Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Cell and Developmental Biology (4)
- Bioinformatics (3)
- Biology (3)
- Biochemistry, Biophysics, and Structural Biology (2)
- Cell Biology (2)
-
- Developmental Biology (2)
- Medicine and Health Sciences (2)
- Neuroscience and Neurobiology (2)
- Social and Behavioral Sciences (2)
- Agriculture (1)
- Allergy and Immunology (1)
- Anthropology (1)
- Artificial Intelligence and Robotics (1)
- Biochemistry (1)
- Biological and Physical Anthropology (1)
- Computer Sciences (1)
- Immunology and Infectious Disease (1)
- Medical Immunology (1)
- Medical Sciences (1)
- Medical Specialties (1)
- Microbiology (1)
- Molecular Biology (1)
- Physical Sciences and Mathematics (1)
- Plant Sciences (1)
- Psychology (1)
- Keyword
-
- Adhesion GPCRs (1)
- Aggregation (1)
- Algorithm (1)
- Arabidopsis thaliana (1)
- B cell lymphoma (1)
-
- Baboons (1)
- Cancer Genomics (1)
- Chaperone (1)
- Chaperone-usher pathway pili (1)
- Chromatin (1)
- Chromosome architecture (1)
- Epigenetics (1)
- Evolution (1)
- Externalizing (1)
- F17-like pili (1)
- Fbxw7 (1)
- Gene expression (1)
- Gene regulation (1)
- Genomics (1)
- Hybridization (1)
- Image-based phenotyping (1)
- Insula (1)
- Introgression (1)
- Leaf development (1)
- Longitudinal (1)
- MRNA surveillance (1)
- Machine Learning (1)
- Mannoside (1)
- Myelin (1)
- Neurogenetics (1)
Articles 1 - 12 of 12
Full-Text Articles in Genetics and Genomics
Mechanism Of Gene Regulation By Coding Polya Tracks, Laura Lea Arthur
Mechanism Of Gene Regulation By Coding Polya Tracks, Laura Lea Arthur
Arts & Sciences Electronic Theses and Dissertations
Regulation of gene expression is essential for cellular development and survival. The great variety and complexity of regulatory mechanisms underscores this fact. Messenger RNA stability and translational efficiency are often key determinants of gene expression. mRNA surveillance pathways, discovered for their role in degradation of aberrant mRNA, are now known to be instrumental in the regulation of physiologically correct mRNA stability. Thus, the study of cis elements in a transcript that can induce mRNA surveillance pathways has become an area of particular interest.
Here I report on the mechanism of gene regulation by coding polyA tracks, defined as a sequence …
Knowledge Driven Approaches And Machine Learning Improve The Identification Of Clinically Relevant Somatic Mutations In Cancer Genomics, Benjamin John Ainscough
Knowledge Driven Approaches And Machine Learning Improve The Identification Of Clinically Relevant Somatic Mutations In Cancer Genomics, Benjamin John Ainscough
Arts & Sciences Electronic Theses and Dissertations
For cancer genomics to fully expand its utility from research discovery to clinical adoption, somatic variant detection pipelines must be optimized and standardized to ensure identification of clinically relevant mutations and to reduce laborious and error-prone post-processing steps. To address the need for improved catalogues of clinically and biologically important somatic mutations, we developed DoCM, a Database of Curated Mutations in Cancer (http://docm.info), as described in Chapter 2. DoCM is an open source, openly licensed resource to enable the cancer research community to aggregate, store and track biologically and clinically important cancer variants. DoCM is currently comprised of 1,364 variants …
Analysis Of Argonaute-Small Rna-Transcription Factor Circuits Controlling Leaf Development, John Steen Hoyer
Analysis Of Argonaute-Small Rna-Transcription Factor Circuits Controlling Leaf Development, John Steen Hoyer
Arts & Sciences Electronic Theses and Dissertations
Experimental studies of plant development have yielded many insights into gene regulation, revealing interactions between core transcriptional and post-transcriptional regulatory pathways present in all land plants. This work describes a direct connection between the three main small RNA-transcription factor circuits controlling leaf shape dynamics in the reference plant Arabidopsis thaliana. We used a high-throughput yeast 1-hybrid platform to identify factors directly binding the promoter of the highly specialized ARGONAUTE7 silencing factor. Two groups of developmentally significant microRNA-targeted transcription factors were the clearest hits from these screens, but transgenic complementation analysis indicated that their binding sites make only a small contribution …
Robust Algorithms For Detecting Hidden Structure In Biological Data, Roman Sloutsky
Robust Algorithms For Detecting Hidden Structure In Biological Data, Roman Sloutsky
Arts & Sciences Electronic Theses and Dissertations
Biological data, such as molecular abundance measurements and protein
sequences, harbor complex hidden structure that reflects its underlying
biological mechanisms. For example, high-throughput abundance measurements
provide a snapshot the global state of a living cell, while homologous
protein sequences encode the residue-level logic of the proteins' function
and provide a snapshot of the evolutionary trajectory of the protein family.
