Complete genome sequence of Salmonella enterica serovar Typhimurium U288

Salmonella enterica serovar Typhimurium U288 has firmly established itself within the United Kingdom pig production industry. The prevalence of this highly pathogenic multidrug-resistant serovar at such a critical point in the food chain is therefore of great concern. To enhance our understanding of this microorganism, whole-genome and plasmid sequencing was performed

Salmonella Typhimurium-specific bacteriophage ΦSH19 and the origins of species specificity in the Vi01-like phage family

<p>Abstract</p> <p>Background</p> <p>Whole genome sequencing of bacteriophages suitable for biocontrol of pathogens in food products is a pre-requisite to any phage-based intervention procedure. Trials involving the biosanitization of <it>Salmonella </it>Typhimurium in the pig production environment identified one such candidate, ΦSH19.</p> <p>Results</p> <p>This phage was sequenced and analysis of its 157,785 bp circular dsDNA genome revealed a number of interesting features. ΦSH19 constitutes another member of the recently-proposed <it>Myoviridae </it>Vi01-like family of phages, containing <it>S</it>. Typhi-specific Vi01 and <it>Shigella</it>-specific SboM-AG3. At the nucleotide level ΦSH19 is highly similar to phage Vi01 (80-98% pairwise identity over the length of the genome), with the major differences lying in the region associated with host-range determination. Analyses of the proteins encoded within this region by ΦSH19 revealed a cluster of three putative tail spikes. Of the three tail spikes, two have protein domains associated with the pectate lyase family of proteins (Tsp2) and P22 tail spike family (Tsp3) with the prospect that these enable <it>Salmonella </it>O antigen degradation. Tail spike proteins of Vi01 and SboM-AG3 are predicted to contain conserved right-handed parallel β-helical structures but the internal protein domains are varied allowing different host specificities.</p> <p>Conclusions</p> <p>The addition or exchange of tail spike protein modules is a major contributor to host range determination in the Vi01-like phage family.</p

The complete plasmid sequences of Salmonella enterica serovar Typhimurium U288.

Salmonella enterica Serovar Typhimurium U288 is an emerging pathogen of pigs. The strain contains three plasmids of diverse origin that encode traits that are of concern for food security and safety, these include antibiotic resistant determinants, an array of functions that can modify cell physiology and permit genetic mobility. At 148,711 bp, pSTU288-1 appears to be a hybrid plasmid containing a conglomerate of genes found in pSLT of S. Typhimurium LT2, coupled with a mosaic of horizontally-acquired elements. Class I integron containing gene cassettes conferring resistance against clinically important antibiotics and compounds are present in pSTU288-1. A curious feature of the plasmid involves the deletion of two genes encoded in the Salmonella plasmid virulence operon (spvR and spvA) following the insertion of a tnpA IS26-like element coupled to a blaTEM gene. The spv operon is considered to be a major plasmid-encoded Salmonella virulence factor that is essential for the intracellular lifecycle. The loss of the positive regulator SpvR may impact on the pathogenesis of S. Typhimurium U288. A second 11,067 bp plasmid designated pSTU288-2 contains further antibiotic resistance determinants, as well as replication and mobilization genes. Finally, a small 4675 bp plasmid pSTU288-3 was identified containing mobilization genes and a pleD-like G-G-D/E-E-F conserved domain protein that modulate intracellular levels of cyclic di-GMP, and are associated with motile to sessile transitions in growth

Determination of insulin secretion from stem cell-derived islet organoids with liquid chromatography-tandem mass spectrometry

