Life Sciences Commons^™

Software For Sequence Analysis Of Variants In Functional Screening Libraries And Personalized Genome Files, Jacklyn Michelle Newsome

UNLV Theses, Dissertations, Professional Papers, and Capstones

Detailed knowledge of protein function is critical for both the study of protein interactions and the development of drugs which target specific proteins. Currently, there are few techniques that directly examine protein function. The techniques that are available are time consuming and can only address one variant of a protein at a time. Our laboratory has designed 3 high throughput protein function screens. We hypothesize that these will address this shortfall.

The first screen is the Chimeric Minimotif Decoy (CMD) Assay. For this screen, we constructed red fluorescent proteins with one or more C-terminal minimotifs. Minimotifs are short, contiguous amino …

Bio-Docklets: Virtualization Containers For Single-Step Execution Of Ngs Pipelines, Baekdoo Kim, Thahmina Ali, Carlos Lijeron, Enis Afgan, Konstantinos Krampis

Publications and Research

Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single …

Using Bioinformatics To Increase The Number Of Tumors That Can Be Treated With Existing Drug Treatments, Jonathan Dayton, Stephen Piccolo

Journal of Undergraduate Research

Typically, tens or even hundreds of mutations are observed in the DNA of a single tumor by the time it has been detected1-4. Knowledge of these mutations may be useful in guiding the way the tumor is treated. In some cases, if a tumor has a mutation in a certain gene, this may indicate that the tumor can be treated with a certain drug. For example, the drug Trastuzumab is a targeted therapy for breast cancer patients with mutations in the HER2 gene5. In other cases, a mutation may be able to be targeted by a drug even if the …

Things Are Getting Hairy: Enterobacteria Bacteriophage Vb_Pcam_Cbb, Colin Buttimer, Hanne Hendrix, Hugo Oliveira, Aidan Casey, Horst Neve, Olivia Mcauliffe, R. Paul Ross, Colin Hill, Jean Paul Noben, Jim O'Mahony, Rob Lavigne, Aidan Coffey

Department of Biological Sciences Publications

© 2017 Buttimer, Hendrix, Oliveira, Casey, Neve, McAuliffe, Ross, Hill, Noben, O'Mahony, Lavigne and Coffey. Enterobacteria phage vB_PcaM_CBB is a "jumbo" phage belonging to the family Myoviridae. It possesses highly atypical whisker-like structures along the length of its contractile tail. It has a broad host range with the capability of infecting species of the genera Erwinia, Pectobacterium, and Cronobacter. With a genome of 355,922 bp, excluding a predicted terminal repeat of 22,456 bp, phage CBB is the third largest phage sequenced to date. Its genome was predicted to encode 554 ORFs with 33 tRNAs. Based on prediction and proteome analysis …

Mrub_1873, Mrub_1872, Mrub_1871 Genes Are Predicted Orthologs Of The B2285, B2284, And B2283 Genes Respectively, Found In Escherichia Coli Coding For Nadh Ubiquinone Oxidoreductase Complex Subunits E, F, And G., Hannah Lohmeier, Dr. Lori R. 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_1873, Mrub_1872, and Mrub_1871.We predict that Mrub_1873 (DNA coordinates 1933743..1934309 on the reverse strand), Mrub_1872 (DNA coordinates 1932430..1933746 on the reverse strand), and Mrub_1871 (DNA coordinates 1930055..1932421 on the reverse strand) are subunits of the NADH ubiquinone oxidoreductase complex (00190). The complex catalyzes both the transfer of protons across the cytoplasmic membrane and the transfer of electrons to ubiquinone during …

Annotation And Identification Of Several Glycerolipid Metabolic Related Ortholog Genes; Mrub_0437, Mrub_1813 And Mrub_2759 In The Organism Meithermus Ruber And Their Predicted Respective Orthologs B3926, B4042 And Bo514 Found In E.Coli., Abdul Rahman Abdul Kader, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

We predict Mrub_0437 encodes the enzyme glycerol kinase (DNA coordinates [417621..419183), which is an intermediary step of the glycerolipid metabolic pathway (KEGG map00561), It catalyzes the conversion of glycerol to sn-Glycerol-3-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3926.

