Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis

2005 ◽  
Vol 54 (11) ◽  
pp. 1031-1035 ◽  
Author(s):  
Niclas Grahn ◽  
Mounira Hmani-Aifa ◽  
Karin Fransén ◽  
Peter Söderkvist ◽  
Hans-Jürg Monstein
Keyword(s):  
16S Rdna ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Limited Information ◽  
Rdna Sequences ◽  
Biopsy Specimens ◽  
16S Rdna Pcr ◽  
H Pylori ◽  
Species Specific ◽  
Pyrosequencing Analysis

Seroepidemiological studies have indicated that Helicobacter pylori infection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or not Helicobacter species are present in CRC tissues. In this study the presence of Helicobacter DNA in 77 CRC biopsies was investigated by means of a Helicobacter species-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence of Helicobacter DNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA sequences corresponding to H. pylori 26695 and H. pylori J99 were most commonly found. Intriguingly, one sequence belonged to Helicobacter mustelae, previously identified in ferrets. No significant correlations were found in the prevalence of Helicobacter DNA between colon and rectum tumour biopsies (P = 0.815), nor between Dukes’ classes A/B and C/D (P = 0.262). 16S rDNA PCR amplification combined with pyrosequencing analysis of 16S rDNA variable V3 regions provides a powerful molecular tool to identify Helicobacter species in human biopsy specimens.

Development of a diagnostic molecular marker for Philonema spp. (Nematoda; Dracunculoidea) infecting salmonids in British Columbia

1995 ◽  
Vol 52 (S1) ◽  
pp. 129-133 ◽  
Author(s):  
L. Després ◽  
M.L. Adamson ◽  
T.E. McDonald
Keyword(s):  
British Columbia ◽  
Sockeye Salmon ◽  
Pcr Amplification ◽  
Base Substitution ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Nematode Parasites ◽  
Rdna Sequences ◽  
Morphological Criteria ◽  
In The Wild ◽  
Species Specific

We developed a species specific DNA probe based on differential PCR amplification that distinguishes two congeneric nematode parasites of salmonids in British Columbia: Philonema agubernaculum Simon and Simon, 1936, usually parasitic in lake resident rainbow trout, Oncorhynchus mykiss; and P. oncorhynchi Kuitunen-Ekbaum, 1933, parasitic in anadromous sockeye salmon, O. nerka. The region differentially amplified was the D3 expansion domain of the 28S rDNA. Sequences of the two species differ in two parts of the domain, one a single base substitution and the other a three base duplication in P. oncorhynchi. A primer specific to P. oncorhynchi (amplifying P. oncorhynchi, not P. agubernaculum) was defined in the duplication region. Using differential amplification, we showed that sockeye smolts are infected with P. agubernaculum, although returning adults harbour only P. oncorhynchi. This technique could conceivably be used to quantify the frequency of heterologous infections in the wild, before infecting worms are identifiable at the species level based on morphological criteria.

Analysis of Fungal Diversity in the Composting by Sequencing of Cloned PCR-Amplified 18S rDNA and Denaturing Gradient Gel Electrophoresis

2011 ◽  
Vol 356-360 ◽  
pp. 1747-1751
Author(s):  
Wan Li ◽  
Xiu Hong Xu ◽  
Jia Lei Xiao ◽  
Bi Xian Zhang ◽  
Hong Tao Li ◽  
...  
Keyword(s):  
Fungal Community ◽  
18S Rdna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Limited Information ◽  
Rdna Sequences ◽  
Microbiological Techniques ◽  
Gradient Gel Electrophoresis ◽  
Realistic View ◽  
Specific Amplification

Like bacteria, fungi play an important role in the composting process as major decomposers of organic substances. As only a small fraction of the fungi present in composting can be cultured because conventional microbiological techniques limited information on the composition of fungal communities in composting. Molecular methods are expected to give a more realistic view of species richness and distribution. For this purpose, we selected universal PCR primer set that allow the specific amplification of fungal 18S-ribosomal-DNA (rDNA) sequences. DNA was extracted from composting samples, and 18S rDNA genes were amplified by EF4/Fung5 (0.6kb) and EF4/NS2-GC (0.4kb). DGGE analysis of the fungal community in the composting of a microcosm experiment was carried out after amplification of total DNA with both primer pairs. Clear banding patterns were obtained with amplified production. 13 different bands excised from the DGGE gel were sequenced and compared with genbank. Sequencing showed that some could not be cultured; some were efficient cellulose-degrading strains. The results showed that diversity and composition of the fungal community in the composting can be analyzed by the combination of 18S rDNA PCR amplification and DGGE.

