A Bioinformatics Study On Whether Or Not Mrub_2763 Gene In M. Ruber Is Similar To The Lpxb Gene In E. Coli And If Mrub_2768 Is Similar To The Lpxd Gene In E. Coli.,
2016
Augustana College, Rock Island Illinois
A Bioinformatics Study On Whether Or Not Mrub_2763 Gene In M. Ruber Is Similar To The Lpxb Gene In E. Coli And If Mrub_2768 Is Similar To The Lpxd Gene In E. Coli., Frank J. Habura, 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 the gene Mrub_2768 and Mrub_2763. We predict that Mrub_2768 (DNA coordinates 2808186..2809178 on the reverse strand) encodes the enzyme UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase (LpxD), which is the third step of the Lipopolysaccharide biosynthesis pathway (KEGG map number 00540). It catalyzes the conversion of UDP-3-O-(3-hydroxymyristoyl)-α-D-glucosamine + a(3R)-3-hydroxymyristoyl-[acp] → a holo-[acyl-carrier protein] + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine. The E. coli K12 MG1655 ortholog is predicted to be b0179, which …
Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway,
2016
Augustana College - Rock Island
Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway, Linnea J. Ritchie, 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. I investigated the biological functions of Mrub_1053 Mrub_2281 and Mrub_2299. I predicted that Mrub_1053 and Mrub_2281 (DNA coordinates 1053364..1054359 on the forward strand and 2333172..2334113 on the forward strand respectively) encodes the enzyme phosphoribose-1-pyrophosphate synthetase (PRS) which is the first step of the purine synthesis pathway (KEGG). I also predicted that Mrub_2299 (DNA coordinates: 2352378..2353775 on the forward strand) encodes for Phosphoribosyl pyrophosphate (PRPP) amidotransferase, which is …
Valine Biosynthesis: Mrub_2994 Is Orthologous To E. Coli B3770 And Mrub_1844 Is Orthologous To E. Coli B3771,
2016
Augustana College, Rock Island Illinois
Valine Biosynthesis: Mrub_2994 Is Orthologous To E. Coli B3770 And Mrub_1844 Is Orthologous To E. Coli B3771, Bennett A. Hartmann, 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 the genes Mrub_2994 and Mrub_1844. We predict that Mrub_1884 encodes the enzyme dihydroxy-acid dehydratase (DNA coordinates 1901362..1903026 on the forward strand), which is the third step of the valine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of 2,3-dihydroxy-3methylbutanoate to 3-methyl-2-oxobutanoate. The E. coli K12 MG1655 ortholog is predicted to be b3771, which has the gene identifier ilvD. …
Bioinformatic Comparison Of Genes In The Leucine Biosynthesis Pathway Of Escherichia Coli To Meiothermus Ruber,
2016
Augustana College, Rock Island Illinois
Bioinformatic Comparison Of Genes In The Leucine Biosynthesis Pathway Of Escherichia Coli To Meiothermus Ruber, Isaac D. Schmied, Benjamin T. Ryan, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
We predict that Mrub_1905 and Mrub_1906 encode the enzyme 2-isopropylmalate synthase (Mrub_1906 DNA coordinates complement(1965044..1966603) Mrub_1905 DNA coordinates complement(1963455..1965041)), which is the first step of the leucine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of (2S)-2-isopropylmalate to 2-isopropylmaleate. The E. coli K12 MG1655 ortholog is predicted to be b0074, which has the gene identifier leuA. We predict that Mrub_1846 encodes the enzyme 3-isopropylmalate dehydrogenase (DNA coordinates complement(1903909..1904961)), which is the third step of the leucine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of (2R,3S)-3-isopropylmalate to (2S)-2-isopropyl-3-oxosuccinate. The E. coli K12 MG1655 ortholog is predicted …
Riboflavin Metabolism: A Study To See If Mrub_1256 Is Orthologous To E. Coli B0415, And If Mrub_1254 Is Orthologous To E. Coli B1662,