In this work I describe algorithmic approaches and analysis software I
developed for uncovering hidden structure in both kinds of data.
Clustering is an unsurpervised machine learning technique commonly used
to map the structure of data collected in high-throughput experiments,
such …
Type 1 And F17-Like Pili Promote The Establishment Of The Uropathogenic E. Coli Intestinal Reservoir, Caitlin Nicole Spaulding
Type 1 And F17-Like Pili Promote The Establishment Of The Uropathogenic E. Coli Intestinal Reservoir, Caitlin Nicole Spaulding
Arts & Sciences Electronic Theses and Dissertations
Urinary tract infections (UTI) affect over 150 million individuals worldwide every year. These infections are associated with significant morbidity and have a sizeable economic impact, with $5 billion being spent on UTI treatment in the USA annually. Uropathogenic E. coli (UPEC) are responsible for 80% of community acquired UTIs and 65% of nosocomial UTI. The current standard of care for UTI is antibiotic therapy. However, 30-50% of women experience recurrent UTI (rUTI) despite receiving antibiotic therapy. The prevalence of single and multi-drug resistant UPEC strains has led to increased reliance on carbepenems, which are primarily reserved for multi-drug resistant infections, …
Neurogenetics Of The Externalizing Spectrum, Caitlin E. Carey
Neurogenetics Of The Externalizing Spectrum, Caitlin E. Carey
Arts & Sciences Electronic Theses and Dissertations
Externalizing spectrum disorders, which include attention-deficit/hyperactivity disorder, oppositional defiant disorder, conduct disorder, alcohol and substance use disorders, and antisocial personality disorder, are characterized by behavioral disinhibition and are thought to be manifestations of a common heritable liability factor throughout the lifespan. However, relatively little is known about their underlying etiology. Here, I probe genetic and neural risk mechanisms for externalizing psychopathology in three complementary studies. First, I report an indirect association between genetic risk for childhood attention-deficit/hyperactivity disorder (ADHD) and problem drinking in young adulthood, mediated by heightened reward-related neural activity within the ventral striatum, among 404 college students. I …
Epigenetic Activation Of The Mouse T Cell Receptor Beta Recombination Center, Jiangyang Zhao
Epigenetic Activation Of The Mouse T Cell Receptor Beta Recombination Center, Jiangyang Zhao
Arts & Sciences Electronic Theses and Dissertations
Lymphocytes are the work horses of adaptive immunity. Compared to the B lymphocyte lineage, early stage progenitors of T lymphocytes maintain considerable potential for differentiation into other hematopoietic lineages. T lineage commitment requires the continuous coordination of transcription factors (TFs) by Notch1 signaling after multi-potent progenitors (MPPs) migrate to thymus. One of the first hall marks of T lineage commitment is expression of the T cell receptor β (TCRβ), which is encoded by the Tcrb locus following its assembly by V(D)J recombination, a somatic shuffling of the genome that joins one V, one D, and one J gene segment. Tcrb …
Genetic And Genomic Dissections Of Myelinating Glial Cell Development, Breanne Leigh Harty
Genetic And Genomic Dissections Of Myelinating Glial Cell Development, Breanne Leigh Harty
Arts & Sciences Electronic Theses and Dissertations
Myelin is a multilamellar sheath made by specialized glial cells that iteratively spiral and compact their plasma membranes around axon segments. In vertebrate nervous systems, myelination facilitates rapid action propagation and provides trophic support critical for neuronal survival. In the central nervous system (CNS), oligodendrocytes (OLs) extend many processes to simultaneously ensheath multiple axons, while in the peripheral nervous system (PNS), myelinating Schwann cells (SCs) pair 1:1 with a single axon segment. Elaboration of the myelin sheath is one of the most exquisite and complex examples of massive coordinated cellular shape changes in the vertebrate nervous system. Furthermore, the importance …