An integrative taxonomic approach to the identification of three new New Zealand endemic earthworm species (Acanthodrilidae, Octochaetidae: Oligochaeta)

Zootaxa ◽  
2011 ◽  
Vol 2994 (1) ◽  
pp. 21 ◽  
Author(s):  
STEPHANE BOYER ◽  
ROBERT J. BLAKEMORE ◽  
STEVE D. WRATTEN
Keyword(s):  
New Species ◽  
New Zealand ◽  
16S Rdna ◽  
Dna Sequences ◽  
Conservation Status ◽  
Earthworm Species ◽  
Holotype Specimen ◽  
Rdna Sequences ◽  
Taxonomic Approach ◽  
Three New Species

This work adds three new species to the ca. 200 currently known from New Zealand. In Acanthodrilidae is Maoridrilus felix and in Octochaetidae are Deinodrilus gorgon and Octochaetus kenleei. All three are endemics that often have restricted ranges; however, little is yet known of their distribution, ecology nor conservation status. DNA barcoding was conducted, which is the first time that New Zealand endemic holotypes have been so characterized. The barcoding region COI (cytochrome c oxidase subunit 1) as well as the 16S rDNA region were sequenced using tissue from the holotype specimen to provide indisputable uniqueness of the species. These DNA sequences are publically available on GenBank to allow accurate cross checking to verify the identification of other specimens or even to identify specimens on the basis of their DNA sequences alone. Based on their 16S rDNA sequences, the position of the three newly described species in the phylogeny of New Zealand earthworms was discussed. The description of new species using this approach is encouraged, to provide a user-friendly identification tool for ecologists studying diverse endemic faunas of poorly known earthworm species.

Clarification of the systematic position ofCercariaeum crassumWesenberg-Lund, 1934 (Digenea), based on karyological analysis and DNA sequences

2011 ◽  
Vol 86 (3) ◽  
pp. 293-301 ◽  
Author(s):  
R. Petkevičiūtė ◽  
V. Stunžėnas ◽  
G. Stanevičiūtė
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Developmental Stages ◽  
Sequence Divergence ◽  
Sister Group ◽  
Systematic Position ◽  
Life Cycles ◽  
Significant Information ◽  
Rdna Sequences ◽  
Species Specific

AbstractChromosome set and rDNA sequences of the larval digeneanCercariaeum crassumwere analysed in order to clarify its systematic position and possible adult form. Parasites were obtained from the sphaeriid bivalvePisidium amnicum, collected in Lithuanian and Finnish rivers. The karyotype is shown to consist of five pairs (2n = 10) of large, up to 14 μm, chromosomes. Complement, composed of a low diploid number of exclusively bi-armed elements, presumably arose through Robertsonian fusions of acrocentric chromosomes. Consistent with a Robertsonian-derived karyotype, one or two small, metacentric, mitotically stable B chromosomes were detected in the cells of parthenitae isolated from some host individuals. A phylogenetic analysis using rDNA internal transcribed spacer 2 (ITS2) and 28S sequences corroborates the allocation ofC. crassumto the family Allocreadiidae. In neighbour-joining and maximum parsimony phylogenetic treesC. crassumclusters into one clade withAllocreadiumspp., and is the closest sister group in relation toA. isoporum; the level of rDNA sequence divergence between them (2.67% for ITS2 and 1.16% for 28S) is consistent with the level expected for intrageneric variation. The present study adds significant information to a database for establishing species-specific characters for confident characterization of different developmental stages of allocreadiid species, clarification of their life cycles and evaluation of intra- and interspecific variability.