2016
Augustana College, Rock Island Illinois
Riboflavin Metabolism: A Study To See If Mrub_1256 Is Orthologous To E. Coli B0415, And If Mrub_1254 Is Orthologous To E. Coli B1662, Anish Sora Reddy, 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 the genes Mrub_1256 and Mrub_1254. We predict that Mrub_1256 encodes the enzyme 6,7-dimethyl-8-ribityllumazine synthase (Dna Coordinates 1282509..1282982 forward strand), which is part of the Riboflavin Metabolism pathway (KEGG map number 00740). It catalyzes the conversion of 3,4-Dihydroxy-2-butanone-4-phosphate or 5-amino-6-ribityl-aminouracil to Quinone. The E. coli K12 MG1655 ortholog is predicted to be E. coli b0415, which has the gene identifier …
The Meiothermus Ruber Mrub_2572 Gene Is An Ortholog Of The Escherichia Coli Pyre B3642 Gene And The Meiothermus Ruber Mrub_2071 Gene Is An Ortholog Of The Escherichia Coli Pyrf B1281 Gene,
2016
Augustana College, Rock Island Illinois
The Meiothermus Ruber Mrub_2572 Gene Is An Ortholog Of The Escherichia Coli Pyre B3642 Gene And The Meiothermus Ruber Mrub_2071 Gene Is An Ortholog Of The Escherichia Coli Pyrf B1281 Gene, Cale J. Mccormick, 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 the genes Mrub_2572 and Mrub_2071. We predict that Mrub_2572 encodes the enzyme orotate phosphoribosyltransferase (DNA coordinates 2617545..2618096 on the forward strand), which is the 5th step of the UMP biosynthesis pathway (KEGG map number 00240). It catalyzes the conversion of orotate + PRPP to orotidine 5’-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3642, which has the gene …
Bioinformatics Indicates That Meiothermus Ruber Genes Mrub_1710 And Mrub_1712 Are Homologs Of The Escherichia Coli Genes B2903 (P-Protein; Glycine Dehydrogenase) And B2905 (T-Protein; Aminomethyltransferase), Respectively,
2016
Augustana College, Rock Island Illinois
Bioinformatics Indicates That Meiothermus Ruber Genes Mrub_1710 And Mrub_1712 Are Homologs Of The Escherichia Coli Genes B2903 (P-Protein; Glycine Dehydrogenase) And B2905 (T-Protein; Aminomethyltransferase), Respectively, Malory J. Groen, 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 the genes Mrub_1710 and Mrub_1712. We predict that Mrub_1710 encodes the enzyme glycine dehydrogenase (DNA coordinates 3046168.. 3049041 on the reverse strand), which is the first step of the glycine degradation pathway (KEGG map number 00260). It catalyzes the conversion of glycine to S-Amino-methyldihydro-lipoylprotein. The E. coli K12 MG1655 ortholog is predicted to be b2903, which has the gene identifier gcvP. …
Mrub_0258 Gene Is An Ortholog Of The B4226 Gene (Ppa) Found In Escherichia Coli; Mrub_1198 Gene Is An Ortholog Of The B2501 Gene (Ppk) Found In Escherichia Coli;,
2016
Augustana College, Rock Island Illinois
Mrub_0258 Gene Is An Ortholog Of The B4226 Gene (Ppa) Found In Escherichia Coli; Mrub_1198 Gene Is An Ortholog Of The B2501 Gene (Ppk) Found In Escherichia Coli;, Brandon M. Wills, 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 the genes Mrub_0258 and Mrub_1198. We predict that Mrub_0258 encodes the enzyme inorganic pyrophosphatase (226403..226942), which is indirectly involved with the oxidative phosphorylation pathway (KEGG map number 00190). It catalyzes the conversion of the diphosphate ions made by Mrub_1198 into two orthophosphate ions, which can then be used by ATP synthase to produce energy. The E. coli K12 MG1655 ortholog is predicted …
Progress In Pathogen Detection By Whole-Genome Sequencing,
2016
University of Missouri–St. Louis
Progress In Pathogen Detection By Whole-Genome Sequencing, Chung Wong
Chemistry & Biochemistry Faculty Works
No abstract provided.
