Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF

BACKGROUND: Diversity Generating Retroelements (DGRs) are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variable region with a strongly mutated cDNA copy generated by the element-encoded reverse transcriptase. In contrast to “selfish” retroelements such as group II introns and retrotransposons, DGRs impart an advantage to their host by increasing its adaptive potential. DGRs were discovered in a bacteriophage, but since then additional examples have been identified in some bacterial genomes. RESULTS: Here we present the program DiGReF that allowed us to comprehensively screen available databases for DGRs. We identified 155 DGRs which are found in all major classes of bacteria, though exhibiting sporadic distribution across species. Phylogenetic analysis and sequence comparison showed that DGRs move between genomes by associating with various mobile elements such as phages, transposons and plasmids. The DGR cassettes exhibit high flexibility in the arrangement of their components and easily acquire additional paralogous target genes. Surprisingly, the genomic data alone provide new insights into the molecular mechanism of DGRs. Most notably, our data suggest that the template RNA is transcribed separately from the rest of the element. CONCLUSIONS: DiGReF is a valuable tool to detect DGRs in genome data. Its output allows comprehensive analysis of various aspects of DGR biology, thus deepening our understanding of the role DGRs play in prokaryotic genome plasticity, from the global down to the molecular level

Randomised, controlled trial of alternating pressure mattresses compared with alternating pressure overlays for the prevention of pressure ulcers : PRESSURE (pressure relieving support surfaces) trial

Objective To compare whether differences exist between alternating pressure overlays and alternating pressure mattresses in the development of new pressure ulcers, healing of existing pressure ulcers, and patient acceptability. Design Pragmatic, open, multicentre, randomised controlled trial. Setting 11 hospitals in six NHS trusts. Participants 1972 people admitted to hospital as acute or elective patients. Interventions Participants were randomised to an alternating pressure mattress (n = 982) of- an alternating pressure overlay (n = 990). Main outcome measures The proportion of participants developing a new pressure ulcer of grade 2 or worse; time to development of new pressure ulcers; proportions of participants developing a new ulcer within 30 days; healing of existing pressure ulcers; and patient acceptability Results Intention to treat analysis found no difference in the proportions of participants developing a new pressure ulcer of grade 2 or worse (10.7% overlay patients, 10.3% mattress patients; difference 0.4%, 95% confidence interval - 23% to 3.1%, P = 0.75). More overlay patients requested change owing to dissatisfaction (23.3%) than mattress patients (18.9%, P = 0.02). Conclusion No difference was found between alternating pressure mattresses and alternating pressure overlays in the proportion of people who develop a pressure ulcer

N=(1,1) super Yang--Mills theory in 1+1 dimensions at finite temperature

We present a formulation of N=(1,1) super Yang-Mills theory in 1+1 dimensions at finite temperature. The partition function is constructed by finding a numerical approximation to the entire spectrum. We solve numerically for the spectrum using Supersymmetric Discrete Light-Cone Quantization (SDLCQ) in the large-N_c approximation and calculate the density of states. We find that the density of states grows exponentially and the theory has a Hagedorn temperature, which we extract. We find that the Hagedorn temperature at infinite resolution is slightly less than one in units of (g^(2) N_c/pi)^(1/2). We use the density of states to also calculate a standard set of thermodynamic functions below the Hagedorn temperature. In this temperature range, we find that the thermodynamics is dominated by the massless states of the theory.Comment: 16 pages, 8 eps figures, LaTe

Persistence of the Chromosome End Regions at Low Copy Number in Mutant Strains of Streptomyces rimosus and Streptomyces lividans

Streptomycetes are important antibiotic producing bacteria that often exhibit genetic instability. One or both ends of the linear Streptomyces chromosome are lost spontaneously, resulting in viable mutant strains sometimes lacking hundreds of genes. We examined some strains of Streptomyces rimosus and Streptomyces lividans, which had been classified as »deletion mutants« and appeared to have lost chromosome end sequences. We discovered that the »deleted« sequences were still present in vegetative mycelium at a very low copy number so that they were normally not detected. The copy number in S. rimosus was estimated as 0.1–1.0 10–3/chromosome. Streptomyces spores contain the disappearing chromosome end sequences at a higher copy number than the vegetative mycelium, promoting their inheritance via spore preparations. This, in effect, represents a separation between germ line and deleted vegetative genomes, which has not been recognised before in Streptomyces, and has practical implications both for strain preservation and genetic studies

