Consistency of genome-based methods in measuring Metazoan evolution

Seven distinct genome-wide divergence measures were applied pairwise to the nine sequenced animal genomes of human, mouse, rat, chicken, pufferfish, fruit fly, mosquito, and two nematode worms (Caenorhabditis briggsae and Caenorhabditis elegans). Qualitatively, all of these divergence measures are found to correlate with the estimated time since speciation; however, marked deviations are observed in a few lineages. The distinct genome divergence measures also correlate well among themselves, indicating that most of the processes shaping genomes are dominated by neutral events. The deviations from the clock-like scenario in some lineages are observed consistently by several measures, implicitly confirming their reliability.     

The effect of radiation on pedicled TRAM flap breast reconstruction: outcomes and implications

The purpose of this study was to examine the effect of postreconstruction radiation therapy on patients undergoing pedicled TRAM flap breast reconstruction. Post-TRAM radiation patients were compared with patients who received pre-TRAM radiation and a control TRAM-only group who received no radiation. Overall aesthetic appearance, evidence of symmetry, flap contracture, and hyperpigmentation were assessed by blinded reviewers. A total of 171 pedicled TRAM reconstructions were performed in 150 patients. Total flap complications were seen in 49.5 percent of the control patients, 57.1 percent of pre-TRAM radiation patients, and 50 percent of post-TRAM radiation patients but were not statistically different. The complete flap necrosis rate was 0.6 percent and the partial flap necrosis rate was 7.6 percent, again with no statistical differences among the groups. Donor-site complications occurred in approximately one third of patients in each of the groups. Deep venous thrombosis and pulmonary embolus each occurred once and only in the post-TRAM radiation group. In terms of overall aesthetic outcome, symmetry, and contracture, the control group consistently rated better than the pre-TRAM (p = 0.021, p = 0.03, p = 0.03, respectively) and the post-TRAM (p = 0.0001, p = 0.0001, and p =0.0001, respectively) radiation groups. The control group also had clinically and statistically significant less hyperpigmentation than the post-TRAM radiation group (p = 0.0002). In contrast, irradiated postreconstruction patients had scores, including aesthetic outcome, symmetry, and contracture, worse than those of irradiated prereconstruction patients. When these two groups were compared with each other, except for contracture, no statistical significance, because of a small patient sample, was found. Neither preoperative nor postoperative radiation increased the risk for flap or donor-site complications. In contrast, radiation of any type did affect aesthetic appearance, symmetry, contracture, and hyperpigmentation. The authors recommend that TRAM flap breast reconstruction be postponed in those patients known or expected to receive postmastectomy radiation.     

Repeat HIV Testing at Voluntary Testing and Counseling Centers in Croatia: Successful HIV Prevention or Failure to Modify Risk Behaviors?

HIV testing plays a critical role in preventing the spread of the virus and identifying infected individuals in need of care. Voluntary counseling and testing centers (VCTs) not only conduct testing but they also provide counseling. Since a proportion of people who test negative for HIV on their previous visit will return for retesting, the frequency of retesting and the characteristics of those who retest may provide insights into the efficacy of testing and counseling strategies. In this cross-sectional, retrospective study of 1,482 VCT clients in Croatia in 2010, 44.3% had been tested for HIV before. The rate of repeat HIV testing is lower in Croatia than in other countries. Men who have sex with men (MSM) clients, those with three or more sexual partners in the last 12 months, consistent condom users with steady partners, and intravenous drug users were more likely to be repeat testers. This finding suggests that clients presenting for repeat HIV testing are those who self-identify as being at a higher risk of infection. Our data showed that testing positive for HIV was not associated with repeat testing. However, the effects of repeat testing on HIV epidemiology needs to be explored.     

SW#db: GPU-Accelerated Exact Sequence Similarity Database Search

In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result–the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4–5 times faster than SSEARCH, 6–25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases     

CYB5A polymorphism increases androgens and reduces risk of rheumatoid arthritis in women

IntroductionRheumatoid arthritis (RA) is characterized by decreased androgen levels, which was the first hormonal abnormality described. Several studies indicated that steroidogenesis is directed towards endogenous glucocorticoids at the expense of androgens. The decisive step governing androgen synthesis is the 17,20-lyase activity of the CYP17A1 gene-encoded enzyme cytochrome P450 17A1. Here, we focused on the role in RA of the critical cofactor for 17,20-lyase activity, cytochrome b5, encoded by the CYB5A gene.MethodsData sets of two genome wide RA association studies (GWAS) were screened for single nucleotide polymorphisms (SNP) in the CYB5A gene. Candidate SNPs in CYB5A were studied in a case–control study population of Slovakia. Expression analyses were done in synovial fibroblasts from RA patients by quantitative real-time polymerase chain reaction, and cytochrome b5–expression was detected by immunohistochemistry. Real-life androgen production after steroid conversion was measured using radiolabeled substrates.ResultsThe study identified the RA-associated intronic SNP rs1790834 in the CYB5A gene in one GWAS and confirmed the same SNP in our study. The minor allele reduced RA risk selectively in women (P = 4.1*10⁻³; OR = 0.63, 95% CI [0.46-0.86]). The protective effect was confined to rheumatoid factor-positive (OR = 0.53, [0.37-0.75]) and anti-cyclic citrullinated peptide-positive (OR = 0.58, [0.41-0.83]) cases, respectively. The protective allele doubles CYB5A mRNA-expression resulting in 2-3fold activation of steroid 17,20-lyase activity, and protective allele was accompanied by a higher density of cytochrome b5-positive cells in synovial tissue.ConclusionsCYB5A is the first RA susceptibility gene involved in androgen synthesis. Our functional analysis of SNP rs1790834 indicates that it contributes to the sex bias observed in RA.     

