Color Gradients and Surface Brightness Profiles of Galaxies in the Hubble Deep Field-North

We fit elliptical isophotes to the Hubble Deep Field-North WFPC-2 and NICMOS data to study the rest-frame UV_{218}-U_{300} color profiles and rest-frame B surface brightness profiles of 33 intermediate redshift galaxies (0.5 <= z <= 1.2) with I_{814} < 25 and 50 high redshift galaxies (2.0 <= z <= 3.5) with H_{160}< 27. From the weighted least-squares fit to the color profiles we find that, at intermediate redshifts, the galaxies possess negative color gradients indicating a reddening towards the center of the profile similar to local samples whereas, at high redshifts, the galaxies possess positive color gradients. This indicates that star formation is more centrally concentrated in the distant galaxy sample which differs from the prevalent mode of extended disk star formation that we observe in the local universe. Additionally, we find that it is critical to correct for PSF effects when evaluating the surface brightness profiles since at small scale lengths and faint magnitudes, an r^{1/4} profile can be smoothed out substantially to become consistent with an exponential profile. After correcting for PSF effects, we find that at higher look-back time, the fraction of galaxies possessing exponential profiles have slightly decreased while the fraction of galaxies possessing r^{1/4} profiles have slightly increased. Our results also suggest a statistically insignificant increase in the fraction of peculiar/irregular type galaxies. We compare our results with recent semi-analytical models which treat galaxy formation and evolution following the cold dark matter hierarchical framework.Comment: 31 pages, 10 JPEG figures. To be published in AJ Vol. 124, October 200

Comprehensive Characterization of Escherichia coil O104:H4 Isolated from Patients in the Netherlands

In 2011, a Shiga toxin-producing Enteroaggregative Escherichia coli (EAEC Stx2a+) O104:H4 strain caused a serious outbreak of acute gastroenteritis and hemolytic-uremic syndrome (HUS) in Germany. In 2013, E. coli O104:H4 isolates were obtained from a patient with HUS and her friend showing only gastrointestinal complaints. The antimicrobial resistance and virulence profiles of these isolates together with three EAEC Stx2a+ O104:H4 isolates from 2011 were determined and compared. Whole-genome sequencing (WGS) was performed for detailed characterization and to determine genetic relationship of the isolates. Four additional genomes of EAEC Stx2a+ O104:H4 isolates of 2009 and 2011 available on NCBI were included in the virulence and phylogenetic analysis. All E. coli O104:H4 isolates tested were positive for stx2a, aatA, and terD but were negative for escV. All, except one 2011 isolate, were positive for aggR and were therefore considered EAEC. The EAEC Stx2a+ O104:H4 isolates of 2013 belonged to sequence type (ST) ST678 as the 2011 isolates and showed slightly different resistance and virulence patterns compared to the 2011 isolates. Core-genome phylogenetic analysis showed that the isolates of 2013 formed a separate cluster from the isolates of 2011 and 2009 by 27 and 20 different alleles, respectively. In addition, only a one-allele difference was found between the isolate of the HUS-patient and that of her friend. Our study shows that EAEC Stx2a+ O104:H4 strains highly similar to the 2011 outbreak clone in their core genome are still circulating necessitating proper surveillance to prevent further outbreaks with these potentially pathogenic strains. In addition, WGS not only provided a detailed characterization of the isolates but its high discriminatory power also enabled us to discriminate the 2013 isolates from the isolates of 2009 and 2011 expediting the use of WGS in public health services to rapidly apply proper infection control strategies

Iron deficiency impairs contractility of human cardiomyocytes through decreased mitochondrial function

Contains fulltext : 191557.pdf (Publisher’s version ) (Open Access

CoNVaDING:Single Exon Variation Detection in Targeted NGS Data

We have developed a tool for detecting single exon copy number variations (CNVs) in targeted next-generation sequencing data: CoNVaDING (Copy Number Variation Detection In Next-generation sequencing Gene panels). CoNVaDING includes a stringent quality control metric, that excludes or flags low quality exons. Since this quality control shows exactly which exons can be reliably analysed and which exons are in need of an alternative analysis method, CoNVaDING is not only useful for CNV detection in a research setting, but also in clinical diagnostics. During the validation phase, CoNVaDING detected all known CNVs in high quality targets in 320 samples analysed, giving 100% sensitivity and 99.998% specificity for 308,574 exons. CoNVaDING outperforms existing tools by exhibiting a higher sensitivity and specificity and by precisely identifying low-quality samples and regions. This article is protected by copyright. All rights reserved.</p

