Recent Changes

Wednesday, November 8

  1. page Undergraduate Research Opportunities edited ... http://www.cur.org/resources/students/undergraduate_journals/ CONFERENCES: Undergraduate Re…
    ...
    http://www.cur.org/resources/students/undergraduate_journals/
    CONFERENCES:
    Undergraduate Research Forum (UT-Austin)
    2018, April 13th
    American Society for Biochemistry and Molecular Biology (ASBMB)
    https://www.asbmb.org/
    2017 - Chicago
    2018 - San Diego - April 22-25th

    The Protein Society (Summer)
    http://www.proteinsociety.org/meetings/symposium/
    Texas Academy of Science
    http://www.texasacademyofscience.org/about-us
    Midland College, March 2-4, 2018
    Texas
    Tech Undergraduate
    ...
    Lubbock, Texas) - March 27, 28th
    http://www.depts.ttu.edu/calue/ConferenceHome/
    ABRCMS (Fall)
    ...
    CNS Student Research Fellowships page:
    http://cns.utexas.edu/honors/scholarships-fellowships/current-students/research-fellowships
    Texas Academy of Science
    http://www.texasacademyofscience.org/about-us

    SACNAS
    (Society for Advancement of Chicanos/Hispanics and Native Americans in Science.)
    (view changes)
    6:18 pm

Tuesday, November 7

  1. page D-alanine ligase (Yersinia pestis) edited ... Current Inhibitors: http://vdsstream.wikispaces.com/file/view/KovacDalanineDalanineLigaseVir…
    ...
    Current Inhibitors:
    http://vdsstream.wikispaces.com/file/view/KovacDalanineDalanineLigaseVirtualScreenJMedChem2008.pdf/261437724/KovacDalanineDalanineLigaseVirtualScreenJMedChem2008.pdf
    ...
    in E. colicoli.
    Purification Method: Ni-NTA
    Image of Protein:
    (view changes)
    10:47 am
  2. page D-alanine ligase (Yersinia pestis) edited ... Is it a monomer or multimer as biological unit? Multimer Complex of Proteins? D-alanine D-ala…
    ...
    Is it a monomer or multimer as biological unit? Multimer
    Complex of Proteins? D-alanine D-alanine ligase consists of three domains, in which four loops, loop 1, loop 2, loop 3 and loop 4, constitute the binding sites for two D-alanine molecules and one ATP molecule.
    ...
    another organism):
    Mycobacterium Tuberculosis
    https://www.ncbi.nlm.nih.gov/pubmed/23286234
    EC#: 6.3.2.4
    Link to BRENDA EC# page: https://www.brenda-enzymes.org/enzyme.php?ecno=6.3.2.4&Suchword=&reference=&UniProtAcc=&organism%5B%5D=Yersinia+pestis&show_tm=0
    (view changes)
    10:46 am

Tuesday, October 31

  1. page TargetSp17- PP2C- family Ser Thr Phosphatase (Mycobacterium tuberculosis) edited ... -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure h…
    ...
    -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
    Primer design results for 'tail' primers (this is just 2 sequences):
    Forward Primer:
    TACTTCCAATCCATGACCCTCGTTCTGCGTTATGC
    Reverse Primer:
    TATCCACCTTTACTGTTAGTGTTCGAGGTCCGCAA

    **
    (view changes)
    6:24 pm
  2. page Target - Protein Tyrosine Phosphatase (Listeria monocytogenes) edited Target (protein/gene (protein / gene name): Protein Protein Tyrosine Phosphatase - lmo1800…

    Target (protein/gene(protein / gene name): ProteinProtein Tyrosine Phosphatase - lmo1800
    *NCBI

    * NCBI
    Gene # or RefSeq#: Project:61583, NC_003210.1,RefSeq #: Project: 61583 , NC_003210.1, Gene ID: 985934
    *Protein

    * Protein
    ID (NP
    ...
    #) or Wolbachia#:Wolbachia #: NP_465325.1 (use
    ...
    B 090313)
    *Organism:

    * Organism:
    Listeria monocytogenes
    Etiologic

    Etiologic
    Risk Group
    ...
    below): Risk groupGroup 2 -
    ...
    including Chlaymidia
    *Background/Disease

    * Background / Disease
    Information: The most deadlyMost Deadly Born food born pathogen. Induces
    ...
    cytosol bacteria maycan reproduce.
    http://www.ncbi.nlm.nih.gov/pubmed/21444667
    ...
    enzymes: No
    *EC#:

