Common genomic features of Campylobacter jejuni subsp. doylei strains distinguish them from C. jejuni subsp. jejuni

<p>Abstract</p> <p>Background</p> <p><it>Campylobacter jejuni </it>has been divided into two subspecies: <it>C. jejuni </it>subsp. <it>jejuni </it>(<it>Cjj</it>) and <it>C. jejuni </it>subsp. <it>doylei </it>(<it>Cjd</it>). Nearly all of the <it>C. jejuni </it>strains isolated are <it>Cjj</it>; nevertheless, although <it>Cjd </it>strains are isolated infrequently, they differ from <it>Cjj </it>in two key aspects: they are obtained primarily from human clinical samples and are associated often with bacteremia, in addition to gastroenteritis. In this study, we utilized multilocus sequence typing (MLST) and a DNA microarray-based comparative genomic indexing (CGI) approach to examine the genomic diversity and gene content of <it>Cjd </it>strains.</p> <p>Results</p> <p>A geographically diverse collection of eight <it>Cjd </it>strains was examined by MLST and determined to be phylogenetically distinct from <it>Cjj </it>strains. Microarray-based CGI approach also supported this. We were able to demonstrate that <it>Cjd </it>strains exhibited divergence from <it>Cjj </it>strains NCTC 11168 and RM1221 in many of the intraspecies hypervariable regions. Moreover, multiple metabolic, transport and virulence functions (e.g. cytolethal distending toxin) were shown to be absent in the <it>Cjd </it>strains examined.</p> <p>Conclusion</p> <p>Our data demonstrate that <it>Cjd </it>are phylogenetically distinct from <it>Cjj </it>strains. Using the CGI approach, we identified subsets of absent genes from amongst the <it>C. jejuni </it>genes that provide clues as to the potential evolutionary origin and unusual pathogenicity of <it>Cjd</it>.</p

Complete Genomic Sequences of Three Salmonella enterica subsp. enterica Serovar Muenchen Strains from an Orchard in San Joaquin County, California.

We present here the complete genome sequences of three Salmonella enterica subsp. enterica serovar Muenchen strains, LG24, LG25, and LG26. All three strains were isolated from almond drupes grown in an orchard in San Joaquin County, California, in 2016. These genomic sequences are nonidentical and will contribute to our understanding of S. enterica genomics

Open Dialogue compared to treatment as usual for adults experiencing a mental health crisis: Protocol for the ODDESSI multi-site cluster randomised controlled trial.

Background 'Open Dialogue' is a social network model of crisis and continuing mental healthcare which involves elements of service delivery such as immediate response and a style of therapeutic meeting called network meetings. Although there are indications from non-randomised studies that it may help people in their recovery from severe mental health crises and improve long-term outcomes, this has yet to be tested in a randomised controlled trial. Methods This paper outlines the protocol for a multi-site cluster-randomised control trial assessing the clinical and cost-effectiveness of Open Dialogue compared to treatment as usual (TAU) for individuals presenting in crisis to six mental health services in England. The primary outcome is time to relapse, with secondary outcomes including measures of recovery and service use. Participants will be followed-up for two years, with data collected from electronic medical records and researcher-led interviews. The analysis will compare outcomes between treatment groups as well as investigating potential mediators of effect: shared decision-making and social network quality and size. Carers of a subsample of participants will be asked about their experiences of shared decision-making, carer burden, and satisfaction. Discussion This trial will provide evidence of whether Open Dialogue services implemented in the English mental health system is an effective alternative to current care and may have important implications for the organization of community mental health services. Trial registration: retrospectively registered (108 participants recruited of 570 target) on 20/12/2019, ISRCTN52653325. [Abstract copyright: Copyright © 2021. Published by Elsevier Inc.

Bioinformatics and the Undergraduate Curriculum Essay

Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their support staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into undergraduate curricula

From Forbidden Coronal Lines to Meaningful Coronal Magnetic Fields

We review methods to measure magnetic fields within the corona using the polarized light in magnetic-dipole (M1) lines. We are particularly interested in both the global magnetic-field evolution over a solar cycle, and the local storage of magnetic free energy within coronal plasmas. We address commonly held skepticisms concerning angular ambiguities and line-of-sight confusion. We argue that ambiguities are in principle no worse than more familiar remotely sensed photospheric vector-fields, and that the diagnosis of M1 line data would benefit from simultaneous observations of EUV lines. Based on calculations and data from eclipses, we discuss the most promising lines and different approaches that might be used. We point to the S-like [Fe {\sc XI}] line (J=2 to J=1) at 789.2nm as a prime target line (for ATST for example) to augment the hotter 1074.7 and 1079.8 nm Si-like lines of [Fe {\sc XIII}] currently observed by the Coronal Multi-channel Polarimeter (CoMP). Significant breakthroughs will be made possible with the new generation of coronagraphs, in three distinct ways: (i) through single point inversions (which encompasses also the analysis of MHD wave modes), (ii) using direct comparisons of synthetic MHD or force-free models with polarization data, and (iii) using tomographic techniques.Comment: Accepted by Solar Physics, April 201

