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Chen, H.,Lim, C.K.,Lee, Y.K.,Chan, Y.N. (2000). Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. International Journal of Systematic and Evolutionary Microbiology 50 (2) : 471-478. ScholarBank@NUS Repository ...
The 2,030 isolates analyzed in the present study comprised 1,235 isolates from stool samples from hospital patients, 395 isolates from stool samples referred via community practitioners, 150 isolates from the hospital environment, 27 isolates from veterinary sources, 89 isolates from the general environment, 1 isolate from an extraintestinal human site, and 133 reference strains held in the National Collection of Type Cultures, the American Type Culture Collection and the Culture Collection, University of Göteborg, and in the personal collections of C. difficile types held by Delmee and others (6, 16) and other members of the International Study Group on C. difficile (3).. PCR ribotyping was performed in duplicate, with slight modifications to a method described previously (13). Briefly, bacteria were harvested from overnight anaerobic cultures on Fastidious Anaerobe Agar (LabM, Bury, United Kingdom) supplemented with 6% horse blood. Crude template nucleic acid was prepared by resuspension of ...
Staphylococcus aureus is an important human and animal pathogen, and is regarded as an important cause of intramammary infection (IMI) in ruminants. Staphylococcus aureus genetic variability and virulence factors have been well studied in veterinary medicine, especially in cows as support for control and management of IMI. The aim of the present study was to genotype 71 Staph. aureus isolates from the bulk tank and foremilk of water buffaloes (n. = 40) and from udder tissue (n. = 7) and foremilk (n. = 24) from small ruminants. The method used was previously applied to bovine Staph. aureus and is based on the amplification of the 16S-23S rRNA intergenic spacer region. The technique applied was able to identify different Staph. aureus genotypes isolated from dairy species other than the bovine species, and cluster the genotypes according to species and herds. Virulence gene distribution was consistent with genotype differentiation. The isolates were also characterized through determination of the ...
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The University of Auckland Library This study describes the extent of variability in biofilm bacterial community structure across a broad range of spatial and temporal scales and assesses whether this may be used as an indicator of stream ecological health and function. A community DNA fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis - ARISA) was used to examine the structure of bacterial communities within freshwater stream biofilms. When compared with macrobenthic invertebrate community assemblages using multi-dimensional scaling techniques, similar broad-scale trends in population structure were revealed between organisms at these different trophic levels. For both communities, spatial variability in community structure was greater between streams than within each site, or compared to temporal variability measured over 1 year. Distance-based redundancy analysis of both bacterial ARISA and macroinvertebrate data estimated that the largest cause of variation in community ...
Freshwater streams display both temporal (time) and spatial (space) differences. Time variation is a result of seasonal influences and space variation is due to flow regime, substrate type, water solutes, suspended materials and incident light exposure. It is believed that bacterial communities are good indicators due to their rapid life cycle. However, if we cant see them, how do we know that they are present and observe changes? Bacteria can be detected using Automated Ribosomal Intergenic Spacer Analysis (ARISA) which creates fingerprints of microbial communities. The fingerprint produced is just like a human fingerprint, because it is unique to a bacteria species just like a fingerprint is unique to a person ...
The Crystal Refinery is a former refinery site in Carson City Michigan that has had historic releases of refined and unrefined crude oil dating back to the late 1940s. The contamination of soil with light non-aqueous phase liquids (LNAPL) has had a dynamic impact on the subsurface environment in adjacent Carson City Park. Very little is known about the complex interactions between microbial communities, geochemistry and geophysics. In order to investigate possible connections between these parameters a multidisciplinary study was undertaken to investigate the hypothesis that the degradation of LNAPL by resident microbial communities causes a local increase in organic acid concentrations, which in turn cause an increase in native mineral weathering and a concurrent decrease in the bulk electrical resistivity of soil.Microbial community structure was analyzed using a 96-well most probable number (MPN) method and rDNA intergenic spacer region analysis (RISA). In addition to the observational study of this
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Under the intluence of 5-tluoro-uridine, the ultrastructure of the rDNA transcription units in Xenopus oocytes is altered. Whereas part of the matrix units maintains anormal aspect or shows various degrees of inhibition, in a strong proportion of the transcription units the alternating pattern of matrix units and fibril-free spacer regions is no longer recognized. Transcriptional complexes are found along the entire DNP axis, including the regions of the spacers. These observations support biochemical data on transcription in rDNA spacer region ...