    * EC #:
    3.1.3.48
    Link

    Link
    to BRENDA EC#EC # page: http://brenda-enzymes.org/php/result_flat.php4?ecno=3.1.3.48
    Enzyme

    Enzyme
    Assay information (spectrophotometric,(spherophophometrics, coupled assay ?,assay, reagents):
    --

    -
    link to
    ...
    reagents (substrates)
    http://www.sigmaaldrich.com/catalog/search?interface=All&term=3.1.3.48&lang=en&region=US&focus=documents&N=0+220003049+219853269+219853286&mode=match%20partialmax

    http://www.sigmaaldrich.com/catalog/search?interface=All&term=3.1.3.48&lang=en®ion=US&focuseddocuments&N = 0 + 220003049 + 219853269 + 219853286 & mode = match% 20partialmax
    ?????
    --

    -
    link to
    ...
    that contains assay information:information Assay:
    http://www.brenda-enzymes.org/literature/lit.php4?e=3.1.3.48&r=663621
    --

    -
    List of cost and quantity ofQUANTITY substrate reagents and supplier
    https://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-679D-5&Template=bacteria
    Structure
    Supplier
    https://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=BAA-679D-5&Template=Bacteria
    Structure
    Available (PDB
    ...
    Homology model) http://www.rcsb.org/pdb /explore/explore.do?structureId=1YWF - QUERY Coverage (Not exposed to direct match): 84% E value - 8 x 10 ^ -22 Druggable Target (see databases for this): Yes Current Inhibitors: None, http: / / www.bindingdb.org/bind/ByMonomersTarget.jsp Expression Information: Purification Method: PyMol or other: Homology model with M. tuberculosis: Blastp gives 47% positives and 83 % query query. * Amino Acid Sequence:
    http://www.rcsb.org/pdb/explore/explore.do?structureId=1YWF
    -- Query Coverage (if not direct match): 84%
    E value - 8 x 10^-22
    Druggable Target (see Databases for this): Yes
    Current Inhibitors: None,
    http://www.bindingdb.org/bind/ByMonomersTarget.jsp
    Expression Information (has it been expressed in bacterial cells):
    Purification Method:
    Image of protein (PyMol or etc):
    Homology model with M. tuberculosis: Blastp gives 47% positives and 83% query coverage.
    *Amino Acid Sequence:
    >gi|16803840|ref|NP_465325.1|
    > gi | 16803840 | ref | NP_465325.1 | lmo1800 hypothetical protein lmo1800 [Listeria monocytogenes EGD-e]
    MKNWVKVTGAGVLSATLLLGGCGAQSEEKAEANVKTEQTLKPGSQIKLEGAVNVRDLGGYKTTDGLTIKPHKLIRSAEL
    ANLSDSDKKKLVNTYDLSHIVDFRTSSEVATKPDPKLTDVDYTHDSVMKDNGTSTSTQDLTASLAKMDNPETFLINANKS
    FITDETSIQAYKDFFDILLANQDGSVLWHCTAGKDRAGFGTALVLSALGVDKNTVIDDYMLSNKYRADENKKAIEAVAAKT
    DNKKVIDGMTAVMEVRESYINAAFDEINAKYGSMDNFLKEKLGLTDAKKEQLKKAYLY
    Molecular

    MKNWVKVTGAGVLSATLLLGGCGAQSEEKAEANVKTEQTLKPGSQIKLEGAVNVRDLGGYKTTDGLTIKPHKLIRSAEL
    ANLSDSDKKKLVNTYDLSHIVDFRTSSEVATKPDPKLTDVDYTHDSVMKDNGTSTSTQDLTASLAKMDNPETFLINANKS
    FITDETSIQAYKDFFDILLANQDGSVLWHCTAGKDRAGFGTALVLSALGVDKNTVIDDYMLSNKYRADENKKAIEAVAAKT
    DNKKVIDGMTAVMEVRESYINAAFDEINAKYGSMDNFLKEKLGLTDAKKEQLKKAYLY
    Molecular
    Weight of your protein in your kiloDaltons using
    ...
    ProtParam website
    Molar

