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Terminal Restriction Fragments (terminal + restriction_fragment)
Terms modified by Terminal Restriction Fragments Selected AbstractsDifferent bacterial communities associated with the roots and bulk sediment of the seagrass Zostera marinaFEMS MICROBIOLOGY ECOLOGY, Issue 1 2007Sheila Ingemann Jensen Abstract The bacterial community of Zostera marina -inhabited bulk sediment vs. root-associated bacteria was investigated by terminal restriction fragment length polymorphism and sequencing, and the spatial extension of the oxygen loss from roots was determined by oxygen microsensors. Extensive oxygen loss was found in the tip region of the youngest roots, and most of the rhizoplane of Z. marina roots was thus anoxic. A significant difference between the bacterial communities associated with the roots and bulk sediment was found. No significant differences were found between differently aged root-bundles. Terminal restriction fragments (TRFs) assigned to sulfate-reducing Deltaproteobacteria showed a relative mean distribution of 12% and 23% of the PCR-amplified bacterial community in the bulk-sediment at the two sites, but only contributed <2% to the root-associated communities. TRFs assigned to Epsilonproteobacteria showed a relative mean distribution of between 5% and 11% in the root-associated communities of the youngest root bundle, in contrast to the bulk-sediment where this TRF only contributed <1.3%. TRFs assigned to Actinobacteria and Gammaproteobacteria also seemed important first root-colonizers, whereas TRFs assigned to Deltaproteobacteria became increasingly important in the root-associated community of the older root bundles. The presence of the roots thus apparently selects for a distinct bacterial community, stimulating the growth of potential symbiotic Epsilon - and Gammaproteobacteria and/or inhibiting the growth of sulfate-reducing Deltaproteobacteria. [source] Bacteria associated with the rapid tissue necrosis of stony coralsENVIRONMENTAL MICROBIOLOGY, Issue 7 2007G. M. Luna Summary The rapid tissue necrosis (RTN) is a common disease of both wild and captive stony corals, which causes a fast tissue degradation (peeling) and death of the colony. Here we report the results of an investigation carried out on the stony coral Pocillopora damicornis, affected by an RTN-like disease. Total abundance of prokaryotes in tissue samples, determined by epifluorescence microscopy, was significantly higher in diseased than in healthy corals, as well as bacterial counts on MB2216 agar plates. Further experiments performed by fluorescent in situ hybridization using a 16S rDNA Vibrio -specific probe showed that vibrios were significantly more abundant in diseased than in healthy corals. Accordingly, bacterial counts on TCBS agar plates were higher in diseased than in healthy tissues. 16S rDNA sequencing identified as Vibrio colonies from diseased tissues only. Cultivated vibrios were dominated by a single ribotype, which displayed 99% of similarity with Vibrio harveyi strain LB4. Bacterial ribotype richness, assessed by terminal-restriction fragment length polymorphism analysis of the 16S rDNA, was significantly higher in diseased than in healthy corals. Using an in silico software, we estimated that a single terminal restriction fragment, putatively assigned to a Vibrio sp., accounted for >,15% and < 5% of the total bacterial assemblage, in diseased and healthy corals respectively. These results let us hypothesize that the RTN in stony corals can be an infectious disease associated to the presence of Vibrio harveyi. However, further studies are needed to validate the microbial origin of this pathology. [source] Use of terminal restriction fragment length polymorphism (T-RFLP) for identification of phytoplasmas in plantsPLANT PATHOLOGY, Issue 3 2007J. Hodgetts A terminal restriction fragment analysis (T-RFLP) technique was developed for the simple and rapid detection and diagnosis of phytoplasmas in plants. The selected primers amplified part of the 23S rRNA gene to provide improved resolution between the taxonomic groups compared to conventional restriction enzyme analysis of the 16S rRNA. Using the restriction enzymes Bsh12361 and MseI on the PCR products, and fragment analysis in the range 68,640 bp, the technique was tested on 37 isolates from 10 of the 16Sr groups. Distinct and unambiguous T-RFLP profiles were produced for nine of the 10 taxonomic groups, such that almost all isolates within a group shared the same profile and could be distinguished from isolates in other groups. The technique also identified the presence of mixtures of phytoplasmas from different groups in samples. Furthermore, the primers were devised to amplify a terminal restriction fragment (TRF) product of a specific defined size (461 bp) from the host plant chloroplast DNA, so that there was a built-in internal control in the procedure to show that the absence of a phytoplasma peak in a sample was the result of no detectable phytoplasma being present, not the result of PCR inhibition. This method offers the possibility of simultaneously detecting and providing a taxonomic grouping for phytoplasmas in test samples using a single PCR reaction. [source] Multiple profiling of soil microbial communities identifies potential genetic markers of metal-enriched sewage sludgeFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Catriona A. Macdonald Abstract The long-term impacts of Cu- and Zn-rich sewage sludge additions on the structure of the microbial community in a field under pasture were