single-cell RNAseq we have identified different molecularly distinct states corresponding to spatiotemporal patterning of the brain. We would like to understand both the causes and the functional implications of the pattern observed. We are interested in investigating how the microenvironment and specific organizers influence or determine this pattern. We expect that paracrine signals are important in inducing those non-autonomous expression changes. Activities The student will culture primary cells obtained from embryonic mice brains at different ages and regions, and evaluate the composition of the cell types generated in vitro. Cocultures will be set up with “majority” cell population from a region, and a “minority” cell population derived from another region. The idea is that the bigger fraction of cells will provide a dominating amount of signaling molecules. Single-cell RNA sequencing will be performed on these cells, allowing a thorough comparison at the transcriptome level.
Keywords: single-cell transcriptomics, neuroscience, stem cells