Evaluation of Human Telomeric G-Quadruplexes: The Influence of Overhanging Sequences on Quadruplex Stability and Folding

To date, various G-quadruplex structures have been reported in human telomeric sequences. Human telomeric repeats can form many topological structures depending on conditions and on base modification; parallel, antiparallel, and hybrid forms. The effect of salts and some specific ligands on conformational switches between different conformers is known, but the influence of protruding sequences has rarely been discussed. In this paper, we analyze different quadruplex-forming oligomers derived from human telomeric sequences which contain 3′- and 5′-protruding nucleotides, not usually associated with the G-quadruplex motif. The study was performed using electrophoresis, CD, and UV spectroscopies. The major findings are (i) protruding nucleotides destabilize the G-quadruplex structure, and (ii) overhanging sequences influence the folding of the quadruplex

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To date, various G-quadruplex structures have been reported in human telomeric sequences. Human telomeric repeats can form many topological structures depending on conditions and on base modification; parallel, antiparallel, and hybrid forms. The effect of salts and some specific ligands on conformational switches between different conformers is known, but the influence of protruding sequences has rarely been discussed. In this paper, we analyze different quadruplex-forming oligomers derived from human telomeric sequences which contain 3 -and 5 -protruding nucleotides, not usually associated with the G-quadruplex motif. The study was performed using electrophoresis, CD, and UV spectroscopies. The major findings are (i) protruding nucleotides destabilize the G-quadruplex structure, and (ii) overhanging sequences influence the folding of the quadruplex

Interplay Between Bacteriophages and Restriction-Modification Systems in Enterococci

The complete genomes of Enterococcus faecalis bacteriophages were analyzed for tetranucleotide words avoidance. Very similar tetranucleotide composition was found in all tested genomes with strong underrepresentation of palindromic GATC and GGCC words. This avoidance could be explained as a protection mechanism against host restriction-modification systems as a clear correlation was found between avoidance of palindromic words and the specificity of E. faecalis restriction and modification systems. No similar avoidance of tetranucleotide words was observed for non-palindromic words. A weak correlation was observed between avoidance of tetranucleotide palindromes in bacteriophage genomes and the possession of phage encoded DNA methyltransferases confirming the interrelation between bacteriophage genomes composition and restriction and modification systems in enterococc

Heterotrophic bacteria associated with Varroa destructor mite

International audienceVarroa bee hive attack is a serious and common problem in bee keeping. In our work, an ecto-microflora of Varroa destructor mites was characterised as a potential source of bacterial bee diseases. Using a cultivation approach, a variable population of bacteria was isolated from the body surface of Varroa mites with frequency of about 150 cfu per mite individual. Nine studied isolates were classified to four genera and six species by a combination of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF)- and 16S ribosomal RNA (rRNA)-based methods, suggesting relatively low diversity of Varroa mite-associated ecto-microflora. The Varroa mite-associated bacterial population was found to be dominated by Gram-positive bacteria of Bacillus and Microbacterium genera. Gram-negative bacteria were represented by members of Brevundimonas and Rhizobium genera. Most of the identified species are not known to be associated with Varroa mite, either honey bee or honey up until now and some of them are probably representatives of new bacterial taxa

The Application of MALDI-TOF MS for a Variability Study of <i>Paenibacillus larvae</i>

In recent decades, the significant deterioration of the health status of honey bees has been observed throughout the world. One of the most severe factors affecting the health of bee colonies worldwide is American foulbrood disease. This devastating disease, with no known cure, is caused by the Gram-positive spore-forming bacteria of Paenibacillus larvae species. At present, DNA-based methods are being used for P. larvae identification and typing. In our study, we compare two of the most advanced DNA-based technologies (rep-PCR and 16S rRNA analyses) with MALDI-TOF MS fingerprinting to evaluate P. larvae variability in Central Europe. While 16S rRNA analysis presents a very limited variation among the strains, MALDI-TOF MS is observed to be more efficient at differentiating P. larvae. Remarkably, no clear correlation is observed between whole-genome rep-PCR fingerprinting and MALDI-TOF MS-based typing. Our data indicate that MALDI-TOF protein profiling provides accurate and cost-effective methods for the rapid identification of P. larvae strains and provides novel perspectives on strain diversity compared to conventional DNA-based genotyping approaches. The current study provides a good foundation for future studies

Biodiversity of rumen ciliates

International audienceThe rumen, a specialized foregut in herbivorous animals (Ruminantia), hosts microbiota of archaea, eubacteria, anaerobic fungi, and ciliated protozoa. Microscopic observations re-veal that the endosymbiotic ciliates account for about 50% of the total microbial mass in the rumen: up to 100 billions of ciliates may populate the rumen of a single cow. These ciliates play an important role in fibre digestion and the modulation of the fermentation pro-files. Classical (morphological) studies have identified more than 250 species of ciliates living in the various ruminants1,2. The number of species in an individual host is known to be highly variable, but the average number of species has been reported about 20 in cat-tle3, but less in sheep3 and goats4. However, as in all protists, the limited number of distinct morphological traits hampers an assessment of the ciliate diversity in the rumen. Molecular studies on rumen ciliates are rare, mainly due to difficulties in culturing these ciliates in vi-tro. Here we describe a molecular approach to study the phylogenetic diversity of rumen protozoa. The diversity of rumen protozoa was analysed by sequencing of 18S rDNA li-braries that have been created from PCR-amplified DNA of total rumen contents of cow, sheep, and a goat. These sequences were compared with the sequences of rumen ciliates obtained from GenBank and ERCULE. The phylogenetic analysis suggests that the ciliate population of the ruminal ecosystem can be much more diverse than previously assumed

Rapid indentification of rumen protozoa by restriction analysis of amplified 18S rRNA gene

A rapid method has been developed for molecular identification of rumen ciliates without the need for cultivation. Total DNA was isolated from single protozoal cells by the Chelex method and nearly complete protozoal 18S rRNA genes were amplified and subjected to restriction fragment length polymorphism analysis. On the basis of restriction patterns generated a molecular key was elaborated allowing identification of protozoa solely by a molecular technique without prior knowledge of morphology. No differences were observed between identical species originating from different animals or geographic locations, or between morphological variants of the same species. The ARDREA analysis described here provides a rapid and convenient way for identification and diversity studies of rumen protozoa