Experts and Doctors on molecular sequence data in Cork, Munster, Ireland

Summary

Locale: Cork, Munster, Ireland
Topic: molecular sequence data

Top Publications

  1. Suda S, Cotter P, Hill C, Ross R. Lacticin 3147--biosynthesis, molecular analysis, immunity, bioengineering and applications. Curr Protein Pept Sci. 2012;13:193-204 pubmed
    ..Here we review the knowledge which has been gained with respect to lacticin 3147 since its discovery in 1995. ..
  2. Scanlan P, Shanahan F, Marchesi J. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol. 2008;8:79 pubmed publisher
  3. O Halloran J, Barbosa T, Morrissey J, Kennedy J, Dobson A, O Gara F. Pseudovibrio axinellae sp. nov., isolated from an Irish marine sponge. Int J Syst Evol Microbiol. 2013;63:141-5 pubmed publisher
    ..The name Pseudovibrio axinellae sp. nov. is proposed, with Ad2(T) (= DSM 24994(T) = NCIMB 14761(T)) as the type strain...
  4. Quane K, Keating K, Healy J, Manning B, Krivosic Horber R, Krivosic I, et al. Mutation screening of the RYR1 gene in malignant hyperthermia: detection of a novel Tyr to Ser mutation in a pedigree with associated central cores. Genomics. 1994;23:236-9 pubmed
    ..This mutation is positioned relatively close to five of the six MHS/CCD mutations known to date and provides further evidence that MHS/CCD mutations may cluster in the amino terminal region of the RYR1 protein. ..
  5. Cashman O, Collins P, Lennon G, Cryan B, Martella V, Fanning S, et al. Molecular characterization of group A rotaviruses detected in children with gastroenteritis in Ireland in 2006-2009. Epidemiol Infect. 2012;140:247-59 pubmed publisher
    ..Moreover, sequence analysis of the VP7 of G1 rotaviruses revealed the onset of a G1 variant, previously unseen in the Irish population. ..
  6. Stanley E, Fitzgerald G, Le Marrec C, Fayard B, van Sinderen D. Sequence analysis and characterization of phi O1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology. 1997;143 ( Pt 11):3417-29 pubmed
    ..The phage attachment site attP, the bacterial attachment site attB, and the two phage/chromosome junctions attL and attR were identified and found to contain a 40 bp common core sequence. ..
  7. O Driscoll J, Heiter D, Wilson G, Fitzgerald G, Roberts R, van Sinderen D. A genetic dissection of the LlaJI restriction cassette reveals insights on a novel bacteriophage resistance system. BMC Microbiol. 2006;6:40 pubmed
  8. Lynch S, Carlsson J, Reilly A, Cotter E, Culloty S. A previously undescribed ostreid herpes virus 1 (OsHV-1) genotype detected in the pacific oyster, Crassostrea gigas, in Ireland. Parasitology. 2012;139:1526-32 pubmed publisher
    ..gigas and in seed and juveniles at both sites, in both years. Analysis suggests that the Irish OsHV-1 ?var variant genotype is closely related to OsHV-1 ?var, first described in France in 2008. ..
  9. Cronin M, Knobel M, O Connell Motherway M, Fitzgerald G, van Sinderen D. Molecular dissection of a bifidobacterial replicon. Appl Environ Microbiol. 2007;73:7858-66 pubmed publisher

More Information

Publications77

  1. Firth A, Chung B, Fleeton M, Atkins J. Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma. Virol J. 2008;5:108 pubmed publisher
    ..The results have implications for alphavirus biology, virion structure, viroporins, ribosomal frameshifting, and bioinformatic identification of novel frameshift-expressed genes, both in viruses and in cellular organisms...
  2. Ventura M, Kenny J, Zhang Z, Fitzgerald G, van Sinderen D. The clpB gene of Bifidobacterium breve UCC 2003: transcriptional analysis and first insights into stress induction. Microbiology. 2005;151:2861-72 pubmed publisher
    ..Moreover the predicted 3D structure of HspR provides further insight into the binding mode of this protein to the clpB promoter region, and highlights the key amino acid residues believed to be involved in the protein-DNA interaction...