Population Genomics Of A Baboon Hybrid Zone In Zambia, Kenneth Lyu Chiou
Population Genomics Of A Baboon Hybrid Zone In Zambia, Kenneth Lyu Chiou
Arts & Sciences Electronic Theses and Dissertations
Hybridization is increasingly recognized as a common, important process shaping the evolution of organisms including humans. Across hybrid zones, the genomes of incipient species are mixed and recombined through hybridization and backcrossing, creating conditions ideal for evaluating the actions of natural selection on gene variants in novel genomic contexts. This dissertation aims to increase our understanding of hybridization using a Zambian baboon study system in which two species, Kinda baboons (Papio kindae) and grayfoot baboons (Papio griseipes), hybridize despite exhibiting pronounced differences in body size and behavior. Using genome-wide genotypic data prepared using double-digest RADseq, I scan for genomic regions …
Factors That Contribute To De Novo Protein Misfolding And Prion Formation In Saccharomyces Cerevisiae, Kathryn Morgan Keefer
Factors That Contribute To De Novo Protein Misfolding And Prion Formation In Saccharomyces Cerevisiae, Kathryn Morgan Keefer
Arts & Sciences Electronic Theses and Dissertations
Protein misfolding is a common phenomenon that can have severe consequences on cellular and organismal health. Despite this, the causes of protein misfolding remain poorly understood. Prions are a class of proteins that, when misfolded, can convert other molecules into a heritable, non-native conformation. The yeast Saccharomyces cerevisiae naturally harbors several diverse prion-forming proteins; thus, it is an ideal model with which to investigate the factors that influence misfolding and aggregation.This thesis utilizes the yeast prions [PSI+] and [RNQ+] to investigate two distinct steps of the protein misfolding pathway: interactions with chaperones and their cofactors, and heterologous templating by other …
Epigenetic Regulation Of Lymphocyte Development And Transformation, Yue Huang
Epigenetic Regulation Of Lymphocyte Development And Transformation, Yue Huang
Arts & Sciences Electronic Theses and Dissertations
Cell identity and function rely on intricately controlled programs of gene regulation, alterations of which underlie many diseases, including cancer. Epigenetic analyses of normal and diseased cells have started to elucidate different facets of epigenetic mechanisms for gene regulation. These include changes in nucleosome density, histone modifications, factor binding and chromosomal architecture. All of these aspects contribute to the activities of regulatory elements conferring promoter, enhancer and insulator functions and the cis-regulatory circuits formed by these elements. Despite this progress, an urgent need remains to profile these features and to study how they cooperatively function in normal and pathogenic settings. …
The Effects Of The Gut Microbiota On The Host Chromatin Landscape, Nicholas Semenkovich
The Effects Of The Gut Microbiota On The Host Chromatin Landscape, Nicholas Semenkovich
Arts & Sciences Electronic Theses and Dissertations
The human gut microbiota is home to tens of trillions of microbes belonging to all three domains of life. The structure and expressed functions of this community have myriad effects on host physiology, metabolism, and immune function. My studies focused on a facet of host-microbial interactions and mutualism that has not been explored to a significant degree in part because of the absence of suitable tools: namely, if, when, and how the gut microbiota produces durable effects on host biology through its impact on the epigenome. To address this area, I turned to gnotobiotic mice and developed a variety of …