Direct evidence for the Maldacena conjecture for N=(8,8) super Yang-Mills theory in 1+1 dimensions

We solve N=(8,8) super Yang-Mills theory in 1+1 dimensions at strong coupling to directly confirm the predictions of supergravity at weak coupling. We do our calculations in the large-N_c approximation using Supersymmetric Discrete Light-Cone Quantization with up to 3*10^{12} basis states. We calculate the stress-energy correlator as a function of the separation r and find that at intermediate values of r the correlator behaves as r^{-5} to within errors as predicted by weak-coupling supergravity. We also present an extension to significantly higher resolution of our earlier results for the same correlator in the N=(2,2) theory and see that in this theory the correlator has very different behavior at intermediate values of r.Comment: 12 pp., 6 figures, LaTe

Od sekvencije DNA do kemijske strukture – pretraživanje mikrobnih genomskih i metagenomskih skupova podataka radi pronalaženja novih prirodnih spojeva

Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene clusters has been achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB) and of predicted entirely novel recombinant products (r-CSDB) that can be used for in silico screening with computer aided drug design technology. The use of these programs has been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic data set and a newly discovered example of a \u27shared metabolic pathway\u27 in marine-microbial endosymbiosis.Brzo pretraživanje genomskih i metagenomskih skupova podataka, modularnih biosintetskih genskih nakupina poliketid sintaza i sintetaza neribosomalno sintetiziranih peptida, postignuto je primjenom generičkih računalnih programskih paketa ClustScan i CompGen. Ti programski paketi provode anotaciju hijerarhijskim strukturiranjem podataka na polipeptide, module i domene, te pohranu i grafičku prezentaciju tih podataka. Na temelju dosadašnjih spoznaja, nastoji se postići najtočnije moguće predviđanje aktivnosti i specifičnosti katalitički aktivnih domena, što vodi prema predviđanju najvjerojatnijih kemijskih struktura koje ti enzimi mogu sintetizirati. Programski paketi ClustScan i CompGen omogućuju generiranje novih genskih nakupina homolognom rekombinacijom anotiranih gena u uvjetima in silico, a upotrijebljeni su i za konstrukciju vlastitih baza podataka poznatih poliketidnih i peptidnih supstancija (CSDB) te potpuno novih poliketidnih i peptidnih supstancija produkata rekombinacije (r-CSDB). Ti će se produkti rekombinacije moći upotrijebiti za izbor supstancija s potencijalnom biološkom aktivnošću pomoću računalom vođenog dizajna lijekova u uvjetima in silico. Primjenjivost programskih paketa ClustScan i CompGen dokazana je u analizi genomskih sekvencija prokariotskih i eukariotskih mikroorganizama što žive u tlu, analizi metagenomske skupine podataka u uzorku iz morske vode, a i na nedavno opisanom primjeru \u27zajedničkog metaboličkoga puta\u27 u mikrobnog endosimbionta morske životinje

White matter changes and confrontation naming in retired aging national football league athletes

Using diffusion tensor imaging (DTI), we assessed the relationship of white matter integrity and performance on the Boston Naming Test (BNT) in a group of retired professional football players and a control group. We examined correlations between fractional anisotropy (FA) and mean diffusivity (MD) with BNT T-scores in an unbiased voxelwise analysis processed with tract-based spatial statistics (TBSS). We also analyzed the DTI data by grouping voxels together as white matter tracts and testing each tract's association with BNT T-scores. Significant voxelwise correlations between FA and BNT performance were only seen in the retired football players (p < 0.02). Two tracts had mean FA values that significantly correlated with BNT performance: forceps minor and forceps major. White matter integrity is important for distributed cognitive processes, and disruption correlates with diminished performance in athletes exposed to concussive and subconcussive brain injuries, but not in controls without such exposure