  3. Foley B, O Mahony J, Hill C, Morgan J. Molecular detection and sequencing of "Norwalk-like viruses" in outbreaks and sporadic cases of gastroenteritis in Ireland. J Med Virol. 2001;65:388-94 pubmed
    ..Further downstream sequence analysis of a number of the isolates confirmed this result. It is concluded that the majority of NLV isolates circulating in Ireland belong to the Bristol/Lordsdale clade. ..
  4. Neville B, Sheridan P, Harris H, Coughlan S, Flint H, Duncan S, et al. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans. PLoS ONE. 2013;8:e68919 pubmed publisher
  5. Kelly E, Horgan C, McCaffrey M. Rab11 proteins in health and disease. Biochem Soc Trans. 2012;40:1360-7 pubmed publisher
    ..We also summarize the protein machinery currently known to regulate or mediate their functions and the cargo molecules which they have been shown to transport. ..
  6. Alvarez Ordóñez A, Begley M, Hill C. Selection for loss of RpoS in Cronobacter sakazakii by growth in the presence of acetate as a carbon source. Appl Environ Microbiol. 2013;79:2099-102 pubmed publisher
    ..This suggests that C. sakazakii is capable of regulating cell fitness through mutation of the rpoS gene. ..
  7. Mac Aogáin M, Mooij M, McCarthy R, Plower E, Wang Y, Tian Z, et al. The non-classical ArsR-family repressor PyeR (PA4354) modulates biofilm formation in Pseudomonas aeruginosa. Microbiology. 2012;158:2598-609 pubmed
    ..Hence, PyeR belongs to a subgroup of non-classical ArsR-family regulators and is the second ArsR regulator shown to be involved in biofilm formation. ..
  8. Floyd S, Favre C, Lasorsa F, Leahy M, Trigiante G, Stroebel P, et al. The insulin-like growth factor-I-mTOR signaling pathway induces the mitochondrial pyrimidine nucleotide carrier to promote cell growth. Mol Biol Cell. 2007;18:3545-55 pubmed
    ..Overall the data indicate that PNC1 is a target of the IGF-I/mTOR pathway that is essential for mitochondrial activity in regulating cell growth and proliferation. ..
  9. McLaughlin H, Xiao Q, Rea R, Pi H, Casey P, Darby T, et al. A putative P-type ATPase required for virulence and resistance to haem toxicity in Listeria monocytogenes. PLoS ONE. 2012;7:e30928 pubmed publisher
    ..The data suggest a potential role for FrvA as a haem exporter that functions, at least in part, to protect the cell against the potential toxicity of free haem. ..
  10. Flynn S, van Sinderen D, Thornton G, Holo H, Nes I, Collins J. Characterization of the genetic locus responsible for the production of ABP-118, a novel bacteriocin produced by the probiotic bacterium Lactobacillus salivarius subsp. salivarius UCC118. Microbiology. 2002;148:973-84 pubmed publisher
    ..This novel bacteriocin is, to the authors' knowledge, the first to be isolated from a known human probiotic bacterium and to be characterized at the genetic level...
  11. MacConaill L, Butler D, O Connell Motherway M, Fitzgerald G, van Sinderen D. Identification of two-component regulatory systems in Bifidobacterium infantis by functional complementation and degenerate PCR approaches. Appl Environ Microbiol. 2003;69:4219-26 pubmed
    ..The conservation of the genetic organization of these three 2CSs in other bacteria, including a number of recently published Bifidobacterium genomes, was investigated...
  12. Vaughan P, McCarthy T. A novel process for mutation detection using uracil DNA-glycosylase. Nucleic Acids Res. 1998;26:810-5 pubmed
    ..Overall, the simplicity, specificity, versatility and flexibility of the GMPD process make it an attractive candidate for both small and large scale application in mutation detection and genome analysis. ..
