DOCSLIB.ORG

Lactate Dehydrogenase – Wikipedia

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Lactate Dehydrogenase – Wikipedia 8/13/2021 Lactate dehydrogenase - Wikipedia Lactate dehydrogenase Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells. LDH catalyzes the conversion of lactate to pyruvate and Lactate dehydrogenase back, as it converts NAD+ to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another. LDH exists in four distinct enzyme classes. This article is specifically about the NAD(P)-dependent L-lactate dehydrogenase. Other LDHs act on D-lactate and/or are dependent on cytochrome c: D-lactate dehydrogenase (cytochrome) and L-lactate dehydrogenase (cytochrome). LDH is expressed extensively in body tissues, such as blood cells and heart muscle. Because it is released during tissue damage, it is a marker of common injuries and disease such as heart failure. Lactate dehydrogenase M tetramer (LDH5), Human Identifiers Contents EC no. 1.1.1.27 (https://www.qmul.ac. Reaction uk/sbcs/iubmb/enzyme/EC1/1/ Active site 1/27.html) Isozymes CAS no. 9001-60-9 (http://www.commo nchemistry.org/ChemicalDetai Protein families l.aspx?ref=9001-60-9&title=) Interactive pathway map Databases Enzyme regulation IntEnz view (https://www.ebi.a Ethanol-induced hypoglycemia IntEnz c.uk/intenz/query?cmd=Searc Substrate regulation hEC&ec=1.1.1.27) Transcriptional regulation BRENDA BRENDA entry (http://www.br Genetics enda-enzymes.org/enzyme.ph Mutations p?ecno=1.1.1.27) Role in muscular fatigue ExPASy NiceZyme view (https://enzym Blood test e.expasy.org/EC/1.1.1.27) Testing in cancer KEGG KEGG entry (https://www.gen Hemolysis ome.jp/dbget-bin/www_bget?e Tissue turnover nzyme+1.1.1.27) HIV MetaCyc metabolic pathway (https://bio Testing in other body fluids cyc.org/META/substring-searc Exudates and transudates h?type=NIL&object=1.1.1.27) Meningitis and encephalitis PRIAM profile (http://priam.prabi.fr/cgi In cancer treatment -bin/PRIAM_profiles_CurrentR Prokaryotes elease.pl?EC=1.1.1.27) See also PDB RCSB PDB (https://www.rcsb. structures org/search?q=rcsb_polymer_e References ntity.rcsb_ec_lineage.id:1.1.1. Further reading 27) PDBe (https://www.ebi.ac. https://en.wikipedia.org/wiki/Lactate_dehydrogenase 1/14 8/13/2021 Lactate dehydrogenase - Wikipedia External links uk/pdbe/entry/search/index?e c_number:1.1.1.27) PDBsum (https://www.ebi.ac.uk/thornto Reaction n-srv/databases/cgi-bin/enzym es/GetPage.pl?ec_number=1. Lactate dehydrogenase catalyzes the interconversion of pyruvate and 1.1.27) lactate with concomitant interconversion of NADH and NAD+. It Gene AmiGO (http://amigo.geneonto converts pyruvate, the final product of glycolysis, to lactate when oxygen is absent or in short supply, and it performs the reverse Ontology logy.org/amigo/term/GO:0004 reaction during the Cori cycle in the liver. At high concentrations of 459) / QuickGO (https://www.e lactate, the enzyme exhibits feedback inhibition, and the rate of bi.ac.uk/QuickGO/term/GO:00 conversion of pyruvate to lactate is decreased. It also catalyzes the 04459) dehydrogenation of 2-hydroxybutyrate, but this is a much poorer Search substrate than lactate. PMC articles (https://www.ncbi.nlm. nih.gov/entrez/query.fcgi?db=p Active site ubmed&term=1.1.1.27%5BE C/RN%20Number%5D%20AN LDH in humans uses His(193) as the proton acceptor, and works in D%20pubmed%20pmc%20loc unison with the coenzyme (Arg99 and Asn138), and substrate (Arg106; al%5Bsb%5D) Arg169; Thr248) binding residues.