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Lactobacillus acetotolerans strain ATCC 43578 16S ribosomal RNA gene,partial sequence; 16S-23S intergenic spacer, complete sequence; and 23Sribosomal RNA gene, partial ...
關於生長在藻類上的真菌研究缺乏,特別是海洋大型藻類,而前人只針對小部份褐藻、綠藻和紅藻進行初部研究。因此本研究選取臺灣北部的優勢紅藻細翼枝菜 (Pterocladiella capillacea) 作為研究對象,以培養法分離真菌及非培養法 (metabarcoding) 結果比較細翼枝菜上的真菌多樣性。於培養法中,將洗淨的健康及死亡藻體置於葡萄糖-酵母萃取物-蛋白腖瓊脂海水培養基 (GYPS) 及人工海水瓊脂培養基 (SWA) 上,待菌絲從藻體生長出來後便繼代於玉米粉瓊脂培養基 (CMAS) 上,依其菌落形態分群。利用聚合酶連鎖反應 (polymerase chain reaction, PCR) 擴增其核醣體基因 (rDNA) 內轉錄間隔區 (internal transcribed spacer, ITS) 及核醣體大亞基 (large subunit, LSU) 並進行測序,最後與NCBI的GenBank資料庫序列進行比較以鑑種。於高通量定序中,從冷凍乾燥後的細翼枝菜藻體萃取總DNA和RNA
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Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were
While the 16S ribosomal gene is the standard for distinguishing among bacterial species, it is insufficiently variable among P. gingivalis strains for resolution. The ribosomal ISR is the most variable portion of the ribosomal operon and is sufficiently variable within a species to resolve strains (18). This locus also offers a technical advantage since it can be amplified with species-specific and conserved primers in the 16S and 23S ribosomal genes, thus avoiding the need to culture bacteria from clinical specimens. There are four copies of the ribosomal operon in P. gingivalis (P. gingivalis genome project [http://www.forsyth.org/pggp/number_of_rrna_operons.htm]). Ribosomal operons in general, including the ISR, are maintained by concerted evolution (2, 4). This correction minimizes replacement by exogenous sequences, so that the operon should closely reflect the evolutionary history of the organism.. We have previously used the ISR for both sequence-based and heteroduplex type-based P. ...
Author contributions: C.L.S. and K.A.S. designed research; K.A.S., V.R., E.B., K.V., P.W.C., A.N.M., M.J.W., M.C.A., K.-D.A., F.-Y.B., R.W.B., D.B., M.-J.B., M. Blackwell, T.B., M. Bogale, N.B., A.R.B., B.B., L.C., Q.C., G.C., P. Chaverri, B.J.C., A.C., P. Cubas, C.C., U.D., Z.W.d.B., G.S.d.H., R.D.-P., B. Dentinger, J.D-U., P.K.D., B. Douglas, M.D., T.A.D., U.E., J.E.E., M.S.E., K.F., M.F., M.A.G., Z.-W.G., G.W.G., K.G., J.Z.G., M. Groenewald, M. Grube, M. Gryzenhout, L.-D.G., F. Hagen, S. Hambleton, R.C.H., K. Hansen, P.H., G.H., C.H., K. Hirayama, Y.H., H.-M.H., K. Hoffmann, V. Hofstetter, F. Högnabba, P.M.H., S.-B.H., K. Hosaka, J.H., K. Hughes, Huhtinen, K.D.H., T.J., E.M.J., J.E.J., P.R.J., E.B.G.J., L.J.K., P.M.K., D.G.K., U.K., G.M.K., C.P.K., S.L., S.D.L., A.S.L., K.L., L.L., J.J.L., H.T.L., H.M., S.S.N.M., M.P.M., T.W.M., A.R.M., A.S.M., W.M., J.-M.M., S.M., L.G.N., R.H.N., T.N., I.N., G.O., I. Okane, I. Olariaga, J.O., T. Papp, D.P., T. Petkovits, R.P.-B., W.Q., H.A.R., D.R., T.L.R., ...