  13. Henry M, Begley M, Neve H, Maher F, Ross R, McAuliffe O, et al. Cloning and expression of a mureinolytic enzyme from the mycobacteriophage TM4. FEMS Microbiol Lett. 2010;311:126-32 pubmed publisher
    ..Evidence of peptidoglycan-degrading activity was observed initially by a chloroform assay and later by conventional zymogram analysis...
  14. Burgess C, Slotboom D, Geertsma E, Duurkens R, Poolman B, van Sinderen D. The riboflavin transporter RibU in Lactococcus lactis: molecular characterization of gene expression and the transport mechanism. J Bacteriol. 2006;188:2752-60 pubmed publisher
    ..The presented transport data are consistent with a uniport mechanism for riboflavin translocation and provide the first detailed molecular and functional analysis of a bacterial protein involved in riboflavin transport...
  15. Baker P, Kennedy J, Dobson A, Marchesi J. Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters. Mar Biotechnol (NY). 2009;11:540-7 pubmed publisher
    ..The data suggests that some fungi live in symbiosis with H. simulans, whereas other fungi may have been ingested from the surrounding seawater...
  16. O Leary N, O Mahony M, Dobson A. Regulation of phenylacetic acid uptake is ?54 dependent in Pseudomonas putida CA-3. BMC Microbiol. 2011;11:229 pubmed publisher
  17. Begley M, Cotter P, Hill C, Ross R. Identification of a novel two-peptide lantibiotic, lichenicidin, following rational genome mining for LanM proteins. Appl Environ Microbiol. 2009;75:5451-60 pubmed publisher
  18. Firth A, Atkins J. Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning. Virol J. 2010;7:17 pubmed publisher
    ..Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively). ..
  19. Bekaert M, Atkins J, Baranov P. ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting. Bioinformatics. 2006;22:2463-5 pubmed
    ..The PHP based web interface of ARFA and the source code are located at http://recode.genetics.utah.edu/arfa ..
  20. O Connell Motherway M, Zomer A, Leahy S, Reunanen J, Bottacini F, Claesson M, et al. Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor. Proc Natl Acad Sci U S A. 2011;108:11217-22 pubmed publisher
    ..Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria. ..
  21. Fallico V, McAuliffe O, Fitzgerald G, Ross R. Plasmids of raw milk cheese isolate Lactococcus lactis subsp. lactis biovar diacetylactis DPC3901 suggest a plant-based origin for the strain. Appl Environ Microbiol. 2011;77:6451-62 pubmed publisher
    ..lactis DPC3901 suggests a plant origin for the raw milk cheese isolate and provides for the first time the genetic basis to support the concept of the plant-milk transition for Lactococcus strains...
  22. Ross P, O Gara F, Condon S. Cloning and characterization of the thymidylate synthase gene from Lactococcus lactis subsp. lactis. Appl Environ Microbiol. 1990;56:2156-63 pubmed
    ..coli. An A-T-rich sequence characteristic of gram-positive promoters was also noted adjacent to the -35 region. The thyA gene has potential as a marker for plasmid maintenance and selection in food systems...
  23. Horgan C, Hanscom S, McCaffrey M. GRAB is a binding partner for the Rab11a and Rab11b GTPases. Biochem Biophys Res Commun. 2013;441:214-9 pubmed publisher
    ..These data identify GRAB as a dual Rab-binding protein that could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. ..
  24. Bullman S, Kearney K, O Mahony M, Kelly L, Whyte P, Fanning S, et al. Identification and genetic characterization of a novel picornavirus from chickens. J Gen Virol. 2014;95:1094-103 pubmed publisher
    ..Further studies are required to investigate the pathogenic potential of this virus within the avian host. ..
  25. Burgess C, O Connell Motherway M, Sybesma W, Hugenholtz J, van Sinderen D. Riboflavin production in Lactococcus lactis: potential for in situ production of vitamin-enriched foods. Appl Environ Microbiol. 2004;70:5769-77 pubmed publisher
    ..The results presented here are an important step toward the development of fermented foods containing increased levels of riboflavin, produced in situ, thus negating the need for vitamin fortification...