Comparative Population Genomics Of Latitudinal Variation In
Drosophila Simulans And Drosophila Melanogaster,
2016
Stanford University
Comparative Population Genomics Of Latitudinal Variation In Drosophila Simulans And Drosophila Melanogaster, Heather E. Machado, Alan O. Bergland, Katherine R. O'Brien, Emily L. Behrman, Paul S. Schmidt, Dmitri A. Petrov
School of Biological Sciences: Faculty Publications
Examples of clinal variation in phenotypes and genotypes across latitudinal transects have served as important models for understanding how spatially varying selection and demographic forces shape variation within species. Here, we examine the selective and demographic contributions to latitudinal variation through the largest comparative genomic study to date of Drosophila simulans and Drosophila melanogaster, with genomic sequence data from 382 individual fruit flies, collected across a spatial transect of 19 degrees latitude and at multiple time points over 2 years. Consistent with phenotypic studies, we find less clinal variation in D. simulans than D. melanogaster, particularly for the autosomes. Moreover, …
Models For Hsv Shedding Must Account For Two Levels Of Overdispersion,
2016
University of Washington - Seattle Campus
Models For Hsv Shedding Must Account For Two Levels Of Overdispersion, Amalia Magaret
UW Biostatistics Working Paper Series
We have frequently implemented crossover studies to evaluate new therapeutic interventions for genital herpes simplex virus infection. The outcome measured to assess the efficacy of interventions on herpes disease severity is the viral shedding rate, defined as the frequency of detection of HSV on the genital skin and mucosa. We performed a simulation study to ascertain whether our standard model, which we have used previously, was appropriately considering all the necessary features of the shedding data to provide correct inference. We simulated shedding data under our standard, validated assumptions and assessed the ability of 5 different models to reproduce the …
Local Admixture Of Amplified And Diversified Secreted Pathogenesis Determinants Shapes Mosaic Toxoplasma Gondii Genomes,
2016
J. Craig Venter Institute
Local Admixture Of Amplified And Diversified Secreted Pathogenesis Determinants Shapes Mosaic Toxoplasma Gondii Genomes, Hernan Lorenzi, Asis Khan, Michael S. Behnke, Sivaranjani Namasivayam, Lakshmipuram S. Swapna, Michalis Hadjithomas, Svetlana Karamycheva, Deborah Pinney, Brian P. Brunk, James W. Ajioka, Daniel Ajzenberg, John C. Boothroyd, Jon P. Boyle, Marie L. Dardé, Maria A. Diaz-Miranda, Jitender P. Dubey, Heather M. Fritz, Solange M. Gennari, Brian D. Gregory, Kami Kim, Jeroen P. J. Saeij, Chunlei Su, Michael W. White, Xing-Quan Zhu, Daniel K. Howe, Benjamin M. Rosenthal, Michael E. Grigg, John Parkinson, Liang Liu, Jessica C. Kissinger
Veterinary Science Faculty Publications
Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure …
Evidence For The Fixation Of Gene Duplications
By Positive Selection In Drosophila,
2016
Cornell University
Evidence For The Fixation Of Gene Duplications By Positive Selection In Drosophila, Margarida Cardoso-Moreira, J. Roman Arguello, Srikanth Gottipati, Lawrence G. Harshman, Jennifer K. Grenier, Andrew G. Clark
Lawrence G. Harshman Publications
Gene duplications play a key role in the emergence of novel traits and in adaptation. But despite their centrality to evolutionary processes, it is still largely unknown how new gene duplicates are initially fixed within populations and later maintained in genomes. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global Diversity Lines (GDL), we have combined genome-wide SNP polymorphism data with a novel set of copy number variant calls and gene expression profiles to characterize the …
Genetic And Genomic Basis Of Antibody Response To Porcine Reproductive And Respiratory Syndrome (Prrs) In Gilts And Sows,
2016
North Carolina State University
Genetic And Genomic Basis Of Antibody Response To Porcine Reproductive And Respiratory Syndrome (Prrs) In Gilts And Sows, Nick V. Serão, Robert A. Kemp, Benny Mote, Philip Willson, John C.S. Harding, Stephen C. Bishop, Graham S. Plastow, Jack C.M. Dekkers
Department of Animal Science: Faculty Publications
Background: Our recent research showed that antibody response to porcine reproductive and respiratory syndrome (PRRS), measured as sample-to-positive (S/P) ratio, is highly heritable and has a high genetic correlation with reproductive performance during a PRRS outbreak. Two major quantitative trait loci (QTL) on Sus scrofa chromosome 7 (SSC7; QTLMHC and QTL130) accounted for ~40 % of the genetic variance for S/P. Objectives of this study were to estimate genetic parameters for PRRS S/P in gilts during acclimation, identify regions associated with S/P, and evaluate the accuracy of genomic prediction of S/P across populations with different prevalences of …
