Effects of Feeding and Confinement on Nitrogen Metabolism and Excretion in the Gulf Toadfish Opsanus Beta
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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. -
Discovery of an Alternate Metabolic Pathway for Urea Synthesis in Adult Aedes Aegypti Mosquitoes
Discovery of an alternate metabolic pathway for urea synthesis in adult Aedes aegypti mosquitoes Patricia Y. Scaraffia*†‡, Guanhong Tan§, Jun Isoe*†, Vicki H. Wysocki*§, Michael A. Wells*†, and Roger L. Miesfeld*† Departments of §Chemistry and *Biochemistry and Molecular Biophysics and †Center for Insect Science, University of Arizona, Tucson, AZ 85721-0088 Edited by Anthony A. James, University of California, Irvine, CA, and approved December 4, 2007 (received for review August 27, 2007) We demonstrate the presence of an alternate metabolic pathway We previously reported that mosquitoes dispose of toxic for urea synthesis in Aedes aegypti mosquitoes that converts uric ammonia through glutamine (Gln) and proline (Pro) synthesis, acid to urea via an amphibian-like uricolytic pathway. For these along with excretion of ammonia, uric acid, and urea (20). By studies, female mosquitoes were fed a sucrose solution containing using labeled isotopes and mass spectrometry techniques (21), 15 15 15 15 15 NH4Cl, [5- N]-glutamine, [ N]-proline, allantoin, or allantoic we have recently determined how the N from NH4Cl is acid. At 24 h after feeding, the feces were collected and analyzed incorporated into the amide side chain of Gln, and then into Pro, in a mass spectrometer. Specific enzyme inhibitors confirmed that in Ae. aegypti (22). In the present article we demonstrate that the 15 15 15 mosquitoes incorporate N from NH4Cl into [5- N]-glutamine nitrogen of the amide group of Gln contributes to uric acid and use the 15N of the amide group of glutamine to produce synthesis in mosquitoes and, surprisingly, that uric acid can be 15 labeled uric acid. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Open Matthew R Moreau Ph.D. Dissertation Finalfinal.Pdf
The Pennsylvania State University The Graduate School Department of Veterinary and Biomedical Sciences Pathobiology Program PATHOGENOMICS AND SOURCE DYNAMICS OF SALMONELLA ENTERICA SEROVAR ENTERITIDIS A Dissertation in Pathobiology by Matthew Raymond Moreau 2015 Matthew R. Moreau Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy May 2015 The Dissertation of Matthew R. Moreau was reviewed and approved* by the following: Subhashinie Kariyawasam Associate Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Bhushan M. Jayarao Professor, Veterinary and Biomedical Sciences Dissertation Adviser Co-Chair of Committee Mary J. Kennett Professor, Veterinary and Biomedical Sciences Vijay Kumar Assistant Professor, Department of Nutritional Sciences Anthony Schmitt Associate Professor, Veterinary and Biomedical Sciences Head of the Pathobiology Graduate Program *Signatures are on file in the Graduate School iii ABSTRACT Salmonella enterica serovar Enteritidis (SE) is one of the most frequent common causes of morbidity and mortality in humans due to consumption of contaminated eggs and egg products. The association between egg contamination and foodborne outbreaks of SE suggests egg derived SE might be more adept to cause human illness than SE from other sources. Therefore, there is a need to understand the molecular mechanisms underlying the ability of egg- derived SE to colonize the chicken intestinal and reproductive tracts and cause disease in the human host. To this end, the present study was carried out in three objectives. The first objective was to sequence two egg-derived SE isolates belonging to the PFGE type JEGX01.0004 to identify the genes that might be involved in SE colonization and/or pathogenesis. -
Nfletffillfl Sm of Nuelieotfl Dles
Nfletffillflsm of Nuelieotfl dles ucleotides \f consistof a nitrogenousbase, a | \ pentose and a phosphate. The pentose sugaris D-ribosein ribonucleotidesof RNAwhile in deoxyribonucleotides(deoxynucleotides) of i Aspariaie--'N.,,,t .J . DNA, the sugaris 2-deoxyD-ribose. Nucleotides t participate in almost all the biochemical processes/either directly or indirectly.They are the structuralcomponents of nucleicacids (DNA, Y RNA), coenzymes, and are involved in tne Glutamine regulationof severalmetabolic reactions. Fig. 17.1 : The sources of individuat atoms in purine ring. (Note : Same colours are used in the syntheticpathway Fig. lZ.2). n T. C4, C5 and N7 are contributedby glycine. Many compoundscontribute to the purine ring of the nucleotides(Fig.t7.l). 