Search results for " RNA"
showing 10 items of 1405 documents
Positive selection in development and growth rate regulation genes involved in species divergence of the genus Radix
2015
AbstractBackgroundLife history traits like developmental time, age and size at maturity are directly related to fitness in all organisms and play a major role in adaptive evolution and speciation processes. Comparative genomic or transcriptomic approaches to identify positively selected genes involved in species divergence can help to generate hypotheses on the driving forces behind speciation. Here we use a bottom-up approach to investigate this hypothesis by comparative analysis of orthologous transcripts of four closely related EuropeanRadixspecies.ResultsSnails of the genusRadixoccupy species specific distribution ranges with distinct climatic niches, indicating a potential for natural …
Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal l…
2004
Three queuosine derivatives (Q-derivatives) have been found at position 34 of four mammalian so-called Q-tRNAs: queuosine (Q) in tRNA(Asn) and tRNA(His), mannosyl-queuosine (manQ) in tRNA(Asp), and galactosyl-queuosine (galQ) in tRNA(Tyr). An analytical procedure based on the combined means of purified tRNA isolation from liver cells and ribonucleoside analysis by reverse-phase high performance liquid chromatography coupled with real-time UV-spectrometry (RPLC-UV) was developed for the quantitative analysis of the three Q-derivatives present in total tRNA from liver tissues and liver cell cultures. Using this analytical procedure, the rates of Q-tRNA modification were studied in total tRNAs…
Mitochondrial compartment: a possible target of cadmium effects on breast epithelial cells.
2009
Cadmium–breast epithelial cell interactions were studied by analyzing some mitochondria-related aspects of stress response. We treated immortalized non-tumor breast cells with 5 or 50 μM CdCl2 for 24 or 96 h demonstrating that the exposure did not cause a significant mitochondrial proliferation, while it induced a significant increase in the respiratory activity and mitochondrial polarization. In addition, we found that hsp60 was up-regulated while hsp70 and COXII and COXIV were down-regulated. The mRNA for hsp70 remained constant and only the inducible form of the 70-kDa heat shock protein was over expressed. The mRNAs for COXII and COXIV remained constant after 24 h and increased after lo…
A Novel Chitin-binding Protein from the Vestimentiferan Riftia pachyptila Interacts Specifically with β-Chitin
2001
Abstract A cDNA from Riftia pachyptila was cloned. It encodes a novel 21.3-kDa protein from the worm protective tube, named RCBP (for Riftia chitin-binding protein). On the basis of partial tube-peptide sequences previously obtained, experiments using reverse transcriptase-mediated polymerase chain reaction and rapid amplification of cDNA ends led to the complete cDNA sequence. Analysis of its deduced amino acid sequence shows the presence of two chitin-binding domains. These domains are closely related to type 2 chitin-binding domains that are restricted to the animal kingdom. We showed by affinity assay and immunogold labeling that RCBP is the first protein so far known that binds specifi…
cDNA Synthesis and Cloning
1998
The isolation of intact messenger RNA and its conversion into cDNA copies by avian or Moloney murine reverse transcriptase, as well as subsequent amplification of gene transcripts by the PCR technique, are becoming increasingly important tools in molecular biology. At present, these techniques have been often necessary and widely used for the analysis of individual mRNA levels in cells and tissues by Northern blot analysis, nuclease protection analysis and in situ hybridization. Another important application of RNA templates is the construction of representative cDNA libraries in order to clone genes, to investigate their molecular structure and to express them in prokaryotic and/or eukary…
DNA-DNA hybridization and ribotyping of Acidovorax delafieldii isolates from eels and aquatic environments
1992
Eleven strains of Acidovorax isolated from a freshwater lake and from healthy and diseased European eels in a hatchery were investigated by genotypic methods. DNA-DNA slot blot hybridization confirmed the identity of all strains as A. delafieldii. Isolates were heterogeneous in EcoR1 ribopatterns with four types recognizable. Most freshwater and healthy eel strains had the same ribotype but differed from the disease-associated strains. Typical ribopatterns of A. delafieldii contained 1·3, 1·5, and 3·2 kb fragments which provided useful additional taxonomic markers for species identification.
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
2019
AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…
Inducible Genetic Code Expansion in Eukaryotes
2020
Abstract Genetic code expansion (GCE) is a versatile tool to site‐specifically incorporate a noncanonical amino acid (ncAA) into a protein, for example, to perform fluorescent labeling inside living cells. To this end, an orthogonal aminoacyl‐tRNA‐synthetase/tRNA (RS/tRNA) pair is used to insert the ncAA in response to an amber stop codon in the protein of interest. One of the drawbacks of this system is that, in order to achieve maximum efficiency, high levels of the orthogonal tRNA are required, and this could interfere with host cell functionality. To minimize the adverse effects on the host, we have developed an inducible GCE system that enables us to switch on tRNA or RS expression whe…
Molecular Identification of Yeasts Associated with Traditional Egyptian Dairy Products
2009
This study aimed to examine the diversity and ecology of yeasts associated with traditional Egyptian dairy products employing molecular techniques in yeast identification. A total of 120 samples of fresh and stored Domiati cheese, kariesh cheese, and "Matared" cream were collected from local markets and examined. Forty yeast isolates were cultured from these samples and identified using the restriction-fragment length polymorphism (RFLPs) of 5.8S-ITS rDNA region and sequencing of the domains D1 and D2 of the 26S rRNA gene. Yeasts were identified as Issatchenkia orientalis (13 isolates), Candida albicans (4 isolates), Clavispora lusitaniae (Candida lusitaniae) (9 isolates), Kodamaea ohmeri (…
Changes in membrane lipid composition in ethanol- and acid-adapted Oenococcus oeni cells: characterization of the cfa gene by heterologous complement…
2008
International audience; Cyclopropane fatty acid (CFA) synthesis was investigated in Oenococcus oeni. The data obtained demonstrated that acid-grown cells or cells harvested in the stationary growth phase showed changes in fatty acid composition similar to those of ethanol-grown cells. An increase of the CFA content and a decrease of the oleic acid content were observed. The biosynthesis of CFAs from unsaturated fatty acid phospholipids is catalysed by CFA synthases. Quantitative real-time-PCR experiments were performed on the cfa gene of O. oeni, which encodes a putative CFA synthase. The level of cfa transcripts increased when cells were harvested in stationary phase and when cells were gr…