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Generated by SRI International Pathway Tools Version 25.0, Authors S 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. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_001806555-HmpCyc: Clostridium sp. HMSC19A11 Cellular Overview Connections between pathways are omitted for legibility.
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  • Table 2. Significant
    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
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  • Generated by SRI International Pathway Tools Version 25.0, Authors S
    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. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000238675-HmpCyc: Bacillus smithii 7_3_47FAA Cellular Overview Connections between pathways are omitted for legibility.
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    US 2014O155567A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0155567 A1 Burk et al. (43) Pub. Date: Jun. 5, 2014 (54) MICROORGANISMS AND METHODS FOR (60) Provisional application No. 61/331,812, filed on May THE BIOSYNTHESIS OF BUTADENE 5, 2010. (71) Applicant: Genomatica, Inc., San Diego, CA (US) Publication Classification (72) Inventors: Mark J. Burk, San Diego, CA (US); (51) Int. Cl. Anthony P. Burgard, Bellefonte, PA CI2P 5/02 (2006.01) (US); Jun Sun, San Diego, CA (US); CSF 36/06 (2006.01) Robin E. Osterhout, San Diego, CA CD7C II/6 (2006.01) (US); Priti Pharkya, San Diego, CA (52) U.S. Cl. (US) CPC ................. CI2P5/026 (2013.01); C07C II/I6 (2013.01); C08F 136/06 (2013.01) (73) Assignee: Genomatica, Inc., San Diego, CA (US) USPC ... 526/335; 435/252.3:435/167; 435/254.2: (21) Appl. No.: 14/059,131 435/254.11: 435/252.33: 435/254.21:585/16 (22) Filed: Oct. 21, 2013 (57) ABSTRACT O O The invention provides non-naturally occurring microbial Related U.S. Application Data organisms having a butadiene pathway. The invention addi (63) Continuation of application No. 13/101,046, filed on tionally provides methods of using Such organisms to produce May 4, 2011, now Pat. No. 8,580,543. butadiene. Patent Application Publication Jun. 5, 2014 Sheet 1 of 4 US 2014/O155567 A1 ?ueudos!SMS |?un61– Patent Application Publication Jun. 5, 2014 Sheet 2 of 4 US 2014/O155567 A1 VOJ OO O Z?un61– Patent Application Publication US 2014/O155567 A1 {}}} Hººso Patent Application Publication Jun.
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  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
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  • Upper and Lower Case Letters to Be Used
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  • Subsistence Strategies in Traditional Societies Distinguish Gut Microbiomes
    UC San Diego UC San Diego Previously Published Works Title Subsistence strategies in traditional societies distinguish gut microbiomes. Permalink https://escholarship.org/uc/item/89g6x2pf Journal Nature communications, 6(1) ISSN 2041-1723 Authors Obregon-Tito, Alexandra J Tito, Raul Y Metcalf, Jessica et al. Publication Date 2015-03-25 DOI 10.1038/ncomms7505 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ARTICLE Received 19 Aug 2014 | Accepted 4 Feb 2015 | Published 25 Mar 2015 DOI: 10.1038/ncomms7505 OPEN Subsistence strategies in traditional societies distinguish gut microbiomes Alexandra J. Obregon-Tito1,2,3,*, Raul Y. Tito1,2,*, Jessica Metcalf4, Krithivasan Sankaranarayanan1, Jose C. Clemente5, Luke K. Ursell4, Zhenjiang Zech Xu4, Will Van Treuren4, Rob Knight6, Patrick M. Gaffney7, Paul Spicer1, Paul Lawson1, Luis Marin-Reyes8, Omar Trujillo-Villarroel8, Morris Foster9, Emilio Guija-Poma2, Luzmila Troncoso-Corzo2, Christina Warinner1, Andrew T. Ozga1 & Cecil M. Lewis1 Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth  26–513) and functional potential character- ization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine.
