Genetics and Genomics Commons^™

An Automatic Framework For Embryonic Localization Using Edges In A Scale Space, Zachary Bessinger

Masters Theses & Specialist Projects

Localization of Drosophila embryos in images is a fundamental step in an automatic computational system for the exploration of gene-gene interaction on Drosophila. Contour extraction of embryonic images is challenging due to many variations in embryonic images. In the thesis work, we develop a localization framework based on the analysis of connected components of edge pixels in a scale space. We propose criteria to select optimal scales for embryonic localization. Furthermore, we propose a scale mapping strategy to compress the range of a scale space in order to improve the efficiency of the localization framework. The effectiveness of the proposed ...

Comparative Analyses Of Microbial Genomes To Identify Molecular Markers For Different Groups Of Prokaryotes, Vaibhav Bhandari

Open Access Dissertations and Theses

Currently centered on molecular data, bacterial and archaeal relationships are often based on their relative branching in 16S rRNA based phylogenetic trees. The availability of numerous bacterial genome sequences over the past two decades has provided new information for insights previously inaccessible to the field of taxonomy. Through utilization of comparative genomics, numerous molecular markers in the form of insertions and deletions within conserved regions of proteins, also known as Conserved Signature Indels or CSIs, have been discovered for various prokaryotic taxa. Using these techniques, we have analyzed relationships among the bacterial phyla of Thermotogae and Synergistetes and the conglomeration ...

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications & Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we ...

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD ...

Unique Small Rna Signatures Uncovered In The Tammar Wallaby Genome, James Lindsay, Dawn M. Carone, Judy Brown, Laura Hall, Sohaib Quershi, Sarah E. Mitchell, Nicholas Jannetty, Greg Hannon, Marilyn B. Renfree, Andrew J. Pask, Michael O'Neill, Rachel J. O'Neill

Open Access Articles

BACKGROUND: Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short ...

Pathway Distiller - Multisource Biological Pathway Consolidation, Mark S. Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander J. R. Bishop, Yidong Chen

Open Access Articles

BACKGROUND: One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets.

METHODS: After gene set enrichment finds representative pathways for large ...

A Specific Family Of Interspersed Repeats (Sines) Facilitates Meiotic Synapsis In Mammals, Matthew E. Johnson, Ross A. Rowsey, Sofia Shirley, Catherine Vandevoort, Jeffrey A. Bailey, Terry Hassold

Open Access Articles

BACKGROUND: Errors during meiosis that affect synapsis and recombination between homologous chromosomes contribute to aneuploidy and infertility in humans. Despite the clinical relevance of these defects, we know very little about the mechanisms by which homologous chromosomes interact with one another during mammalian meiotic prophase. Further, we remain ignorant of the way in which chromosomal DNA complexes with the meiosis-specific structure that tethers homologs, the synaptonemal complex (SC), and whether specific DNA elements are necessary for this interaction.

RESULTS: In the present study we utilized chromatin immunoprecipitation (ChIP) and DNA sequencing to demonstrate that the axial elements of the mammalian ...

Delayed Thrombus Resolution And Fibroproliferative Vascular Wound Healing From Deficiency Of Type Iii Collagen: A Paradoxical Mechanism For Tissue Fragility, Amy J. Reid

UT GSBS Dissertations and Theses (Open Access)

Vascular Ehlers-Danlos syndrome is a heritable disease of connective tissue caused by mutations in COL3A1, conferring a tissue deficiency of type III collagen. Cutaneous wounds heal poorly in these patients, and they are susceptible to spontaneous and catastrophic rupture of expansible hollow organs like the gut, uterus, and medium-sized to large arteries, which leads to premature death. Although the predisposition for organ rupture is often attributed to inherent tissue fragility, investigation of arteries from a haploinsufficient Col3a1 mouse model (Col3a1^+/-) demonstrates that mutant arteries withstand even supraphysiologic pressures comparably to wild-type vessels. We hypothesize that injury that elicits occlusive thrombi ...

The Torsion Angle Of Random Walks, Mu He

Masters Theses & Specialist Projects

In this thesis, we study the expected mean of the torsion angle of an n-step
equilateral random walk in 3D. We consider the random walk is generated within a confining sphere or without a confining sphere: given three consecutive vectors ^→e₁ , ^→e₂ , and ^→e₃ of the random walk then the vectors ^→e₁ and ^→e₂ define a plane and the vectors ^→e₂ and ^→e₃ define a second plane. The angle between the two planes is called the torsion angle of the three vectors. Algorithms are described to generate random walks which are used in ...