5. C6 directly comes from COr. 1. purine N1 of is derivedfrom amino group It should be rememberedthat purine bases of aspartate. are not synthesizedas such,but they are formed as ribonucleotides. The purines 2. C2 and Cs arise from formate of N10- are built upon a formyl THF. pre-existing ribose S-phosphate. Liver is the major site for purine nucleotide synthesis. 3. N3 and N9 are obtainedfrom amide group Erythrocytes,polymorphonuclear leukocytes and of glutamine. brain cannot producepurines. 388 BIOCHEMISTF|Y m-gg-o-=_ |l Formylglycinamide ribosyl S-phosphate Kn H) Glutam H \-Y OH +ATt OH OH Glutame cl-D-Ribose-S-phosphate + ADP orr-l t'1 PRPPsYnthetase ,N o"t*'] \cH + Hrcl-itl HN:C-- O EO-qn2-O.- H -NH l./ \l KH H) I u \.]_j^/ r,\-iEl-/^\-td Ribose5-P II Formylglycinamidineribosyl-s-phosphate -
Arginase Specific Activity and Nitrogenous Excretion of Penaeus Japonicus Exposed to Elevated Ambient Ammonia
MARINE ECOLOGY PROGRESS SERIES Published July 10 Mar Ecol Prog Ser Arginase specific activity and nitrogenous excretion of Penaeus japonicus exposed to elevated ambient ammonia Jiann-Chu Chen*,Jiann-Min Chen Department of Aquaculture. National Taiwan Ocean University. Keelung, Taiwan 20224, Republic of China ABSTRACT: Mass-specific activity of arginase and nitrogenous excretion of Penaeus japonicus Bate (10.3 * 3.7 g) were measured for shrimps exposed to 0.029 (control), 1.007 and 10.054 mg 1-' ammonia- N at 32%, S for 24 h. Arginase specific activity of gill, hepatopancreas and midgut increased directly with ambient ammonia-N, whereas arginase specific activity of muscle was inversely related to ambient ammonia-N. Excretion of total-N (total nitrogen), organic-N and urea-N increased, whereas excretion of ammonia-N, nitrate-N and nitrite-N decreased significantly with an increase of ambient ammonia- N. In the control solution, japonlcus excreted 68.94% ammonia-N, 25.39% organic-N and 2.87% urea-N. For the shrimps exposed to 10 mg 1" ammonia-N, ammonia-N uptake occurred, and t.he con- tribution of organic-N and urea-N excretion increased to 90.57 and 8.78%, respectively, of total-N. High levels of arginase specific activity in the gill, midgut and hepatopancreas suggest that there is an alternative route of nitrogenous waste for P. japonicus under ammonia exposure. KEY WORDS: Penaeus japonicus - Ammonia . Arginase activity . Nitrogenous excretion . Metabolism INTRODUCTION processes. Therefore, accumulation of ammonia and its toxicity are of primary concern. Kuruma shrimp Penaeus japonicus Bate, which is Ammonia has been reported to increase molting fre- distributed in Pacific rim countries, is also found in the quency, reduce growth, and even cause mortality of Mediterranean. -
Generated by SRI International Pathway Tools Version 25.0, Authors S
Authors: Pallavi Subhraveti Ron Caspi Quang Ong 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_000725805Cyc: Streptomyces xanthophaeus Cellular Overview Connections between pathways are omitted for legibility. -
CUMMINGS-DISSERTATION.Pdf (4.094Mb)
D-AMINOACYLASES AND DIPEPTIDASES WITHIN THE AMIDOHYDROLASE SUPERFAMILY: RELATIONSHIP BETWEEN ENZYME STRUCTURE AND SUBSTRATE SPECIFICITY A Dissertation by JENNIFER ANN CUMMINGS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2010 Major Subject: Chemistry D-AMINOACYLASES AND DIPEPTIDASES WITHIN THE AMIDOHYDROLASE SUPERFAMILY: RELATIONSHIP BETWEEN ENZYME STRUCTURE AND SUBSTRATE SPECIFICITY A Dissertation by JENNIFER ANN CUMMINGS Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Frank Raushel Committee Members, Paul Lindahl David Barondeau Gregory Reinhart Head of Department, David Russell December 2010 Major Subject: Chemistry iii ABSTRACT D-Aminoacylases and Dipeptidases within the Amidohydrolase Superfamily: Relationship Between Enzyme Structure and Substrate Specificity. (December 2010) Jennifer Ann Cummings, B.S., Southern Oregon University; M.S., Texas A&M University Chair of Advisory Committee: Dr. Frank Raushel Approximately one third of the genes for the completely sequenced bacterial genomes have an unknown, uncertain, or incorrect functional annotation. Approximately 11,000 putative proteins identified from the fully-sequenced microbial genomes are members of the catalytically diverse Amidohydrolase Superfamily. Members of the Amidohydrolase Superfamily separate into 24 Clusters of Orthologous Groups (cogs). Cog3653 includes proteins annotated as N-acyl-D-amino acid deacetylases (DAAs), and proteins within cog2355 are homologues to the human renal dipeptidase. The substrate profiles of three DAAs (Bb3285, Gox1177 and Sco4986) and six microbial dipeptidase (Sco3058, Gox2272, Cc2746, LmoDP, Rsp0802 and Bh2271) were examined with N-acyl-L-, N-acyl-D-, L-Xaa-L-Xaa, L-Xaa-D-Xaa and D-Xaa-L-Xaa substrate libraries. -