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  • (12) United States Patent (10) Patent No.: US 9,169.496 B2 Marliere (45) Date of Patent: Oct
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  • Supplementary Table 1. the List of 1,675 All Stages of AD-Related Upregulated Genes
    Supplementary Table 1. The list of 1,675 all stages of AD-related upregulated genes Gene ID Gene symbol Gene name 51146 A4GNT ALPHA-1,4-N-ACETYLGLUCOSAMINYLTRANSFERASE 9625 AATK APOPTOSIS-ASSOCIATED TYROSINE KINASE 19 ABCA1 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 1 20 ABCA2 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 2 10058 ABCB6 ATP-BINDING CASSETTE, SUB-FAMILY B (MDR/TAP), MEMBER 6 89845 ABCC10 ATP-BINDING CASSETTE, SUB-FAMILY C (CFTR/MRP), MEMBER 10 5826 ABCD4 ATP-BINDING CASSETTE, SUB-FAMILY D (ALD), MEMBER 4 25 ABL1 V-ABL ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1 3983 ABLIM1 ACTIN BINDING LIM PROTEIN 1 30 ACAA1 ACETYL-COENZYME A ACYLTRANSFERASE 1 (PEROXISOMAL 3-OXOACYL-COENZYME A THIOLASE) 35 ACADS ACYL-COENZYME A DEHYDROGENASE, C-2 TO C-3 SHORT CHAIN 8310 ACOX3 ACYL-COENZYME A OXIDASE 3, PRISTANOYL 56 ACRV1 ACROSOMAL VESICLE PROTEIN 1 2180 ACSL1 ACYL-COA SYNTHETASE LONG-CHAIN FAMILY MEMBER 1 86 ACTL6A ACTIN-LIKE 6A 93973 ACTR8 ACTIN-RELATED PROTEIN 8 91 ACVR1B ACTIVIN A RECEPTOR, TYPE IB 8747 ADAM21 ADAM METALLOPEPTIDASE DOMAIN 21 27299 ADAMDEC1 ADAM-LIKE, DECYSIN 1 56999 ADAMTS9 ADAM METALLOPEPTIDASE WITH THROMBOSPONDIN TYPE 1 MOTIF, 9 105 ADARB2 ADENOSINE DEAMINASE, RNA-SPECIFIC, B2 (RED2 HOMOLOG RAT) 109 ADCY3 ADENYLATE CYCLASE 3 113 ADCY7 ADENYLATE CYCLASE 7 120 ADD3 ADDUCIN 3 (GAMMA) 125 ADH1C ALCOHOL DEHYDROGENASE 1A (CLASS I), ALPHA POLYPEPTIDE 9370 ADIPOQ ADIPONECTIN, C1Q AND COLLAGEN DOMAIN CONTAINING 165 AEBP1 AE BINDING PROTEIN 1 4299 AFF1 AF4/FMR2 FAMILY, MEMBER 1 173 AFM AFAMIN 79814 AGMAT AGMATINE
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  • Data Mining of the Transcriptome of Plasmodium Falciparum: the Pentose Phosphate Pathway and Ancillary Processes Zbynek Bozdech1 and Hagai Ginsburg*2
    Malaria Journal BioMed Central Research Open Access Data mining of the transcriptome of Plasmodium falciparum: the pentose phosphate pathway and ancillary processes Zbynek Bozdech1 and Hagai Ginsburg*2 Address: 1School of Biological Sciences, Nanyang Technological University, 637551 Singapore and 2Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel Email: Zbynek Bozdech - [email protected]; Hagai Ginsburg* - [email protected] * Corresponding author Published: 18 March 2005 Received: 15 January 2005 Accepted: 18 March 2005 Malaria Journal 2005, 4:17 doi:10.1186/1475-2875-4-17 This article is available from: http://www.malariajournal.com/content/4/1/17 © 2005 Bozdech and Ginsburg; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract The general paradigm that emerges from the analysis of the transcriptome of the malaria parasite Plasmodium falciparum is that the expression clusters of genes that code for enzymes engaged in the same cellular function is coordinated. Here the consistency of this perception is examined by analysing specific pathways that metabolically-linked. The pentose phosphate pathway (PPP) is a fundamental element of cell biochemistry since it is the major pathway for the recycling of NADP+ to NADPH and for the production of ribose-5-phosphate that is needed for the synthesis of nucleotides. The function of PPP depends on the synthesis of NADP+ and thiamine pyrophosphate, a co-enzyme of the PPP enzyme transketolase.
