Search results for " RNA"

BlotBase: a northern blot database.

2008

With the availability of high-throughput gene expression analysis, multiple public expression databases emerged, mostly based on microarray expression data. Although these databases are of significant biomedical value, they do hold significant drawbacks, especially concerning the reliability of single gene expression profiles obtained by microarray data. Simultaneously, reliable data on an individual gene's expression are often published as single northern blots in individual publications. These data were not yet available for high-throughput screening. To reduce the gap between high-throughput expression data and individual highly reliable expression data, we designed a novel database "Blo…

Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example

2008

ABSTRACT We investigated the effects of internal primer-template mismatches on the efficiency of PCR amplification using the 16S rRNA gene as the model template DNA. We observed that the presence of a single mismatch in the second half of the primer extension sequence can result in an underestimation of up to 1,000-fold of the gene copy number, depending on the primer and position of the mismatch.

Morphological and molecular taxonomy ofPythium longisporangiumsp. nov. isolated from the Burgundian region of France

2005

During the course of an investigation on the Pythiaceous oomycetes occurring in the Burgundian vineyards, some species of Pythium possessing mainly hypogynous antheridia were found. These had been classified as oomycetes belonging to the ‘‘Pythium rostratum’’ group for a long time. Three of these isolates, having similar structures and growth, are very closely related to a recently described species, Pythium bifurcatum Paul. A close look at these, however, underlines some fundamental differences with the latter. Not all of them produce zoospores but have very large sporangia. The type specimen is F-1200 (B 76a) which is a medium-slow growing saprophyte. The sequence of the ITS region of the…

Identification of Lactobacilli from Deep Carious Lesions by Means of Species-Specific PCR and MALDI-TOF Mass Spectrometry

2014

SUMMARY Background: The aim of the present study was to compare MALDI-TOF results for the identification of 87 lactobacilli, isolated from soft or hard carious dentin from 70 first molars of 7- to 8-year-old children with those obtained by species-specific PCR. Methods: The 87 isolates were analyzed by MALDI-TOF MS (Microflex LT, MALDI Biotyper 3.0, Bruker Daltonik, Bremen, Germany), using a reference data base of 4110 strains including > 90 lactobacillus species. For the identification with species-specific PCR, oligonucleotide primers (16S rRNA) specific for L. casei, L. paracasei, L. rhamnosus, L. gasseri, L. plantarum, and L. acidophilus were used; type strains served as controls. The P…

Pythium prolatumisolated from soil in the Burgundy region: a new record for Europe

1999

Pythium prolatum Hendrix and Campbell has been isolated from a soil sample taken in the Burgundy region in France. The fungus is easily recognisable by its heavily ornamented oogonia with conical to mammiform spines, elongated sporangia, and its diclinous antheridia forming or originating from a tangled mass of hyphae. Descriptions of the morphological and reproductive aspects of Pythium prolatum, the polymerase chain reaction of the internal transcribed spacer (ITS1) of the ribosomal nuclear DNA as well as the nucleotide sequences of ITS1 coding for 5.8 S rRNA are given.

2015

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m(1)A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m(1)A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol was tailored…

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly

2020

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared to bacteria and eukaryotes. Here, we use parallel high‐resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large‐scale latitudinal, climatic (nemoral to arctic), and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea‐specific sequencing revealed that freshwa…

Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent Pseudomonads

2003

ABSTRACT The diversity of the membrane-bound nitrate reductase ( narG ) and nitrous oxide reductase ( nosZ ) genes in fluorescent pseudomonads isolated from soil and rhizosphere environments was characterized together with that of the 16S rRNA gene by a PCR-restriction fragment length polymorphism assay. Fragments of 1,008 bp and 1,433 bp were amplified via PCR with primers specific for the narG and nosZ genes, respectively. The presence of the narG and nosZ genes in the bacterial strains was confirmed by hybridization of the genomic DNA and the PCR products with the corresponding probes. The ability of the strains to either reduce nitrate or totally dissimilate nitrogen was assessed. Overa…

Regulatory factor for the transcription of the ribosomal genes in amphibian oocytes.

1970

AMPHIBIAN oocytes provide very convenient material for the study of the mechanisms that control ribosomal RNA synthesis because their pattern of ribosomal RNA synthesis does not change greatly during oogenesis. During the lampbrush stage of oogenesis (stage 4) more than 97 per cent of the RNA synthesized per unit time in the oocytes is ribosomal. This happens because the genes for ribosomal RNA are specifically amplified3–5 to such an extent that the oocyte nucleus (germinal vesicle) has an rDNA content approximately 1,500 times more than the haploid amount4. On the other hand, in mature oocytes (stage 6) no ribosomal RNA is synthesized1,2, although the extra copies of the ribosomal cistron…

Electrochemical probe for the monitoring of DNA-protein interactions.

2010

Self-assembly of thiol-terminated oligonucleotides on gold substrates provides a convenient way for DNA-functionalized surfaces. Here we describe the development of an electrochemical assay for the detection of DNA-protein interactions based on the modification of the electrochemical response of methylene blue (MB) intercalated in the DNA strands. Using a functionalized electrode with double stranded DNA carrying T3 RNA polymerase binding sequence, we show a substantial attenuation of the current upon the DNA-protein interaction. Moreover, a Langmuir binding isotherm for T3 RNA polymerase (T3 Pol) gives a dissociation constant K(D) equal to 0.46+/-0.23 microM. Such value is 100 times lower …