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Sequence and Annotation of the 314-Kb MT325 and the 321-Kb FR483 Viruses That Infect Chlorella Pbi”: Appendix B: Gene Names M001L Through M807R

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University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Virology Papers Virology, Nebraska Center for 2-20-2007 Supplementary Data for “Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi”: Appendix B: Gene Names M001L through M807R Lisa A. Fitzgerald University of Nebraska-Lincoln, [email protected] Michael V. Graves University of Massachusetts–Lowell, [email protected] Xiao Li University of Massachusetts–Lowell Tamara Feldblyum The Institute for Genomic Research, Rockville, MD James Hartigan Agencourt Bioscience Corporation, Beverly, MA See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/virologypub Part of the Virology Commons Fitzgerald, Lisa A.; Graves, Michael V.; Li, Xiao; Feldblyum, Tamara; Hartigan, James; and Van Etten, James L., "Supplementary Data for “Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi”: Appendix B: Gene Names M001L through M807R" (2007). Virology Papers. 3. https://digitalcommons.unl.edu/virologypub/3 This Article is brought to you for free and open access by the Virology, Nebraska Center for at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Virology Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Lisa A. Fitzgerald, Michael V. Graves, Xiao Li, Tamara Feldblyum, James Hartigan, and James L. Van Etten This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ virologypub/3 Published in Virology 358:2 (February 20, 2007), pp. 459–471. doi:10.1016/j.virol.2006.08.034 Copyright © 2006 Elsevier Inc. Used by permission. Submitted July 27, 2006; revised August 18, 2006; accepted August 23, 2006; published online October 4, 2006. Supplementary data originally published online at doi:10.1016/j.virol.2006.08.034. SUPPLEMENTARY DATA FOR Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi Lisa A. Fitzgeralda, Michael V. Gravesb, Xiao Lib, Tamara Feldblyumc, James Hartigand, and James L. Van Ettene, f, * aDepartment of Chemistry, University of Nebraska–Lincoln, Lincoln, NE 68588-0304 bDepartment of Biological Sciences, University of Massachusetts–Lowell, Lowell, MA 01854 cThe Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850 dAgencourt Bioscience Corporation, 500 Cummings Center, Suite 2450, Beverly, MA 01915 eDeparment of Plant Pathology, University of Nebraska–Lincoln, Lincoln, NE 68583-0722 fNebraska Center for Virology, University of Nebraska, Lincoln, NE 68588-0666 *Corresponding author. Email: [email protected] Abstract: Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335- bp genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in public databases, including some that are the first of their kind to be detected in a virus. For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion transporter protein and an alkyl sulfatase in FR483, and a dTDP–glucose pyrophosphorylase in both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three viruses. Supplementary data associated with this article is archived in this repository as 4 separate files: Appendices A–D. Each document, in spreadsheet format, shows Gene Name, Genome Position, A.A. length, Peptid e Mw, pI, CDD Hit Number, COGs, COG Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, Hit from-to, BLASTp Hit Number, Hit Accession, BLASTp Definition, Bit Score, E-value, % Identity, % Positive, Query from-to, and Hit from-to. Appendix A: Gene Names m002R through m843L Appendix B: Gene Names M001L through M807R Appendix C: Gene Names n001L through n849R Appendix D: Gene Names N003L through N847R Appendix B: Gene Names M001L through M807R BLASTp Gene Genome A.A. Peptide CDD Hit Bit % % Query Hit Hit Bit % % Query Hit from- pI COGs COG Definition E-value Hit BLASTp Definition E-value Name Position length Mw Number Score Identity Positive from-to from-to Accession Score Identity Positive from-to to Number M001L 1052--384 223 26,253 6.70 No Hit Found 1 ZP_00575949 RepA / Rep+ protein KID 55.45 1.41E-06 25% 59% 14--113 61--160 2 NP_705165 hypothetical malaria antigen 51.60 2.03E-05 24% 51% 1--136 1993--2129 3 YP_161395 hypothetical protein BGP110 49.68 7.73E-05 27% 54% 27--137 91--194 M003L 1521--1147 125 13,988 9.87 No Hit Found No Hit Found No Hit Found M005L 2294--1755 180 20,424 10.16 No Hit Found 1 NP_048429 A81L 110.92 1.71E-23 40% 60% 33--158 21--163 M007L 2839--2330 170 19,447 6.12 No Hit Found 1 NP_048432 A84L 73.94 1.97E-12 33% 57% 11--135 10--149 Exostosin, Exostosin family. The EXT family is a family of tumour suppressor genes. Mutations of EXT1 on 8q24.1, EXT2 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other M009L 3736--2930 269 31,504 6.02 1 pfam03016 45.82 4.20E-06 25% 51% 159--235 221--292 1 NP_048423 A75L 233.42 5.34E-60 40% 61% 8--268 7--276 EXT genes suggest association with other forms of neoplasia. EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities. The nature of the defect in heparan sulphate biosynthesis in HME is unclear.. nucleoside_deaminase, Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia M010L 4146--3790 119 13,199 9.97 1 cd01285 and is a member of the pyrimidine salvage pathway. Cytosine deaminase 57.97 9.98E-10 35% 