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Articles 1 - 6 of 6
Full-Text Articles in Life Sciences
Selection Pressure On Surface Exposed Virus Proteins, Sareh Bagherichimeh
Selection Pressure On Surface Exposed Virus Proteins, Sareh Bagherichimeh
Electronic Thesis and Dissertation Repository
Viral infection requires the interaction between virus surface-exposed (SE) proteins and host cell receptors. This can result in an “arms race” that is assumed to drive accelerated rates of evolution, and some well known examples of diversifying selection involve surface pro- teins (HIV-1 env, influenza hemagglutinin). We conducted a systematic analysis to determine whether this is truly a distinctive feature of SE virus proteins, in comparison to non-SE proteins encoded by the same genomes.
We obtained reference and all neighbour genomes of 52 human viruses from the NCBI Viral Genomes database. The coding sequences (CDS) of each genome extracted by …
Chromatin Regulation By Rb-Interacting Proteins In Cellular Immune Functions, Seung June Kim
Chromatin Regulation By Rb-Interacting Proteins In Cellular Immune Functions, Seung June Kim
Electronic Thesis and Dissertation Repository
The retinoblastoma protein (RB) is historically known for its function in cell cycle control. However, mice carrying targeted Rb1 mutations have revealed that RB serves various non-cell cycle control roles. Notably, RB acts as a scaffold that recruits chromatin regulatory proteins, condensin II and enhancer of zeste homolog 2 (EZH2). These complexes protect the genome integrity through maintaining proper chromosome condensation, long range contacts, and transcriptionally repressive histone modification. This thesis explores the mechanistic links that regulate such RB-condensin II complex or that are leveraged upon pharmacological inhibition of the RB-EZH2 complex. First, I identified potential phosphorylation sites in the …
Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris
Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris
Electronic Thesis and Dissertation Repository
Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.
Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …
Characterizing The Transcriptome Of Sirt6-Deficient Aortic Smooth Muscle Cells, Ryan J. Wong
Characterizing The Transcriptome Of Sirt6-Deficient Aortic Smooth Muscle Cells, Ryan J. Wong
Electronic Thesis and Dissertation Repository
Several vascular diseases are marked by dysfunctional vascular smooth muscle cells (VSMCs). Our group has found that the knockout of the NAD+-dependent histone deacetylase sirtuin 6 (Sirt6), specifically in VSMCs, increases oxidative stress-induced DNA damage, inflammation, and aortic aneurysms in mice. To study the molecular mechanisms that drive VSMC dysfunction in Sirt6-deficiency, I established a primary culture model of Sirt6 deletion in VSMCs with Cre-lox technology. Through RNA sequencing of Sirt6-deficient VSMCs, we have identified modest but coordinated upregulations in transcripts involved in nucleosome assembly, inflammation, cell death, and autoimmunity. Immunostaining in histological sections of VSMC-specific …
Applications Of Nanopore Dna Sequencing For Improved Genome Assembly, Daniel Giguere
Applications Of Nanopore Dna Sequencing For Improved Genome Assembly, Daniel Giguere
Electronic Thesis and Dissertation Repository
An organism's genome is the ultimate determinant of its functional potential. Understanding genomes is therefore essential to understand function, and a foundational knowledge of a genome is required transfer functions to and from microorganisms of interest. Sequencing DNA using nanopores is a recent advance that resolves limitations of previous technologies, enabling an improved understanding of genomes. For this thesis, I improved our understanding of microbial genomes by developing novel approaches to analyze long read sequencing data, setting the foundation for future synthetic biology work.
Long sequencing reads have enabled routine assembly of complete bacterial genomes by directly sequencing DNA extracted …
The Genetics Of Pain: An Exploration Of Gene-By-Environment Interactions And Their Effects On Pain, Mohamad F. Fakhereddin
The Genetics Of Pain: An Exploration Of Gene-By-Environment Interactions And Their Effects On Pain, Mohamad F. Fakhereddin
Electronic Thesis and Dissertation Repository
The findings presented in this dissertation are part of the bigger SYMBIOME project which aims to use the biopsychosocial model of pain to develop a prognostic clinical phenotype for people that experience musculoskeletal (MSK) trauma. Chapter 2 presents an exploratory analysis to assess the relationships between genetic polymorphisms and pain severity and interference. Early childhood trauma was also explored as a moderator between genetic polymorphisms and pain outcomes. For pain severity, major allele carriers (A/A and G/A) of FKBP5 rs9394314 reported significantly higher scores than minor allele carriers (G/G). Further, major allele carriers who had at least one adverse childhood …