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat

Profound Pathogen-Specific Alterations in Intestinal Microbiota Composition Precede Late-Onset Sepsis in Preterm Infants:A Longitudinal, Multicenter, Case-Control Study

BACKGROUND: The role of intestinal microbiota in the pathogenesis of late-onset sepsis (LOS) in preterm infants is largely unexplored but could provide opportunities for microbiota-targeted preventive and therapeutic strategies. We hypothesized that microbiota composition changes before the onset of sepsis, with causative bacteria that are isolated later in blood culture. METHODS: This multicenter case-control study included preterm infants born under 30 weeks of gestation. Fecal samples collected from the 5 days preceding LOS diagnosis were analyzed using a molecular microbiota detection technique. LOS cases were subdivided into 3 groups: gram-negative, gram-positive, and coagulase-negative Staphylococci (CoNS). RESULTS: Forty LOS cases and 40 matched controls were included. In gram-negative LOS, the causative pathogen could be identified in at least 1 of the fecal samples collected 3 days prior to LOS onset in all cases, whereas in all matched controls, this pathogen was absent (P = .015). The abundance of these pathogens increased from 3 days before clinical onset. In gram-negative and gram-positive LOS (except CoNS) combined, the causative pathogen could be identified in at least 1 fecal sample collected 3 days prior to LOS onset in 92% of the fecal samples, whereas these pathogens were present in 33% of the control samples (P = .004). Overall, LOS (expect CoNS) could be predicted 1 day prior to clinical onset with an area under the curve of 0.78. CONCLUSIONS: Profound preclinical microbial alterations underline that gut microbiota is involved in the pathogenesis of LOS and has the potential as an early noninvasive biomarker

Decabromodiphenylether trends in the European environment: bird eggs, sewage sludge and surficial sediments

Concern on relatively high levels and the potential bioaccumulation of decabromodiphenylether (BDE209) has led to a European 8-year monitoring program on trends in BDE209 concentrations in birds, sewage sludge and sediments from seven countries. BDE209 was analysed in four environmental matrices: sparrowhawk eggs (UK), glaucous gull eggs (Bear Island, Norway), sewage sludge (UK, Ireland and the Netherlands) and sediment (France, Germany, the Netherlands, UK and Ireland). BDE209 was detected in most of the glaucous gull and sparrow hawk eggs but neither increasing nor decreasing trends in these BDE209 levels were observed. An indication for debromination of BDE209 in sparrowhawk eggs was found. BDE209 concentrations in sediments ranged from very low ng/g (88 ng/g on an organic carbon (OC) basis) concentrations, in the rivers Elbe, Ems, Seine and the Outer Humber, to high μg/g (120 μg/g OC), in the Western Scheldt, Liverpool Bay and River Mersey. Apart from decreasing values in the Western Scheldt sediment no further decreases in BDE209 concentrations were observed over time, neither in sediment nor in sewage sludge showing that the voluntary emissions control program of the bromine industry only had a local effect. In contrast to the sewage sludge samples from the Netherlands (mean 355 ng/g dry weight (dw) or 1026 ng/g OC), the BDE209 concentrations in the UK increased at all sites from 2006 to 2011 (8092 ng/g dw or 22,367 ng/g OC). The BDE209 levels in several UK sediments and sewage sludge were still very high at the end of the program in 2012, most likely caused by frequent use of BDE209 in the textile industry. This may be indicative of the persistence of BDE209 and the limited degradation into lower brominated congeners in sediment, although it cannot be excluded that ongoing BDE209 emissions have played a role as well

Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5

Mutations in genes critical for proper intra-Golgi transport can cause human syndromes due to defects in glycosylation of proteins. Here, the authors identify a human variant of Syntaxin-5 that causes fatal multisystem disease and mislocalization of glycosyltransferases due to altered Golgi transport