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Sequences Specific (sequence + specific)
Selected AbstractsIdentification of a Brevibacterium marker gene specific to poultry litter and development of a quantitative PCR assayJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2010J.L. Weidhaas Abstract Aim:, To identify a DNA sequence specific to a bacterium found in poultry litter that was indicative of faecal contamination by poultry sources. Methods and Results:, Faecally contaminated poultry litter and soils were used as source material for the development of a quantitative polymerase chain reaction (qPCR) method targeting the 16S rRNA gene of a Brevibacterium sp. The identified sequence had 98% nucleotide identity to the 16S rRNA gene of Brevibacterium avium. The qPCR method was tested on 17 soiled litter samples; 40 chicken faecal samples; and 116 nontarget faecal samples from cattle, swine, ducks, geese, and human sewage collected across the United States. The 571-bp product was detected in 76% of poultry-associated samples, but not in 93% of faecal samples from other sources. Marker concentrations were 107,109 gene copies per gram in soiled litter, up to 105 gene copies per gram in spread-site soils, and 107 gene copies per litre in field run-off water. Results were corroborated by a blinded study conducted by a second laboratory. Conclusion:, The poultry-specific PCR product is a useful marker gene for assessing the impact of faecal contamination as a result of land-applied poultry litter. Significance and Impact of the Study:, This study describes the first quantitative, sensitive and specific microbial source tracking method for the detection of poultry litter contamination. [source] Multiparasitism of Choristoneura fumiferana by the ichneumonid Tranosema rostrale and the tachinid Actia interrupta: occurrence in the field and outcome of competition under laboratory conditionsENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 2 2002Michel Cusson Abstract Tranosema rostrale (Brishke) (Hymenoptera, Ichneumonidae) and Actia interrupta Curran (Hymenoptera: Tachinidae) are the two endoparasitoids most frequently encountered in low-density populations of the spruce budworm, Choristoneura fumiferana (Clemens) (Lepidoptera, Tortricidae), in the Quebec City region. Monitoring of attack rates of implanted C. fumiferana larvae at two different study sites suggested the possible existence of competition between the two parasitoids, with A. interrupta seemingly displacing T. rostrale. Here, we show that multiparasitism involving these two species does occur in the field, but at a frequency too low to explain the seasonal pattern of decline in apparent parasitism by T. rostrale that accompanies the rise of A. interrupta attack rates. We also provide preliminary evidence, from laboratory experiments, that A. interrupta has a competitive advantage over T. rostrale and that the success of parasitism by A. interrupta may be enhanced by prior parasitism by T. rostrale under certain conditions, possibly due to the presence of the latter species' polydnavirus. In addition, we describe a PCR-based method that we developed to help detect the presence of T. rostrale eggs which often escape detection by simple visual examination of the dissected host larvae; DNA sequences specific to the polydnavirus injected by the female wasp at the time of oviposition can be readily amplified from whole host larvae. [source] Herpetic Folliculitis is Usually a Consequence of Varicella Zoster Virus InfectionJOURNAL OF CUTANEOUS PATHOLOGY, Issue 1 2005J Blair Skin biopsies of 8 patients diagnosed with herpetic folliculitis by light microscopy were retrieved from the files of the UCSF Dermatopathology Service. Clinical and microscopical features were reviewed and tabulated, and PCR analysis was employed to seek DNA sequences specific for herpes simplex virus (HSV) and varicella zoster virus (VZV). The study group included 4 women and 4 men, ages 15 to 54. Five patients (62%) were immunosuppressed, with underlying conditions including HIV infection, leukemia, rheumatoid arthritis, and lupus erythematosus with polyarteritis nodosa. Microscopically, herpetic cytopathic changes involved the isthmus in 7/8 cases (87%), and involved the sebaceous apparatus in 4/8 cases (50%). Herpetic viropathic changes were not found within eccrine epithelium. A moderate to dense perifollicular infiltrate, comprised mostly of lymphocytes, was evident in 7/8 cases (87%). After PCR expansion of genetic material extracted from the original paraffin blocks, VZV-specific DNA sequences were detected in 8/8 cases. We conclude that herpetic folliculitis is a consequence of VZV infection. Because follicular herpetic infection is often accompanied by a dense perifollicular lymphoid infiltrate, the microscopical presentation can simulate inflammatory skin diseases such as lupus erythematosus. Level sections may be required for a specific diagnosis to be made. [source] Poster Sessions BP06: Neurogenesis, Stem Cells and ApoptosisJOURNAL OF NEUROCHEMISTRY, Issue 2002J. Qiu The NF-,B transcription factor regulates bcl-x gene expression, which may determine hypoxia-induced neuronal apoptosis. We examined hypoxia-induced NF-,B and Bcl-xL changes in rat hippocampus. We showed differential hypoxia-induced NF-,B binding to the bcl-x promoter CS4 and