[1][2] The His(193) active site, is not PubMed articles (https://www.ncbi.nlm. only found in the human form of LDH, but is found in many different nih.gov/entrez/query.fcgi?db=p animals, showing the convergent evolution of LDH. The two different ubmed&term=1.1.1.27%5BE subunits of LDH (LDHA, also known as the M subunit of LDH, and C/RN%20Number%5D) LDHB, also known as the H subunit of LDH) both retain the same NCBI proteins (https://www.ncbi.nlm. active site and the same amino acids participating in the reaction. The nih.gov/protein?term=1.1.1.2 noticeable difference between the two subunits that make up LDH's 7%5BEC/RN%20Number%5 tertiary structure is the replacement of alanine (in the M chain) with a D) glutamine (in the H chain). This tiny but notable change is believed to be the reason the H subunit can bind NAD faster, and the M subunit's catalytic activity isn't reduced in the presence of acetylpyridine adenine dinucleotide, whereas the H subunit's activity is reduced fivefold.[3] Isozymes Reaction catalyzed by lactate dehydrogenase Lactate dehydrogenase is composed of four subunits (tetramer). The two most common subunits are the LDH-M and LDH-H protein, encoded by the LDHA and LDHB genes, respectively. These two subunits can form five possible tetramers (isoenzymes): 4H, 4M, and the three mixed tetramers (3H1M, 2H2M, 1H3M). These five isoforms are enzymatically similar but show different tissue distribution: The major isoenzymes of skeletal muscle and liver, M4, has four muscle (M) subunits, while H4 is the main isoenzymes for heart muscle in most species, containing four heart (H) subunits. LDH-1 (4H)—in the heart and in RBC (red blood cells), as well as the brain[4] Arrow pushing mechanism for the reaction catalyzed by lactate LDH-2 (3H1M)—in the reticuloendothelial dehydrogenase system LDH-3 (2H2M)—in the lungs LDH-4 (1H3M)—in the kidneys, placenta, and pancreas https://en.wikipedia.org/wiki/Lactate_dehydrogenase 2/14 8/13/2021 Lactate dehydrogenase - Wikipedia LDH-5 (4M)—in the liver and striated muscle,[5] also present in the brain[4] LDH-2 is usually the predominant form in the serum. An LDH-1 level higher than the LDH-2 level (a "flipped pattern") suggests myocardial infarction (damage to heart tissues releases heart LDH, which is rich in LDH-1, into the bloodstream). The use of this phenomenon to diagnose infarction has been largely superseded by the use of Troponin I or T measurement. There are two more mammalian LDH subunits that can be included in LDH tetramers: LDHC and LDHBx. LDHC is a testes-specific LDH protein, that is encoded by the LDHC gene. LDHBx is a peroxisome-specific LDH protein. LDHBx is the readthrough-form of LDHB. LDHBx is generated by translation of the LDHB mRNA, but the stop codon is interpreted as an amino acid-encoding codon. In consequence, translation continues to the next stop codon. This leads to the addition of seven amino acid residues to the normal LDH-H protein. The extension contains a peroxisomal targeting signal, so that LDHBx is imported into the peroxisome.[6] lactate dehydrogenase A lactate dehydrogenase B lactate dehydrogenase C (subunit M) (subunit H) Crystal structure of Mouse Testicular Crystal structure of B-lactate Lactate dehydrogenase (C4). From dehydrogenase. From PDB: 1T2F (htt PDB: 2LDX (https://www.rcsb.org/stru Human lactate dehydrogenase M4 (the isoenzyme found in skeletal ps://www.rcsb.org/structure/1T2F). cture/2LDX) . muscle). From PDB: 1I10 (https://ww Identifiers Identifiers w.rcsb.org/structure/1I10) . Symbol LDHB Symbol LDHC Identifiers Alt. LDHL NCBI 3948 (https://www.ncbi.nlm. Symbol LDHA symbols gene nih.gov/gene?cmd=retrieve Alt. LDHM NCBI 3945 (https://www.ncbi.nl &dopt=default&list_uids=39 symbols gene m.nih.gov/gene?cmd=retrie 48&rn=1) NCBI 3939 (https://www.ncbi.nl ve&dopt=default&list_uids= HGNC 6544 (https://www.genenam gene m.nih.gov/gene?cmd=retrie 3945&rn=1) es.org/data/gene-symbol-re ve&dopt=default&list_uids= HGNC 6541 (https://www.genena port/#!/hgnc_id/HGNC:654 3939&rn=1) mes.org/data/gene-symbol- 4) HGNC 6535 (https://www.genena report/#!/hgnc_id/HGNC:65 OMIM 150150 (https://omim.org/15 mes.org/data/gene-symbol- 41) 0150) report/#!