(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. -
An Updated Overview on the Regulation of Seed Germination
An Updated Overview on the Regulation of Seed Germination Table S1. Selected recent reviews on seed germination-related aspects. Subject (Keywords) References Generalists ABA, Arabidopsis, dormancy, germination, GA, seed maturation. [3] GAs and ABA GAs, ABA, hormone signaling, seed germination, abiotic stresses, crosstalk of [10] hormone signaling. DELLAs, GAs, hormone crosstalk, phenotypic plasticity, plant development. [20] DELLA, GRAS, GAs, Arabidopsis, rice, GID1, crosstalk, [22] ABA, ABA synthesis, ABA signaling, ABA response. [35] PYR1, RCAR, ABA transduction, SnRK2, PP2C. [42] ABI5, abiotic stress response, phytohormone crosstalk, ABA, brassinosteroids, GAs, [81] jasmonates, posttranslational modification. Hormones transport GA biosynthesis, GA action, GA transport, evolution, Gibberella fujikuroi. [48] GA, plant hormone, hormone transport and localization, GA transporters, NPF, [49] SWEET. ABA; guard cell; transporter; water stress. [50] GA metabolism, GA transport, GA gradients, cellular growth. [51] Plant NRT1/PTR transporters, phylogenetic relationships, substrates. [72] Glucosinolate, hormone, nitrate, nitrite, peptide, transporter. [73] NIN-like protein (NLP), nitrate, nitrate-responsive gene expression, post- translational regulation, transcription factor, [77] nitrate signalling. Light regulation PIF signaling, Phytochromes, plant development. [109] Chromatin dynamics Shoot apical meristem, quiescent center, floral homeotic gene, polycomb repression, [162] seed development, dormancy, germination and greening. DNA methylation, -
Phosphate Availability and Ectomycorrhizal Symbiosis with Pinus Sylvestris Have Independent Effects on the Paxillus Involutus Transcriptome
This is a repository copy of Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/168854/ Version: Published Version Article: Paparokidou, C., Leake, J.R. orcid.org/0000-0001-8364-7616, Beerling, D.J. et al. (1 more author) (2020) Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome. Mycorrhiza. ISSN 0940- 6360 https://doi.org/10.1007/s00572-020-01001-6 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Mycorrhiza https://doi.org/10.1007/s00572-020-01001-6 ORIGINAL ARTICLE Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome Christina Paparokidou1 & Jonathan R. Leake1 & David J. Beerling1 & Stephen A. Rolfe1 Received: 16 June 2020 /Accepted: 29 October 2020 # The Author(s) 2020 Abstract Many plant species form symbioses with ectomycorrhizal fungi, which help them forage for limiting nutrients in the soil such as inorganic phosphate (Pi). -
Supplementary Information
Supplementary information (a) (b) Figure S1. Resistant (a) and sensitive (b) gene scores plotted against subsystems involved in cell regulation. The small circles represent the individual hits and the large circles represent the mean of each subsystem. Each individual score signifies the mean of 12 trials – three biological and four technical. The p-value was calculated as a two-tailed t-test and significance was determined using the Benjamini-Hochberg procedure; false discovery rate was selected to be 0.1. Plots constructed using Pathway Tools, Omics Dashboard. Figure S2. Connectivity map displaying the predicted functional associations between the silver-resistant gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S3. Connectivity map displaying the predicted functional associations between the silver-sensitive gene hits; disconnected gene hits not shown. The thicknesses of the lines indicate the degree of confidence prediction for the given interaction, based on fusion, co-occurrence, experimental and co-expression data. Figure produced using STRING (version 10.5) and a medium confidence score (approximate probability) of 0.4. Figure S4. Metabolic overview of the pathways in Escherichia coli. The pathways involved in silver-resistance are coloured according to respective normalized score. Each individual score represents the mean of 12 trials – three biological and four technical. Amino acid – upward pointing triangle, carbohydrate – square, proteins – diamond, purines – vertical ellipse, cofactor – downward pointing triangle, tRNA – tee, and other – circle.