DOCSLIB.ORG

Table 10: H. Sapiens Recon 1 Network Confidence Scores and Citations

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Table 10: H. Sapiens Recon 1 Network Confidence Scores and Citations Table 10: H. sapiens Recon 1 network confidence scores and citations. Alphabetized list of reactions and their corresponding confidence scores, literature citations, and curator notes. Confidence scores (ranging from 0 to 3) are defined in the text. Reaction Abbreviation Score Authors Article or Book Title Journal Year PubMed ID Curation Notes This reaction takes place in kidney Human 25-hydroxyvitamin D 24-hydroxylase based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, Labuda M, Lemieux N, Tihy cytochrome P450 subunit maps to a different 24,25VITD2Hm 3 J Bone Miner Res 1993 8266831 1st ed (book) pg.196 F, Prinster C, Glorieux FH. chromosomal location than that of pseudovitamin D- 1-4 ng/ml blood deficient rickets. is produced if neither ca2+ nor pi i needed (regulated by these compounds concentration) IT This reaction takes place in kidney Kusudo T, Sakaki T, Abe D, based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, Fujishima T, Kittaka A, Metabolism of A-ring diastereomers of 1alpha,25- Biochem Biophys Res 24,25VITD2Hm 3 2004 15358094 1st ed (book) pg.196 Takayama H, Hatakeyama S, dihydroxyvitamin D3 by CYP24A1. Commun 1-4 ng/ml blood Ohta M, Inouye K. is produced if neither ca2+ nor pi i needed (regulated by these compounds concentration) IT This reaction takes place in kidney St-Arnaud R, Messerlian S, The 25-hydroxyvitamin D 1-alpha-hydroxylase gene based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, 25VITD3Hm 3 Moir JM, Omdahl JL, Glorieux maps to the pseudovitamin D-deficiency rickets J Bone Miner Res 1997 9333115 1st ed (book) pg.196 FH. (PDDR) disease locus. this form is the biological acitve hormon (25-70pg/ml blood) IT is produced if ca2+ or pi i needed (regulated by these compounds concentration) This reaction takes place in kidney Yokomura K, Suda T, Sasaki Increased expression of the 25-hydroxyvitamin D(3)- based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, J Clin Endocrinol 25VITD3Hm 3 S, Inui N, Chida K, Nakamura 1alpha-hydroxylase gene in alveolar macrophages of 2003 14671156 1st ed (book) pg.196 Metab H. patients with lung cancer. this form is the biological acitve hormon (25-70pg/ml blood) IT is produced if ca2+ or pi i needed (regulated by these compounds concentration) The reference indicates this is a spontaneous reaction. It is needed to get rid of 2amac that is a byproduct of thyroid hormone synthesis. Gavaret JM, Cahnmann HJ, The fate of the "lost side chain" during thyroid 2AMACHYD 3 J Biol Chem 1979 500639 Nunez J hormonogenesis added by MM- PMID 14596599: Formation of pyruvate by SDH is a two-step reaction in which the hydroxyl group of serine is cleaved to produce aminoacrylate, and then the aminoacrylate is deaminated by nonenzymatic hydrolysis to produce pyruvate. -L-cysteate can be synthesized from 2-aminoacrylate in rat (PMID: 6351723) -this is a lumped rxn w/ an inferred reduction rxn that occurs in conjunction w/ the sulfotransferase step; this reduction step has 2AMACSULT 2 Cooper AJ Biochemistry of sulfur-containing amino acids. 