We predict Mrub_1813 encodes the enzyme diacylglycerol kinase (DNA coordinates [1864659..1865063), which is an intermediary step of the glycerolipid metabolic pathway (KEGG map00561), It catalyzes the conversion of 1,2-diacyl-sn-glycerol to 1,2-diacyl-sn-glycerol 3-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b4042.

We predict Mrub_2759 encodes the enzyme glycerol kinase (DNA coordinates [2799712..2800665), which is an intermediary …

Serine Biosynthesis And Glycine Biosynthesis/Degradation: Mrub_0173 Is Orthologous To E. Coli B2913 (Sera); Mrub_0125 Is Orthologous To E. Coli B4388 (Serb); Mrub_2910 Is Orthologous To E. Coli B2551 (Glya)., Megan M. Janssen, Dr. Lori R. 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_0173, Mrub_0125, and Mrub_ 2910. We predict that Mrub_0173 encodes the enzyme phosphoglycerate dehydrogenase (DNA coordinates 152982 ... 154347), which is the 1st step of the serine biosynthesis pathway (KEGG map number 00680). It catalyzes the conversion of NAD+ + 3-phospho-D-glycerate → NADH H+ + 3-phospho-hydroxypyruvate. The E. coli K12 MG1655 ortholog is predicted to be b2913, which has …

Mrub_3029, Mrub_2052, Are Predicted Orthologs Of B_0688, B_0394, While Mrub_0759 And Mrub_2365 Are Not Predicted Orthologs Of B_1309, In Escherichia Coli, Which Code For Enzymes Involved In Starch And Sucrose Metabolism, Max A. Benstine, Dr. Lori R. Scott

Meiothermus ruber Genome Analysis Project

We predict that Mrub__[0759] encodes the enzyme [Meiothermus ruber Fruktokinase] (DNA coordinates [741282..742202 on the forward strand] which is the 00500 step of the Starch and Sucrose Metabolism pathway (KEGG map number [2.7.1.4]). It catalyzes the conversion of [ATP + D-fructoseADP + D-fructose 6-phosphate]. The E. coli K12 MG1655 ortholog is predicted to be b1309, which has the gene identifier [ycjM] We predict that Mrub__[ 2365] encodes the enzyme [Meiothermus ruber Fruktokinase] (DNA coordinates [2417118..2418059 on the forward strand], which is the [00500] step of the [Starch and Sucrose Metabolism] pathway (KEGG map number [2.7.1.4]). It catalyzes the …

Mrub_2642, Mrub_1054, And Mrub_1059 Genes Are Orthologs Of The Escherichia Coli Genes B2942, B0159, And B2687 Genes, Respectively, Which Code For Methionine Adenosyltransferase, Adenosylhomocysteine Nucleosidase, And S-Ribosylhomocysteine Lyase, Nicholas M. Orslini, Dr. Lori R. 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_2642, Mrub_1054, and Mrub_1059.

We predict that Mrub_2642 encodes the enzyme methionine adenosyltransferase (DNA coordinates [2677251…2678426] on the reverse strand), the first step of the methionine degradation pathway (KEGG map number 00270). Methionine adenosyltransferase catalyzes the conversion of the substrates, ATP, L-methionine, and water, to yield the products S-adenosyl-L-methionine (SAM), inorganic phosphate, and diphosphate. Mrub_1054 encodes adenosylhomocysteine nucleosidase (DNA …

Mrub_0860, Mrub_0701 And Mrub_2285 Are Orthologous To E. Coli B2892, B2562 And B3863 Within The Recfor Pathway For Homologous Recombination, Bailey Englund, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tool associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict the gene function. We investigated the biological function of the genes Mrub_0860, Mrub_0701,and Mrub_2285. We predicted that Mrub_0860 (DNA coordinates 842934..844868 on the forward strand) encodes for the enzyme single-stranded DNA-specific exonuclease, which is in the first step of homologous recombination via the RecFOR pathway (KEGG map number 03440). The E. coli K12 MG1655 ortholog is predicted to be b2892, which has the gene identifier …

