Electronic structures of B-2p and C-2p of boron-doped diamond film by soft X-ray absorption and emission spectroscopy

X-ray absorption (XAS) and emission (XES) spectroscopy near B-K and C-K edges have been performed on metallic (~1at%B, B-diamond) and semiconducting (~0.1at%B and N, BN-diamond) doped-diamond films. Both B-K XAS and XES spectra shows metallic partial density of state (PDOS) with the Fermi energy of 185.3 eV, and there is no apparent boron-concentration dependence in contrast to the different electric property. In C-K XAS spectrum of B-diamond, the impurity state ascribed to boron is clearly observed near the Fermi level. The Fermi energy is found to be almost same with the top of the valence band of non-doped diamond, E_V, 283.9 eV. C-K XAS of BN-diamond shows both the B-induced shallow level and N-induced deep-and-broad levels as the in-gap states, in which the shallow level is in good agreement with the activation energy (E_a=0.37 eV) estimated from the temperature dependence of the conductivity, namely the change in C-2p PDOS of impurity-induced metallization is directly observed. The electric property of this diamond is mainly ascribed to the electronic structure of C-2p near the Fermi level. The observed XES spectra are compared with the DVX-alpha cluster calculation. The DVX-alpha result supports the strong hybridization between B-2p and C-2p observed in XAS and XES spectra, and suggests that the small amount of borons (<1at%) in diamond occupy the substitutional site rather than interstitial site.Comment: submitted to Phys. Rev. B, 5 pages and 5 figure

High-Quality and -Quantity DNA Extraction from Frozen Archival Blood Clots for Genotyping of Single-Nucleotide Polymorphisms

Background: The recovery of biological samples for genetic epidemiological studies can be cumbersome. Blood clots are routinely collected for serological examinations. However, the extraction of DNA from blood clots can be difficult and often results in low yields. Aim: The aim was to compare the efficiency of commercial purification kits for extracting DNA from long-term frozen clotted blood. Methods: Serum tubes with clotted blood were stored at -20°C for 1 to 2.5 years before DNA extraction. DNA was extracted from 10 blood clot samples using PureGene (Qiagen) with and without glycogen, the QIAamp DNA Micro kit (Qiagen), and the Nucleospin 96 Blood kit (Macherey-Nagel). Furthermore, blood clots from 1055 inflammatory bowel disease patients were purified using the Maxwell 16 Blood purification kit (Promega). The DNA was extracted according to the manufacturers` instructions and real-time PCR and the A260/A280 ratio were used to evaluate the quality of the extracted DNA. Results: The highest DNA yield was obtained by the Maxwell 16 Blood purification kit (Promega) with a median of 4.90 μg (range 0.8-25 μg) pr 300 μL total blood. PureGene with glycogen (Qiagen) had the second highest yield with a median of 0.65 μg (range 0.5-2.6 μg) pr 300 μL total blood. Conclusion: The yield obtained by the different commercial kits varied considerably. Our work demonstrates that high-quality and -quantity DNA can be extracted with the Maxwell 16 Blood purification kit (Promega) from cryopreserved blood clots, even after prolonged storage. The recovered DNA served as a reliable PCR template for single-nucleotide polymorphism assays

Genome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys

Objective: Clostridium perfringens causes gastrointestinal diseases in both humans and domestic animals. Type A strains expressing the NetB toxin are the main cause of necrotic enteritis (NE) in chickens, which has remarkable impact on animal welfare and production economy in the international poultry industry. Three pathogenicity loci NELoc-1, -2 and -3 and a collagen adhesion gene cnaA have been found to be associated with NE in chickens, whereas the presence of these has not been investigated in diseased turkeys. The purpose was to investigate the virulence associated genome content and the genetic relationship among 30 C. perfringens isolates from both healthy and NE infected chickens and turkeys, applying whole-genome sequencing. Results: NELoc-1, -3, netB and cnaA were significantly associated with NE isolates from chickens, whereas only NELoc-2 was commonly observed in both diseased turkeys and chickens. A putative collagen adhesion gene that encodes a von Willebrand Factor (vWF) domain was identified in all diseased turkeys and designated as cnaD. The phylogenetic analysis based on single nucleotide polymorphisms showed that the isolates generally were not closely related. These results indicate that virulence factors and pathogenicity loci associated with NE in chickens are not important to the same extent in diseased turkeys except for NELoc-2. A putative collagen adhesion gene which potentially could be of importance in regard to the NE pathogenesis in turkeys was identified and need to be further investigated. Thus, the pathogenesis of NE in turkeys appears to be different from that of broiler chickens