1983 6351723 to occur in order for the transformation (2amac-->Lcyst) to be valid -used NADPH as electron donor since it is a common cofactor involved in biosynthetic steps utilizing oxygen (see Neema for further explanations) MM Determination of isoenzyme contents of lactic Komoda T, Sakagishi Y, dehydrogenase activity and 2-hydroxybutyric 2HBO 3 Clin Chim Acta 1976 10108 Mizushima H dehydrogenase activity in lactic dehydrogenase - another function of L-lactate dehydrogenase [Naghizadeh, preparations Clin Chim Acta 1977], [Komoda, Clin Chim Acta 1976] 2HBO 3 Naghizadeh F Oxidation of alpha-hydroxybutyrate by human serum Clin Chim Acta 1977 21765 - another function of L-lactate dehydrogenase [Naghizadeh, Clin Chim Acta 1977], [Komoda, Clin Chim Acta 1976] The Metabolic and Molecular Bases of 2OXOADOXm 2 Cox, RP Errors of lysine metabolism 2001 Inherited Disease, 8th ed 0 Fiermonte G, Dolce V, Identification of the human mitochondrial Palmieri L, Ventura M, oxodicarboxylate carrier. Bacterial expression, 2OXOADPTm 3 J Biol Chem 2001 11083877 Runswick MJ, Palmieri F, reconstitution, functional characterization, tissue reference says other transport reactions done by this gene as Walker JE distribution, and chromosomal location well Mardh G, Dingley AL, Auld Human class II (pi) alcohol dehydrogenase has a Proc Natl Acad Sci U S 34DHOXPEGOX 3 1986 3466164 DS, Vallee BL redox-specific function in norepinephrine metabolism A Citation in abstract indicates that ADH does this reaction. Two different mechanisms of noradrenaline release Kurz T, Richardt G, Hagl S, 34DHOXPEGt 2 during normoxia and simulated ischemia in human J Mol Cell Cardiol 1995 7473774 Citation indicates that this compound is found in the blood. Seyfarth M, Schomig A cardiac tissue Mechanism and gene unknown. First citation has catalytic constants. Human aldehyde dehydrogenase. Activity with 34DHPLACOX(NAD 3 Ambroziak W, Pietruszko R aldehyde metabolites of monoamines, diamines, and J Biol Chem 1991 2071588 P) Only Aldh3a1 is known to use NADP, but the other two have polyamines not yet been determined. First citation has catalytic constants. Biogenic aldehyde(s) derived from the action of 34DHPLACOX(NAD 3 Keung WM monoamine oxidase may mediate the antidipsotropic Chem Biol Interact 2001 11306106 P) Only Aldh3a1 is known to use NADP, but the other two have effect of daidzin not yet been determined. First citation indicates that aldh1a3 does not use NADP. Kawamura M, Eisenhofer G, Aldh3b1, 3b2 are yet to be determined according to citation and 34DHXMANDACOX( Kopin IJ, Kador PF, Lee YS, Aldose reductase, a key enzyme in the oxidative 3 Biochem Pharmacol 1999 10424772 left with both forms of the reaction. NADP) Tsai JY, Fujisawa S, Lizak deamination of norepinephrine in rats MJ, Sinz A, Sato S Second citation is based on evidence in rats. This reaction is left reversible because the loop was eliminated by making the NAD dependent reaction irreversible. Reaction Abbreviation Score Authors Article or Book Title Journal Year PubMed ID Curation Notes IT the enzyme responsible for this reaction has not been identified Ubiquinone. Biosynthesis of quinone ring and its 3DPHBH1 2 Szkopinska A. Acta Biochim Pol 2000 11051212 in any organism. Szekopinspka (2000) describes reaction as isoprenoid side chain. Intracellular localization. hydroxylation, Stryer (Biochemistry) notes that NADPH is a required secondary metabolite for the hydroxylation reaction of sterols. Based on these information the reaction was created (plus for NADH since we cannot exclude the action of NADH instead of NADPH) Malherbe P, Kohler C, Da Prada M, Lang G, Kiefer V, Molecular cloning and functional expression of 3HAO 3 J Biol Chem 1994 7514594 Schwarcz R, Lahm HW, human 3-hydroxyanthranilic-acid dioxygenase Cesura AM Reaction and gene detailed in citation. The citation states that the same enzyme that takes Lkynr as a 3HKYNAKGAT 2 BONNER DM, JAKOBY WB Kynurenine transaminase from neurospora J Biol Chem 1956 13357462 substrate in neurospora also takes this as a substrate. Physiological data was chosen for this reaction, but that characterization may not be entirely accurate. Hawes JW, Jaskiewicz J, Primary structure and tissue-specific expression of Shimomura Y, Huang B, 3HPCOAHYD 3 human beta-hydroxyisobutyryl-coenzyme