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Authors: Pallavi Subhraveti Ron Caspi Peter Midford Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_005519305Cyc: Acinetobacter radioresistens DD78 Cellular Overview Connections between pathways are omitted for legibility.

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METACYC ID Description A0AR23 GO:0004842 (Ubiquitin-Protein Ligase
Electronic Supplementary Material (ESI) for Integrative Biology This journal is © The Royal Society of Chemistry 2012 Heat Stress Responsive Zostera marina Genes, Southern Population (α=0.
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Mycobacterium Haemophilum Sp. Nov., a New Pathogen of Humanst
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The Genome of Nanoarchaeum Equitans: Insights Into Early Archaeal Evolution and Derived Parasitism
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism Elizabeth Waters†‡, Michael J. Hohn§, Ivan Ahel¶, David E. Graham††, Mark D. Adams‡‡, Mary Barnstead‡‡, Karen Y. Beeson‡‡, Lisa Bibbs†, Randall Bolanos‡‡, Martin Keller†, Keith Kretz†, Xiaoying Lin‡‡, Eric Mathur†, Jingwei Ni‡‡, Mircea Podar†, Toby Richardson†, Granger G. Sutton‡‡, Melvin Simon†, Dieter So¨ ll¶§§¶¶, Karl O. Stetter†§¶¶, Jay M. Short†, and Michiel Noordewier†¶¶ †Diversa Corporation, 4955 Directors Place, San Diego, CA 92121; ‡Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182; §Lehrstuhl fu¨r Mikrobiologie und Archaeenzentrum, Universita¨t Regensburg, Universita¨tsstrasse 31, D-93053 Regensburg, Germany; ‡‡Celera Genomics Rockville, 45 West Gude Drive, Rockville, MD 20850; Departments of ¶Molecular Biophysics and Biochemistry and §§Chemistry, Yale University, New Haven, CT 06520-8114; and ʈDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 Communicated by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, August 21, 2003 (received for review July 22, 2003) The hyperthermophile Nanoarchaeum equitans is an obligate sym- (6–8). Genomic DNA was either digested with restriction en- biont growing in coculture with the crenarchaeon Ignicoccus. zymes or sheared to provide clonable fragments. Two plasmid Ribosomal protein and rRNA-based phylogenies place its branching libraries were made by subcloning randomly sheared fragments point early in the archaeal lineage, representing the new archaeal of this DNA into a high-copy number vector (Ϸ2.8 kbp library) kingdom Nanoarchaeota. The N. equitans genome (490,885 base or low-copy number vector (Ϸ6.3 kbp library). DNA sequence pairs) encodes the machinery for information processing and was obtained from both ends of plasmid inserts to create repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide ‘‘mate-pairs,’’ pairs of reads from single clones that should be biosyntheses.
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Enzymatic Encoding Methods for Efficient Synthesis Of
(19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN,
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Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
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(12) Patent Application Publication (10) Pub. No.: US 2003/0082511 A1 Brown Et Al
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Mullergliaregnerationtranscriptome
gene.id fc1 fc2 fc3 fc4 p1 p2 p3 p4 FDR.pvalue-1 Gene Symbol Gene Title Pathway go biological process term go molecular function term go cellular component term Dr.10016.1.A1_at -2.33397 -3.86923 -4.38335 -2.39965 0.935201 0.320614 0.208 0.917227 0.208 zgc:77556 zgc:77556 --- proteolysis arylesterase activity /// metallopeptidase activity /// zinc ion --- binding Dr.10024.1.A1 at 1.483417 2.531269 2.089091 1.698761 1 0.613 0.998961 1 0.613 zgc:171808 zgc:171808--- cell-cell signaling --- --- Dr.10051.1.A1 at -1.78449 -2.22024 -1.70922 -1.99464 1 0.901663 1 0.999955 0.9017 ccng2 cyclin G2 --- --- --- --- Dr.10061.1.A1 at 2.065955 2.274632 2.248958 2.507754 0.992 0.718655 0.83 0.600609 0.6006 zgc:173506 zgc:173506--- --- --- --- Dr.10061.2.A1 at 2.131883 2.616483 2.49378 2.815337 0.983443 0.711513 0.805599 0.519115 0.5191 zgc:173506 Zgc:17350 --- --- --- --- Dr.10065.1.A1 at -1.02315 -2.01596 -2.29343 -1.88944 1 0.999955 0.957199 1 0.9572 zgc:114139 zgc:114139--- --- --- cytoplasm /// centrosome Dr.10070.1.A1_at -1.74365 -2.52206 -2.39093 -1.86817 1 0.741254 0.885401 1 0.7413 fbp1a fructose-1, --- carbohydrate metabolic process hydrolase activity /// phosphoric ester hydrolase activity --- Dr.10074.1.S1_at 6.035545 10.44051 7.880519 5.020371 0.1104 0.044 0.062491 0.144679 0.044 pdgfaa platelet-der--- multicellular organismal development /// cell proliferation growth factor activity membrane Dr.10095.1.A1 at -1.73408 -2.11615 -1.47234 -2.19919 1 0.997562 1 0.978177 0.9782 wu:fk95g04 wu:fk95g04--- --- --- --- Dr.10110.1.S1 a at 3.929761 5.798708
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1/05661 1 Al
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date _ . ... - 12 May 2011 (12.05.2011) W 2 11/05661 1 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/00 (2006.0 1) C12Q 1/48 (2006.0 1) kind of national protection available): AE, AG, AL, AM, C12Q 1/42 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) Number: International Application DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US20 10/054171 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 26 October 2010 (26.10.2010) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, (26) Publication Language: English TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 61/255,068 26 October 2009 (26.10.2009) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, (71) Applicant (for all designated States except US): ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, MYREXIS, INC.
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(10) Patent No.: US 8119385 B2
US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides.
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Calorie Restriction and the Exercise of Chromatin
Downloaded from genesdev.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW Calorie restriction and the exercise of chromatin Alejandro Vaquero1,4 and Danny Reinberg2,3 1Chromatin Biology Laboratory, Cancer Epigenetics and Biology Program (PEBC), ICREA, and IDIBELL, L’Hospitalet de Llobregat, Barcelona 08907, Spain; 2Howard Hughes Medical Institute, Department of Biochemistry, New York University-Medical School, New York, New York 10016, USA Since the earliest stages of evolution, organisms have (Masoro2005).Inahallmarkstudyin1935,McCayetal. faced the challenge of sensing and adapting to environ- (1935) demonstrated that, compared with rats fed with mental changes for their survival under compromising a standard diet, rats fed under CR lived longer, weighed less, conditions such as food depletion or stress. Implicit in showed heart hypertrophy, and had smaller livers, which these responses are mechanisms developed during evolu- they explained at the time as an effect of growth retarda- tion that include the targeting of chromatin to allow or tion. Since then, considerable research efforts have revealed prevent expression of fundamental genes and to protect that, surprisingly, the effects of CR on life span are highly genome integrity. Among the different approaches to similar among diverse eukaryotes (e.g., yeast, insects, fish, study these mechanisms, the analysis of the response to and mammals) (Kennedy et al. 2007). Although we can only a moderate reduction of energy intake, also known as speculate on these findings, they suggest that the follow- calorie restriction (CR), has become one of the best sources ing general survival strategy has been conserved through- of information regarding the factors and pathways in- out eukaryotic evolution: In low-nutrient conditions, volved in metabolic adaptation from lower to higher metabolism is adjusted to enable more efficient use of eukaryotes.
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