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Articles 1 - 7 of 7
Full-Text Articles in Life Sciences
Characterizing The Function Of B Cells That Accumulate In The Inflamed Central Nervous System In Anti-Myelin Autoimmunity, Lika Chowdhury
Characterizing The Function Of B Cells That Accumulate In The Inflamed Central Nervous System In Anti-Myelin Autoimmunity, Lika Chowdhury
Electronic Thesis and Dissertation Repository
While the role of autoimmune T cells has been extensively studied in anti-myelin
autoimmunity, little is known about the function of B cells in multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system (CNS). B cells form clusters with T cells in the meninges directly adjacent to demyelinating lesions. Previous studies have shown that disease progression is dependent on the depletion of specific populations of B cells, but it is not clear which contributes to pathology or how. The purpose of this thesis is to characterize the population of meningeal B cells to determine how they differ …
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 …
Gene Regulatory Context Of Honey Bee Worker Sterility, Rahul Choorakkat Unnikrishnan
Gene Regulatory Context Of Honey Bee Worker Sterility, Rahul Choorakkat Unnikrishnan
Electronic Thesis and Dissertation Repository
Honey bee workers deactivate their ovaries and are functionally sterile when a queen is present in the colony. I adopt a bioinformatics approach to up-date a model transcriptional regulatory network (TRN) to study gene-regulatory processes that regulate fecundity in workers. On splitting the network, I obtained nine clusters and each cluster conformed to properties associated with real-world networks. Two of the nine clusters are enriched for 'sterility genes' and contained single well-connected hub genes (GB44769, ftz-f1). The genes in the two clusters were functionally enriched for nucleic acid binding (GO:0003676) and nucleotide binding (GO:0000166). I identified homologous genes for …
Capturing Within Host Hiv-1 Evolution Dynamics Using Simulation Methods, Emmanuel Wong
Capturing Within Host Hiv-1 Evolution Dynamics Using Simulation Methods, Emmanuel Wong
Electronic Thesis and Dissertation Repository
The persistent latent reservoir of long-lived cells carrying integrated HIV DNA is the source of reinfection upon treatment interruption, and a primary focus for cure research. The reservoir is difficult to study because these cells are relatively rare or located in tissues that are difficult to sample. Sequencing proviral DNA in the latent reservoir is an important source of information about reservoir establishment and persistence, especially from the presence of identical (clonal) sequences. I evaluated the relationship between select measures of these clonal sequences and drivers of reservoir persistence, e.g., clonal expansion, by implementing a simulation model of within-host HIV …
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 …
Manipulating The Root Mycobiome To Improve Plant Performance And Reduce Pathogen Pressure In Corn (Zea Mays), Noor F. Saeed Cheema
Manipulating The Root Mycobiome To Improve Plant Performance And Reduce Pathogen Pressure In Corn (Zea Mays), Noor F. Saeed Cheema
Electronic Thesis and Dissertation Repository
Crop yield often varies within a field of a single genetically uniform crop plant, with the causes presumed to be a mix of both biotic and abiotic factors. Manipulating crop root mycobiomes could potentially increase yield by reducing pathogen impacts and improving access to soil water and nutrients. This study aimed to identify different fungal inoculation treatments that could increase the growth of corn seedlings sown in low productivity soils to that in high productivity soils and shift the root mycobiome composition. Fungal inoculation treatments did not have significantly different root mycobiome composition than seedlings grown in low yield control …
Identification Of Dna Methylation Episignatures For Classification And Phenotype/Genotype Correlation In Mendelian Neurodevelopmental Disorders, John Reilly
Electronic Thesis and Dissertation Repository
ABSTRACT: Diagnosis for neurodevelopmental disorders poses numerous challenges, related to the lack of specific findings and limited understanding of clinical impact of the majority of genetic variation. Epigenomics mechanisms involve chemical modifications in DNA that involve a range of cellular mechanisms. DNA methylation is an epigenetic mechanism involving addition and removal of methyl groups to cytosine residues. These methylation signals form episignatures; patterns of methylation that can be used as biomarkers capable of differentiating neurodevelopmental disorders. EpiSigns have enabled molecular diagnosis of a number of genetic conditions, classification of variants of unknown significance, and provided insights into the pathophysiology of …