    Molar
    Extinction coefficient
    ...
    nm wavelength:
    *CDS

    * CDS
    Gene Sequence:
    Partial
    >gi|16802048:c1873620-1872724
    sequence:
    Partial
    > gi | 16802048: c1873620- 1872724
    Listeria monocytogenes EGD-e, complete genome ATGAAAAATTGGGTAAAAGTAACAGGAGCAGGGGTACTAAGCGCGACTTTACTATTAGGTGGATGCGGGGgenomeATGAAAAATTGGGTAAAAGTAACAGGAGCAGGGGTACTAAGCGCGACTTTACTATTAGGTGGATGCGGGG CGCAGTCAGAAGAAAAAGCAGAAGCAAATGTTAAAACCGAGCAAACACTCAAACCAGGAAGCCAAATTAA ATTAGAAGGCGCTGTAAATGTCCGGGACTTAGGCGGATACAAAACAACGGATGGACTAACCATTAAGCCA
    ...
    AAAAACACGGTCATTGACGATTATATGCTGTCCAATAAATATCGTGCTGACGAAAATAAAAAAGCAATTG AAGCCGTTGCAGCAAAAACAGATAATAAAAAAGTGATTGATGGAATGACAGCCGTAATGGAAGTTCGTGA ATCTTATATCAATGCAGCCTTCGATGAAATTAATGCAAAATATGGTTCGATGGACAACTTTTTAAAAGAA AAACTCGGACTAACCGATGCTAAAAAAGAACAACTAAAAAAAGCATATCTTTATTAA
    *GC%
    ATCTTATATCAATGCAGCCTTCGATGAAATTAATGCAAAATATGGTTCGATGGACAACTTTTTAAAAGAAAAACTCGGACTAACCGATGCTAATAACAACAACTAAAAAAAGCATATCTTTATTAA
    * GC%
    Content for gene: 37.9%
    *CDS

    * CDS
    Gene Sequence
    ...
    TCTAACAAATACCGTGCTGACGAAAATAAGAAAGCGATCGAAGCGGTAGCGGCGAAAACC GACAACAAAAAAGTGATCGACGGTATGACGGCAGTTATGGAAGTTCGTGAATCTTACATC AACGCGGCGTTCGATGAGATCAATGCGAAATATGGTTCTATGGATAACTTCCTCAAAGAA AAGCTGGGCCTCACTGATGCGAAGAAAGAGCAGCTGAAAAAAGCATACCTGTACTAA
    *GC% Content
    AACGCGGCGTTCGATGAGATCAATGCGAAATATGGTTCTATGGATAACTTCCTCAAAGAAAAGCTGGGCCTCACTGATGCGAAGAAAGAGCAGCTGAAAAAAGCATACCTGTACTAA
    *% GC content
    for geneGene (codon optimized): 50.9%
    Primer

    primer
    design results
    ...
    cloning (list seqeunces of all of your ~40seqeunces ~ 40 nt long primers):primers)
    Oligos Sequencesequence
    Lmon_PTP_1 || ATGAAGAATTGGGTTAAAGTTACCGGTGCAGGTGTTCTGTCCGCGACCCTGCTGCT ||
    ||

    ||
    Lmon_PTP_2 || ACGTTCGCTTCCGCTTTTTCCTCAGACTGCGCACCACAACCACCCAGCAGCAGGGTCGCGACGTTCGCTTCCGCTTTTCCTCAGACTGCGCACCACAACCACCCAGCAGCAGGGTCGCG ||
    ||

    ||
    Lmon_PTP_3 || AAAAGCGGAAGCGAACGTTAAAACTGAACAGACCCTGAAACCGGGTTCTCAAATCAAACTWHERE YOU SHOULD BE A BETWEEN YOUCCCCECCAACCGGTCTCTCAAATCAAACT ||
    ||

    ||
    Lmon_PTP_4 || TTATAACCGCCGAGATCGCGCACGTTAACCGCACCTTCCAGTTTGATTTGAGAACCCGGT ||
    ||

    ||
    Lmon_PTP_5 || GCGATCTCGGCGGTTATAAGACTACCGACGGTCTCACGATCAAACCGCATAAACTGATCC ||
    ||

    ||
    Lmon_PTP_6 || TCTTATCAGAGTCAGACAGATTCGCCAGTTCCGCAGAACGGATCAGTTTATGCGGTTTGATCTTATCAGAGTCAGACAGATTCGCCAGTTCCGCAGAACGGATCAGTTTGGGTTTGA ||
    || Lmon_PTP_7 || CGAATCTGTCTGACTCTGATAAGAAAAAACTGGTTAACACCTACGACCTGTCTCACATCG ||
    ...
    TCCGGTTTGGTCGCAACTTCAGAAGAGGTGCGAAAGTCAACGATGTGAGACAGGTCGTAG ||
    ||

