Search results for " RNA"

Larval morphology, genetic divergence, and contrasting levels of host manipulation between forms of Pomphorhynchus laevis (Acanthocephala)

2004

Studies on parasite species with a wide geographic and ecological range may be confounded by still equivocal taxonomic identification. Here, we investigated genetic polymorphism and behavioural changes induced in a common intermediate host, in two different forms of Pomphorhynchus laevis based on the morphology of the larval infective stage (cystacanth). A 'smooth type' (S) and a 'wrinkled type' (W) of cystacanth were distinguished based on their surface and shape. We analysed sequence divergence at both nuclear (ribosomal gene 18S rDNA, and ribosomal internal transcribed spacers, ITS1/ITS2) and mitochondrial (cytochrome c oxidase subunit 1) genes of P. laevis cystacanths and adults at vari…

A ceRNA approach may unveil unexpected contributors to deletion syndromes, the model of 5q- syndrome.

2015

In genomic deletions, gene haploinsufficiency might directly configure a specific disease phenotype. Nevertheless, in some cases no functional association can be identified between haploinsufficient genes and the deletion-associated phenotype. Transcripts can act as microRNA sponges. The reduction of transcripts from the hemizygous region may increase the availability of specific microRNAs, which in turn may exert in-trans regulation of target genes outside the deleted region, eventually contributing to the phenotype. Here we prospect a competing endogenous RNA (ceRNA) approach for the identification of candidate genes target of epigenetic regulation in deletion syndromes. As a model, we an…

rRNA gene restriction patterns and biotypes of Shigella sonnei.

1993

SUMMARYShigella sonneiis a major agent of diarrhoeal disease in developed as well as in developing countries. Several phenotypic methods to define strain differences have been applied to this species ofShigellaincluding, more recently, analysis of extrachromosomal and chromosomal DNA.In this study, 432 endemic and epidemic strains isolated between 1975 and 1991 in Italy, France and Switzerland were submitted to rRNA gene restriction pattern analysis, after digestion of whole-cell DNA byHincII, and to concomitant biotyping.Thirteen ribotypes, HI to H13, and five biotypes, a, d, e, f, g, were detected. Xinety-five percent of the sporadic strains were assigned to ribotypes HI to H4, which coul…

Real-time PCR detection of Pseudomonas aeruginosa in clinical and municipal wastewater and genotyping of the ciprofloxacin-resistant isolates

2006

Real-time quantification of Pseudomonas aeruginosa was performed in various wastewater systems including clinical, municipal wastewaters and inflow from a wastewater treatment plant. The highest concentrations of P. aeruginosa-specific targets were detected in clinical wastewaters. Limitations of the detection system resulting from inhibition or cross-reaction were identified. Ciprofloxacin-resistant P. aeruginosa strains were isolated after specific enrichment from clinical and municipal wastewaters. In some cases they were also cultivated from effluent of a wastewater treatment plant, and from its downstream river water. A total of 119 isolates were phenotypically characterized as ciprofl…

Quantitative Detection of the nosZ Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA, narG , nirK , and nosZ Genes…

2006

ABSTRACT Nitrous oxide (N 2 O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N 2 O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the nosZ gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of nosZ primers flanking the nosZ fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the nosZ gene present in six different …

16S rRNA sequences as diagnostic tools to elucidate potential symbiotic relationships between bacteria and the marine sponge Halichondria panicea : r…

1999

Specific roles of 5′ RNA secondary structures in stabilizing transcripts in chloroplasts

2005

RNA secondary structures, e.g. stem-loops that are often found at the 5' and 3' ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem-loop at the 5' end of rbcL gene transcripts in Chlamydomonas that it neither prevents ribonucleases from binding to the RNA nor impedes their movement along the RNA strand. The stem-loop has a formative function in that it mediates folding of a short sequence around its base into a specific RNA conformation, consisting of a helical and single-stranded region, i.e. the real structure required for longevit…

Stage, tissue, and cell specific distribution of alternative Ultrabithorax mRNAs and protein isoforms in the Drosophila embryo

1996

The homeotic gene Ultrabithorax encodes a family of six homeoproteins translated from alternatively spliced mRNAs. The structures of these UBX isoforms have been conserved among anciently diverged Drosoph-ila species and functional distinctions between some isoforms have been reported that suggest subtle but important roles in Ubx action. We present a detailed analysis of the expression patterns of Ubx mRNAs and proteins during embryogenesis, using isoform-specific monoclonal antibodies and synthetic oligonucleotide probes. These patterns are remarkably complex, each mRNA and corresponding protein isoform being expressed in a partially overlapping but distinct stage and tissue-specific patt…

Impact of Insertion Sequences and RNAs on Genomic Inversions in Pseudomonas aeruginosa

2022

Abstract In this article, a bioinformatics pipeline is proposed that focuses on two types of elements, namely the mobile genetic elements (MGE) and Ribonucleic acids (RNAs). The MGEs are called insertion sequences (ISs) in the prokaryotic domain. The objective of this research work is to study the behaviour of RNAs and MGEs genes, and the effects of their presence around inversions in genome sequences. The proposed pipeline finds the relation between the transposase gene types (e.g., DDE and DEDD) located within insertion sequences according to their IS family and sub-family, and RNAs (tRNA and rRNA) on the one hand, and genomic inversion on the other hand. More precisely, we wonder whether…

rDNA Sequences of <I>Anopheles</I> Species from the Iberian Peninsula and an Evaluation of the 18S rRNA Gene as Phylogenetic Marker in An…

2006

The complete 18S rDNA and internal transcribed spacer (ITS)-2 rDNA sequences were obtained from Anopheles atroparvus Van Thiel and Anopheles plumbeus Stephens from two areas of Spain. The number of nucleotide differences in the 18S rDNA of the two species is high compared with differences in the same gene of other invertebrate vectors. In Anopheles, short 18S rDNA sequences are richer in AT than the longer sequences, which are richer in GC and include extremely GC-biased expanded regions. Four small regions in the variable regions V4 and V7 contain the majority of nucleotide differences. The results did not support the use of partial sequences for relationship analyses. Genetic distances an…