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Full-Text Articles in Life Sciences
Cataloging And Engineering Temperate Coliphages Of The Human Urinary Microbiome, Elias Crum
Cataloging And Engineering Temperate Coliphages Of The Human Urinary Microbiome, Elias Crum
Master's Theses
In the US, around 60% of females will be diagnosed with a Urinary Tract Infection (UTI) in their lifetime, and Escherichia coli is the most implicated etiological agent in UTIs. Despite its frequent association with lower urinary tract symptoms, recent studies have found that the urinary microbiome (UMB), the viral, bacterial, and fungal resident members of the urinary tract, of healthy females can also consist of E. coli. While most research has focused on the bacterial constituents of the UMB, bacteriophages, viruses that infect bacteria, are far more abundant. Bacteriophages (phages) of other human microbiomes have been shown to play …
Genomic Survey Of E. Coli From The Bladders Of Women With And Without Lower Urinary Tract Symptoms, Andrea Garretto, Taylor Miller-Ensminger, Adriana Ene, Zubia Merchant, Aashaka Shah, Athina Gerodias, Anthony Biancofiori, Stacey Canchola, Stephanie Canchola, Emanuel Castillo, Tasnim Chowdhury, Nikita Gandhi, Sarah Hamilton, Kyla Hatton, Syed Hyder, Koty Krull, Demetrios Lagios, Thinh Lam, Kennedy Mitchell, Christine Mortensen, Amber Murphy, Joseph Richburg, Meghan Rokas, Suzanne Ryclik, Pauline Sulit, Thomas Szwajnos, Manuel Widuch, Jessica Willis, Mary Woloszyn, Bridget Brassil, Genevieve Johnson, Rita Mormando, Laura Maskeri, Mary Batrich, Nicole Stark, Jason W. Shapiro, Cesar Montelongo Hernandez, Swarnali Banerjee, Alan J. Wolfe, Catherine Putonti
Genomic Survey Of E. Coli From The Bladders Of Women With And Without Lower Urinary Tract Symptoms, Andrea Garretto, Taylor Miller-Ensminger, Adriana Ene, Zubia Merchant, Aashaka Shah, Athina Gerodias, Anthony Biancofiori, Stacey Canchola, Stephanie Canchola, Emanuel Castillo, Tasnim Chowdhury, Nikita Gandhi, Sarah Hamilton, Kyla Hatton, Syed Hyder, Koty Krull, Demetrios Lagios, Thinh Lam, Kennedy Mitchell, Christine Mortensen, Amber Murphy, Joseph Richburg, Meghan Rokas, Suzanne Ryclik, Pauline Sulit, Thomas Szwajnos, Manuel Widuch, Jessica Willis, Mary Woloszyn, Bridget Brassil, Genevieve Johnson, Rita Mormando, Laura Maskeri, Mary Batrich, Nicole Stark, Jason W. Shapiro, Cesar Montelongo Hernandez, Swarnali Banerjee, Alan J. Wolfe, Catherine Putonti
Bioinformatics Faculty Publications
Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female …
Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott
Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …
Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott
Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
In this project we investigated the biological function of the genes b3725, b3726, b3727, b3728 and Mrub_2518, Mrub_2519, Mrub_2520 and Mrub_2521 (KEGG map number 02010). We predict that these genes encode the components of a Phosphate ABC transporter: Orthologous genes Mrub_2518 (DNA coordinates 2565359..2566438) and b3728 encodes the periplasmic phosphate binding component; Orthologous genes Mrub_2519 (DNA coordinates 2566499..2567485) and b3727, and Mrub_2520 (DNA coordinates 2567496..2568326) and b3726 encode for the two transmembrane proteins; Orthologous genes Mrub_2521 (DNA coordinates 2568338..2569159) and b3725 encode for the ATP binding protein within the cytoplasm. Within the two species, M. ruber and E. coli, …
Confirmation That Mrub_1751 Is Homologous To E. Coli Xylf, Mrub_1752 Is Homologous To E. Coli Xylh, And Mrub_1753 Is Homologous To E. Coli Xylg, Ben Price, Dr. Lori Scott
Confirmation That Mrub_1751 Is Homologous To E. Coli Xylf, Mrub_1752 Is Homologous To E. Coli Xylh, And Mrub_1753 Is Homologous To E. Coli Xylg, Ben Price, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
In this project we investigated the biological function of the genes Mrub_1751, Mrub_1752 and Mrub_1753 (KEGG map number 02010). We predict these genes encode components of a D-xylose ATP Binding Cassette (ABC) transporter: 1) Mrub_1752 (DNA coordinates 1809004-1810224 on the forward strand) encodes the permease component (aka transmembrane domain), predicted to be an ortholog and 2) Mrub_1753 (DNA coordinates 1810227-1811000 on the forward strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1751 (DNA coordinates 1807855-1808892 on the forward strand) encodes the solute binding protein. The ABC-transporter for M. ruber to transport D-xylose is homologous with the transporter …
Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams
Using Hadoop To Identify False Positives In Bacterial Strain Typing From Dna Fingerprints, Colin C. Adams
Computer Science and Software Engineering
Pyroprinting is a novel technique used by the Department of Biological Sciences to obtain “fingerprints” from the DNA of E. coli isolates in order to categorize them into strains. To determine the number of false positives that occur in the pyroprinting process, isolates with the same pyroprints needed to be sequenced to see if their underlying alleles match. If they do match, this shows they are indeed the same strain and are a true positive. If the alleles don’t match, they are different strains and are a false positive. To do this 100 isolates with nucleotide identifiers were sequenced. Over …
Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott
Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2874 and Mrub_1349. We predict that Mrub_2874 encodes the enzyme ribulose-5-phosphate 3-epimerase (DNA coordinates 2912530..2913204 on the reverse strand), which is the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3386, which has the gene …