A J Biol Chem 1996 8824301 Bunting J, Harper ET, Harris Citation has details. It is unclear why it is included in this hydrolase. RA. pathway. SAB The relationship between body size and the urinary Johansson AC, Lonnqvist B, 3MLDAt 2 excretion of the main histamine metabolite tele- Inflamm Res 2001 11411609 Granerus G Added because this compound is known to be in the urine. methylimidazoleacetic acid in man Mechanism and gene unknown. PMID 8428987: transport of branched chain alpha-keto acid via proton symport shown in rat mitochondria; possibly a Identification of the mitochondrial branched chain bifunctional activity of mitochondrial branched chain 3MOPt2im 3 Hutson SM, Hall TR. aminotransferase as a branched chain alpha-keto acid 1993 8428987 aminotransferase transport protein. MM Jonsson EG, Norton N, A promoter polymorphism in the monoamine oxidase 3MOXTYROX 3 Gustavsson JP, Oreland L, A gene and its relationships to monoamine metabolite J Psychiatr Res 2000 10867119 MAOA seems to participate a bit more than MAOB in this Owen MJ, Sedvall GC concentrations in CSF of healthy volunteers reaction nucleotide monophosphates come from DNA and RNA degradation in lysosome (by acid exonucleoase and acid ribonuclease). Will be dead-end in model as well as their efflux transport systems. Lysosomal Nucleic Acid and Phosphate Metabolism 3NTD7l 3 R.L. Pisoni 1996 and Related Metabolic Reactions, Chapter 9 IT Their is also a acid nucleotidase which carries out these reactions but i could not find the gene for this lysososmal enzyme - needed in the degradation of 4abut (GABA) in the mitochondria Medina-Kauwe LK, Tobin AJ, -allows 4abut (which resides/is synthesized in cytosol) De Meirleir L, Jaeken J, 4-Aminobutyrate aminotransferase (GABA- 4ABUTtm 2 1999 10407778 degradation to succ, which occurs in the mitochondria; Jakobs C, Nyhan WL, Gibson transaminase) deficiency. transport mechanism not found/specified for humans so this rxn KM. is used for the time being, although there is a possible 4abut/glu L antiport mechanism based on evidence in rat mitochondria (PMID:10407778) MM IT I assumed that reaction takes place in mito as whole ubiquinone biosynthesis.- first reaction from tyr to 34hpp has also been assigned to the mito 4HBZCOAFm 2 Meganathan R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol Lett 2001 11583838 Booth et al proposed this mechanism from tyrosine to 4hbz. Loescher + Heide found this mechanism in higher plant cells and these results make it highly probable that this mechanism also occurs in mammalian cells. IT I assumed that reaction takes place in mito as whole ubiquinone Biosynthesis of p-Hydroxybenzoate from p- biosynthesis.- first reaction from tyr to 34hpp has also been Coumarate and p-Coumaroyl-Coenzyme A in Cell- assigned to the mito 4HBZCOAFm 2 Loscher R, Heide L.
Load more

Recommended publications
  • Gene Expression Polarization
    Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression This information is current as of September 27, 2021. Fernando O. Martinez, Siamon Gordon, Massimo Locati and Alberto Mantovani J Immunol 2006; 177:7303-7311; ; doi: 10.4049/jimmunol.177.10.7303 http://www.jimmunol.org/content/177/10/7303 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2006/11/03/177.10.7303.DC1 Material http://www.jimmunol.org/ References This article cites 61 articles, 22 of which you can access for free at: http://www.jimmunol.org/content/177/10/7303.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 27, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2006 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Transcriptional Profiling of the Human Monocyte-to-Macrophage Differentiation and Polarization: New Molecules and Patterns of Gene Expression1 Fernando O.
