Towards a unified paradigm for sequence‐based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database ( http://unite.ut.ee ) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released ( http://unite.ut.ee/repository.php ) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.     

Middle East and North Africa consensus on osteoporosis

With the increasing life expectancy, osteoporosis is becoming a major worldwide health problem. The magnitude of the disease may become larger in developing countries, more particularly in the Middle East region where the prevalence of low bone mass is higher than in western countries. Although several local organizations and countries have developed guidelines for osteoporosis, no previous regional guidelines have been developed encompassing all Middle-Eastern and North African countries. The present document reviews all the regional published data on bone mineral density, risk factors, fracture prevalence and vitamin D status. It also gives simple recommendations applicable to all these countries. This document was endorsed by leading members of all the different regional countries including, Iran, Egypt, Tunisia, Jordan, Palestine, Syria, Iraq, Libya, Oman, Kuwait, Saudi Arabia and Bahrain.     

Two new Neuratelia Rondani (Diptera,Mycetophilidae) species from Western Palaearctic: a case of limited congruence between morphology and DNA sequence data

Two new Mycetophilidae species, Neuratelia jabalmoussae sp. n. and Neuratelia salmelai sp. n. are described on the basis of material collected from Lebanon, Estonia and Finland. Detailed figures of male terminalia and photographs of general facies are provided along with discussions of their morphological distinction from sibling species. For the first time molecular characters are used to distinguish new fungus gnat species. Molecular analysis relies on cytochrome oxidase subunit one (COI) but has additionally been corroborated by information from the 28S and ITS2 regions of nuclear ribosomal DNA. Situations where morphological and molecular data provide conflicting evidence for species delimitation are discussed. A new country record from Georgia is provided for Neuratelia caucasica.     

Prediction of a deletion copy number variant by a dense SNP panel

Background

A newly recognized type of genetic variation, Copy Number Variation (CNV), is detected in mammalian genomes, e.g. the cattle genome. This form of variation can potentially cause phenotypic variation. Our objective was to determine whether dense SNP (single nucleotide polymorphisms) panels can capture the genetic variation due to a simple bi-allelic CNV, with the prospect of including the effect of such structural variations into genomic predictions.

Methods

A deletion type CNV on bovine chromosome 6 was predicted from its neighboring SNP with a multiple regression model. Our dataset consisted of CNV genotypes of 1,682 cows, along with 100 surrounding SNP genotypes. A prediction model was fitted considering 10 to 100 surrounding SNP and the accuracy obtained directly from the model was confirmed by cross-validation.

Results and conclusions

The accuracy of prediction increased with an increasing number of SNP in the model and the predicted accuracies were similar to those obtained by cross-validation. A substantial increase in accuracy was observed when the number of SNP increased from 10 to 50 but thereafter the increase was smaller, reaching the highest accuracy (0.94) with 100 surrounding SNP. Thus, we conclude that the genotype of a deletion type CNV and its putative QTL effect can be predicted with a maximum accuracy of 0.94 from surrounding SNP. This high prediction accuracy suggests that genetic variation due to simple deletion CNV is well captured by dense SNP panels. Since genomic selection relies on the availability of a dense marker panel with markers in close linkage disequilibrium to the QTL in order to predict their genetic values, we also discuss opportunities for genomic selection to predict the effects of CNV by dense SNP panels, when CNV cause variation in quantitative traits.     

Kinetic investigation on aqueous decomposition of 2-chloroethylnitrososulfamide

The kinetics decomposition of 2-chloroethylnitrososulfamides (CENS) was studied in aqueous buffered solutions with pH ranging from 0 to 14. The study was monitored by RP-LC-MS and conventional UV spectrophotometry. The reaction proceeded via a pseudo-first-order kinetic with significant correlation coefficient. The major decomposition products from CENS after incubation in phosphate buffer were isolated and identified by NMR and mass spectrometry. The results indicate that the mechanism pathway involves a denitrosation of the CENS and competitive hydrolysis with nucleophilic attack on the sulfur atom and formation of sulfamate compounds.     