Respiratory infection in cystic fibrosis (CF) is polymicrobial, but standard sputum microbiology does not account for the lung microbiome or detect changes in microbial diversity associated with disease. As a clinically applicable CF microbiome surveillance scheme, total sputum nucleic acids isolated by a standard high-throughput robotic method for accredited viral diagnosis were profiled for bacterial diversity using ribosomal intergenic spacer analysis (RISA) PCR. Conventional culture and RISA were performed on 200 paired sputum samples from 93 CF adults; pyrosequencing of the 16S rRNA gene was applied to 59 patients to systematically determine bacterial diversity. Compared to the microbiology data, RISA profiles clustered into two groups: the emerging nonfermenting Gram-negative organisms (eNFGN) and Pseudomonas groups. Patients who were culture positive for Burkholderia, Achromobacter, Stenotrophomonas, and Ralstonia clustered within the eNFGN group. Pseudomonas group RISA profiles were ...
In recent years, DNA barcoding is considered as a universal species identification method for plants. It mainly involves discrimination of species through standardized molecular marker gene and is gaining support from the taxonomists as well. DNA barcoding has wider applications in different studies namely to predict cryptic species, to study biological samples in forensics and conservation sciences for characterization of biodiversity; to track inventory for plants identity or purity and in ecological species diversity studies [1-4]. Various molecular markers have been used for DNA barcoding studies. A 650 base pair (bp) of the mitochondrial cytochrome c oxidase unit I (COI) gene was used as a barcode in various organisms such as animals, birds, fishes, insects and nematodes [4-8]. A specific region of the nuclear ribosomal internal transcribed spacer (ITS) gene is the well-studied DNA barcode for fungi [9]. In plant DNA barcoding, there has been extensive debate about the locus choice; several ...
TY - JOUR. T1 - Report of the second internal workshop on human chromosome 5 mapping. AU - Westbrook, C. A.. AU - Neuman, W. L.. AU - Mcpherson, John Douglas. AU - Camper, S.. AU - Wasmuth, J.. AU - Plaetke, R.. AU - Williamson, R.. PY - 1992. Y1 - 1992. UR - http://www.scopus.com/inward/record.url?scp=0026677059&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0026677059&partnerID=8YFLogxK. M3 - Article. C2 - 1362532. AN - SCOPUS:0026677059. VL - 61. SP - 226. EP - 231. JO - Cytogenetic and Genome Research. JF - Cytogenetic and Genome Research. SN - 1424-8581. IS - 4. ER - ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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Spacer 9 is a triethylene glycol chain that is 9 atoms long (6 carbons + 3 oxygens), and is used to incorporate a spacer arm into an oligonucleotide. Spacer 9 can be incorporated in consecutive additions whenever a longer spacer is required. Spacer 9 has been used to form non-nucleotide bridges in hairpin loops in oligonucleotides (1), for linking oligonucleotides to epitopes for drug development (2), and for solid-phase immobilization of hybridization probes (3). Multiple incorporation of Spacer 9 has been used to form long, flexible linker arms between the two domains (double-helix forming and triple-helix forming, respectively) of a bifunctional DNA oligonucleotide, in order to maximize the binding flexibility of the two domains for their respective targets (4). This oligo was used to form a peptide nucleic acid (PNA)-DNA conjugate for use in site-directed recombination applications.. References ...
We explored the potential of the cox1 gene in the species resolution of soil fungi and compared it with the nuclear internal transcribed spacer (ITS) and small subunit (SSU)-rDNA. Conserved primers allowing the amplification of the fungal cox1 gene were designed, and a total of 47 isolates of Zygomycota and Ascomycota were investigated. The analysis revealed a lack of introns in >90% of the isolat ...
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Lactobacillus kefiranofaciens strain ATCC 43761 16S ribosomal RNA gene,partial sequence; 16S-23S intergenic spacer, complete sequence; and 23Sribosomal RNA gene, partial ...
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The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Schultz, J.; Muller, T.; Achtziger, M.; Seibel, P. N.; Dandekar, T.; Wolf, M. in Nucleic Acids Res. (2006). 34 W704--707. ...
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