Multipixel characterization of imaging CZT detectors for hard X-ray imaging and spectroscopy

We report our in-depth study of Cd-Zn-Te (CZT) crystals to determine an optimum pixel and guard band configuration for Hard X-ray imaging and spectroscopy. We tested 20x20x5mm crystals with 8x8 pixels on a 2.46mm pitch. We have studied different types of cathode / anode contacts and different pixel pad sizes. We present the measurements of leakage current as well as spectral response for each pixel. Our I-V measurement setup is custom designed to allow automated measurements of the I-V curves sequentially for all 64 pixels, whereas the radiation properties measurement setup allows for interchangeable crystals with the same XAIM3.2 ASIC readout from IDEAS. We have tested multiple crystals of each type, and each crystal in different positions to measure the variation between individual crystals and variation among the ASIC channels. We also compare the same crystals with and without a grounded guard band deposited on the crystal side walls vs. a floating guard band and compare results to simulations. This study was carried out to find the optimum CZT crystal configuration for prototype detectors for the proposed Black-Hole Finder mission, EXIST.Comment: To appears in the SPIE 2004 proceedings (5540: Hard X-ray and gamma-ray detector physics V

Heme metabolism genes Downregulated in COPD Cachexia.

IntroductionCachexia contributes to increased mortality and reduced quality of life in Chronic Obstructive Pulmonary Disease (COPD) and may be associated with underlying gene expression changes. Our goal was to identify differential gene expression signatures associated with COPD cachexia in current and former smokers.MethodsWe analyzed whole-blood gene expression data from participants with COPD in a discovery cohort (COPDGene, N = 400) and assessed replication (ECLIPSE, N = 114). To approximate the consensus definition using available criteria, cachexia was defined as weight-loss &gt; 5% in the past 12 months or low body mass index (BMI) (&lt; 20 kg/m2) and 1/3 criteria: decreased muscle strength (six-minute walk distance &lt; 350 m), anemia (hemoglobin &lt; 12 g/dl), and low fat-free mass index (FFMI) (&lt; 15 kg/m2 among women and &lt; 17 kg/m2 among men) in COPDGene. In ECLIPSE, cachexia was defined as weight-loss &gt; 5% in the past 12 months or low BMI and 3/5 criteria: decreased muscle strength, anorexia, abnormal biochemistry (anemia or high c-reactive protein (&gt; 5 mg/l)), fatigue, and low FFMI. Differential gene expression was assessed between cachectic and non-cachectic subjects, adjusting for age, sex, white blood cell counts, and technical covariates. Gene set enrichment analysis was performed using MSigDB.ResultsThe prevalence of COPD cachexia was 13.7% in COPDGene and 7.9% in ECLIPSE. Fourteen genes were differentially downregulated in cachectic versus non-cachectic COPD patients in COPDGene (FDR &lt; 0.05) and ECLIPSE (FDR &lt; 0.05).DiscussionSeveral replicated genes regulating heme metabolism were downregulated among participants with COPD cachexia. Impaired heme biosynthesis may contribute to cachexia development through free-iron buildup and oxidative tissue damage

Влияние механической активации гидрида титана на его взаимодействие с азотом и кислородом

Показано, что размол гидрида титана в планетарной мельнице приводит к повышению удельной поверхности порошка, росту микроискажений кристаллической решетки, уменьшению содержания в нем водорода и повышению химической активности, что позволяет получать нитрид титана из него в среде азота уже при температуре 500 °С. За счет кислорода, адсорбирован ного механически активированным порошком при нагревании в атмосфере азота, происходят реакции окисления атомов титана, в результате чего образуется низший оксид Tі2О.Показано, що подрібнення гідриду титану в планетарному млині приводить до підвищення питомої поверхні порошку, зростанню дефектів кристалічної ґратки, зменшенню вмісту в ній водню і підвищенню хімічної активності. Це дає змогу досягти повного перетворення механічно активованого гідриду в нітрид титану вже за температури 500 °С і витримці упродовж однієї години в середовищі азоту. За рахунок кисню, адсорбованого механічно активованим порошком при нагрівання в атмосфері азоту, проходять реакції окиснення, в результаті чого утворюється нижчий оксид Ti2O.Milling of titanium hydride in planetary mill is shoun to increase the speci surface area of powder, to decrease the hydrogen content in it and to intensity chemical activity. This makesit possible to obtain titanium nitride from the titanium hydride in a nitrogen atmosphere at as low temperature as 500 °C . Thanks to the presence of oxygen adsorbed by mechanically activated powder under heating in a nitrogen atmosphere? Reaction of intramolecular oxidation -reduction, of titanium takes place, which results in forming the lower oxide Ti2O