  26. Keating K, Giblin L, Lynch P, Quane K, Lehane M, Heffron J, et al. Detection of a novel mutation in the ryanodine receptor gene in an Irish malignant hyperthermia pedigree: correlation of the IVCT response with the affected and unaffected haplotypes. J Med Genet. 1997;34:291-6 pubmed
    ..The results show that the normal RYR1 allele is unlikely to play a role in IVCT variation. ..
  27. Horgan C, Walsh M, Zurawski T, McCaffrey M. Rab11-FIP3 localises to a Rab11-positive pericentrosomal compartment during interphase and to the cleavage furrow during cytokinesis. Biochem Biophys Res Commun. 2004;319:83-94 pubmed
    ..It is likely that Rab11-FIP3 is involved in trafficking events other than Tfn trafficking; these may include the transport of endosomally derived membrane to the cleavage furrow during cytokinesis. ..
  28. Forde A, Fitzgerald G. Molecular organization of exopolysaccharide (EPS) encoding genes on the lactococcal bacteriophage adsorption blocking plasmid, pCI658. Plasmid. 2003;49:130-42 pubmed
    ..Evidence of a gene encoding UDP-glucose dehydrogenase is also presented and this is the first description of such a gene in Lactococcus...
  29. Firth A, Atkins J. Bioinformatic analysis suggests that the Cypovirus 1 major core protein cistron harbours an overlapping gene. Virol J. 2008;5:62 pubmed publisher
    ..The ORFX amino acid sequences are hydrophilic and basic, with between 12 and 16 Arg/Lys residues in each though, at 7.5-10.2 kDa, the putative ORFX product is too small to appear on typical published protein gels...
  30. O Toole P, Snelling W, Canchaya C, Forde B, Hardie K, Josenhans C, et al. Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen. BMC Genomics. 2010;11:164 pubmed publisher
    ..mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome...
  31. Flemer B, Kennedy J, Margassery L, Morrissey J, O Gara F, Dobson A. Diversity and antimicrobial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp. J Appl Microbiol. 2012;112:289-301 pubmed publisher
    ..To evaluate the diversity and antimicrobial activity of bacteria from the marine sponges Suberites carnosus and Leucosolenia sp...
  32. Wallace D, Lindsay A, Hendrick A, McCaffrey M. Rab11-FIP4 interacts with Rab11 in a GTP-dependent manner and its overexpression condenses the Rab11 positive compartment in HeLa cells. Biochem Biophys Res Commun. 2002;299:770-9 pubmed
    ..It is likely that Rab11-FIP4 serves as a Rab11 effector in a Rab11 mediated function other than transferrin recycling. ..
  33. Lindsay A, Hendrick A, Cantalupo G, Senic Matuglia F, Goud B, Bucci C, et al. Rab coupling protein (RCP), a novel Rab4 and Rab11 effector protein. J Biol Chem. 2002;277:12190-9 pubmed
    ..RCP is a homologue of Rip11 and therefore belongs to the recently described Rab11-FIP family. ..
  34. Garvey P, Fitzgerald G, Hill C. Cloning and DNA sequence analysis of two abortive infection phage resistance determinants from the lactococcal plasmid pNP40. Appl Environ Microbiol. 1995;61:4321-8 pubmed
    ..The predicted protein product of abiF shows significant homology to the products of two other lactococcal abortive infection genes, abiD and abiD1...
  35. Rosberg Cody E, Liavonchanka A, Gobel C, Ross R, O Sullivan O, Fitzgerald G, et al. Myosin-cross-reactive antigen (MCRA) protein from Bifidobacterium breve is a FAD-dependent fatty acid hydratase which has a function in stress protection. BMC Biochem. 2011;12:9 pubmed publisher
  36. Claesson M, Cusack S, O Sullivan O, Greene Diniz R, de Weerd H, Flannery E, et al. Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4586-91 pubmed publisher
    ..We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability. ..
