Experts and Doctors on molecular sequence data in Palmerston North, Manawatu Wanganui, New Zealand


Locale: Palmerston North, Manawatu Wanganui, New Zealand
Topic: molecular sequence data

Top Publications

  1. Bloomer R, Juenger T, Symonds V. Natural variation in GL1 and its effects on trichome density in Arabidopsis thaliana. Mol Ecol. 2012;21:3501-15 pubmed publisher
  2. Mercadante D, Melton L, Jameson G, Williams M, De Simone A. Substrate dynamics in enzyme action: rotations of monosaccharide subunits in the binding groove are essential for pectin methylesterase processivity. Biophys J. 2013;104:1731-9 pubmed publisher
    ..This investigation is one of the few reported examples of a process where the dynamics of a substrate are vitally important. ..
  3. Sun X, Xue B, Jones W, Rikkerink E, Dunker A, Uversky V. A functionally required unfoldome from the plant kingdom: intrinsically disordered N-terminal domains of GRAS proteins are involved in molecular recognition during plant development. Plant Mol Biol. 2011;77:205-23 pubmed publisher
    ..This study enables us to propose a conceptual framework that guides future experimental approaches to understand structure-function relationships of the entire GRAS family. ..
  4. McComish B, Hills S, Biggs P, Penny D. Index-free de novo assembly and deconvolution of mixed mitochondrial genomes. Genome Biol Evol. 2010;2:410-24 pubmed publisher
    ..The general approach has considerable potential, especially when combined with indexed sequencing of different groups of genomes...
  5. Englebretsen D, Harding D. Fmoc SPPS using Perloza beaded cellulose. Int J Pept Protein Res. 1994;43:546-54 pubmed
    ..The overall aim of our work with Perloza is synthesis of resin-bound peptide ligands for affinity chromatography and antibody generation.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  6. Stayner C, Tweedie J. Cloning and characterisation of the cDNA for sheep liver cytosolic aldehyde dehydrogenase. Adv Exp Med Biol. 1995;372:61-6 pubmed
  7. Coupe S, Sinclair B, Watson L, Heyes J, Eason J. Identification of dehydration-responsive cysteine proteases during post-harvest senescence of broccoli florets. J Exp Bot. 2003;54:1045-56 pubmed
    ..The putative cysteine protease mRNAs are expressed before measurable increases in endo-protease activity, loss of protein, chlorophyll or tissue chlorosis...
  8. Overhage J, Schemionek M, Webb J, Rehm B. Expression of the psl operon in Pseudomonas aeruginosa PAO1 biofilms: PslA performs an essential function in biofilm formation. Appl Environ Microbiol. 2005;71:4407-13 pubmed
    ..These data suggest that constitutive expression of the psl operon enables efficient attachment to surfaces and that regulated localized psl operon expression is required for biofilm differentiation. ..
  9. McLenachan P, Lockhart P, Faber H, Mansfield B. Evolutionary analysis of the multigene pregnancy-specific beta 1-glycoprotein family: separation of historical and nonhistorical signals. J Mol Evol. 1996;42:273-80 pubmed
    ..The N-terminal domains show a nonrandom pattern of amino acid substitutions clustered in the immunoglobulin complementarity-determining region (CDR)-like regions, which appear to be important in the function of the protein. ..

More Information


  1. Stowell K, Rado T, Funk W, Tweedie J. Expression of cloned human lactoferrin in baby-hamster kidney cells. Biochem J. 1991;276 ( Pt 2):349-55 pubmed
    ..The protein was secreted into the tissue-culture medium and was subsequently purified to homogeneity in a single step. Initial characterization suggests that the protein expressed by BHK cells is identical with native human lactoferrin. ..
  2. Winichayakul S, Scott R, Roldan M, Hatier J, Livingston S, Cookson R, et al. In vivo packaging of triacylglycerols enhances Arabidopsis leaf biomass and energy density. Plant Physiol. 2013;162:626-39 pubmed publisher
    ..The Cys-oleosins have applications in biofuels, animal feed, and human nutrition as well as in providing a tool for investigating fatty acid biosynthesis and catabolism...
  3. Clark A, Sawyer G, Robertson S, Sutherland Smith A. Skeletal dysplasias due to filamin A mutations result from a gain-of-function mechanism distinct from allelic neurological disorders. Hum Mol Genet. 2009;18:4791-800 pubmed publisher
    ..These data provide the first biochemical evidence for a gain-of-function mechanism for the OPD disorders, and mechanistically distinguishes them from the loss-of-function phenotypes that manifest as disorders of neuronal migration. ..