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  • Enzymes Important in the KREBS-HENSELEIT UREA SYNTHESIZING CYCLE* ARGINASE ORNITHINE CARBAMOYLTRANSFERASE (E.C. 3.5,3,1) from Beef Liver (E.C
    enzymes important in the KREBS-HENSELEIT UREA SYNTHESIZING CYCLE* ARGINASE ORNITHINE CARBAMOYLTRANSFERASE (E.C. 3.5,3,1) from Beef Liver (E.C. 2.1.3.3) from Streptococcus faecalis (L-Arginine Ureohydrolase; (Ornithine Transcarbamylase; Carbamoylphosphate: L-Arginine amidinohydrolase) L-Ornithine Carbamoyltransferase) Lyophilized powder Lyophilized with Trizma ® buffer. Catalyzes the following reaction: SuitableforthedeterminationofCarbamyl Phosphate L-Arginine + H~O-*L-Ornithine + Urea and Ornithine, One unit will convert approximately one micromole One unit will form one micromole of Citrulline from of L(+) Arginine to L-Ornithine and Urea per minute Ornithine and Carbamyl Phosphate I~er minute at at pH 9.5 at 37°C. pH 8.5 at 37°C. Order Sigma Product No. A-2137 Order Sigma Product No. O-2501 Approx. 60 units per mg. Protein (Biuret) Approx. 600 units per mg. Protein (Lowry) 2500 units $ 4.85 12,500 units $20.00 30 units $5.00 300 units $40.00 6250 units 11.00 25,000 units 30.00 *Ref.: Krebs, H. A. and Henseleit, K., Z. Physiol. Chem., 210:33 ().932). Other enzymes related to AMMONIA NITROGEN METABOLISM: L-Asparaginase Glutamic Oxalacetic Transaminase Glutaminase L-Aspartase Glutamic-Pyruvic Transaminase L-Histidase Creatininase Gabase Adenosine Deaminase L-Glutamic Dehydrogenase Useful for assay of'r-Aminobutyric Acid. 5'-AMP Deaminase See the Sigma Catalog for further details. ~//~"~ CARBOXYPEPTIDASE - B (E. C. No. 3.4.2.2.) catalyzes hydrolysis of the basic amino acids Arginine and Lysine from the carboxyl terminal position in polypeptides. One of the major pancreatic proteases, Carboxypeptidase-B also functions in the further degradation of products of tryptic digestion.
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  • Structure and Function of Metallohydrolases in the Arginase- Deacetylase Family
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Structure and Function of Metallohydrolases in the Arginase- Deacetylase Family Yang Hai University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons Recommended Citation Hai, Yang, "Structure and Function of Metallohydrolases in the Arginase-Deacetylase Family" (2016). Publicly Accessible Penn Dissertations. 1753. https://repository.upenn.edu/edissertations/1753 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1753 For more information, please contact [email protected]. Structure and Function of Metallohydrolases in the Arginase-Deacetylase Family Abstract Arginases and deacetylases are metallohydrolases that catalyze two distinct chemical transformations. The arginases catalyze the hydrolysis of the guanidinium group of arginine by using a hydroxide ion 2+ 2+ bridging the binuclear manganese cluster (Mn A-Mn B) for nucleophilic attack. The deacetylases catalyze the hydrolysis of amide bonds by using a mononuclear Zn2+-ion activated water molecule as the nucleophile. Despite the diverse functions, metallohydrolases of the arginase-deacetylase superfamily 2+ share the same characteristic α/β hydrolase core fold and a conserved metal binding site (the Mn B site in arginase corresponds to the catalytic Zn2+ site in deacetylase) which is essential for catalysis in both enzymes. We report crystal structure of formiminoglutamase from the parasitic protozoan Trypanosoma cruzi and confirm that formiminoglutamase is a Mn2+-requiring hydrolase that belongs to the arginase- deacetylase superfamily. We also report the crystal structure of an arginase-like protein from Trypanosoma brucei (TbARG) with unknown function. Although its biological role remains enigmatic, the 2+ evolutionarily more conserved Mn B site can be readily restored in TbARG through side-directed mutagenesis.
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