    [Show full text]
  • Downloaded from GEO
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.252007; this version posted November 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Oxylipin metabolism is controlled by mitochondrial b-oxidation during bacterial inflammation. Mariya Misheva1, Konstantinos Kotzamanis1*, Luke C Davies1*, Victoria J Tyrrell1, Patricia R S Rodrigues1, Gloria A Benavides2, Christine Hinz1, Robert C Murphy3, Paul Kennedy4, Philip R Taylor1,5, Marcela Rosas1, Simon A Jones1, Sumukh Deshpande1, Robert Andrews1, Magdalena A Czubala1, Mark Gurney1, Maceler Aldrovandi1, Sven W Meckelmann1, Peter Ghazal1, Victor Darley-Usmar2, Daniel White1, and Valerie B O’Donnell1 1Systems Immunity Research Institute and Division of Infection and Immunity, and School of Medicine, Cardiff University, UK, 2Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA, 4Cayman Chemical 1180 E Ellsworth Rd, Ann Arbor, MI 48108, United States, 5UK Dementia Research Institute at Cardiff, Cardiff University, UK Address correspondence: Valerie O’Donnell, [email protected] or Daniel White, [email protected], Systems Immunity Research Institute, Cardiff University *Both authors contributed equally to the study 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.252007; this version posted November 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Mouse Adh4 Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Adh4 Knockout Project (CRISPR/Cas9) Objective: To create a Adh4 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Adh4 gene (NCBI Reference Sequence: NM_011996 ; Ensembl: ENSMUSG00000037797 ) is located on Mouse chromosome 3. 9 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 9 (Transcript: ENSMUST00000013458). Exon 2~7 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 1.68% of the coding region. Exon 2~7 covers 84.17% of the coding region. The size of effective KO region: ~9976 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 9 Legends Exon of mouse Adh4 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of Exon 2 is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 936 bp section downstream of Exon 7 is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • HHS Public Access Author Manuscript
    HHS Public Access Author manuscript Author Manuscript Author ManuscriptAm J Med Author Manuscript Genet B Neuropsychiatr Author Manuscript Genet. Author manuscript; available in PMC 2015 December 01. Published in final edited form as: Am J Med Genet B Neuropsychiatr Genet. 2014 December ; 0(8): 673–683. doi:10.1002/ajmg.b.32272. Association and ancestry analysis of sequence variants in ADH and ALDH using alcohol-related phenotypes in a Native American community sample Qian Peng1,2,*, Ian R. Gizer3, Ondrej Libiger2, Chris Bizon4, Kirk C. Wilhelmsen4,5, Nicholas J. Schork1, and Cindy L. Ehlers6,* 1 Department of Human Biology, J. Craig Venter Institute, La Jolla, CA 92037 2 Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037 3 Department of Psychological Sciences, University of Missouri-Columbia, Columbia, MO 65211 4 Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517 5 Department of Genetics and Neurology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 6 Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037 Abstract Higher rates of alcohol use and other drug-dependence have been observed in some Native American populations relative to other ethnic groups in the U.S. Previous studies have shown that alcohol dehydrogenase (ADH) genes and aldehyde dehydrogenase (ALDH) genes may affect the risk of development of alcohol dependence, and that polymorphisms within these genes may differentially affect risk for the disorder depending on the ethnic group evaluated. We evaluated variations in the ADH and ALDH genes in a large study investigating risk factors for substance use in a Native American population.
    [Show full text]
  • 35 Disorders of Purine and Pyrimidine Metabolism
    35 Disorders of Purine and Pyrimidine Metabolism Georges van den Berghe, M.- Françoise Vincent, Sandrine Marie 35.1 Inborn Errors of Purine Metabolism – 435 35.1.1 Phosphoribosyl Pyrophosphate Synthetase Superactivity – 435 35.1.2 Adenylosuccinase Deficiency – 436 35.1.3 AICA-Ribosiduria – 437 35.1.4 Muscle AMP Deaminase Deficiency – 437 35.1.5 Adenosine Deaminase Deficiency – 438 35.1.6 Adenosine Deaminase Superactivity – 439 35.1.7 Purine Nucleoside Phosphorylase Deficiency – 440 35.1.8 Xanthine Oxidase Deficiency – 440 35.1.9 Hypoxanthine-Guanine Phosphoribosyltransferase Deficiency – 441 35.1.10 Adenine Phosphoribosyltransferase Deficiency – 442 35.1.11 Deoxyguanosine Kinase Deficiency – 442 35.2 Inborn Errors of Pyrimidine Metabolism – 445 35.2.1 UMP Synthase Deficiency (Hereditary Orotic Aciduria) – 445 35.2.2 Dihydropyrimidine Dehydrogenase Deficiency – 445 35.2.3 Dihydropyrimidinase Deficiency – 446 35.2.4 Ureidopropionase Deficiency – 446 35.2.5 Pyrimidine 5’-Nucleotidase Deficiency – 446 35.2.6 Cytosolic 5’-Nucleotidase Superactivity – 447 35.2.7 Thymidine Phosphorylase Deficiency – 447 35.2.8 Thymidine Kinase Deficiency – 447 References – 447 434 Chapter 35 · Disorders of Purine and Pyrimidine Metabolism Purine Metabolism Purine nucleotides are essential cellular constituents 4 The catabolic pathway starts from GMP, IMP and which intervene in energy transfer, metabolic regula- AMP, and produces uric acid, a poorly soluble tion, and synthesis of DNA and RNA. Purine metabo- compound, which tends to crystallize once its lism can be divided into three pathways: plasma concentration surpasses 6.5–7 mg/dl (0.38– 4 The biosynthetic pathway, often termed de novo, 0.47 mmol/l). starts with the formation of phosphoribosyl pyro- 4 The salvage pathway utilizes the purine bases, gua- phosphate (PRPP) and leads to the synthesis of nine, hypoxanthine and adenine, which are pro- inosine monophosphate (IMP).