  4. Ward L, Beresford T, Lubbers M, Jarvis B, Jarvis A. Sequence analysis of the lysin gene region of the prolate lactococcal bacteriophage c2. Can J Microbiol. 1993;39:767-74 pubmed
    ..A codon usage table for the lysin genes of several phages as well as for reported gene sequences from L. lactis and lactococcal bacteriophages is presented. ..
  5. Fleetwood D, Scott B, Lane G, Tanaka A, Johnson R. A complex ergovaline gene cluster in epichloe endophytes of grasses. Appl Environ Microbiol. 2007;73:2571-9 pubmed
    ..This work provides a genetic foundation for elucidating biochemical steps in the ergovaline pathway, the ecological role of individual ergot alkaloid compounds, and the regulation of their synthesis in planta...
  6. Lubbers M, Waterfield N, Beresford T, Le Page R, Jarvis A. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. Appl Environ Microbiol. 1995;61:4348-56 pubmed
    ..The identification of direct nucleotide repeats flanking these sequences indicated that recombination may be important in the evolution of these phages.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  7. Moore S, Ronimus R, Roberson R, Morgan H. The structure of a pyrophosphate-dependent phosphofructokinase from the Lyme disease spirochete Borrelia burgdorferi. Structure. 2002;10:659-71 pubmed
    ..Asn181 blocks the binding of the adenine moiety of ATP. Lys203 hydrogen bonds to a sulfate anion that likely mimics PP(i) substrate binding. ..
  8. Gatehouse L, Sutherland P, Forgie S, Kaji R, Christeller J. Molecular and histological characterization of primary (betaproteobacteria) and secondary (gammaproteobacteria) endosymbionts of three mealybug species. Appl Environ Microbiol. 2012;78:1187-97 pubmed publisher
    ..The data from this model are consistent with a role for the primary endosymbiont in mealybug transmission of Grapevine leafroll-associated virus 3...
  9. Li F, Parry D, Scott M. The amino-terminal region of Drosophila MSL1 contains basic, glycine-rich, and leucine zipper-like motifs that promote X chromosome binding, self-association, and MSL2 binding, respectively. Mol Cell Biol. 2005;25:8913-24 pubmed publisher
    ..We propose that the basic region may mediate DNA binding and that the glycine-rich region may promote the association of MSL complexes to closely adjacent sites on the X chromosome...
  10. Dupont C, Thompson K, Heuer C, Gicquel B, Murray A. Identification and characterization of an immunogenic 22 kDa exported protein of Mycobacterium avium subspecies paratuberculosis. J Med Microbiol. 2005;54:1083-92 pubmed publisher
    ..Antibody to P22 was detected by Western blot analysis in 10 out of 11 vaccinated sheep, in two out of two clinically affected cows and in 11 out of 13 subclinically infected cows...
  11. Coupe S, Watson L, Ryan D, Pinkney T, Eason J. Molecular analysis of programmed cell death during senescence in Arabidopsis thaliana and Brassica oleracea: cloning broccoli LSD1, Bax inhibitor and serine palmitoyltransferase homologues. J Exp Bot. 2004;55:59-68 pubmed publisher
    ..AtBI-1 expression was constitutively expressed during detached senescence, AtLSD1 expression remained constitutively low, and AtSPT1 expression increased during detached senescence...
  12. Sawyer G, Clark A, Robertson S, Sutherland Smith A. Disease-associated substitutions in the filamin B actin binding domain confer enhanced actin binding affinity in the absence of major structural disturbance: Insights from the crystal structures of filamin B actin binding domains. J Mol Biol. 2009;390:1030-47 pubmed publisher
    ..0 microM. The increased F-actin binding affinity of the mutants presents a biochemical mechanism that differentiates the autosomal dominant gain-of-function FLNB disorders from those that arise through the complete loss of FLNB protein. ..
  13. Xu F, Pearce L, Yu P. Genetic analysis of a lactococcal plasmid replicon. Mol Gen Genet. 1991;227:33-9 pubmed
    ..The genetic organization of this lactococcal plasmid replicon shares significant similarity with pE194 group plasmids. ..
  14. Brophy B, Macdonald R, McLenachan P, Mansfield B. cDNA sequence of the pregnancy-specific beta 1-glycoprotein-11s (PSG-11s). Biochim Biophys Acta. 1992;1131:119-21 pubmed
    ..Minor differences between the four clones sequenced included a restriction site polymorphic for ApaI that may differentiate between alleles of the PSG-11 gene. ..