    ||
    Lmon_PTP_9 || GTTGCGACCAAACCGGACCCAAAGCTGACCGACGTGGATTACACCCACGACTCTGTTATG ||
    ||

    ||
    Lmon_PTP_10 || GGTCAGGTCTTGGGTGGAGGTAGAGGTACCGTTGTCTTTCATAACAGAGTCGTGGGTGTA ||
    ||

    ||
    Lmon_PTP_11 || TCCACCCAAGACCTGACCGCGTCTCTCGCGAAGATGGATAACCCGGAAACCTTCCTGATC ||
    ||

    ||
    Lmon_PTP_12 || TGGATAGAGGTTTCATCGGTGATAAAAGATTTGTTCGCATTGATCAGGAAGGTTTCCGGG ||
    ||

    ||
    Lmon_PTP_13 || CACCGATGAAACCTCTATCCAGGCGTACAAAGACTTCTTCGACATCCTGCTCGCAAACCA ||
    ||

    ||
    Lmon_PTP_14 || CGGTCTTTACCCGCAGTGCAGTGCCACAGGACAGAGCCGTCTTGGTTTGCGAGCAGGATG ||
    ||

    ||
    Lmon_PTP_15 || CACTGCGGGTAAAGACCGTGCTGGTTTCGGCACCGCGCTGGTTCTCTCTGCACTCGGTGTCACTGCGGTAAAGACCGTGCTGGTTTCGGCACCGCGCTGGTCTCTCTGCACTCGGTGT ||
    || Lmon_PTP_16 || TGTTAGACAGCATGTAGTCGTCAATAACGGTGTTTTTGTCCACACCGAGTGCAGAGAGAA ||
    ...
    ACGACTACATGCTGTCTAACAAATACCGTGCGGACGAAAACAAAAAGGCGATCGAAGCGG ||
    ||

    ||
    Lmon_PTP_18 || GTCATACCGTCGATAACTTTCTTGTTGTCGGTTTTCGCCGCAACCGCTTCGATCGCCTTTGTCATACCGTCGATAACTTTCTTGTTGTCGGTTTTCGCCGCAACCGTTTCGATCGCCTTT ||
    ||

    ||
    Lmon_PTP_19 || CAAGAAAGTTATCGACGGTATGACCGCAGTTATGGAAGTTCGTGAATCTTACATTAACGC ||
    ||

    ||
    Lmon_PTP_20 || ATAGAACCGTATTTTGCGTTGATTTCGTCGAACGCCGCGTTAATGTAAGATTCACGAACT ||
    ||

    ||
    Lmon_PTP_21 || ATCAACGCAAAATACGGTTCTATGGACAACTTCCTCAAGGAGAAACTGGGTCTGACGGAC ||
    ||

    ||
    Lmon_PTP_22 || TTAGTACAGGTACGCTTTCTTCAGCTGTTCTTTTTTCGCGTCCGTCAGACCCAGTTTCTTAGTACAGGTACGCTTTCTTCAGCTGTTCTTTTTCTCGCGTCCGTCAGACCCAGTTTC ||
    Primers
    LmPTP-for

    Primers
    LmPTP-for
    imc TACTTCCAATCCATGAAGAACTGGGTTAAAGTTTACTTCCAATCC ATG AAGAACTGGGTTAAAGTT
    LmPTP-rev imc AAAAGGCATACCTGTACTAACAGTAAAGGTGGATA
    (link
    AAAAGGCATACCTGTACTAA CAGTAAAGGTGGATA
    Primers - C. Burns - Underlined is partial nucleotide sequence - middle black are start and stop codons
    Forward - TACTTCCAATCCATGACCCTCGTTCTGCGTTAT
    Reverse - TATCCACCTTTACTGTTAGTGTTCGAGGTCCGC
    ( link
    to DNA
    ...
    text file - that-that should be
    ...
    did the primerprimary design protocol)
    --