51% 4--106 1--94 1 NP_048547 contains cytidine and deoxycytidine deaminase Zn-binding region 161.38 7.13E-39 62% 83% 1--118 1--118 is found in bacteria and fungi but is not present in mammals; for this signature reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protein synthesis. Other members of the family are guanine deaminases which deaminate guanine to xanthine as part of the utilization of guanine as a nitrogen source.. CumB, Cytosine/adenosine deaminases [Nucleotide transport and 2 COG0590 52.65 3.33E-08 31% 47% 2--106 10--105 2 AAR26853 FirrV-1-A29 50.83 1.36E-05 27% 50% 22--111 24--105 metabolism / Translation, ribosomal structure and biogenesis]. dCMP_cyt_deam, Cytidine and deoxycytidylate deaminase zinc-binding 3 pfam00383 43.43 2.04E-05 30% 47% 4--106 7--101 3 AAX51127 tRNA-specific adenosine deaminase 48.52 6.74E-05 31% 49% 4--108 10--104 region.. Riboflavin_deaminase-reductase, Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 4 cd01284 5'-phosphate, which is an intermediate step in the biosynthesis of 36.76 0.002101 26% 45% 4--107 1--95 4 AAC68441 cytosine deaminase 48.14 8.80E-05 31% 49% 4--108 10--104 riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.. M011L 4524--4237 96 10,637 10.49 No Hit Found 1 NP_048546 A199R 73.17 2.59E-12 43% 68% 1--79 1--82 M012R 4552--5019 156 17,894 7.66 No Hit Found 1 NP_048543 A196L 185.27 4.65E-46 56% 72% 1--151 1--151 PCNA_N, Proliferating cell nuclear antigen, N-terminal domain. N- M014R 5076--5867 264 29,728 5.00 1 pfam00705 terminal and C-terminal domains of PCNA are topologically identical. 92.25 4.08E-20 28% 57% 9--132 1--125 1 NP_048540 similar to human PCNA, corresponds to Swiss-Prot Accession Number 368.24 1.34E-100 68% 85% 9--261 7--259 Three PCNA molecules are tightly associated to form a closed ring P12004 encircling duplex DNA.. PCNA_C, Proliferating cell nuclear antigen, C-terminal domain. N- terminal and C-terminal domains of PCNA are topologically identical. 2 pfam02747 79.98 2.27E-16 34% 55% 137--261 2--127 2 XP_534355 PREDICTED: similar to proliferating cell nuclear antigen 158.69 1.61E-37 32% 55% 5--264 202--461 Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.
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    Paul R Thompson Department of Biochemistry and Molecular Pharmacology Voice: (508) 856-8492 UMass Medical School FAX: (508) 856-6215 Worcester, MA, 01605 Email: [email protected] PROFESSIONAL PREPARATION Institution Major Area Degree & Year McMaster University Biochemistry Honors B.S.c. – 1994 McMaster University Biochemistry Ph.D. – 2000 Johns Hopkins University SOM Pharmacology PDF – 2000-2003 PROFESSIONAL EXPERIENCE Dates Title Institution Department 2014-present Professor and Director University of Massachusetts Biochemistry and of Chemical Biology Medical School Molecular with tenure Pharmacology 2010-2014 Associate Professor The Scripps Research Chemistry with tenure Institute, Scripps Florida 2009-2010 Associate Professor University of South Carolina Chemistry with Tenure 2004-2008 Assistant Professor University of South Carolina Chemistry 2003-2004 Visiting Assistant Professor University of South Carolina Chemistry 2000-2003 Postdoctoral Fellow Johns University SOM Pharmacology 1994-2000 Teaching and McMaster University Biochemistry Research Assistant 1993-1994 Teaching Assistant McMaster University Chemistry HONORS, AWARDS AND OTHER SIGNIFICANT ACTIVITIES • Consultant to Disarm Therapeutics, 2018 to present • Chair, Bioorganic Chemistry Gordon Research Conference 2017 • Permanent Member, Synthetic Biological Chemistry B (SBCB) Study Section, NIH October 2016- present. • Consultant to Celgene, 2018 to present. • Associate Chair, Bioorganic Chemistry Gordon Research Conference 2017 • Consultant to Bristol Myers Squibb,
  • Leeds Thesis Template

    Leeds Thesis Template

    Determining the Link Between Genome Integrity and Seed Quality Robbie Michael Gillett Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds Faculty of Biological Sciences School of Biology January, 2017 - ii - The candidate confirms that the work submitted is his own and that appropriate credit has been given where reference has been made to the work of others. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Robbie M. Gillett to be identified as Author of this work has been asserted by him in accordance with the Copyright, Designs and Patents Act 1988. © 2016 The University of Leeds and Robbie Michael Gillett - iii - Acknowledgements I would like to thank my supervisor Dr Christopher West and co-supervisor Dr. Wanda Waterworth for all of their support, expertise and incredible patience and for always being available to help. I would like to thank Aaron Barrett, James Cooper, Valérie Tennant, and all my other friends at university for their help throughout my PhD. Thanks to Vince Agboh and Grace Hoysteed for their combined disjointedness and to Ashley Hines, Daniel Johnston and Darryl Ransom for being a source of entertainment for many years. I would like to thank my international Sona friends, Lindsay Hoffman and Jan Maarten ten Katen. Finally unreserved thanks to my loving parents who supported me throughout the tough times and to my Grandma and Granddad, Jean and Dennis McCarthy, who were always very vocal with their love, support and pride.