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.     

Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides

Background  

The hybridization of synthetic Streptococcus pneumoniae tmRNA on a detection microarray is slow at 34°C resulting in low signal intensities.     

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.     

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.