  37. Phelan R, O Halloran J, Kennedy J, Morrissey J, Dobson A, O Gara F, et al. Diversity and bioactive potential of endospore-forming bacteria cultured from the marine sponge Haliclona simulans. J Appl Microbiol. 2012;112:65-78 pubmed publisher
    ..The main aims of this study were to isolate and characterize the spore-forming bacteria from the marine sponge Haliclona simulans and to examine their potential as a source for bioactive compounds...
  38. Wallace D, Cotter T. Histone deacetylase activity in conjunction with E2F-1 and p53 regulates Apaf-1 expression in 661W cells and the retina. J Neurosci Res. 2009;87:887-905 pubmed publisher
    ..Overall, we propose a role for HDAC activity, E2F-1, and p53 in the regulation of Apaf-1 expression in 661W cells; initial data also indicate a regulatory role in the retina. ..
  39. Cotter P, Emerson N, Gahan C, Hill C. Identification and disruption of lisRK, a genetic locus encoding a two-component signal transduction system involved in stress tolerance and virulence in Listeria monocytogenes. J Bacteriol. 1999;181:6840-3 pubmed
  40. Scanlan P, Marchesi J. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J. 2008;2:1183-93 pubmed publisher
  41. Sriramulu D, Liang M, Hernandez Romero D, Raux Deery E, Lünsdorf H, Parsons J, et al. Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1,2-propanediol by disproportionation. J Bacteriol. 2008;190:4559-67 pubmed publisher
    ..reuteri. The metabolosome-associated diol dehydratase we describe is the only candidate glycerol dehydratase present on inspection of the L. reuteri F275 genome sequence...
  42. Ryan R, Fouhy Y, Garcia B, Watt S, Niehaus K, Yang L, et al. Interspecies signalling via the Stenotrophomonas maltophilia diffusible signal factor influences biofilm formation and polymyxin tolerance in Pseudomonas aeruginosa. Mol Microbiol. 2008;68:75-86 pubmed publisher
  43. Loughran G, Healy N, Kiely P, Huigsloot M, Kedersha N, O Connor R. Mystique is a new insulin-like growth factor-I-regulated PDZ-LIM domain protein that promotes cell attachment and migration and suppresses Anchorage-independent growth. Mol Biol Cell. 2005;16:1811-22 pubmed
    ..The data indicate that Mystique is an IGF-IR-regulated adapter protein located at the actin cytoskeleton that is necessary for the migratory capacity of epithelial cells. ..
  44. Reen F, Boyd E. Molecular typing of epidemic and nonepidemic Vibrio cholerae isolates and differentiation of V. cholerae and V. mimicus isolates by PCR-single-strand conformation polymorphism analysis. J Appl Microbiol. 2005;98:544-55 pubmed
    ..cholerae and Vibrio mimicus isolates...
  45. McLellan A, Zimmermann W, Moore T. Conservation of pregnancy-specific glycoprotein (PSG) N domains following independent expansions of the gene families in rodents and primates. BMC Evol Biol. 2005;5:39 pubmed
    ..Partial conservation of RGD and RGD-like tri-peptides in primate and rodent N and N1 domains, respectively, supports a role for these motifs in PSG function. ..
  46. Loughran G, Firth A, Atkins J. Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome. Proc Natl Acad Sci U S A. 2011;108:E1111-9 pubmed publisher
    ..Unlike previous cases of programmed -1 frameshifting, here frameshifting is modulated by virus infection, thus suggesting a novel regulatory role for frameshifting in these viruses. ..
  47. Garvey P, Rince A, Hill C, Fitzgerald G. Identification of a recA homolog (recALP) on the conjugative lactococcal phage resistance plasmid pNP40: evidence of a role for chromosomally encoded recAL in abortive infection. Appl Environ Microbiol. 1997;63:1244-51 pubmed
    ..Interestingly, it was shown that the chromosomally encoded recA is necessary for complete expression of the AbiF phenotype, confirming a role for RecA in this abortive infection system...