    [Show full text]
  • TRANSCRIPTION REGULATION of the CLASS IV ALCOHOL DEHYDROGENASE 7 (ADH7) Sowmya Jairam Submitted to the Faculty of the University
    TRANSCRIPTION REGULATION OF THE CLASS IV ALCOHOL DEHYDROGENASE 7 (ADH7) Sowmya Jairam Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Department of Biochemistry and Molecular Biology, Indiana University May 2014 Accepted by the Graduate Faculty, of Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Howard J. Edenberg, Ph.D., Chair Brian P. Herring, Ph.D. Doctoral Committee David G. Skalnik, Ph.D. January 21, 2014 Ronald C. Wek, Ph.D. ii ACKNOWLEDGEMENTS I would like to thank my advisor, Dr. Howard Edenberg, for his guidance and support throughout my time in his lab. He fostered the ability to think independently by asking questions and letting me find the answers, even those I didn’t have readily, while making sure I was on the right track. I know the lessons I have learnt and the training I have received will stand me in good stead in my career. I would also like to thank all the current and former lab members at both the MS building and BRTC, particularly Jun Wang, Dr. Jeanette McClintick, Ron Jerome and Dr. Sirisha Pochareddy for their mentoring and friendship. They have been a great help and an immense support whenever I needed to get a second opinion on a technique or a research idea, and I have enjoyed discussing both scientific and non-scientific topics with them. I would like to thank my committee members Dr. Paul Herring, Dr. David Skalnik and Dr.
    [Show full text]
  • Metabolism of Purines and Pyrimidines in Health and Disease
    39th Meeting of the Polish Biochemical Society Gdañsk 16–20 September 2003 SESSION 6 Metabolism of purines and pyrimidines in health and disease Organized by A. C. Sk³adanowski, A. Guranowski 182 Session 6. Metabolism of purines and pyrimidines in health and disease 2003 323 Lecture The role of DNA methylation in cytotoxicity mechanism of adenosine analogues in treatment of leukemia Krystyna Fabianowska-Majewska Zak³ad Chemii Medycznej IFiB, Uniwersytet Medyczny, ul. Mazowiecka 6/8, 92 215 £ódŸ Changes in DNA methylation have been recognized tory effects of cladribine and fludarabine on DNA as one of the most common molecular alterations in hu- methylation, after 48 hr growth of K562 cells with the man neoplastic diseases and hypermethylation of drugs, are non-random and affect mainly CpG rich is- gene-promoter regions is one of the most frequent lands or CCGG sequences but do not affect sepa- mechanisms of the loss of gene functions. For this rea- rately-located CpG sequences. The analysis showed son, DNA methylation may be a tool for detection of that cladribine (0.1 mM) reduced the methylated early cell transformations as well as predisposition to cytosines in CpG islands and CCGG sequences to a sim- metastasis process. Moreover, DNA methylation seems ilar degree. The inhibition of cytosine methylation by to be a promissing target for new preventive and thera- fludarabine (3 mM) was observed mainly in CCGG se- peutic strategies. quences, sensitive to HpaII, but the decline in the meth- Our studies on DNA methylation and cytotoxicity ylated cytosine, located in CpG island was 2-fold lower mechanism of antileukemic drugs, cladribine and than that with cladribine.