  15. Brummell D, Chen R, Harris J, Zhang H, Hamiaux C, Kralicek A, et al. Induction of vacuolar invertase inhibitor mRNA in potato tubers contributes to cold-induced sweetening resistance and includes spliced hybrid mRNA variants. J Exp Bot. 2011;62:3519-34 pubmed publisher
    ..Evidence for increased RNA splicing activity was detected in several resistant lines, a mechanism that in some circumstances may generate a range of proteins with additional functional capacity to aid adaptability...
  16. Roussel A, Anderson B, Baker H, Fraser J, Baker E. Crystal structure of the streptococcal superantigen SPE-C: dimerization and zinc binding suggest a novel mode of interaction with MHC class II molecules. Nat Struct Biol. 1997;4:635-43 pubmed
    ..Consideration of the SPE-C dimer suggests a novel mechanism for promotion of MHC aggregation and T-cell activation. ..
  17. Xiao Q, Moore C. The primary structure of phosphofructokinase from Lactococcus lactis. Biochem Biophys Res Commun. 1993;194:65-71 pubmed publisher
  18. Scott M, Pan L, Cleland S, Knox A, Heinrich J. MSL1 plays a central role in assembly of the MSL complex, essential for dosage compensation in Drosophila. EMBO J. 2000;19:144-55 pubmed
    ..The MSL1 C-terminal domain shows similarity to a region of mouse CBP, a transcription co-activator. We conclude that a main role of MSL1 is to serve as the backbone for assembly of the MSL complex. ..
  19. Veit B, Briggs S, Schmidt R, Yanofsky M, Hake S. Regulation of leaf initiation by the terminal ear 1 gene of maize. Nature. 1998;393:166-8 pubmed
    ..The tel gene product contains conserved RNA-binding motifs, indicating that it may function through an RNA-binding activity. ..
  20. McLenachan P, Rutherfurd K, Beggs K, Sims S, Mansfield B. Characterization of the PSG11 gene. Genomics. 1994;22:356-63 pubmed
    ..Comparison of the C-terminal sequences of the three subgroups of genes shows that the subgroup 2 and 3 genes are more closely related than, and are distinct from, the subgroup 1 genes. ..
  21. Fleetwood D, Khan A, Johnson R, Young C, Mittal S, Wrenn R, et al. Abundant degenerate miniature inverted-repeat transposable elements in genomes of epichloid fungal endophytes of grasses. Genome Biol Evol. 2011;3:1253-64 pubmed publisher
    ..This work provides insight into the potential impact of MITEs on epichloae evolution and provides a foundation for analysis in other fungal genomes...
  22. Weake V, Scott M. The non-dosage compensated Lsp1alpha gene of Drosophila melanogaster escapes acetylation by MOF in larval fat body nuclei, but is flanked by two dosage compensated genes. BMC Mol Biol. 2007;8:35 pubmed
    ..The X-linked Larval serum protein one alpha (Lsp1alpha) gene has long been known to be not dosage compensated. Here we have examined possible explanations for why the Lsp1alpha gene is not dosage compensated...
  23. Shang Y, Venail J, Mackay S, Bailey P, Schwinn K, Jameson P, et al. The molecular basis for venation patterning of pigmentation and its effect on pollinator attraction in flowers of Antirrhinum. New Phytol. 2011;189:602-15 pubmed publisher
    ..Venation may be the ancestral trait, with full-red pigmentation a derived, polyphyletic trait. Venation patterning is probably not fixed once species evolve full-red floral pigmentation...
  24. Marincs F, White D. Nopaline causes a conformational change in the NocR regulatory protein-nocR promoter complex of Agrobacterium tumefaciens Ti plasmid pTiT37. Mol Gen Genet. 1993;241:65-72 pubmed
    ..These results suggest that nopaline-induced alterations in the NocR protein-nocR promoter complex might control gene expression in the noc operon. ..