Comparison Of Multilocus Sequence Analysis And Virulence Genotyping Of Escherichia Coli From Live Birds, Retail Poultry Meat, And Human Extraintestinal Infection, Jessica L. Danzeisen, Yvonne Wannemuehler, Lisa K. Nolan, Timothy J. Johnson

Veterinary Microbiology and Preventive Medicine Publications and Papers

To examine the correlations between virulence genotyping and multilocus sequence analysis of Escherichia coli from poultry and humans, 88 isolates were examined. The isolates were selected from a population of over 1000 based on their assignment to nine different virulence genotyping clusters. Clustering based on multilocus sequence analysis mostly correlated with virulence genotyping, although multilocus sequence analysis demonstrated higher discriminatory ability and greater reliability related to inferred phylogenetic relationships. No distinct patterns in host source were observed using inferred phylogeny through multilocus sequence analysis, indicating that human, avian, and retail meat isolates are diverse, and some belong to multiple shared ...

Characterization Of The Apoptotic Functions Of The Hid Hmolog Isolated From Megaselia Scalaris, Shannon Smith

University of Tennessee Honors Thesis Projects

No abstract provided.

Prevalence Of Avian-Pathogenic Escherichia Coli Strain O1 Genomic Islands Among Extraintestinal And Commensal E. Coli Isolates, Timothy J. Johnson, Yvonne Wannemuehler, Subhashinie Kariyawasam, James R. Johnson, Catherine M. Logue, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications and Papers

Escherichia coli strains that cause disease outside the intestine are known as extraintestinal pathogenic E. coli (ExPEC) and include pathogens of humans and animals. Previously, the genome of avian-pathogenic E. coli (APEC) O1:K1:H7 strain O1, from ST95, was sequenced and compared to those of several other E. coli strains, identifying 43 genomic islands. Here, the genomic islands of APEC O1 were compared to those of other sequenced E. coli strains, and the distribution of 81 genes belonging to 12 APEC O1 genomic islands among 828 human and avian ExPEC and commensal E. coli isolates was determined. Multiple islands ...

Genotypic And Phenotypic Traits That Distinguish Neonatal Meningitis-Associated Escherichia Coli From Fecal E. Coli Isolates Of Healthy Human Hosts, Catherine M. Logue, Curt Doetkott, Paul M. Mangiamele, Yvonne Wannemuehler, Timothy J. Johnson, Kelly A. Tivendale, Ganwu Li, Julie S. Sherwood, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications and Papers

Neonatal meningitis Escherichia coli (NMEC) is one of the top causes of neonatal meningitis worldwide. Here, 85 NMEC and 204 fecal E. coli isolates from healthy humans (HFEC) were compared for possession of traits related to virulence, antimicrobial resistance, and plasmid content. This comparison was done to identify traits that typify NMEC and distinguish it from commensal strains to refine the definition of the NMEC subpathotype, identify traits that might contribute to NMEC pathogenesis, and facilitate choices of NMEC strains for future study. A large number of E. coli strains from both groups were untypeable, with the most common serogroups ...

Escherichia Coli Isolates That Carry Vat, Fyua, Chua, And Yfcv Efficiently Colonize The Urinary Tract, Rachel R. Spurbeck, Paul C. Dinh Jr., Seth T. Walk, Ann E. Stapleton, Thomas M. Hooton, Lisa K. Nolan, Kwang Sik Kim, James R. Johnson, Harry L. T. Mobley

Veterinary Microbiology and Preventive Medicine Publications and Papers

Extraintestinal Escherichia coli (ExPEC), a heterogeneous group of pathogens, encompasses avian, neonatal meningitis, and uropathogenic E. coli strains. While several virulence factors are associated with ExPEC, there is no core set of virulence factors that can be used to definitively differentiate these pathotypes. Here we describe a multiplex of four virulence factor-encoding genes, yfcV, vat,fyuA, and chuA, highly associated with uropathogenic E. coli strains that can distinguish three groups of E. coli: diarrheagenic and animal-associated E. colistrains, human commensal and avian pathogenic E. coli strains, and uropathogenic and neonatal meningitis E. coli strains. Furthermore, human intestinal isolates that encode ...

Complete Genome Sequence Of The Avian Pathogenic Escherichia Coli Strain Apec O78, Paul M. Mangiamele, Bryon A. Nicholson, Yvonne Wannemuehler, Torsten Seemann, Catherine M. Logue, Ganwu Li, Kelly A. Tivendale, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications and Papers

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is a significant disease, causing extensive animal and financial losses globally. Because of the significance of this disease, more knowledge is needed regarding APEC's mechanisms of virulence. Here, we present the fully closed genome sequence of a typical avian pathogenic E. coli strain belonging to the serogroup O78.