    [Show full text]
  • Age-Dependent Protein Abundance of Cytosolic Alcohol and Aldehyde Dehydrogenases in Human Liver S
    Supplemental material to this article can be found at: http://dmd.aspetjournals.org/content/suppl/2017/08/21/dmd.117.076463.DC2 http://dmd.aspetjournals.org/content/suppl/2017/06/12/dmd.117.076463.DC1 1521-009X/45/9/1044–1048$25.00 https://doi.org/10.1124/dmd.117.076463 DRUG METABOLISM AND DISPOSITION Drug Metab Dispos 45:1044–1048, September 2017 Copyright ª 2017 by The American Society for Pharmacology and Experimental Therapeutics Age-dependent Protein Abundance of Cytosolic Alcohol and Aldehyde Dehydrogenases in Human Liver s Deepak Kumar Bhatt, Andrea Gaedigk, Robin E. Pearce, J. Steven Leeder, and Bhagwat Prasad Department of Pharmaceutics, University of Washington, Seattle, Washington (D.K.B., B.P.); Department of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children’s Mercy-Kansas City, Missouri and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri (A.G., R.E.P., J.S.L.) Received April 21, 2017; accepted June 5, 2017 ABSTRACT Hepatic cytosolic alcohol and aldehyde dehydrogenases (ADHs and the adult levels, respectively. For all proteins, the abundance steeply ALDHs) catalyze the biotransformation of xenobiotics (e.g., cyclo- increased during the first year of life, which mostly reached adult Downloaded from phosphamide and ethanol) and vitamin A. Because age-dependent levels during early childhood (age between 1 and 6 years). Only for hepatic abundance of these proteins is unknown, we quantified ADH1A protein abundance in adults (age > 18 year) was ∼40% lower protein expression of ADHs and ALDH1A1 in a large cohort of pediatric relative to the early childhood group. Abundances of ADHs and and adult human livers by liquid chromatography coupled with tandem ALDH1A1 were not associated with sex in samples with age > 1 year mass spectrometry proteomics.
    [Show full text]
  • ACSL6 (C) Antibody, Rabbit Polyclonal
    Order: (888)-282-5810 (Phone) (818)-707-0392 (Fax) [email protected] Web: www.Abiocode.com ACSL6 (C) Antibody, Rabbit Polyclonal Cat#: R2712-2 Lot#: Refer to vial Quantity: 100 ul Application: WB Predicted I Observed M.W.: 78 kDa Uniprot ID: Q9UKU0 Background: Activation of long-chain fatty acids for both synthesis of cellular lipids, and degradation via beta- oxidation. ACSL6 plays an important role in fatty acid metabolism in brain and the acyl-CoAs produced may be utilized exclusively for the synthesis of the brain lipid. Translocations with the ETV6 gene are causes of myelodysplastic syndrome with basophilia, acute myelogenous leukemia with eosinophilia, and acute eosinophilic leukemia. Other Names: Long-chain-fatty-acid--CoA ligase 6, Long-chain acyl-CoA synthetase 6, LACS 6, ACS2, FACL6, KIAA0837, LACS5 Source and Purity: Rabbit polyclonal antibodies were produced by immunizing animals with a GST-fusion protein containing C-terminal region of human ACSL6. Antibodies were purified by affinity purification using immunogen. Storage Buffer and Condition: Supplied in 1 x PBS (pH 7.4), 100 ug/ml BSA, 40% Glycerol, 0.01% NaN3. Store at -20 °C. Stable for 6 months from date of receipt. Species Specificity: Human, Mouse Tested Applications: WB: 1:1,000-1:3,000 (detect endogenous protein*) *: The apparent protein size on WB may be different from the calculated M.W. due to modifications. For research use only. Not for therapeutic or diagnostic purposes. Abiocode, Inc., 29397 Agoura Rd., Ste 106, Agoura Hills, CA 91301 Order: (888)-282-5810 (Phone) (818)-707-0392 (Fax) [email protected] Web: www.Abiocode.com Product Data: kDa A B C 175 80 58 46 Fig 1.