/hgnc_id/HGNC:65 OMIM 150100 (https://omim.org/1 RefSeq NM_002301 (https://genom 35) 50100) e.ucsc.edu/cgi-bin/hgTrack OMIM 150000 (https://omim.org/1 RefSeq NM_002300 (https://genom s?Submit=Submit&position= 50000) e.ucsc.edu/cgi-bin/hgTrack NM_002301&rn=1) RefSeq NM_005566 (https://genom s?Submit=Submit&position UniProt P07864 (https://www.unipro e.ucsc.edu/cgi-bin/hgTrack =NM_002300&rn=1) t.org/uniprot/P07864) s?Submit=Submit&position UniProt P07195 (https://www.unipr Other data =NM_005566&rn=1) ot.org/uniprot/P07195) EC 1.1.1.27 (https://www.geno UniProt P00338 (https://www.unipr Other data number me.jp/dbget-bin/www_bget? ot.org/uniprot/P00338) EC 1.1.1.27 (https://www.geno enzyme+1.1.1.27) https://en.wikipedia.org/wiki/Lactate_dehydrogenase 3/14 8/13/2021 Lactate dehydrogenase - Wikipedia Other data number me.jp/dbget-bin/www_bge Locus Chr. 11 p15.5–15.3 (https://o EC 1.1.1.27 (https://www.geno t?enzyme+1.1.1.27) mim.org/search/?index=gen number me.jp/dbget-bin/www_bge Locus Chr. 12 p12.2–12.1 (https:// eMap&search=11p15.5–15. t?enzyme+1.1.1.27) omim.org/search/?index=g 3) Locus Chr. 11 p15.4 (https://omi eneMap&search=12p12.2– Search for m.org/search/?index=gene 12.1) Structures Swiss-model (https://swissm Map&search=11p15.4) Search for odel.expasy.org/repository/u niprot/P07864) Search for Structures Swiss-model (https://swissm odel.expasy.org/repository/u Domains InterPro (https://www.ebi.ac. Structures Swiss-model (https://swissm niprot/P07195) uk/interpro/protein/P07864) odel.expasy.org/repository/u niprot/P00338) Domains InterPro (https://www.ebi.ac. uk/interpro/protein/P07195) Domains InterPro (https://www.ebi.ac. uk/interpro/protein/P00338) Protein families D-lactate dehydrogenase, lactate/malate lactate/malate membrane binding dehydrogenase, NAD dehydrogenase, alpha/beta binding domain C-terminal domain Identifiers Identifiers Symbol Ldh_1_N Symbol Ldh_1_C Pfam PF00056 (http://pfam.xfam.
Load more

Recommended publications
  • PIR Brochure
    Protein Information Resource Integrated Protein Informatics Resource for Genomic & Proteomic Research For four decades the Protein Information Resource (PIR) has provided databases and protein sequence analysis tools to the scientific community, including the Protein Sequence Database, which grew out from the Atlas of Protein Sequence and Structure, edited by Margaret Dayhoff [1965-1978]. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PIRSF protein pir.georgetown.edu classification, and iv) iProLINK protein literature mining and ontology development. UniProt – Universal Protein Resource What is UniProt? UniProt is the central resource for storing and UniProt (Universal Protein Resource) http://www.uniprot.org interconnecting information from large and = + + disparate sources and the most UniProt: the world's most comprehensive catalog of information on proteins comprehensive catalog of protein sequence and functional annotation. UniProt Knowledgebase UniProt Reference UniProt Archive (UniProtKB) Clusters (UniRef) (UniParc) When to use UniProt databases Integration of Swiss-Prot, TrEMBL Non-redundant reference A stable, and PIR-PSD sequences clustered from comprehensive Use UniProtKB to retrieve curated, reliable, Fully classified, richly and accurately UniProtKB and UniParc for archive of all publicly annotated protein sequences with comprehensive or fast available protein comprehensive information on proteins. minimal redundancy and extensive sequence searches at 100%, sequences for Use UniRef to decrease redundancy and cross-references 90%, or 50% identity sequence tracking from: speed up sequence similarity searches. TrEMBL section UniRef100 Swiss-Prot, Computer-annotated protein sequences TrEMBL, PIR-PSD, Use UniParc to access to archived sequences EMBL, Ensembl, IPI, and their source databases.
