Similar mutation rates but different mutation spectra in moderate and extremely halophilic archaea.

Archaea are a major part of Earth's microbiota and extremely diverse. Yet, we know very little about the process of mutation that drives such diversification. To expand beyond previous work with the moderate halophilic archaeal species Haloferax volcanii, we performed a mutation-accumulation experiment followed by whole-genome sequencing in the extremely halophilic archaeon Halobacterium salinarum.

Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium .

Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0-8.

Low Base-Substitution Mutation Rate but High Rate of Slippage Mutations in the Sequence Repeat-Rich Genome of .

We describe the rate and spectrum of spontaneous mutations for the social amoeba , a key model organism in molecular, cellular, evolutionary and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates and Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in are highly A/T biased.

Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species .

Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth's biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing.

Evolutionary determinants of genome-wide nucleotide composition.

One of the long-standing mysteries of evolutionary genomics is the source of the wide phylogenetic diversity in genome nucleotide composition (G + C versus A + T), which must be a consequence of interspecific differences in mutation bias, the efficiency of selection for different nucleotides or a combination of the two. We demonstrate that although genomic G + C composition is strongly driven by mutation bias, it is also substantially modified by direct selection and/or as a by-product of biased gene conversion. Moreover, G + C composition at fourfold redundant sites is consistently elevated above the neutral expectation-more so than for any other class of sites.

The Rate and Spectrum of Spontaneous Mutations in Mycobacterium smegmatis, a Bacterium Naturally Devoid of the Postreplicative Mismatch Repair Pathway.

Mycobacterium smegmatis is a bacterium that is naturally devoid of known postreplicative DNA mismatch repair (MMR) homologs, mutS and mutL, providing an opportunity to investigate how the mutation rate and spectrum has evolved in the absence of a highly conserved primary repair pathway. Mutation accumulation experiments of M. smegmatis yielded a base-substitution mutation rate of 5.

Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans.

Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments, we find that the GC-rich Deinococcus radiodurans has an overall background genomic mutation rate similar to that of E.

Association of VNTR polymorphisms in DRD4, 5-HTT and DAT1 genes with obesity.

Objective: To investigate the association between VNTR polymorphisms of DRD4, DAT1 and 5-HTT genes and obesity.

Material And Methods: Peripheral blood samples of 234 obese (BMI ≥ 30) and 148 healthy individuals (BMI ≤ 25) were objected to PCR to detect the VNTR of the 2nd intron of 5-HTT, 3rd exon of DRD4 and 3'UTR of DAT1 genes.

Results: The association between obesity and genotype distributions of 5-HTT, DAT1 and DRD4 genes and between obesity and distributions of allele frequencies were tested by Chi Square (χ(2)) test and were not found statistically significant.

Promoter hypermethylation of p16 and APC in gastrointestinal cancer patients.

Background/aims: Cancer is a consequence of the disruption of cellular regulation. Epigenetic is one of the reasons of this disruption. Epigenetic factors play a role in the carcinogenesis by affecting proto-oncogenes and tumor suppressor genes and it is one of the most popular research areas in recent years.

Genetic structures of sand fly (Diptera: Psychodidae) populations in a leishmaniasis endemic region of Turkey.

The object of this study was to determine the genetic structures of three vector species, Phlebotomus tobbi, Phlebotomus papatasi, and Phlebotomus sergenti, in the Cukurova Region of Turkey, an endemic focus of cutaneous leishmaniasis. The genetic diversity indices, neutrality tests and hierarchical analysis of molecular variance (AMOVA) were performed using partial sequences of ITS2 and cytochrome b gene regions. In all species, within population genetic variation was higher than between population variation for ITS2 gene region.

A prospective study of serotonin transporter gene promoter (5-HTT gene linked polymorphic region) and intron 2 (variable number of tandem repeats) polymorphisms as predictors of trauma response to mild physical injury.

The aim of this study was to examine the effect of both promoter and intron polymorphisms of the serotonin transporter (5HTT) gene on posttraumatic stress disorder (PTSD) development. For this purpose, two polymorphisms of the 5-HTT gene, which are found in the promoter (5-HTT gene-linked polymorphic region) and second intron (variable number of tandem repeats) of the gene, were analyzed in 100 patients who were admitted to the Emergency Department after a mild physical trauma. None of the 5-HTT polymorphisms studied have an effect on PTSD development after a mild physical injury, but having L allele for 5-HTT gene-linked polymorphic region may cause milder hyperarousal symptoms in those patients who have developed PTSD.

The zymographic evaluation of gelatinase (MMP-2 and -9) levels in acute and chronic periapical abscesses.

Objective: This study investigated the presence and levels of matrix metalloproteinases (MMP)-2 and -9 in periapical abscesses.

Study Design: Eighteen samples of intracanal exudates containing pus were collected from teeth with clinically and radiographically verified primary or secondary acute and chronic apical abscesses. Pro- and active forms of MMP-2 and MMP-9 levels were analyzed by using substrate gel zymography followed by an image analysis system.