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Jared Fath, MSC Defence, Earth Sciences
2:00 PM - 5:00 PM
March 14, 2014No Description
Saeed Saberi Modaber, PhD Thesis Defence, Physics
11:00 AM - 2:00 PM
March 17, 2014DEPARTMENT OF PHYSICS THESIS DEFENCE DOCTOR OF PHILOSOPHY Monday, March 17, 2014 11:00 AM Room P8445.2, SFU Department of Physics Candidate: Mr. Saeed Saberi Modaber MSc, BSc, Sharif University of Technology Examining Committee Chair: Dr.Jeffrey McGuirk Senior Supervisor: Dr.Eldon Emberly Supervisor: Dr. John Bechhoefer Supervisor: Dr. Eric Cytrynbaum, University of British Columbia SFU Examiner: Dr. Erikur Palsson, Department of Biological Sciences External Examiner: Dr. Anirvan Sengupta, Rutgers University Models for Protein Localization in Bacteria and Chromatin Structure in Eukaryotes In the first part of this thesis, we focus on the problem of how proteins localize within the cytoplasm of bacteria. Experimentally, it is found that proteins that have attractive interactions are able to localize to one or both of the poles in cylindrical bacteria. We put forward a model that only relies on the aggregating tendency of proteins and the occlusion by the bacterial nucleoid. Monte-Carlo simulations enabled us to find the stable and metastable localization patterns patterns, allowing us to explore the phase space of parameters in our model. Our findings provide an explanation for the different patterns observed for PopZ localization in Escherichia coli and Caulobacter crescentus as well as misfolded proteins. We find the kinetics of expressing proteins has a crucial role: unipolar patterning is an energetically favorable state while other polar patterns can be achieved at higher rates of protein expression. Using sets of different GFP tagged aggregating proteins we are able to experimentally test this prediction and alter the localization from unipolar to bipolar simply by increasing the rate of expression. In the second part of the thesis, we consider the structuring of the DNA within the eukaryotic nucleous and its associated proteins. A new high-throughput experimental technique, Hi-C, is able to measure the looping frequencies between all parts of the genome. We transform the measured data and are able to extract a distance independent free energyby subtracting out the background free energy of interactions due to the polymer nature of DNA. Our mean-field model quantifies the interaction strengths between chromatin factors and loops along the chromosomes in a protein pairwise interaction matrix Jμ, υ. Since the Hi-C data carries different biases, using our approach we are able to assess the best sets of corrections that lead to the free energy having the most mutual information with the underlying chromatin profiles. Further to this, we use Principal Component Analysis (PCA) to identify the frequent modes of genome wide looping. Hence we are able to correlate these with known domain structures such as boundaries between active and silent regions of the genome.
Andrew Adams, M.Sc. Thesis Defence, Mathematics Room: IRMACS 10901
10:30 AM - 12:30 PM
March 20, 2014Sr. Supervisor: Ralf Wittenberg Title: Using Viral Dynamics to Connect Clinical Markers of Disease Progression to Sequence Evolution during HIV-1 Infection. Abstract: HIV-1 remains a global health challenge, with over 35 million people infected. The high rates of turnover and evolutionary adaptability exhibited by HIV-1 pose a particular challenge to HIV-1 vaccine development. We developed a dynamic model of HIV-1 infection that uses equilibration, adaptation, and inheritance to model the initial infection and successive generations of viral lineages. The model allows viruses to generate new lineages in proportion to their viral load. These lineages compete for immune cells to infect. We use this model to demonstrate how viruses with a sufficiently high mutation rate could overcome the immune system, even when most changes are expected to be detrimental to viral fitness. We have calibrated our model to match averages of CD4+ T cells/mm3 and HIV-1 RNA/ml derived from 91 HIV-infected individuals studied longitudinally during various disease stages. We also explore the use of phylogenies to validate the underlying composition of viral load.
Event: Pi Day Celebration at the IRMACS Centre! March 11, 2014
Pi Day trivia at the IRMACS Centre with free pie
Professional Development Opportunity: High Impact Communication with Dr. Mark L. Winston March 10, 2014
Improve your ability to speak and write so that people listen and understand with widely published Bio Science Professor and Semester in Dialogue Director, Dr. Mark Winston