    [Show full text]
  • Cdna Cloning, Expression and Homology Modeling of a Luciferase from the Firefly Lampyroidea Maculata
    Journal of Biochemistry and Molecular Biology, Vol. 39, No. 5, September 2006, pp. 578-585 cDNA Cloning, Expression and Homology Modeling of a Luciferase from the Firefly Lampyroidea maculata Abdo Rahman Emamzadeh1, Saman Hosseinkhani1,*, Majid Sadeghizadeh2, Maryam Nikkhah3, Mohammad Javad Chaichi4 and Mojtaba Mortazavi1 1Department of Biochemistry, Faculty of Basic Sciences, Tarbiat Modarres University, Tehran, Iran 2Department of Genetics, Faculty of Basic Sciences, Tarbiat Modarres University, Tehran, Iran 3Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran 4Department of Chemistry, Mazandaran University, Babolsar, Iran Received 7 April 2006, Accepted 23 May 2006 The cDNA of a firefly luciferase from lantern mRNA of Introduction Lampyroidea maculata has been cloned, sequenced and functionally expressed. The cDNA has an open reading Firefly luciferase (EC 1.13.12.7) is a well-characterized enzyme frame of 1647 bp and codes for a 548-residue-long that is responsible for the bioluminescence reaction. It polypeptide. Noteworthy, sequence comparison as well as catalyzes the oxidation of firefly luciferin with molecular homology modeling showed the highest degree of similarity oxygen in the presence of ATP and Mg2+ to emit yellow-green with H. unmunsana and L. mingrelica luciferases, light (McElroy, 1969; White et al., 1971; DeLuca, 1976; suggesting a close phylogenetic relationship despite the Wood, 1995). The initial reaction catalyzed by firefly geographical distance separation. The deduced amino acid luciferase is the formation of luciferyl adenylate with the sequence of the luciferase gene of firefly L. maculata release of inorganic pyrophosphate. The luciferase-bound showed 93% identity to H. unmunsana. Superposition of luciferyl adenylate reacts rapidly with molecular oxygen to the three-dimensional model of L.
    [Show full text]
  • Letters to Nature
    letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997).
    [Show full text]
  • The Interpro Database, an Integrated Documentation Resource for Protein
    The InterPro database, an integrated documentation resource for protein families, domains and functional sites R Apweiler, T K Attwood, A Bairoch, A Bateman, E Birney, M Biswas, P Bucher, L Cerutti, F Corpet, M D Croning, et al. To cite this version: R Apweiler, T K Attwood, A Bairoch, A Bateman, E Birney, et al.. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research, Oxford University Press, 2001, 29 (1), pp.37-40. 10.1093/nar/29.1.37. hal-01213150 HAL Id: hal-01213150 https://hal.archives-ouvertes.fr/hal-01213150 Submitted on 7 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. © 2001 Oxford University Press Nucleic Acids Research, 2001, Vol. 29, No. 1 37–40 The InterPro database, an integrated documentation resource for protein families, domains and functional sites R. Apweiler1,*, T. K. Attwood2,A.Bairoch3, A. Bateman4,E.Birney1, M. Biswas1, P. Bucher5, L. Cerutti4,F.Corpet6, M. D. R. Croning1,2, R. Durbin4,L.Falquet5,W.Fleischmann1, J. Gouzy6,H.Hermjakob1,N.Hulo3, I. Jonassen7,D.Kahn6,A.Kanapin1, Y. Karavidopoulou1, R.