  25. Borich S, Murray A, Gormley E. Genomic arrangement of a putative operon involved in maltose transport in the Mycobacterium tuberculosis complex and Mycobacterium leprae. Microbios. 2000;102:7-15 pubmed
  26. Day C, Dupont C, Lackmann M, Vaux D, Hinds M. Solution structure and mutagenesis of the caspase recruitment domain (CARD) from Apaf-1. Cell Death Differ. 1999;6:1125-32 pubmed
  27. Mead P, Tweedie J. cDNA and protein sequence of bovine lactoferrin. Nucleic Acids Res. 1990;18:7167 pubmed
  28. Young C, Felitti S, Shields K, Spangenberg G, Johnson R, Bryan G, et al. A complex gene cluster for indole-diterpene biosynthesis in the grass endophyte Neotyphodium lolii. Fungal Genet Biol. 2006;43:679-93 pubmed
    ..paxilli paxM and paxC, respectively. This work provides a genetic foundation for elucidating the metabolic grid responsible for the diversity of indole-diterpenes synthesized by N. lolii...
  29. Bryant M, May K, Bryan G, Scott B. Functional analysis of a beta-1,6-glucanase gene from the grass endophytic fungus Epichloƫ festucae. Fungal Genet Biol. 2007;44:808-17 pubmed
    ..Growth of DeltagcnA and gcnA-overexpressing strains in vegetative grass tissues was indistinguishable from wild type strains. ..
  30. Libich D, Schwalbe M, Kate S, Venugopal H, Claridge J, Edwards P, et al. Intrinsic disorder and coiled-coil formation in prostate apoptosis response factor 4. FEBS J. 2009;276:3710-28 pubmed publisher
    ..Interruption of self-association by urea also resulted in loss of secondary structure. These results are consistent with the stabilization of the coiled-coil motif through an intramolecular association. ..
  31. Khan H, Flint S, Yu P. Determination of the mode of action of enterolysin A, produced by Enterococcus faecalis B9510. J Appl Microbiol. 2013;115:484-94 pubmed publisher
    ..This is the first report identifying the cleavage site of enterolysin A within the cell walls of sensitive bacteria. This will help in identifying potential applications for enterolysin A. ..
  32. Cumming M, Leung S, McCallum J, McManus M. Complex formation between recombinant ATP sulfurylase and APS reductase of Allium cepa (L.). FEBS Lett. 2007;581:4139-47 pubmed
    ..The significance of an interaction between chloroplastidic ATPS and APR in A. cepa is evaluated with respect to the control of the reductive assimilation of sulfate. ..
  33. Loo T, Patchett M, Norris G, Lott J. Using secretion to solve a solubility problem: high-yield expression in Escherichia coli and purification of the bacterial glycoamidase PNGase F. Protein Expr Purif. 2002;24:90-8 pubmed
    ..coli periplasm. Single-step purification using immobilized metal affinity chromatography yielded 8 mg of pure enzyme per liter of culture, which is fully active on a range of protein and peptide substrates. ..
  34. Ward L, Brown J, Davey G. Identification and sequence analysis of IS1297, an ISS1-like insertion sequence in a Leuconostoc strain. Gene. 1996;174:259-63 pubmed
    ..This is the first sequence of an ISS1-like element from a genus other than Lactococcus; however, IS1297 has close similarity to the lactococcal iso-ISS1 elements, especially the iso-ISS1 element from the lactose plasmid, pTD1. ..
  35. Chagn D, Lin Wang K, Espley R, Volz R, How N, Rouse S, et al. An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol. 2013;161:225-39 pubmed publisher
    ..Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity...
  36. Schwinn K, Venail J, Shang Y, Mackay S, Alm V, Butelli E, et al. A small family of MYB-regulatory genes controls floral pigmentation intensity and patterning in the genus Antirrhinum. Plant Cell. 2006;18:831-51 pubmed
    ..Set in the context of our understanding of the regulation of anthocyanin production in other genera, the activity of MYB-related genes is probably a primary cause of natural variation in anthocyanin pigmentation in plants...
  37. Reid J, Coolbear T, Pillidge C, Pritchard G. Specificity of hydrolysis of bovine kappa-casein by cell envelope-associated proteinases from Lactococcus lactis strains. Appl Environ Microbiol. 1994;60:801-6 pubmed
    ..abstract truncated at 250 words) ..
  38. Carpenter M, Broad T. The cDNA sequence of horse transferrin. Biochim Biophys Acta. 1993;1173:230-2 pubmed
    ..The horse transferrin sequence had the duplicated structure and conserved iron binding and cysteine residues which are characteristic of the transferrin family...
  39. Collins L, Biggs P, Voelckel C, Joly S. An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Inform. 2008;21:3-14 pubmed
    ..Our approach demonstrates that transcriptome analysis using high-throughput short-read sequencing need not be restricted to the genomes of model organisms. ..