Mrub_2052, Mrub_0628, And Mrub_2034 Genes Are Predicted To Be Orthologous To B0688, B2039, And B3789 Genes Found In Escherichia Coli, Which Are Involved In Streptomycin Biosynthesis, James P. Hartnett, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

We predict that Mrub_2052 encodes the enzymephosphoglucomutase (DNA coordinates 2088542..2090185 on the complement strand which is the 00521 step of the Streptomycin Biosynthesis pathway (KEGG map number 5.4.2.2). It catalyzes the conversion of D-Glucose- 6P (also known as D-glucopyranose 6-phosphate) to D-Glucose-1P (also known as α-D-glucopyranose 1-phosphate). The E. coli K12 MG1655 ortholog is predicted to be b0688, which has the gene identifier pgm. We predict that Mrub__0628 encodes the enzyme glucose-1-phosphate thymidylyltransferase (DNA coordinates 605559..606635 on the complement strand, which is the 00521 step of the Streptomycin Biosynthesis pathway (KEGG map number 2.7.7.24). It catalyzes the conversion of D-Glucose-1P …

Annotation Of Genes Involved With Biosynthetic Production Of Peptidoglycan Within Meiothermus Ruber Involving Supposed Orthologous Genes: Mrub_0981 And B1069, Mrub_1162 And B063, Mrub_1999 And B0084., Marckus Simmons, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

Using bioinformatics tools, the genes within Meiothermus ruber that are involved with peptidoglycan production were annotated. We predict that Mrub_0981 encodes the enzyme Lipid II Flippase (DNA coordinates970078…971580 on the reverse strand), which is the 9th step of the Peptidoglycan biosynthesis pathway (KEGG map number 00550) It catalyzes the conversion of Meso-2,6-diaminopimelate to Peptidoglycan. The E. coli K12 MG1655 ortholog is predicted to be b1069, which has the gene identifier mviN. We also predict that Mrub_1162 encodes the enzyme Penicillin binding protein II (DNA coordinates 1176079…1177836 on the reverse strand), which is the 12th step of the Peptidoglycan biosynthesis …

Mrub_1867, Mrub_1868, And Mrub_1869 Genes Are Predicted Orthologs Of The B2279, B2280, And B2281 Genes Found In Escherichia Coli Coding For The Nadh Dehydrogenase Subunits K, J, And I Respectively, Wade Smith, Dr. Lori R. 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_1867, Mrub_1868, and Mrub_1869. We predict that Mrub_1867 (DNA coordinates 1927237..1927527 on the reverse strand), Mrub_1868 (DNA coordinates 1927524..1928123 on the reverse strand), and Mrub_1869 (DNA coordinates 1928248..1928781 on the reverse strand) are subunits of the NADH: ubiquinone oxidoreductase complex (KEGG map number 00190). This complex catalyzes the translocation of H+ across the cytoplasmic …

K-Shell Decomposition Reveals Structural Properties Of The Gene Coexpression Network Forneurodevelopment, Abdullah Ercüment Çi̇çek

Turkish Journal of Biology

Neurodevelopment is a dynamic and complex process, which involves interactions of thousands of genes. Understanding the mechanisms of brain development is important for uncovering the genetic architectures of neurodevelopmental disorders such as autism spectrum disorder and intellectual disability. The BrainSpan dataset is an important resource for studying the transcriptional mechanisms governing neurodevelopment. It contains RNA-seq and microarray data for 13 developmental periods in 8?16 brain regions. Various important studies used this dataset, in particular to generate gene coexpression networks. The topology of the BrainSpan gene coexpression network yielded various important gene clusters, which are found to play key roles in …