Genetics and Genomics Commons^™

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, 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, 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, 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, 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, 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 5^th 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, 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;, 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, Chung Wong

Chemistry & Biochemistry Faculty Works

No abstract provided.

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, 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, 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, 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, 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; QTL_MHC 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, 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, 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, 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, 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, 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, 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 …

A Comprehensive Benchmarking Study Of Protocols And Sequencing Platforms For 16s Rrna Community Profiling, Rosalinda D’Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John G. Kenny, Richard Gregory, Alistair C. Darby, Migun Shakya

Dartmouth Scholarship

In the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. Therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. The most common phylogenetic marker for microbial community diversity studies is the 16S ribosomal RNA gene and in the last 10 years the field has moved from sequencing a small number of amplicons and samples to more complex studies where thousands of samples and multiple different gene regions are interrogated. …

Phenotypic And Genetic Analyses Of Adaptation To Geothermal Soils In Yellow Monkeyflowers Of Yellowstone National Park, Peter Breigenzer

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Microgeographic adaptation, which occurs on a spatial scale smaller than the dispersal distance of the evolving organisms, provides a fertile context for understanding the genetic processes that shape natural variation and contribute to biological diversity. In plants, mosaics of distinct soil conditions can select for microgeographic divergence in the face of gene flow, leading to major life history transitions and novel trait evolution. Mimulus (monkeyflowers) is an emerging model genus for ecological genomics, due to tremendous diversity, experimental tractability, and a wealth of genomic resources. In Yellowstone National Park, Mimulus guttatus occurs in both geothermal soils and nearby nonthermal bogs …

Resolving Gnetum Evolutionary History, Angela Mcfadden

All Master's Theses

Gnetum are non-flowering seed plants of the tropics, indigenous to South America, Africa, and Asia. This group of about 40 species is fascinating to botanists because it shares distinctive morphological characteristics with flowering plants, such as broad leaves, woody stems, and flower-like strobili. There are still questions surrounding the relationships within the genus of Gnetum. With that in mind, I focused my work on generating phylogenetic hypotheses, using two molecular data sets: a concatenation of over 60 different chloroplast genes (66,815 base pairs), and the whole chloroplast genome (128,772 base pairs). This allowed me to compare the two phylogenies …

Toward The Elucidation Of Cytoplasmic Diversity In North American Grape Breeding Programs, Jonathan Fresnedo-Ramirez, Qi Sun, Chin-Feng Hwang, Craig A. Ledbetter, David W. Ramming, Anne Fennell, M. Andrew Walker, James J. Luby, Matthew D. Clark, Jason P. Londo, Lance Cadle-Davidson, Gan-Yuan Zhong

Agronomy, Horticulture and Plant Science Faculty Publications

Plants have an intriguing tripartite genetic system: Nuclear genome 9 Mitochondria 9 Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid …

System Genetic Analysis Of Mechanisms Underlying Excessive Alcohol Consumption, Maren L. Smith

Theses and Dissertations

Increased alcohol consumption over time is one of the characteristic symptoms of Alcohol Use Disorder (AUD). The molecular mechanisms underlying this escalation in intake is still the subject of study. However, the mesocortical and mesolimbic dopamine pathways, and the extended amygdala, because of their involvement in reward and reinforcement are believed to play key roles in these behavioral changes. Multiple gene expression studies have shown that alcohol affects the expression of thousands of genes in the brain. The studies discussed in this document use the systems biology technique of co-expression network analysis to attempt to find

patterns within genome-wide expression …

Population Genetic Structure Of Necturus Maculosus In Central And Eastern Kentucky, Mason Owen Murphy

Theses and Dissertations--Biology

Population structure is influenced by extrinsic factors, such as landscape architecture and dispersal barriers. Lotic network architecture is known to constrain ecological, demographic and evolutionary processes, including population genetic structure. I assessed the population structure of a widespread aquatic salamander, Necturus maculosus, across three river basins in central and eastern Kentucky. I examined the role of network architecture, anthropogenic barriers, and spatial scale on patterns of population structure. I also provided a review of N. maculosus capture methods and offer an improved trap design. I identified significant structuring between the combined Licking/Kinniconick basin and the Kentucky River basin, with …

Characterization Of Somatically-Eliminated Genes During Development Of The Sea Lamprey (Petromyzon Marinus), Stephanie A. Bryant

Theses and Dissertations--Biology

The sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangements (PGRs) during early development that facilitate the elimination of ~20% of the genome from the somatic cell lineage, resulting in distinct somatic and germline genomes. To improve our understanding of the evolutionary/developmental logic of PGR, we generated computational predictions to identify candidate germline-specific genes within a transcriptomic dataset derived from adult germline and the embryonic stages encompassing PGR. Validation studies identified 44 germline-specific genes and characterized patterns of transcription and DNA loss during early embryogenesis. Expression analyses reveal that several of these genes are differentially expressed during early embryogenesis …

Genomic Prediction Of Gene Bank Wheat Landraces, José Crossa, Diego Jarquin, Jorge Franco, Paulino Pérez-Rodríguez, Juan Burgueño, Carolina Saint-Pierre, Prashant Vikram, Carolina Sansaloni, Cesar Petroli, Denis Akdemir, Clay Sneller, Matthew Reynolds, Maria Tattaris, Thomas Payne, Carlos Guzman, Roberto J. Peña, Peter Wenzl, Sukhwinder Singh

Department of Agronomy and Horticulture: Faculty Publications

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% …

The Effects Of Manufactured Nanomaterial Transformations On Bioavailability, Toxicity And Transcriptomic Responses Of Caenorhabditis Elegans, Daniel L. Starnes

Theses and Dissertations--Plant and Soil Sciences

In recent decades, there has been a rapid expansion in the use of manufactured nanoparticles (MNPs). Experimental evidence and material flow models predict that MNPs enter wastewater treatment plants and partition to sewage sludge and majority of that sludge is land applied as biosolids. During wastewater treatment and after land application, MNPs undergo biogeochemical transformations (aging). The primary transformation process for silver MNPs (Ag-MNPs) is sulfidation, while zinc oxide MNPs (ZnO-MNPs) most likely undergo phosphatation and sulfidation. Our overall goal was to assess bioavailability and toxicogenomic impacts of both pristine, defined as-synthesized, and aged Ag- and ZnO-MNPs, as well as …

Whole-Genome Sequencing And Disability In The Nicu: Exploring Practical And Ethical Challenges., Michael J. Deem

Manuscripts, Articles, Book Chapters and Other Papers

Clinical whole-genome sequencing (WGS) promises to deliver faster diagnoses and lead to better management of care in the NICU. However,several disability rights advocates have expressed concern that clinical use of genetic technologies may reinforce and perpetuate stigmatization of and discrimination against disabled persons in medical and social contexts. There is growing need, then, for clinicians and bioethicists to consider how the clinical use of WGS in the newborn period might exacerbate such harms to persons with disabilities. This article explores ways to extend these concerns to clinical WGS in neonatal care. By considering these perspectives during the early phases of …