    [Show full text]
  • Bioinformatics Analysis and Characterization of a Secretory Cystatin from Thelohanellus Kitauei
    Bioinformatics analysis and characterization of a secretory cystatin from Thelohanellus kitauei Fengli Zhang Chinese Academy of Agricultural Sciences Feed Research Institute Yalin Yang Chinese Academy of Agricultural Sciences Feed Research Institute Chenchen Gao Chinese Academy of Agricultural Sciences Feed Research Institute Yuanyuan Yao Chinese Academy of Agricultural Sciences Feed Research Institute Rui Xia Chinese Academy of Agricultural Sciences Feed Research Institute Juan Hu Chinese Academy of Agricultural Sciences Feed Research Institute Chao Ran Chinese Academy of Agricultural Sciences Feed Research Institute Zhen Zhang Chinese Academy of Agricultural Sciences Feed Research Institute Zhigang Zhou ( [email protected] ) Chinese Academy of Agricultural Sciences Feed Research Institute Original article Keywords: TK-cystatin, Thelohanellus kitauei, Bioinformatics analysis, Protease inhibitor, Inhibitory activity, Molecular docking Posted Date: June 15th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-26747/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on June 23rd, 2020. See the published version at https://doi.org/10.1186/s13568-020-01052-0. Page 1/20 Abstract Thelohanellus kitauei , is a group of obligate parasitic Myxozoans, which causes intestinal giant-cystic disease of common carp ( Cyprinus carpio) and has resulted in signicant economic losses in carp farms. Cystatin secreted by parasites can regulate the immune response of host to facilitate parasite’s survival. In this study, the secretory TK-cystatin gene, encoding a protein of 120 amino acid residues (13.65 kDa), was cloned from T. kitauei genome. Phylogenetic analysis showed that TK-cystatin gene is closely related to the cystatin-A from Hydra vulgaris .
    [Show full text]
  • Data Resources and Tools
    6/22/2012 Introductory Bioinformatic Techniques 2012 Wits Bioinformatics Shaun Aron Sequence Structure Function Introductory Bioinformatics 2012 - Shaun Aron Introductory Bioinformatics 2012 - Shaun Aron A variety of protein resources online Evolutionary relationships between proteins Several websites/portals dedicated to Detection of local similarities between providing a single interface to multiple proteins to detect functional domains resources Functional predictions Important to differentiate between Protein structural predictions databases, websites and portals Protein-Protein interactions Protein-Nucleotide interactions Protein engineering and design Introductory Bioinformatics 2012 - Shaun Aron Introductory Bioinformatics 2012 - Shaun Aron Domain identification Protein classification Multiple domains in eukaryotic proteins . Families Sequence based methods Domain Prediction Structure based methods . Sequence based . SCOP . Structure based . CATH Introductory Bioinformatics 2012 - Shaun Aron Introductory Bioinformatics 2012 - Shaun Aron 1 6/22/2012 Experimental determination of structures . X-ray crystallography (requires crystallisation of protein) Sequence and information databases . NMR (for smaller proteins) . NCBI Entrez Protein Database – contains protein . EM (For large complex structures) Structural comparisons sequences from GenBank, RefSeq , as well as Protein folding records from SwissProt, PIR, PRF, and PDB . Folding simulations . UniProtKB – the “Protein knowledgebase”, a Structure prediction comprehensive
    [Show full text]
  • Mouse Ldhb Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Ldhb Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Ldhb conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ldhb gene (NCBI Reference Sequence: NM_008492 ; Ensembl: ENSMUSG00000030246 ) is located on Mouse chromosome 6. 8 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 8 (Transcript: ENSMUST00000032373). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Ldhb gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-134H20 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Electrophoretic variants of LDHB are determined by: the a allele with fast anodal mobility in all inbred strains tested; and the b allele with slower mobility in Peru-Coppock stock. Three additional variants are known in wild M. spretus from southern France and Spain. Alleles are codominant. Exon 3 starts from about 12.97% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 3954 bp, and the size of intron 3 for 3'-loxP site insertion: 2661 bp. The size of effective cKO region: ~1353 bp. The transcript Ldhb-202 may not be affected by deleting this cKO region.