    -
    Ask a
    ...
    how to.
    https://docs.google.com/document/d/1zCGuvqj1KwDp46nAn3SRRWRO2oCQd2O1F9vGN3blrsI/edit
    TMpred Output:
    (view changes)
    6:22 pm
  3. page TargetSp17 - Inogranic pyrophosphatase (Burkholderia pseudomallei) edited ... Reverse Primer: 5’ TATCCACCTTTACTGTCATTTTTTGAAGTTCGCAAC 3’ 36_ bp Primers as designed by To…
    ...
    Reverse Primer:
    5’ TATCCACCTTTACTGTCATTTTTTGAAGTTCGCAAC 3’ 36_ bp
    Primers as designed by Todd:
    Forward Primer: 5' TACTTCCAATCCATGTCTTTCTCTAACGTTCCA 3' 33 bp 1.5 mM Mg++ 68.4 C
    Reverse Primer: 5' TATCCACCTTTACTGTCATTTTTTGAAGTTCGCA 3' 34 bp 1.5 mM Mg++ 68.4 C

    **
    (view changes)
    6:21 pm
  4. page Target - Protein Tyrosine Phosphatase (Listeria monocytogenes) edited ... || Lmon_PTP_21 || ATCAACGCAAAATACGGTTCTATGGACAACTTCCTCAAGGAGAAACTGGGTCTGACGGAC || || Lmon_PTP…
    ...
    || Lmon_PTP_21 || ATCAACGCAAAATACGGTTCTATGGACAACTTCCTCAAGGAGAAACTGGGTCTGACGGAC ||
    || Lmon_PTP_22 || TTAGTACAGGTACGCTTTCTTCAGCTGTTCTTTTTTCGCGTCCGTCAGACCCAGTTTC ||
    Primers
    LmPTP-for imc TACTTCCAATCCATGAAGAACTGGGTTAAAGTT
    LmPTP-rev imc AAAAGGCATACCTGTACTAACAGTAAAGGTGGATA

    (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
    -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
    (view changes)
    5:51 pm

Monday, October 30

  1. page TargetSp17 - Inogranic pyrophosphatase (Burkholderia pseudomallei) edited ... (link to DNA Works output text file - that should be saved in your Google Docs folder after yo…
    ...
    (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
    -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
    https://drive.google.com/open?id=0B4O2KqKh2q_-dGI1bVBqY2pXcEE
    Primer design results for 'tail' primers (this is just 2 sequences):
    Forward Primer:
    5’ TACTTCCAATCCATGTCTTTCTCTAACGTTCCA 3’ 33 bp
    Reverse Primer:
    5’ TATCCACCTTTACTGTCATTTTTTGAAGTTCGCAAC 3’ 36_ bp

    **
    (view changes)
    6:28 pm
  2. page Undergraduate Research Opportunities edited ... Journal of Student Research http://www.jofsr.com/index.php/path Texas Undergraduate Researc…
    ...
    Journal of Student Research
    http://www.jofsr.com/index.php/path
    Texas Undergraduate Research Journal (TURJ)
    http://texasurj.com/wp/

    J Med Chem
    Bioorganic and Medicinal Chemistry Letters
    (view changes)
    6:01 pm

Sunday, October 22

  1. page TargetSp17 - Inogranic pyrophosphatase (Burkholderia pseudomallei) edited ... http://www.rcsb.org/pdb/explore.do?structureId=3GVF Current Inhibitors: 4-{2-[3-(2-Amino-a…
    ...
    http://www.rcsb.org/pdb/explore.do?structureId=3GVF
    Current Inhibitors:
    4-{2-[3-(2-Amino-acetyl)-thioureido]-ethyl}-benzenesulfonamide; compound with GENERIC INORGANIC NEUTRAL COMPONENT CHEMBL178560 BDBM50171016
    CHEMBL103102 CHEMBL216318 BDBM50037981 Piperidine-1-carboxamidine; compound with GENERIC INORGANIC NEUTRAL COMPONENT
    http://www.bindingdb.org/bind/tabLuceneResult.jsp?thisInput=inorganic+pyrophosphatase&submit=Go
    N-(pyridin-3-ylmethyl)aniline (DB06851)
    5-amino-1-(4-chlorophenyl)-1H-pyrazole-4-carbonitrile (DB07291)
    https://www.drugbank.ca/biodb/polypeptides/Q3JUV5

    Expression Information (has it been expressed in bacterial cells): Yes
    Purification Method:
    (view changes)
    8:59 pm

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