Analyzing the potential use of reovirus as an oncolytic agent

Thesis (M.A.)--Boston UniversityReovirus, which belongs to the Reoviridae family, is a non-enveloped, dsRNA viruse. Known to infect a wide range of hosts including humans, this virus is generally asymptomatic, and a majority of the population expresses anti- reoviurs antibodies from exposure during childhood. Within the last 70 years, this seemingly obscure virus has gained significant attention as a possible oncolytic virus, which as a group possess a number of qualities that make them theoretically ideal as cancer therapeutics. Namely, they are both safe and well tolerated, and specifically infect and destroy malignant cells. Theorizing that reovirus type-3 dearing would selectively infect and mediate cell death in ras activated cells, researchers have attempted to exploit this non-attenuated strain as an oncolytic virus. By analyzing pre-clinical and clinical studies of reovirus, both as a monotherapy and as part of a variety of combination therapies, I show that reovirus therapy is both safe and well tolerated, but with poorly understood efficacy. Further work is required to elucidate the mechanism behind reovirus mediated oncolysis, to fully maximize its oncolytic potential

Modulation of Rab GTPase function by a protein phosphocholine transferase.

The intracellular pathogen Legionella pneumophila modulates the activity of host GTPases to direct the transport and assembly of the membrane-bound compartment in which it resides. In vitro studies have indicated that the Legionella protein DrrA post-translationally modifies the GTPase Rab1 by a process called AMPylation. Here we used mass spectrometry to investigate post-translational modifications to Rab1 that occur during infection of host cells by Legionella. Consistent with in vitro studies, DrrA-mediated AMPylation of a conserved tyrosine residue in the switch II region of Rab1 was detected during infection. In addition, a modification to an adjacent serine residue in Rab1 was discovered, which was independent of DrrA. The Legionella effector protein AnkX was required for this modification. Biochemical studies determined that AnkX directly mediates the covalent attachment of a phosphocholine moiety to Rab1. This phosphocholine transferase activity used CDP-choline as a substrate and required a conserved histidine residue located in the FIC domain of the AnkX protein. During infection, AnkX modified both Rab1 and Rab35, which explains how this protein modulates membrane transport through both the endocytic and exocytic pathways of the host cell. Thus, phosphocholination of Rab GTPases represents a mechanism by which bacterial FIC-domain-containing proteins can alter host-cell functions

Author response: Effects of orthostatic hypotension on cognition in Parkinson disease

OBJECTIVE: To investigate the relation between orthostatic hypotension (OH) and posture-mediated cognitive impairment in persons with Parkinson's disease (PD) without dementia. METHODS: There were 55 participants: 37 non-demented individuals with idiopathic PD, including 18 with OH (PDOH), and 19 without (PDWOH), and18 control participants (C). All participants completed neuropsychological tests in the supine and in the upright tilted position. Blood pressure was assessed in each posture using a standardized oscillometric cuff at the right brachial artery. RESULTS: The two PD groups performed similarly while supine, with a profile notable for executive dysfunction consisting of deficits in sustained attention, response inhibition, and semantic verbal fluency, as well as reduced verbal memory encoding and retention. When upright, these deficits were exacerbated and broadened to include additional cognitive functions in the PDOH group: deficits in phonemic verbal fluency, psychomotor speed, and both basic and complex aspects of auditory working memory. When group-specific supine scores were used as baseline anchors, both PD groups showed cognitive changes following tilt, though the PDOH group had a wider range of deficits in the executive functioning and memory domains and was the only group to show significant changes in visuospatial skills. CONCLUSIONS: Cognitive deficits in idiopathic PD have been widely reported, though assessments are typically performed in the supine position. While both PD groups had supine deficits that aligned with prior studies and clinical findings, we demonstrated that those with PD and orthostatic hypotension had transient, posture-mediated changes in excess of those found in PD without autonomic failure. These observed changes suggest an acute, reversible effect, and as orthostatic hypotension is a significant comorbid factor in PD, an independent target for clinical intervention. Further understanding of the effects of autonomic failure on cognition in other disorders is desirable, particularly in the context of neuroimaging studies and clinical assessments where data are collected only in the supine or seated positions. Identification of a distinct neuropsychological profile in PD with autonomic failure also has implications for functional activities of daily living and overall quality of life.Accepted manuscrip

Effects of orthostatic hypotension on cognition in Parkinson's disease

OBJECTIVE: To investigate the relation between orthostatic hypotension (OH) and posture-mediated cognitive impairment in Parkinson disease (PD) using a cross-sectional and within-group design. METHODS: Individuals without dementia with idiopathic PD included 18 with OH (PDOH) and 19 without OH; 18 control participants were also included. Neuropsychological tests were conducted in supine and upright-tilted positions. Blood pressure was assessed in each posture. RESULTS: The PD groups performed similarly while supine, demonstrating executive dysfunction in sustained attention and response inhibition, and reduced semantic fluency and verbal memory (encoding and retention). Upright posture exacerbated and broadened these deficits in the PDOH group to include phonemic fluency, psychomotor speed, and auditory working memory. When group-specific supine scores were used as baseline anchors, both PD groups showed cognitive changes following tilt, with the PDOH group exhibiting a wider range of deficits in executive function and memory as well as significant changes in visuospatial function. CONCLUSIONS: Cognitive deficits in PD have been widely reported with assessments performed in the supine position, as seen in both our PD groups. Here we demonstrated that those with PDOH had transient, posture-mediated changes in excess of those found in PD without OH. These observed changes suggest an acute, reversible effect. Understanding the effects of OH due to autonomic failure on cognition is desirable, particularly as neuroimaging and clinical assessments collect data only in the supine or seated positions. Identification of a distinct neuropsychological profile in PD with OH has quality of life implications, and OH presents itself as a possible target for intervention in cognitive disturbance.Accepted manuscriptAccepted manuscrip