    [Show full text]
  • Chuanxiong Rhizoma Compound on HIF-VEGF Pathway and Cerebral Ischemia-Reperfusion Injury’S Biological Network Based on Systematic Pharmacology
    ORIGINAL RESEARCH published: 25 June 2021 doi: 10.3389/fphar.2021.601846 Exploring the Regulatory Mechanism of Hedysarum Multijugum Maxim.-Chuanxiong Rhizoma Compound on HIF-VEGF Pathway and Cerebral Ischemia-Reperfusion Injury’s Biological Network Based on Systematic Pharmacology Kailin Yang 1†, Liuting Zeng 1†, Anqi Ge 2†, Yi Chen 1†, Shanshan Wang 1†, Xiaofei Zhu 1,3† and Jinwen Ge 1,4* Edited by: 1 Takashi Sato, Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of 2 Tokyo University of Pharmacy and Life Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China, Galactophore Department, The First 3 Sciences, Japan Hospital of Hunan University of Chinese Medicine, Changsha, China, School of Graduate, Central South University, Changsha, China, 4Shaoyang University, Shaoyang, China Reviewed by: Hui Zhao, Capital Medical University, China Background: Clinical research found that Hedysarum Multijugum Maxim.-Chuanxiong Maria Luisa Del Moral, fi University of Jaén, Spain Rhizoma Compound (HCC) has de nite curative effect on cerebral ischemic diseases, *Correspondence: such as ischemic stroke and cerebral ischemia-reperfusion injury (CIR). However, its Jinwen Ge mechanism for treating cerebral ischemia is still not fully explained. [email protected] †These authors share first authorship Methods: The traditional Chinese medicine related database were utilized to obtain the components of HCC. The Pharmmapper were used to predict HCC’s potential targets. Specialty section: The CIR genes were obtained from Genecards and OMIM and the protein-protein This article was submitted to interaction (PPI) data of HCC’s targets and IS genes were obtained from String Ethnopharmacology, a section of the journal database.
    [Show full text]
  • Gene and Pathway-Based Second-Wave Analysis of Genome-Wide Association Studies
    European Journal of Human Genetics (2010) 18, 111–117 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 $32.00 www.nature.com/ejhg ARTICLE Gene and pathway-based second-wave analysis of genome-wide association studies Gang Peng1, Li Luo2, Hoicheong Siu1, Yun Zhu1, Pengfei Hu1, Shengjun Hong1, Jinying Zhao3, Xiaodong Zhou4, John D Reveille4, Li Jin1, Christopher I Amos5 and Momiao Xiong*,2 Despite the great success of genome-wide association studies (GWAS) in identification of the common genetic variants associated with complex diseases, the current GWAS have focused on single-SNP analysis. However, single-SNP analysis often identifies only a few of the most significant SNPs that account for a small proportion of the genetic variants and offers only a limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis of 13 published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single-SNP analysis, but also detected new genes in which each single SNP conferred a small disease risk; however, their joint actions were implicated in the development of diseases. The results also showed that the new paradigm for GWAS was able to identify biologically meaningful pathways associated with the diseases, which were confirmed by a gene-set-rich analysis using gene expression
    [Show full text]
  • Variation in Protein Coding Genes Identifies Information
    bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 1 1 2 3 4 5 Variation in protein coding genes identifies information flow as a contributor to 6 animal complexity 7 8 Jack Dean, Daniela Lopes Cardoso and Colin Sharpe* 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 Institute of Biological and Biomedical Sciences 25 School of Biological Science 26 University of Portsmouth, 27 Portsmouth, UK 28 PO16 7YH 29 30 * Author for correspondence 31 [email protected] 32 33 Orcid numbers: 34 DLC: 0000-0003-2683-1745 35 CS: 0000-0002-5022-0840 36 37 38 39 40 41 42 43 44 45 46 47 48 49 Abstract bioRxiv preprint doi: https://doi.org/10.1101/679456; this version posted June 21, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Animal complexity and information flow 2 1 Across the metazoans there is a trend towards greater organismal complexity. How 2 complexity is generated, however, is uncertain. Since C.elegans and humans have 3 approximately the same number of genes, the explanation will depend on how genes are 4 used, rather than their absolute number.
    [Show full text]