investigated using a combination of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) and T-RFLP profiling approaches. Changes in the community structure of bacteria, fungi, archaea and actinobacteria were observed in soils that had previously received Cu- (50,200 mg kg,1 soil) and Zn- (150,450 mg kg,1 soil) rich sewage sludge additions. Changes in the structure of all microbial groups measured were observed at Cu and Zn rates below the current EU guidelines (135 mg kg,1 Cu and 300 mg kg,1 Zn). The response of the fungal community, and to a lesser extent the bacterial and archaeal community, to Cu was dose dependent. The fungal community also showed a dose-dependent response to Zn, which was not observed in the other microbial groups assessed. Redundancy analysis demonstrated that individual terminal restriction fragments responded to both Cu and Zn and these may have potential as genetic markers of long-term metal effects in soil. [source] Soil parent material is a key determinant of the bacterial community structure in arable soilsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Andreas Ulrich Abstract The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes. [source] Structure and diversity of Gram-negative sulfate-reducing bacteria on rice rootsFEMS MICROBIOLOGY ECOLOGY, Issue 2-3 2001Daniel Scheid Abstract Specific PCR assays were used to amplify the 16S rRNA genes of the Desulfobacteriaceae and the Desulfovibrionaceae from extracted environmental DNA from rice roots. 16S rDNA-based community patterns of the Desulfobacteriaceae were generated via terminal restriction fragment length polymorphism analysis from rice roots and compared with bulk soil. The molecular fingerprints showed no significant difference between rice roots and bulk soil, but changes during the vegetation period. 16S rDNA clone libraries and sequencing showed that the predominant terminal restriction fragments represented distinct phylogenetic groups. The 16S rDNA clone sequences of the Desulfobacteriaceae fell in the phylogenetic radiation of Desulfonema and Desulfosarcina or grouped within the Desulforhabdus,Syntrophobacter assemblage. Three of the latter sequences were closely affiliated with the MPN isolate EZ-2C2 from rice roots. All Desulfovibrionaceae 16S rDNA clone sequences, with one exception, were affiliated with the MPN isolate F1-7b from rice roots. The clustering of the clone sequences and the close phylogenetic affiliation with isolates from MPN enrichments from the same habitat in two cases indicated that these sequence clusters may represent predominant Gram-negative sulfate reducers on rice roots. Quantification of the bacterial abundances was accomplished by rRNA dot blot hybridization. In total the Gram-negative sulfate reducers accounted for approximately 2,3% of the total rRNA content. The relative rRNA abundance of the Desulfobacteriaceae was, at 1.4%, higher than that of the Desulfovibrionaceae (0.5%). [source] Telomerase activity and hTERT mRNA expression can be heterogeneous and does not correlate with telomere length in soft tissue sarcomasINTERNATIONAL JOURNAL OF CANCER, Issue 6 2002Pu Yan Abstract In a previous study, we showed that telomerase activity (TA) and human telomerase reverse transcriptase (hTERT) mRNA expression were undetectable in benign mesenchymal lesions and low-grade soft tissue sarcomas (STSs), but detectable in about 50% of intermediate-/high-grade STSs. We wondered if this lack of TA or hTERT mRNA expression could be related to the tumor sample examined and if there was a relationship between the former 2 parameters and telomere length. Two separate tumor samples from 37 STSs were examined for telomerase activity, using the telomerase repeat amplification protocol (TRAP) assay and for hTERT mRNA expression, using RT-PCR. Telomere length was determined in each tumor sample, using the terminal restriction fragments (TRF) technique. Significant variations in telomere length, TA and hTERT mRNA expression between 2 samples of the same tumor were observed in 27%, 11% and 27% of STSs, respectively. Telomere length did not correlate with TA or hTERT mRNA expression. Despite great intratumoral heterogeneity in telomere length, short and long telomeres were more often seen in the low/intermediate-grade and high-grade STS categories, respectively. Few STSs that showed a TRF pattern suggestive of alternative lengthening of telomeres (ALT) may contain ALT subpopulations. © 2002 Wiley-Liss, Inc. [source] Telomere length and obesityACTA PAEDIATRICA, Issue 7 2008Raffaella Zannolli Abstract Aim: To assess the telomere length in apparently healthy obese and normal-weight subjects. Methods: Seventy-six Caucasian subjects were chosen including 53 children (age 8.2 ± 3.5 years) and 23 adults (age 40.5 ± 8.4 years). Among these, 22 (12 children and 10 adults) were obese with a body mass index (BMI, kg/m2) > 2 SD above the norm. Bioelectrical impedance analysis (BIA), measured with a multiple frequency analyzer, was used to estimate body composition. DNA extraction from white blood cells was used to estimate the telomere length by detection of terminal restriction fragments (TRF). Results: No difference was found between the TRF lengths of obese and normal children. Obese adults had shorter TRF lengths than adults who were not obese (mean TRF length difference, ,884.5; 95% confidence intervals ,1727 to ,41.8; t= 2.183; df = 17; p < 0.041). Conclusions: Obese adults have shorter telomeres than their normal-weight counterparts, while this phenomenon is not present in childhood. [source] | |||||||||||||