Spread of avian pathogenic Escherichia coli ST117 O78:H4 in Nordic broiler production

BACKGROUND: Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in general been characterized as being a genetically diverse population. In the Nordic countries, poultry farmers depend on import of Swedish broiler breeders which are part of a breeding pyramid. During 2014 to 2016, an increased occurrence of colibacillosis on Nordic broiler chicken farms was reported. The aim of this study was to investigate the genetic diversity among E. coli isolates collected on poultry farms with colibacillosis issues, using whole genome sequencing. METHODS: Hundred and fourteen bacterial isolates from both broilers and broiler breeders were whole genome sequenced. The majority of isolates were collected from poultry with colibacillosis on Nordic farms. Subsequently, comparative genomic analyses were carried out. This included in silico typing (sero- and multi-locus sequence typing), identification of virulence and resistance genes and phylogenetic analyses based on single nucleotide polymorphisms. RESULTS: In general, the characterized poultry isolates constituted a genetically diverse population. However, the phylogenetic analyses revealed a major clade of 47 closely related ST117 O78:H4 isolates. The isolates in this clade were collected from broiler chickens and breeders with colibacillosis in multiple Nordic countries. They clustered together with a human ST117 isolate and all carried virulence genes that previously have been associated with human uropathogenic E. coli. CONCLUSIONS: The investigation revealed a lineage of ST117 O78:H4 isolates collected in different Nordic countries from diseased broilers and breeders. The data indicate that the closely related ST117 O78:H4 strains have been transferred vertically through the broiler breeding pyramid into distantly located farms across the Nordic countries. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3415-6) contains supplementary material, which is available to authorized users

Vancomycin gene selection in the microbiome of urban <i>Rattus norvegicus</i> from hospital environment

Background and objectives: Widespread use of antibiotics has resulted in selection pressure on genes that make bacteria non-responsive to antibiotics. These antibiotic-resistant bacteria are currently a major threat to global health. There are various possibilities for the transfer of antibiotic resistance genes. It has been argued that animal vectors such as Rattus norvegicus (R. norvegicus) living in hospital sewage systems are ideal for carrying pathogens responsible for fatal diseases in humans. Methodology: Using a metagenomic sequencing approach, we investigated faecal samples of R. norvegicus from three major cities for the presence of antibiotic resistance genes. Results: We show that despite the shared resistome within samples from the same geographic locations, samples from hospital area carry significantly abundant vancomycin resistance genes. Conclusions and implications: The observed pattern is consistent with a selection for vancomycin genes in the R. norvegicus microbiome, potentially driven by the outflow of antibiotics and antibiotic-resistant bacteria into the wastewater systems. Carriage of vancomycin resistance may suggest that R. norvegicus is acting as a reservoir for possible transmission to the human population

Synthesis and characterization of atomically-thin graphite films on a silicon carbide substrate

This paper reports the synthesis and detailed characterization of graphite thin films produced by thermal decomposition of the (0001) face of a 6H-SiC wafer, demonstrating the successful growth of single crystalline films down to approximately one graphene layer. The growth and characterization were carried out in ultrahigh vacuum (UHV) conditions. The growth process and sample quality were monitored by low-energy electron diffraction, and the thickness of the sample was determined by core level x-ray photoelectron spectroscopy. High-resolution angle-resolved photoemission spectroscopy shows constant energy map patterns, which are very sharp and fully momentum-resolved, but nonetheless not resolution limited. We discuss the implications of this observation in connection with scanning electron microscopy data, as well as with previous studies

Scattered Data Approximation by LR B-Spline Surfaces: A Study on Refinement Strategies for Efficient Approximation

Locally refined B-spline (LRB) surfaces provide a representation that is well suited to scattered data approximation. When a data set has local details in some areas and is largely smooth elsewhere, LR B-splines allow the spatial distribution of degrees of freedom to follow the variations of the data set. An LRB surface approximating a data set is refined in areas where the accuracy does not meet a required tolerance. In this paper we address, in a systematic study, different LRB refinement strategies and polynomial degrees for surface approximation. We study their influence on the resulting data volume and accuracy when applied to geospatial data sets with different structural behaviour. The relative performance of the refinement strategies is reasonably coherent for the different data sets and this paper concludes with some recommendations. An overall evaluation indicates that bi-quadratic LRB are preferable for the use cases tested, and that the strategies we denote as “full span" have the overall best performance.publishedVersio