Surgical outcomes of the brachial plexus lesions caused by gunshot wounds in adults

Background

The management of brachial plexus injuries due to gunshot wounds is a surgical challenge. Better surgical strategies based on clinical and electrophysiological patterns are needed. The aim of this study is to clarify the factors which may influence the surgical technique and outcome of the brachial plexus lesions caused by gunshot injuries.

Methods

Two hundred and sixty five patients who had brachial plexus lesions caused by gunshot injuries were included in this study. All of them were male with a mean age of 22 years. Twenty-three patients were improved with conservative treatment while the others underwent surgical treatment. The patients were classified and managed according to the locations, clinical and electrophysiological findings, and coexisting lesions.

Results

The wounding agent was shrapnel in 106 patients and bullet in 159 patients. Surgical procedures were performed from 6 weeks to 10 months after the injury. The majority of the lesions were repaired within 4 months were improved successfully. Good results were obtained in upper trunk and lateral cord lesions. The outcome was satisfactory if the nerve was intact and only compressed by fibrosis or the nerve was in-contunuity with neuroma or fibrosis.

Conclusion

Appropriate surgical techniques help the recovery from the lesions, especially in patients with complete functional loss. Intraoperative nerve status and the type of surgery significantly affect the final clinical outcome of the patients.     

Demographic response to shading and defoliation in two woodland orchids

Many woodland herbs are long-lived, clonal geophytes that have evolved life histories favoring survival over reproduction. We examined the life history responses of natural populations of two woodland orchid species,Cypripedium calceolus andCephalanthera longifolia to defoliation and heavy shading conducted early in the growing seasons of 2002 and 2003. We asked whether, in view of the importance of growth for the survival of geophytes, treated plants were more likely to exhibit reduced flowering than reduced vegetative growth in the seasons following treatment. We also asked whether plants would suffer reduced ramet performance. Both treatments led to significant declines in flower number per ramet, number of leaves per ramet, and mean ramet height relative to controls inCypripedium. However, inCephalanthera, only shaded plants exhibited significant declines in flower number per ramet, and only defoliated plants exhibited declines in mean ramet height. The number of ramets per plant did not decline relative to controls in either species. Thus, these orchids, especiallyCypripedium, appeared to allocate resources preferentially to vegetative growth functions over sexual reproduction. Per-plant variation in leaf and flower number per ramet, as well as in mean ramet height, consistently declined in response to treatment, significantly so in the case of mean ramet height, suggesting that ramets became more similar within genets. These results suggest both similarities and differences in the ways in whichCephalanthera andCypripedium mobilize resources in response to stress.     

Quercetin protects human granulosa cells against oxidative stress via thioredoxin system

Granulosa Cells (GCs) are sensitive to excessive production of reactive oxygen species (ROS). Quercetin (QUR) is a free radical scavenger which can alleviate oxidative stress through nuclear factor (erythroid-derived 2)-like 2 (Nrf2)/antioxidant response element (ARE) pathway and thioredoxin (Trx) system. We aimed to explore the probable protective role of QUR on cultured human GCs treated with hydrogen peroxide (H₂O₂) as an inducer of oxidative stress. MTT assay was applied for evaluating the cell cytotoxicity of QUR and H₂O₂. The rate of apoptotic cells and intracellular ROS generation were determined by Annexin V-FITC/PI staining and 2′-7′-dichlorodihydro?uorescein diacetate ?uorescent probes (DCFH-DA), respectively. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis and western blot analysis were used to evaluate the gene and protein expression of Nrf2 and kelch-like ech-associated protein 1 (Keap1)1. The Nrf2 and Trx activities were measured by Enzyme-linked Immunosorbent Assay (ELISA). The results indicated that QUR pretreatment can decrease ROS production and apoptosis induced by H₂O₂. In addition, QUR increased Nrf2 gene and protein expression, as well as its nuclear translocation. Moreover, in QUR-treated group, a lower level of Keap1 protein was observed, which was not reported as significant. The results also indicated a significant correlation between the expression of Nrf2 and Keap1 in QUR-treated group. Further, QUR protected GCs from oxidative stress by increasing Trx gene expression and activity. This study suggests that QUR as a supplementary factor may protect GCs from oxidative stress in diseases related to this condition.