Bacterial endophytes of the wildflowerCrocus albiflorusanalyzed by characterization of isolates and by a cultivation-independent approach

2006 ◽  
Vol 52 (2) ◽  
pp. 140-149 ◽  
Author(s):  
Birgit Reiter ◽  
Angela Sessitsch
Keyword(s):  
16S Rdna ◽  
Clone Library ◽  
Pcr Amplification ◽  
Rflp Analysis ◽  
Community Analysis ◽  
Culture Collection ◽  
Phylogenetic Affiliation ◽  
16S Rdna Pcr ◽  
Wide Range ◽  
Cold Tolerant

The presence and taxonomy of endophytic bacteria of the entire aerial parts of crocus (Crocus albiflorus), a wildflower native in the Alps, were investigated. A combination of plating of plant macerates, isolation and sequence identification of isolates, and direct 16S rDNA PCR amplification followed by whole-community fingerprinting (T-RFLP) and by construction of a bacterial clone library was used. The results clearly indicated that a wide range of bacteria from diverse phylogenetic affiliation, mainly γ-Proteobacteria and Firmicutes, live in association with plants of C. albiflorus. The community composition of the culturable component of the microflora was remarkably different from that of the clone library. Only three bacterial divisions were found in the culture collection, which represented 17 phylotypes, whereas six divisions were identified in the clonal analysis comprising 38 phylotypes. The predominant group in the culture collection was the low G + C Gram-positive group, whereas in the clone library, the γ-Proteobacteria predominated. Interestingly, the most prominent bacterium within the uncultured bacterial community was a pseudo monad closely related to a cold-tolerant Pseudomonas marginalis strain. The results suggest that Crocus supports a diverse bacterial microflora resembling the microbial communities that have been described for other plants and containing species that have not been described in association with plants.Key words: crocus, endophytes, 16S rRNA, 16S rDNA clone library, T-RFLP analysis, community analysis.

Microbial 16S rDNA diversity in an anaerobic digester

1997 ◽  
Vol 36 (6-7) ◽  
pp. 49-55 ◽  
Author(s):  
Jean-Jacques Godon ◽  
Emmanuelle Zumstein ◽  
Patrick Dabert ◽  
Frédéric Habouzit ◽  
René Moletta
Keyword(s):  
Phylogenetic Analysis ◽  
Community Structure ◽  
16S Rdna ◽  
Bacterial Community Structure ◽  
Bacterial Population ◽  
Pcr Amplification ◽  
Operational Taxonomic Unit ◽  
Fluidized Bed Reactor ◽  
Rdna Sequences ◽  
Rdna Clone

The bacterial community structure of a fluidized bed reactor fed by vinasses was analysed by molecular identification. After PCR amplification, three 16S rDNA clone libraries of Bacteria, Archaea, and Procarya populations were established. Community structure was determined by phylogenetic analysis of 556 partial rDNA sequences (about 500 bp long). 139 OTUs (Operational Taxonomic Unit) were found among which 133 and 6 were from the Bacteria and Archaea domains respectively. The majority of bacterial OTUs are not closely related to all other hitherto-determined sequences. The ratio Archaea/Bacteria is 1/4 and the most frequent bacterial OTU represents less than 5% of the characterised bacterial population.

Genetic structure of the endangered species Pinna nobilis (Mollusca: Bivalvia) inferred from mtDNA sequences

Biologia ◽  
2008 ◽  
Vol 63 (3) ◽  
Author(s):  
Vassilios Katsares ◽  
Anna Tsiora ◽  
Sofia Galinou-Mitsoudi ◽  
Anastasia Imsiridou
Keyword(s):  
Genetic Structure ◽  
Endangered Species ◽  
16S Rdna ◽  
Dna Sequences ◽  
Population Sample ◽  
Nucleotide Sequences ◽  
Mtdna Sequences ◽  
Pinna Nobilis ◽  
Rdna Sequences ◽  
Haplotypic Diversity

AbstractThis study examines the population genetic structure of the endangered bivalve Pinna nobilis (Mollusca: Bivalvia), based on novel mtDNA sequences (partial COI and 16S rDNA mtDNA genes). The analyzed nucleotide sequences of COI were 729 bp in size, coding for a 243 amino acid peptide, while the analyzed nucleotide sequences of 16S rDNA were 489 bp in size. These sequences of P. nobilis were the first DNA sequences of the species submitted to any Genetic Data Base. Population samples from four geographic regions from Greece, as well as a population sample of Atrina fragilis (as an outgroup) were used. High values of haplotypic diversity were found in the population samples of P. nobilis, based on the COI sequences. A single base in the analyzed 16S rDNA sequences was different in all analyzed individuals from a single population sample (Chios island) differentiating it from the other ones. These mtDNA sequences could be informative for further genetic analyses of the endangered species, contributing in conservation plans for its protection and/or aquaculture investigations.

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