Genetic structure and expansion of golden jackals (Canis aureus) in the north-western distribution range (Croatia and eastern Italian Alps)

The golden jackal, widely distributed in Europe, Asia and Africa, is one of the less studied carnivores in the world and the genetic structure of the European populations is unknown. In the last century jackals strongly declined mainly due to human persecution, but recently they expanded again in eastern Europe. With the aim to determine the genetic structure and the origin of expanding jackals, we analyzed population samples obtained from Bulgaria, Serbia, Croatia (Dalmatia and Slavonia) and individuals sampled in north-eastern Italy. Samples were typed at the hypervariable part of the mitochondrial DNA control-region (mtDNA CR1) and at 15 canine autosomal microsatellite loci (STR), and analyzed using multivariate, Bayesian and landscape genetic methods. The mtDNA CR1 was monomorphic, showing a single haplotype shared among all the populations. The STR loci were variable, with 2–14 alleles and intermediate values of heterozygosity (Ho = 0.47; He = 0.51). Genetic diversity was significantly partitioned (θ_ST = 0.07; P < 0.001) and the populations were partially distinct, perhaps in consequence of recent fragmentations. Jackals from Dalmatia were the most genetically differentiated. Assignment testing and gene flow analyses suggested that jackals colonizing Italy have admixed origins from Dalmatian and Slavonian populations. They are not first generation migrants, suggesting that dispersal towards north-eastern Italy is a stepping-stone process. Golden jackal and wolf colonization patterns might be different, with prevalent short-distance dispersal in jackals versus prevalent long distance dispersal in wolves. The admixed origin of jackals in the Alps ensures abundant genetic variability, which may enhance adaptive fitness and expectancy of population growth. The intersections between Dinaric–Balkan and Eastern Alps are areas of population expansion and admixture, highlighting their conservation, ecological and evolutionary values.     

Glucosinolate distribution in aerial parts of Degenia velebitica

The glucosinolates present in the leaf, stem, and seed extracts of Degenia velebitica (Degen) Hayek were characterized and quantified according to the ISO 9167-1 method, which is based on the HPLC analysis of desulfoglucosinolates. The stems contained glucoalyssin (3a) as the major compound as well as glucoberteroin (1a) and glucoaubrietin (4a). The leaves contained three glucosinolates, the major one being 3a, followed by glucobrassicanapin (2a) and 1a. Glucoberteroin (1a) was the major glucosinolate in the seeds, along with the two minor glucosinolates 3a and glucoerucin (5a). The content of 1a in the whole, non-defatted seeds amounted to 4% (w/w). The compound was characterized as its desulfo counterpart by spectroscopic techniques.     

Evidence for Distinct Functions of MRE11 in Arabidopsis Meiosis

The evolutionary conserved Mre11/Rad50/Nbs1 complex functions as one of the guardians of genome integrity in eukaryotes; it is required for the double-strand break repair, meiosis, DNA checkpoint, and telomere maintenance. To better understand the role of the MRE11 gene in Arabidopsis, we performed comparative analysis of several mre11 alleles with respect to genome stability and meiosis. The mre11-4 and mre11-2 alleles presumably produce truncated MRE11 proteins composed of the first 499 and 529 amino acids, respectively. Although the putative MRE11 truncated proteins differ only by 30 amino acids, the mutants exhibited strikingly different phenotypes in regards to growth morphology, genome stability and meiosis. While the mre11-2 mutants are fully fertile and undergo normal meiosis, the mre11-4 plants are sterile due to aberrant repair of meiotic DNA breaks. Structural homology analysis suggests that the T-DNA insertion in the mre11-4 allele probably disrupted the putative RAD50 interaction and/or homodimerization domain, which is assumed to be preserved in mre11-2 allele. Intriguingly, introgression of the atm-2 mutant plant into the mre11-2 background renders the double mutant infertile, a phenotype not observed in either parent line. This data indicate that MRE11 partially compensates for ATM deficiency in meiosis of Arabidopsis.