The goal of the M. ruber genome analysis project is to study the genes and genome organization of the bacterium Meiothermus ruber, a thermophilic bacterium found in hot springs and a few warm artificial environments. The M. ruber genome was sequenced as part of the Department of Energy Joint Genome Institute’s GEBA project (Wu et al.,2009), the goal for which was to broaden our understanding of microbial genome structure and function across the microbial Tree of Life.

The M. ruber project gives students an authentic research experience in genome analysis by performing: 1) gene annotations - using bioinformatics tools to study gene function, and 2) functional genomics - using benchtop tools common to a molecular biology lab to study gene function. The papers uploaded into this site reflect student work in both these fields of study. Students perform these projects as part of the course Molecular Genetics/BIOL375 or as independent research experiences.

Wu D et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

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Submissions from 2017

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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 and Dr. Lori R. Scott

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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 and Dr. Lori R. Scott

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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 and Dr. Lori Scott

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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 and Dr. Lori Scott

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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 and Dr. Lori R. Scott

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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 and Dr. Lori R. Scott

Mrub_2813, Mrub_2815, and Mrub_2024 genes are orthologs of E. coli b0758, b0757, and b2036 genes respectively, found in the galactose metabolism pathway., Hunter Lyon and Dr. Lori R. Scott

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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 and Dr. Lori R. Scott

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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 and Dr. Lori Scott

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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 and Dr. Lori R. Scott

Submissions from 2016

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Bioinformatics Comparison of M. ruber Mrub_2507 to E. coli pdxK/b1636 and M. ruber Mrub_2888 to E. coli pdxH/b1638 to Determine the Orthologous Nature, Adam Bernardi and Dr. Lori Scott

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Comparison of genes in Meiothermus ruber and Escherichia coli in the Thiamine Biosynthesis Pathway, Erin E. Frye and Dr. Lori Scott

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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 and Dr. Lori Scott

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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 and Dr. Lori Scott

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Valine Biosynthesis: Mrub_2994 is Orthologous to E. coli b3770 and Mrub_1844 is Orthologous to E. coli b3771, Bennett A. Hartmann and Dr. Lori Scott

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Genomic Analysis of Meiothermus ruber Mrub_1907 and Meiothermus ruber Mrub_1844 with Potential Ortholog Escherichia coli b3774 IlvC and Escherichia coli b3771 IlvC Gene through Bioinformatics, Felipe A. Hernandez and Dr. Lori Scott

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Pyruvate metabolism in m. ruber when compared to e. coli, Amanda M. Johnson and Dr. Lori Scott

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Confirmation of the function of Mrub1080 as γ-glutamyl kinase (ProB) in Meiothermus ruber, Cale J. McCormick and Dr. Lori Scott

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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 and Dr. Lori Scott

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Mrub_2874 is homologous to b3386 and Mrub_1349 is homologous to b2914, but Mrub_1349 is not homologous to b4090, Samantha Murad and Dr. Lori Scott

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Can The Insertion Of An E. coli Shine-Dalgarno Sequence Upstream Of M. ruber proA Of The proBA Operon Enhance Its Expression, As Measured By A Complementation Assay Using E. coli Null Strains?, Matthew D. Murphy and Dr. Lori Scott

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Mrub_2765 is the version of E. coli FabZ in Meiothermus ruber, while Mrub_0266 is the version of E. coli FabI in Meiothermus ruber, Amanda M. Narkis and Dr. Lori Scott

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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 and Dr. Lori Scott

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Comparing Meiothermus ruber and Myxococcus xanthus in the Purine Metabolism Pathway, Linnea J. Ritchie and Dr. Lori Scott

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Bioinformatic Comparison of Genes in the Leucine Biosynthesis Pathway of Escherichia coli to Meiothermus ruber, Isaac D. Schmied, Benjamin T. Ryan, and Dr. Lori Scott