    [Show full text]
  • Predicting Protein Structure and Function with Interpro
    Predicting protein structure and function with InterPro Phil Jones, Alex Mitchell, Amaia Sangrador (V4.0, Jun 2011) www.ebi.ac.uk Contents Course Information ........................................................................................... 3 Course learning objectives ............................................................................... 3 An introduction to InterPro ............................................................................... 4 I. Searching InterPro using a text search ........................................................ 7 Learning objectives ............................................................................................. 7 What information can be found in the InterPro entry page? ................................. 8 How do I interpret an InterPro protein view? ........................................................ 9 Summary ........................................................................................................... 11 Exercises .......................................................................................................... 11 Exercise 1 – Searching InterPro using a UniPro identifier ........................... 11 Exercise 2 – Exploring InterPro entries: General annotation ....................... 12 Exercise 3 – Exploring InterPro entries: Relationships ................................ 13 Exercise 4 – Exploring InterPro entries: Structure ....................................... 14 II. InterPro Scan ..............................................................................................
    [Show full text]
  • Introduction to Bioinformatics
    INTRODUCTION TO BIOINFORMATICS > Please take the initial BIOINF525 questionnaire: < http://tinyurl.com/bioinf525-questions Barry Grant University of Michigan www.thegrantlab.org BIOINF 525 http://bioboot.github.io/bioinf525_w16/ 12-Jan-2016 Barry Grant, Ph.D. [email protected] Ryan Mills, Ph.D. [email protected] Hongyang Li (GSI) [email protected] COURSE LOGISTICS Lectures: Tuesdays 2:30-4:00 PM Rm. 2062 Palmer Commons Labs: Session I: Thursdays 2:30 - 4:00 PM Session II: Fridays 10:30 - 12:00 PM Rm. 2036 Palmer Commons Website: http://tinyurl.com/bioinf525-w16 Lecture, lab and background reading material plus homework and course announcements MODULE OVERVIEW Objective: Provide an introduction to the practice of bioinformatics as well as a practical guide to using common bioinformatics databases and algorithms 1.1. ‣ Introduction to Bioinformatics 1.2. ‣ Sequence Alignment and Database Searching 1.3 ‣ Structural Bioinformatics 1.4 ‣ Genome Informatics: High Throughput Sequencing Applications and Analytical Methods TODAYS MENU Overview of bioinformatics • The what, why and how of bioinformatics? • Major bioinformatics research areas. • Skepticism and common problems with bioinformatics. Bioinformatics databases and associated tools • Primary, secondary and composite databases. • Nucleotide sequence databases (GenBank & RefSeq). • Protein sequence database (UniProt). • Composite databases (PFAM & OMIM). Database usage vignette • Searching with ENTREZ and BLAST. • Reference slides and handout on major databases. HOMEWORK Complete the initial
    [Show full text]
  • Cloning and Sequence Analysis of Glyceraldehyde-3-Phosphate Dehydrogenase Gene in Yak*
    1673 Asian-Aust. J. Anim. Sci. Vol. 21, No. 11 : 1673 - 1679 November 2008 www.ajas.info Cloning and Sequence Analysis of Glyceraldehyde-3-Phosphate Dehydrogenase Gene in *Yak Sheng-wei Li, Ming-feng Jiang**, Yong-tao Liu, Tu-feng Yang, Yong Wang and Jin-cheng Zhong College of Life Sciences and Technology, Southwest University for Nationalities, ChengDu, 610041, China ABSTRACT :In order to study the biological function of gapdh gene in yak, and prove whether the gapdh gene was a useful intra­ reference gene that can be given an important role in molecular biology research of yak, the cDNA sequence encoding glyceraldehyde- 3-phosphate dehydrogenase from yak was cloned by the RT-PCR method using gene specific PCR primers. The sequence results indicated that the cloned cDNA fragment (1,008 bp) contained a 1,002 bp open reading frame, encoding 333 amino acids (AAs) with a molecular mass of 35.753 kDa. The deduced amino acids sequence showed a high level of sequence identity to Bos Taurus (99.70%), Xenopus laevis (94.29%), Homo sapiens (97.01%), Mus musculus (97.90%) and Sus scrofa (98.20%). The expression of yak’s gapdh gene in heart, spleen, kidney and brain tissues was also detected; the results showed that the gapdh gene was expressed in all these tissues. Further analysis of yak GAPDH amino acid sequence implied that it contained a complete glyceraldehyde-3-phosphate dehydrogenase active site (ASCTTNCL) which ranged from 148 to 155 amino acid residues. It also contained two conserved domains, a NAD binding domain in its N-terminal and a complete catalytic domain of sugar transport in its C-terminal.