  48. Colleran A, Collins P, O Carroll C, Ahmed A, Mao X, McManus B, et al. Deubiquitination of NF-?B by Ubiquitin-Specific Protease-7 promotes transcription. Proc Natl Acad Sci U S A. 2013;110:618-23 pubmed publisher
    ..These findings reveal a unique mechanism controlling NF-?B activity and demonstrate that the deubiquitination of NF-?B by USP7 is critical for target gene transcription. ..
  49. Wang Y, Birkenhead K, Boesten B, Manian S, O Gara F. Genetic analysis and regulation of the Rhizobium meliloti genes controlling C4-dicarboxylic acid transport. Gene. 1989;85:135-44 pubmed
    ..Under micro-aerobic conditions, however, NifA induction alone is not sufficient for expression of the dctA promoter, even though the NifA-dependent nifHDK promoter is highly expressed under these conditions...
  50. Collins P, Kiely P, Carmody R. Inhibition of transcription by B cell Leukemia 3 (Bcl-3) protein requires interaction with nuclear factor ?B (NF-?B) p50. J Biol Chem. 2014;289:7059-67 pubmed publisher
  51. O Flaherty S, Ross R, Coffey A. Bacteriophage and their lysins for elimination of infectious bacteria. FEMS Microbiol Rev. 2009;33:801-19 pubmed publisher
    ..Such developments have prompted this review into the status of phage research as it pertains to the control of infectious bacteria. ..
  52. Stanton C, Ross P, Hutson S, Wallin R. Evidence for competition between vitamin K-dependent clotting factors for intracellular processing by the vitamin K-dependent gamma-carboxylase. Thromb Res. 1995;80:63-73 pubmed
    ..The variations in the concentrations of the prothrombin and the factor X precursors that were as associated with the ER membrane correlated with the available prothrombin and factor X substrate pools for the gamma-carboxylase. ..
  53. Begley M, Bron P, Heuston S, Casey P, Englert N, Wiesner J, et al. Analysis of the isoprenoid biosynthesis pathways in Listeria monocytogenes reveals a role for the alternative 2-C-methyl-D-erythritol 4-phosphate pathway in murine infection. Infect Immun. 2008;76:5392-401 pubmed publisher
    ..In vivo bioluminescence imaging also confirmed in vivo expression of the gcpE gene (MEP pathway) during murine infection...
  54. Kennedy J, Codling C, Jones B, Dobson A, Marchesi J. Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ Microbiol. 2008;10:1888-902 pubmed publisher
    ..Analyses of these clones revealed a diverse collection of PKS sequences which were most closely affiliated with PKS from members of the Cyanobacteria, Myxobacteria and Dinoflagellata...
  55. O Sullivan T, van Sinderen D, Fitzgerald G. Structural and functional analysis of pCI65st, a 6.5 kb plasmid from Streptococcus thermophilus NDI-6. Microbiology. 1999;145 ( Pt 1):127-34 pubmed
    ..In addition, plasmid-free mutants were lysed in broth by bacteriophages to which the parent culture was resistant...
  56. O Connell Motherway M, van Sinderen D, Morel Deville F, Fitzgerald G, Ehrlich S, Morel P. Six putative two-component regulatory systems isolated from Lactococcus lactis subsp. cremoris MG1363. Microbiology. 2000;146 ( Pt 4):935-47 pubmed
    ..Mutational analysis of the remaining four systems revealed that they are implicated in susceptibility to extreme pH, osmotic or oxidative conditions, or the regulation of phosphatase activity in L. lactis. ..
  57. Stack H, Sleator R, Bowers M, Hill C, Gahan C. Role for HtrA in stress induction and virulence potential in Listeria monocytogenes. Appl Environ Microbiol. 2005;71:4241-7 pubmed
    ..Our findings suggest that L. monocytogenes lmo0292 encodes an HtrA-like serine protease that is not part of the classical heat shock response but is involved in stress responses and virulence. ..
  58. Ventura M, Zink R, Fitzgerald G, van Sinderen D. Gene structure and transcriptional organization of the dnaK operon of Bifidobacterium breve UCC 2003 and application of the operon in bifidobacterial tracing. Appl Environ Microbiol. 2005;71:487-500 pubmed publisher
    ..The use of these genes in bifidobacterial species as an alternative or complement to the 16S rRNA gene marker provides sequence signatures that allow a high level of discrimination between closely related species of this genus...