Power Analysis In Applied Linear Regression For Cell Type-Specific Differential Expression Detection,
2016
Virginia Commonwealth University
Power Analysis In Applied Linear Regression For Cell Type-Specific Differential Expression Detection, Edmund Glass
Theses and Dissertations
The goal of many human disease-oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from any tissues suffer from variability of cell composition. This variability hinders the detection of differentially expressed genes and is often ignored. However, this variability may actually be advantageous, as heterogeneous gene expression measurements coupled with cell counts may provide deeper insights into the gene expression differences on the cell type-specific level. Published computational methods use linear regression to estimate cell type-specific differential expression. Yet, they do not consider many artifacts hidden in high-dimensional gene expression …
Genomic Comparisons And Genome Architecture Of Divergent Trypanosoma Species,
2016
Virginia Commonwealth University
Genomic Comparisons And Genome Architecture Of Divergent Trypanosoma Species, Katie Bradwell
Theses and Dissertations
Virulent Trypanosoma cruzi, and the non-pathogenic Trypanosoma conorhini and Trypanosoma rangeli are protozoan parasites with divergent lifestyles. T. cruzi and T. rangeli are endemic to Latin America, whereas T. conorhini is tropicopolitan. Reduviid bug vectors spread these parasites to mammalian hosts, within which T. rangeli and T. conorhini replicate extracellularly, while T. cruzi has intracellular stages. Firstly, this work compares the genomes of these parasites to understand their differing phenotypes. Secondly, genome architecture of T. cruzi is examined to address the effect of a complex hybridization history, polycistronic transcription, and genome plasticity on this organism, and study its highly …
Synthetic Biology For Autotrophic And Heterotrophic Production Of Ethanol,
2016
South Dakota State University
Synthetic Biology For Autotrophic And Heterotrophic Production Of Ethanol, Nathanael Braselton
Electronic Theses and Dissertations
Growing energy demand and rising levels of greenhouse gases has put massive strain on the global environment. Alternatives to fossil fuels are being developed in an attempt to curb climate change. Biotechnology has made large strides in order to create a completely renewable energy source by genetically modifying microbes to produce biofuels and other “green” high value compounds. In this thesis project, (1) E. coli ATCC9637 (E. coli W) was genetically modified to produce bioethanol from beet juice which contains mainly sucrose. The ethanol productivity by engineered E. coli W was 18.8 mg/L/H/OD600.
(2) Cyanobacterium Anabaena sp. PCC7120 …
Genomics Of Mature And Immature Olfactory Sensory Neuron,
2016
University of Kentucky
Genomics Of Mature And Immature Olfactory Sensory Neuron, Timothy S. Mcclintock
Physiology Research Data
The Excel file contains probabilistic predictions of which genes are expressed in mature versus immature olfactory sensory neurons, versus the sum of all other cell types in the olfactory epithelium. Responses to bulbectomy, which differentially affects mature and immature olfactory sensory neurons, supports these predictions.
Mouse Osns Express 10,000 Genes,
2016
University of Kentucky
Mouse Osns Express 10,000 Genes, Timothy S. Mcclintock
Physiology Research Data
This Excel file (both full and compressed versions are available) contains processed GeneChip microarray data that allows predictions of whether a gene is expressed in mature olfactory sensory neurons of mice.
An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing,
2016
Old Dominion University
An Alignment-Free "Metapeptide" Strategy For Metaproteomic Characterization Of Microbiome Samples Using Shotgun Metagenomic Sequencing, Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan, H. Rodger Harvey, Elhanan Borenstein, Brook L. Nunn, William S. Noble
OES Faculty Publications
In principle, tandem mass spectrometry can be used to detect and quantify the peptides present in a microbiome sample, enabling functional and taxonomic insight into microbiome metabolic activity. However, the phylogenetic diversity constituting a particular microbiome is often unknown, and many of the organisms present may not have assembled genomes. In ocean microbiome samples, with particularly diverse and uncultured bacterial communities, it is difficult to construct protein databases that contain the bulk of the peptides in the sample without losing detection sensitivity due to the overwhelming number of candidate peptides for each tandem mass spectrum. We describe a method for …
