Life Sciences Commons^™

S-Plot2: Rapid Visual And Statistical Analysis Of Genomic Sequences, Laurynas Kalesinskas, Evan Cudone, Yuriy Fofanov, Catherine Putonti

Biology: Faculty Publications and Other Works

With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool …

Molecular Determinants Of Trim5Α Restriction And Recruitment Of Autophagic Effectors, Sabrina Imam

Dissertations

TRIM5α is an anti-viral restriction factor that inhibits the lifecycle of retroviruses. TRIM5α binds to and forms a hexameric lattice around the retroviral capsid, thereby initiating its antiviral activities, which include: (1) inhibition of viral infection; (2) inhibition of viral reverse transcription; (3) disassembly of the capsid; and (4), activation of innate signaling pathways. The formation of this assembly also activates the E3 ubiquitin ligase function of TRIM5α. Ubiquitin modification is associated with directing substrates to particular cellular pathways. We and others have shown that TRIM5α cytoplasmic bodies colocalize with proteins involved in the autophagy pathway, and we hypothesized that …

S-Plot2: Rapid Visual And Statistical Analysis Of Genomic Sequences, Laurynas Kalensinskas, Evan Cudone, Yuriy Fofanov, Catherine Putonti

Bioinformatics Faculty Publications

With the daily release of data from whole genome sequencing projects, tools to facilitate comparative studies are hard-pressed to keep pace. Graphical software solutions can readily recognize synteny by measuring similarities between sequences. Nevertheless, regions of dissimilarity can prove to be equally informative; these regions may harbor genes acquired via lateral gene transfer (LGT), signify gene loss or gain, or include coding regions under strong selection. Previously, we developed the software S-plot. This tool employed an alignment-free approach for comparing bacterial genomes and generated a heatmap representing the genomes’ similarities and dissimilarities in nucleotide usage. In prior studies, this tool …

Clusters Of Alpha Satellite On Human Chromosome 21 Are Dispersed Far Onto The Short Arm And Lack Ancient Layers, William Ziccardi, Chongjian Zhao, Valery Shepelev, Lev Uralsky, Ivan Alexandrov, Tatyana Andreeva, Evgeny Rogaev, Christopher Bun, Emily Miller, Catherine Putonti, Jeffrey Doering

Bioinformatics Faculty Publications

Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the …

Mechanism By Which Commensal Bacteria Limit Inflammation, Mallory Paynich

Dissertations

Trillions of bacteria live within the gastrointestinal tract and are critical for maintaining intestinal homeostasis; however, the mechanisms utilized by specific bacterial molecules to contribute to homeostasis are not well understood. We utilize a mouse model in which a single oral dose of the probiotic, Bacillus subtilis, protects mice from acute colitis induced by the enteric pathogen Citrobacter rodentium. Our goal is to elucidate the mechanism by which B. subtilis prevents inflammation.

We identified exopolysaccharides (EPS) to be the active molecule of B. subtilis, and a single dose of EPS protects mice from disease. EPS binds F4/80+CD11b+ peritoneal macrophages, and …

Dna Methylation Patterns Of Specific L1 Loci On The Short Arm Of Chromosome 21, Sarah Ann Tincher

Master's Theses

While 10-15% of the human genome is composed of heterochromatic DNA, these regions are not included in the completed genome sequence. The short arm of chromosome 21 (HC21p) serves as a model for understanding the structure and function of heterochromatin. LINE-1 (L1) retrotransposons are underrepresented in heterochromatin, including HC21p, and have not been extensively studied in these regions. However, there are disproportionately more full length L1s on HC21p than in euchromatic genomic regions. Decreased DNA methylation in the promoters of these L1s on HC21p may allow them to facilitate heterochromatin formation, which would be analogous to their proposed role in …

Functional Characterization Of A Novel Thioredoxin Domain-Containing Protein Of The Malaria Parasite Plasmodium, Rachel Kooistra

Master's Theses

A novel thioredoxin domain-containing protein of the malaria parasite Plasmodium was identified and found to be conserved among eukaryotes. This protein belongs to the phosducin-like family of proteins (PhLPs), and was therefore assigned the name PhLP1, since it is the first phosducin-like protein to be identified in Plasmodium. PhLPs have been found to have various roles in G-protein signaling, cell cycle progression, and protein folding. However, the biochemical mechanism by which PhLPs perform their function is unknown. Here is described the cloning and biochemical characterization of both PhLP1 and its human homolog TXNDC9. Both purified PhLP1 and TXNDC9 showed enzymatic …

Organization And Composition Of The Α21-Ii Region Of Human Chromosome 21, William Ziccardi

Master's Theses

The purpose of this project was to develop a better map of the alpha 21-II region of human chromosome 21 in regards to size and primary sequence of the five alphoid clusters that comprise the region and to explore the evolutionary relationships that exist within and between these clusters. Several HC21 BACs were identified as containing strong sequence identities to alpha 21-II clones and were mapped to various alpha 21-II clusters. It was revealed that both monomeric and HOR alphoid clusters can be found in the alpha 21-II region. Phylogenetic analysis revealed separate evolutionary histories for the monomeric and HOR …

The Non-Teratogenic Effects In Mice Progeny By Maternal Treatment With Amygdalin, Victoria Ann Rowe

Master's Theses

No abstract provided.