IgG,,B enhancer sequences by rat hippocampal nuclear extracts. The differential NF-,B binding to these two promoter sequences was also determined in a contused spinal cord injury model and in vitro studies with LPS-treated Hela cells. There was tissue-, gene promoter-specific and time-dependent regulation of bcl-x gene expression by NF-,B in support of the hypothesis that NF-,B has tissue- and gene-specific regulatory effects and that these effects may account for both the pro- and anti-apoptotic roles assigned to NF-,B in different apoptotic processes. We applied ,decoy' oligonucleotides with sequences specific to different promoters to the rat hippocampus and measured ,decoy' inhibitory effects on nuclear NF-,B binding. The IgG-,B enhancer sequence ,decoy' showed stronger inhibition on nuclear NF-,B c-Rel/p50 binding to the bcl-x gene promoter CS4 sequence when compared to NF-,B p50/p50 binding to the same sequence. This result suggests that the ,decoy' approach has the potential to selectively manipulate NF-,B regulation of gene expression in response to hypoxia. Acknowledgements:, Supported by NINDS NS-39161, Shriner Grant 8710 and a Grant from the Sealy Center on Aging to J. Qiu. [source] The Occurrence of Phytoplasmas in Apple Trees Showing Branch TwistingJOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2005J. Fránová Abstract Apple trees showing malformation of branches were found at different locations in the Czech Republic. Ultrathin sections of tissues from diseased trees showed the presence of pleomorphic bodies resembling phytoplasma. Nested-polymerase chain reaction (PCR) assays with primers amplifying16S,23S ribosomal RNA (rRNA) sequences specific for phytoplasma and the subsequent restriction fragment length polymorphism (RFLP) analyses allowed to classify the detected phytoplasmas in the aster yellows group, subgroup 16SrI-C in 12 trees, single (11 plants) or mixed with phytoplasma belonging to subgroup 16SrI-B (1 plant). Phytoplasma of apple proliferation group (16SrX-A subgroup) were identified in cv. Mat,ino. Apple tree cv. P,e,tické r,,ové was infected by phytoplasma of the 16SrX-A and 16SrI-B subgroups. No phytoplasmas were detected in asymptomatic apple trees. [source] Selective amplification of bacterial RNA: use of a DNA primer containing mismatched bases near its 3, terminus to reduce false-positive signalsLETTERS IN APPLIED MICROBIOLOGY, Issue 3 2000K. Koo A reverse transcription PCR (RT,PCR) method designed to reduce false-positive results due to the co-amplification of contaminating genomic DNA is reported. Feasibility of the method was evaluated using 16S rRNA sequences specific to Bacillus cereus. A DNA oligonucleotide primer, consisting of 22-bases containing three consecutive mismatched bases near its 3, terminus (primer B16RT), was used for reverse transcription and in subsequent cDNA amplification. Specific rRNA was reverse transcribed at low temperature (40 °C or 45 °C) in the presence of primer B16RT. As subsequent PCR using primer B16RT at high (62 °C) annealing temperatures is not nearly as efficient as amplification using the specific primer, amplification of genomic DNA was hindered relative to the amplification of cDNA. The method was readily adapted to the selective amplification of mRNA of the Listeria monocytogenes listeriolysin O (hly) gene. [source] Insights into Sequence,Activity Relationships amongst Baeyer,Villiger Monooxygenases as Revealed by the Intragenomic Complement of Enzymes from Rhodococcus jostii RHA1CHEMBIOCHEM, Issue 7 2009Claudia Szolkowy Abstract TheRhodococcus jostiiRHA1 genome encodes a number of enzymes that can be exploited as biocatalysts. Study of the substrate spectrum and enantioselectivity of Baeyer,Villiger monooxygenases from R. jostii allowed the identification of short amino acid sequences specific to groups displaying certain catalytic characteristics. The gel illustrates the substrate acceptance spectra and selectivities of the different proteins. Microbial genome sequences are providing a wealth of information on new enzymes that have considerable potential as biocatalysts. The recently sequenced genome of Rhodococcus jostii RHA1, for example, has revealed an impressive array of catabolic enzymes, including many putative Baeyer,Villiger monooxygenases (BVMOs). We have cloned 23 target BVMO sequences from the genome of R. jostii RHA1 and heterologously expressed 13 of these as soluble proteins to unearth new substrate specificities and selectivities. Whole-cell biocatalysts expressing the genes were screened against seven different test substrates. Each of these catalysts displayed activity toward at least three ketones. We observed a remarkable diversity of both regio- and enantioselectivity among the BVMOs from R. jostii RHA1 for the transformation of two chiral substrates, with some enzymes displaying high enantioselectivity for the isomers of 2-methylcyclopentanone. With the notable exception of the product of gene ro03437, named MO14, the biocatalysts' sequences correlated well with their respective activities and selectivities. This correlation allowed the identification of sequence motifs specific to subgroups of the BVMOs from R. jostii and other organisms. Overall, the data improve predictive models of BVMO activity from sequence and suggest new avenues to pursue in engineering these enzymes. [source] |