Available Master Projects SV

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. Over the past decade, our understanding of insect endosymbionts has shifted from seeing them as fascinating oddities to being ubiquitous and central to the biology of their hosts, including many of high economic and medical importance. However, 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, genetics, insects

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. Until recently, a detailed understanding of the fly immune response was hampered by the difficulty of generating loss-of-function mutations as well as the technological limits of the RNAi approach. 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.
Keywords: Immunology, innate immunity, Drosophila, genetics

Objective: design, chemically synthesize and test a fluorescent probe specifically targeting the microtubule-doublets present in centrioles and axonemes.
Keywords: Structural analysis, synthetic chemistry, cell biology

Objective: combine experimental 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.
Keywords: CRISPR/Cas9-mediated genome engineering, super-resolution microscopy, mathematical modeling

Objective: test whether centrioles can be formed in human cells with a SAS-6 protein that assembles into a spiral rather than a cartwheel.
Keywords: Live cell imaging, Parthenogenetic development, centrioles, protein expression and purification, antibody generation

Objective: investigate how centrioles are inherited/formed in embryos generated through asexual reproduction, where oocytes develop without fertilization by sperm.
Keywords: Live cell imaging, parthenogenetic development, centrioles, protein expression and purification, Antibody generation

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

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