  59. Ventura M, Canchaya C, Zink R, Fitzgerald G, van Sinderen D. Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: genetic, transcriptional, and phylogenetic analyses. Appl Environ Microbiol. 2004;70:6197-209 pubmed publisher
  60. Duranti S, Turroni F, Lugli G, Milani C, Viappiani A, Mangifesta M, et al. Genomic characterization and transcriptional studies of the starch-utilizing strain Bifidobacterium adolescentis 22L. Appl Environ Microbiol. 2014;80:6080-90 pubmed publisher
    ..Such extracellular structures include so-called sortase-dependent and type IVb pili, which may be involved in gut colonization of 22L through adhesion to extracellular matrix proteins. ..
  61. Marsh A, O Sullivan O, Ross R, Cotter P, Hill C. In silico analysis highlights the frequency and diversity of type 1 lantibiotic gene clusters in genome sequenced bacteria. BMC Genomics. 2010;11:679 pubmed publisher
    ..These clusters represent a rich repository which can yield a large number of valuable novel antimicrobials and biosynthetic enzymes. ..
  62. Collins B, Bebeacua C, Mahony J, Blangy S, Douillard F, Veesler D, et al. Structure and functional analysis of the host recognition device of lactococcal phage tuc2009. J Virol. 2013;87:8429-40 pubmed publisher
    ..In the case of Tuc2009, such adsorption-blocking ability was reduced in tripods that lacked BppATuc2009, indicating that this protein increases the binding specificity and/or affinity of the Tuc2009 tripod to its host receptor. ..
  63. O Callaghan J, Caddick M, Dobson A. A polyketide synthase gene required for ochratoxin A biosynthesis in Aspergillus ochraceus. Microbiology. 2003;149:3485-91 pubmed
    ..A mutant in which the pks gene has been interrupted cannot synthesize ochratoxin A. This report is the first of the cloning and characterization of a gene involved in ochratoxin A biosynthesis...
  64. Stockley J, O NEILL C. The proteins BACE1 and BACE2 and beta-secretase activity in normal and Alzheimer's disease brain. Biochem Soc Trans. 2007;35:574-6 pubmed
    ..This article gives a brief review of studies which have examined BACE1 protein levels and beta-secretase activity in control and AD brain, considering further the expression of BACE2 in the human brain. ..
  65. Ivanov I, Atkins J. Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res. 2007;35:1842-58 pubmed
    ..Among these are RNA pseudoknots, RNA stem-loops, conserved primary RNA sequences, nascent peptide sequences and branch-specific 'shifty' codons. ..
  66. O Riordan K, Fitzgerald G. Molecular characterisation of a 5.75-kb cryptic plasmid from Bifidobacterium breve NCFB 2258 and determination of mode of replication. FEMS Microbiol Lett. 1999;174:285-94 pubmed
    ..Two other ORFs, par (199 amino acids) and an ftsK-like gene (286 amino acids), were assigned putative functions based on the presence of conserved motifs in their deduced proteins...
  67. Moynihan J, Morrissey J, Coppoolse E, Stiekema W, O Gara F, Boyd E. Evolutionary history of the phl gene cluster in the plant-associated bacterium Pseudomonas fluorescens. Appl Environ Microbiol. 2009;75:2122-31 pubmed publisher
    ..The possible evolutionary and functional implications for retention of the phl cluster and 2,4-DAPG production in some lineages of P. fluorescens are discussed. ..
  68. Menton J, Cremin S, Canier L, Horgan M, Fanning L. Molecular epidemiology of sexually transmitted human papillomavirus in a self referred group of women in Ireland. Virol J. 2009;6:112 pubmed publisher
    ..Positive samples were then genotyped by means of a commercially available assay (LiPA). A comparison of genotyping results determined by the LiPA assay and direct amplicon DNA sequencing was also performed...