    [Show full text]
  • The Genome Sequence of the Facultative Intracellular Pathogen Brucella Melitensis
    The genome sequence of the facultative intracellular pathogen Brucella melitensis Vito G. DelVecchio*†, Vinayak Kapatral‡, Rajendra J. Redkar*, Guy Patra*, Cesar Mujer*, Tamara Los‡, Natalia Ivanova‡, Iain Anderson‡, Anamitra Bhattacharyya‡, Athanasios Lykidis‡, Gary Reznik‡, Lynn Jablonski‡, Niels Larsen‡, Mark D’Souza‡, Axel Bernal‡, Mikhail Mazur‡, Eugene Goltsman‡, Eugene Selkov‡, Philip H. Elzer§, Sue Hagius§, David O’Callaghan¶, Jean-Jacques Letessonʈ, Robert Haselkorn‡, Nikos Kyrpides‡, and Ross Overbeek‡ *Institute of Molecular Biology and Medicine, University of Scranton, Scranton, PA 18510; ‡Integrated Genomics, Incorporated, 2201 West Campbell Park Drive, Chicago, IL 60612; §Department of Veterinary Science, Louisiana State University Ag Center, 111 Dalrymple Building, Baton Rouge, LA 70803; ¶Institut National de la Sante´et de la Recherche Me´dicale, U431, Faculte´deMe´ decine, Avenue Kennedy, 30900 Nıˆmes,France; and ʈUnite´de Recherche en Biologie Mole´culaire, Laboratoire d’Immunologie et de Microbiologie, Universite´of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium Contributed by Robert Haselkorn, October 29, 2001 Brucella melitensis is a facultative intracellular bacterial pathogen Brucella melitensis (15–17). However, each biovar exhibits a pref- that causes abortion in goats and sheep and Malta fever in humans. erence for specific hosts: B. melitensis infects goats and sheep, The genome of B. melitensis strain 16M was sequenced and found Brucella abortus causes abortion in cattle, and Brucella suis infects to contain 3,294,935 bp distributed over two circular chromosomes swine. Brucella canis, Brucella ovis, and Brucella neotomae are of 2,117,144 bp and 1,177,787 bp encoding 3,197 ORFs. By using the pathogenic to dogs, sheep, and desert wood rats, respectively.
    [Show full text]
  • Mouse Ldhc Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Ldhc Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Ldhc conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ldhc gene (NCBI Reference Sequence: NM_013580 ; Ensembl: ENSMUSG00000030851 ) is located on Mouse chromosome 7. 8 exons are identified, with the ATG start codon in exon 2 and the TAA stop codon in exon 8 (Transcript: ENSMUST00000014545). Exon 3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Ldhc gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP24-169L3 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Homozygous male mice are infertile. Spermatogenesis appears normal, but sperm motility decreases rapidly after their release from the epididymus. In vitro fertilization is blocked unless the zona pellucida is removed; even then, the rate of sperm penetration is lower than for wild-type sperm. Exon 3 starts from about 12.75% of the coding region. The knockout of Exon 3 will result in frameshift of the gene. The size of intron 2 for 5'-loxP site insertion: 4513 bp, and the size of intron 3 for 3'-loxP site insertion: 3072 bp. The size of effective cKO region: ~618 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 3 8 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Ldhc Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]