Multi-critical behavior of Z2×O(2)Z_2\times O(2) Gross-Neveu-Yukawa theory in graphene

Multi-critical behavior of interacting fermions in graphene's honeycomb lattice is presented. In particular, we considered the spin triplet insulating orders, where the spin rotational symmetry of the order parameter is explicitly broken. By casting the problem in terms of Gross-Neveu-Yukawa theory we show that such symmetry-breaking terms are irrelevant near the metal-insulator critical point. A finite Yukawa coupling among bosons and fermions improves the stability of such critical point against the symmetry-breaking perturbations. Physical sources of such symmetry-breaking terms are pointed out. Critical exponents are calculated near the transitions as well.Comment: 4 pages, 1 figure, Published Version with corrections and new reference

Cross-Linguistic Twitter Analysis of Discussion Themes before, during and after Ramadan

© 2019 IEEE. This study represents the first comprehensive analysis of Twitter data for the United Arab Emirates using both Arabic and English texts. Particular attention is given to the impact of the holy period of Ramadan on the thematic content of Twitter discourse. We examine users\u27 tweet frequency, tweet length and tweet content for different languages (English/Arabic) using statistical methods and topic modeling. The results indicate that Arabic language tweets, during the Ramadan period, included more religious themes than did English tweets. Also, relative to English, Arabic tweets showed greater consistency of content during the three months of the study (before, during and after Ramadan). English content varied significantly over the three months with notable fluctuations in the frequency of content centering on the music, shopping, and health categories. These results suggest that such analytic methods applied to social media data can provide a useful indicator of societal discussion themes. Further research is merited with larger datasets over longer timeframes

Symbolic Execution for Randomized Programs

We propose a symbolic execution method for programs that can draw random samples. In contrast to existing work, our method can verify randomized programs with unknown inputs and can prove probabilistic properties that universally quantify over all possible inputs. Our technique augments standard symbolic execution with a new class of \emph{probabilistic symbolic variables}, which represent the results of random draws, and computes symbolic expressions representing the probability of taking individual paths. We implement our method on top of the \textsc{KLEE} symbolic execution engine alongside multiple optimizations and use it to prove properties about probabilities and expected values for a range of challenging case studies written in C++, including Freivalds' algorithm, randomized quicksort, and a randomized property-testing algorithm for monotonicity. We evaluate our method against \textsc{Psi}, an exact probabilistic symbolic inference engine, and \textsc{Storm}, a probabilistic model checker, and show that our method significantly outperforms both tools.Comment: 47 pages, 9 figures, to appear at OOPSLA 202

On the challenges and rewards of analyzing molecular dynamics at the terabyte and millisecond scale

Molecular Dynamics (MD) and Markov state models (MSMs) are powerful tools for estimating and concisely representing the conformational ensemble accessible to biological macromolecules, particularly proteins. Conformational ensembles are of special importance biological function, both in health and disease, because biology derives from molecules’ entire conformational distribution rather than any single structure. Consequently, MD is poised to become a powerful tool for personalized medicine and for the study of molecular sequence-function relationships generally. However, because of their hyperdimensionality and size, just generating MD datasets and Markov state models (MSMs) that represent biologically relevant molecules is a substantive technical challenge. Then, even once these models are generated, it is not immediately obvious how the conformational ensemble represented by an MSM encodes function. In this thesis, I first present enspara, a python library that makes it possible to build and analyze MSMs at an unprecedented scale. Then, I present “exposons,” an unsupervised machine learning method for discovering substructure these colossal datasets by searching for cooperative changes in a protein’s surface. This method is applied to several small systems of biological interest. Finally, I demonstrate the power these technologies to analyze the kinetic diversity of motor protein myosin, the longest-studied protein in all biochemistry, and in so doing address a longstanding mystery in the field of myosin biochemistry. The applicability of these technologies is almost certainly not limited to the handful of systems I study here. Therefore, this work likely has broad implications for the future of biochemistry, personalized medicine, and the study of biology

A study into the effect of RBM5 expression on a small cell lung cancer cell line

RNA Binding Motif domain protein 5 (RBM5) has been described as a lung cancer tumour suppressor gene. It influences the cell cycle, apoptosis, and the alternative splicing of various genes. In this study, the function of RBM5 was examined in a small cell lung cancer cell line, GLC20, in which RBM5 is deleted. GLC20 sublines expressing RBM5 were used for this study. It was observed that increased RBM5 expression associated with an increase in GLC20 cell death in the presence of cisplatin and a decrease in GLC20 cell proliferation. Increased RBM5 expression also resulted in a decrease in the EC50 of GLC20 cells towards cisplatin. The type of cell death triggered by both RBM5 expression and cisplatin treatment was observed to be apoptosis. Increased RBM5 expression resulted in changes in RBM10 alternative splicing. These results suggest that RBM5 expression may be important in the development of small cell lung cancer.Master of Science (MSc) in Chemical Science