  40. Faber H, Groom C, Baker H, Morgan W, Smith A, Baker E. 1.8 A crystal structure of the C-terminal domain of rabbit serum haemopexin. Structure. 1995;3:551-9 pubmed
    ..The capacity to bind both cations and anions, together with the disc shape of the domain, suggests that such domains may be used widely for macromolecular recognition. ..
  41. Chen X, White W, Collins L, Penny D. Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis. PLoS ONE. 2008;3:e3106 pubmed publisher
    ..Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes. ..
  42. Huynen L, Millar C, Lambert D. A DNA test to sex ratite birds. Mol Ecol. 2002;11:851-6 pubmed
    ..Polymerase chain reaction (PCR) primers designed to this locus allow the assignment of sex in all species of living ratites...
  43. Skillman L, Evans P, Strompl C, Joblin K. 16S rDNA directed PCR primers and detection of methanogens in the bovine rumen. Lett Appl Microbiol. 2006;42:222-8 pubmed
    ..To assess the diversity of ruminal methanogens in a grazing cow, and develop PCR primers targeting the predominant methanogens...
  44. Christeller J, Poulton J, Markwick N, Simpson R. The effect of diet on the expression of lipase genes in the midgut of the lightbrown apple moth (Epiphyas postvittana Walker; Tortricidae). Insect Mol Biol. 2010;19:9-25 pubmed publisher
  45. White D. PEAPOD regulates lamina size and curvature in Arabidopsis. Proc Natl Acad Sci U S A. 2006;103:13238-43 pubmed
  46. Fraser R, Parry D. Molecular packing in the feather keratin filament. J Struct Biol. 2008;162:1-13 pubmed publisher
  47. Kenters N, Henderson G, Jeyanathan J, Kittelmann S, Janssen P. Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. J Microbiol Methods. 2011;84:52-60 pubmed publisher
    ..This strategy has therefore allowed us to cultivate many novel rumen bacteria, opening the way to overcoming the lack of cultures of many of the groups detected using cultivation-independent methods. ..
  48. Starck C, Sutherland Smith A. Cytotoxic aggregation and amyloid formation by the myostatin precursor protein. PLoS ONE. 2010;5:e9170 pubmed publisher
    ..These novel results show that the myostatin precursor protein is capable of forming amyloid structures in vitro with implications for a role in sIBM pathogenesis. ..
  49. Concha C, Edman R, Belikoff E, Schiemann A, Carey B, Scott M. Organization and expression of the Australian sheep blowfly (Lucilia cuprina) hsp23, hsp24, hsp70 and hsp83 genes. Insect Mol Biol. 2012;21:169-80 pubmed
    ..The isolation of these hsp gene promoters will facilitate constitutive or conditional expression of a gene of interest in transgenic Lucilia...
  50. Jameson G, Anderson B, Norris G, Thomas D, Baker E. Structure of human apolactoferrin at 2.0 A resolution. Refinement and analysis of ligand-induced conformational change. Acta Crystallogr D Biol Crystallogr. 1998;54:1319-35 pubmed
    ..It shows that a stable closed structure, essentially identical to that of the iron-bound form, can be formed in the absence of iron binding. ..
  51. Daly T, Sutherland Smith A, Penny D. Beyond BLASTing: tertiary and quaternary structure analysis helps identify major vault proteins. Genome Biol Evol. 2013;5:217-32 pubmed publisher
    ..Two of these sequences are predicted to be structurally similar to rat MVP, despite being in excess of 300 residues shorter. The method can be used generally to help test predictions of homology via structural analysis. ..
  52. Stepper J, Shastri S, Loo T, Preston J, Novak P, Man P, et al. Cysteine S-glycosylation, a new post-translational modification found in glycopeptide bacteriocins. FEBS Lett. 2011;585:645-50 pubmed publisher
    ..Genomic context analysis identified diverse putative glycopeptide bacteriocins in Firmicutes. One of these, the reputed lantibiotic sublancin, was shown to contain a hexose S-linked to Cys22. ..
  53. Langbein L, Eckhart L, Fischer H, Rogers M, Praetzel Wunder S, Parry D, et al. Localisation of keratin K78 in the basal layer and first suprabasal layers of stratified epithelia completes expression catalogue of type II keratins and provides new insights into sequential keratin expression. Cell Tissue Res. 2016;363:735-50 pubmed publisher
    ..Moreover, the K78 expression pattern and the decoupled K1/K10 and K4/K13 expression define the existence of a hitherto unperceived early differentiation stage in the parabasal layer characterized by K78/K10 or K78/K13 expression. ..