Deep Sequencing-Based Transcriptome Analysis Of Chicken Spleen In Response To Avian Pathogenic Escherichia Coli (Apec) Infection, Qinghua Nie, Xiquan Zhang, Erin E. Sandford, Susan J. Lamont, Lisa K. Nolan

Veterinary Microbiology and Preventive Medicine Publications and Papers

Avian pathogenic Escherichia coli (APEC) leads to economic losses in poultry production and is also a threat to human health. The goal of this study was to characterize the chicken spleen transcriptome and to identify candidate genes for response and resistance to APEC infection using Solexa sequencing. We obtained 14422935, 14104324, and 14954692 Solexa read pairs for non-challenged (NC), challenged-mild pathology (MD), and challenged-severe pathology (SV), respectively. A total of 148197 contigs and 98461 unigenes were assembled, of which 134949 contigs and 91890 unigenes match the chicken genome. In total, 12272 annotated unigenes take part in biological processes (11664), cellular ...

Genome Analysis And Phylogenetic Relatedness Of Gallibacterium Anatis Strains From Poultry, Timothy J. Johnson, Jessica L. Danzeisen, Darrell W. Trampel, Lisa K. Nolan, Torsten Seemann, Ragnhild J. Bager, Anders M. Bojesen

Veterinary Microbiology and Preventive Medicine Publications and Papers

Peritonitis is the major disease problem of laying hens in commercial table egg and parent stock operations. Despite its importance, the etiology and pathogenesis of this disease have not been completely clarified. Although avian pathogenic Escherichia coli (APEC) isolates have been incriminated as the causative agent of laying hen peritonitis, Gallibacterium anatis are frequently isolated from peritonitis lesions. Despite recent studies suggesting a role for G. anatis in the pathogenesis of peritonitis, little is known about the organism’s virulence mechanisms, genomic composition and population dynamics. Here, we compared the genome sequences of three G. anatis isolates in an effort ...

Cellular Adaptation Of Macrophages To Anthrax Lethal Toxin-Induced Pyroptosis Via Epigenetic Mechanisms, Chae Young Han

University of Western Ontario - Electronic Thesis and Dissertation Repository

Cellular adaptation to microbial stresses has been demonstrated in several cell types. Macrophages (MФ) are sentinel immune cells fending off invading microbes. Anthrax lethal toxin (LeTx) is a key virulence factor released by Bacillus anthracis that causes rapid cell death, pyroptosis. A small number of RAW246.7 macrophages (~4%) exposed to a non-lethal dose of LeTx become resistant to LeTx-induced pyroptosis for ~ 4 weeks, termed “toxin-induced resistance (TIR)”. Here, I showed that high levels of DNA methyl transferase1 (DNMT1) expression were maintained although global genomic methylation levels were not high in TIR. TIR cells treated with the DNMT inhibitor 5-azacitidine ...

Expressional Alterations In Functional Ultra-Conserved Non-Coding Rnas In Response To All-Trans Retinoic Acid - Induced Differentiation In Neuroblastoma Cells., Karen M. Watters, Kenneth Bryan, Niamh H. Foley, Maria Meehan, Raymond L. Stallings

Cancer Genetics Articles

BACKGROUND: Ultra-conserved regions (UCRs) are segments of the genome (≥ 200 bp) that exhibit 100% DNA sequence conservation between human, mouse and rat. Transcribed UCRs (T-UCRs) have been shown to be differentially expressed in cancers versus normal tissue, indicating a possible role in carcinogenesis. All-trans-retinoic acid (ATRA) causes some neuroblastoma (NB) cell lines to undergo differentiation and leads to a significant decrease in the oncogenic transcription factor MYCN. Here, we examine the impact of ATRA treatment on T-UCR expression and investigate the biological significance of these changes.

METHODS: We designed a custom tiling microarray to profile the expression of 481 T-UCRs ...

Regulation Of Mrna Export By The Pi3 Kinase / Akt Signal Transduction Pathway, Alexandre Jose Christino Quaresma, Rachel Sievert, Jeffrey A. Nickerson

Cell and Developmental Biology Publications and Presentations

UAP56, ALY/REF, and NXF1 are mRNA export factors that sequentially bind at the 5' end of a nuclear mRNA, but are also reported to associate with the Exon Junction Complex (EJC). To screen for signal transduction pathways regulating mRNA export complex assembly we used Fluorescence Recovery after Photobleaching (FRAP) to measure the binding of mRNA export and EJC core proteins in nuclear complexes. The fraction of UAP56, ALY/REF, and NXF1 tightly bound in complexes was reduced by drug inhibition of the PI3 kinase / AKT pathway, as was the tightly bound fraction of the core EJC proteins eIF4A3, MAGOH ...