Organoids are laboratory-grown 3D organ models, mimicking human organs for e.g. drug development and personalized therapy. Islet organoids (typically 100–200 µm), which can be grown from the patient́s own cells, are emerging as prototypes for transplantation-based therapy of diabetes. Selective methods for quantifying insulin production from islet organoids are needed, but sensitivity and carry-over have been major bottlenecks in previous efforts. We have developed a reverse phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) method for studying the insulin secretion of islet organoids. In contrast to our previous attempts using nano-scale LC columns, conventional 2.1 mm inner diameter LC column (combined with triple quadrupole mass spectrometry) was well suited for sensitive and selective measurements of insulin secreted from islet organoids with low microliter-scale samples. Insulin is highly prone to carry-over, so standard tubings and injector parts were replaced with shielded fused silica connectors. As samples were expected to be very limited, an extended Box-Behnken experimental design for the MS settings was conducted to maximize performance. The finale method has excellent sensitivity, accuracy and precision (limit of detection: ≤0.2 pg/µL, relative error: ≤±10%, relative standard deviation: <10%), and was well suited for measuring 20 µL amounts of Krebs buffer containing insulin secreted from islet organoids.publishedVersio

A comparison of the survival and migratory behavior of hatchery-reared and naturally reared steelhead smolts in the Alsea River and estuary, Oregon, using acoustic telemetry

We tracked three groups of steelhead Oncorhynchus mykiss smolts implanted with acoustic transmitters to determine whether the degree of hatchery domestication or the juvenile rearing environment (hatchery raceway versus natural stream) influenced migration timing and survival in the Alsea River and estuary, Oregon. Two groups consisted of age-1 smolts reared in concrete raceways. One hatchery-reared group (traditional brood group) was derived from the traditional Alsea River broodstock initially developed in the 1950s. The second hatchery-reared group (new brood group) was derived from naturally reared Alsea River adult steelhead that were captured and spawned at the hatchery beginning in the winter of 2000-2001. The third group (naturally reared group) consisted of age-2 naturally reared smolts captured in a downstream migrant trap located in a tributary stream near the hatchery. We placed transmitters in 74 traditional brood smolts, 76 new brood smolts, and 72 naturally reared smolts. Thirty-one acoustic receivers were located throughout the Alsea River and estuary and in the ocean offshore of the river mouth to monitor smolt movement. We found no significant difference between groups in their survival to the head of tide or to the mouth of the estuary. Most smolts from all three groups were detected at the head of tide (87% of fish from the traditional brood group, 78% from the new brood group, and 84% from the naturally reared group). However, survival was poor in the lower estuary for all three groups; we estimated that only 37% of the traditional brood group, 45% of the new brood group, and 47% of the naturally reared group survived to the ocean. The timing of migration through the river was highly variable in all three groups, and we found no significant differences in the rate of downstream movement from the release site to the head of tide. Mean residence time within the estuary was similar for all groups, although smolts from the naturally reared group showed less variability in estuary residence time than hatchery-reared smolts.Keywords: marine survival, Oncorhynchus mykiss, juvenile salmonid

Electronic Health Record Functionality Needed to Better Support Primary Care

Electronic health records (EHRs) must support primary care clinicians and patients, yet many clinicians remain dissatisfied with their system. This manuscript presents a consensus statement about gaps in current EHR functionality and needed enhancements to support primary care. The Institute of Medicine primary care attributes were used to define needs and Meaningful Use (MU) objectives to define EHR functionality. Current objectives remain disease- rather than whole-person focused, ignoring factors like personal risks, behaviors, family structure, and occupational and environmental influences. Primary care needs EHRs to move beyond documentation to interpreting and tracking information over time as well as patient partnering activities, support for team based care, population management tools that deliver care, and reduced documentation burden. While Stage 3 MU’s focus on outcomes is laudable, enhanced functionality is still needed including EHR modifications, expanded use of patient portals, seamless integration with external applications, and advancement of national infrastructure and policies

Research priorities in hypertrophic cardiomyopathy: report of a Working Group of the National Heart, Lung, and Blood Institute.

Hypertrophic cardiomyopathy (HCM) is a myocardial disorder characterized by left ventricular (LV) hypertrophy without dilatation and without apparent cause (ie, it occurs in the absence of severe hypertension, aortic stenosis, or other cardiac or systemic diseases that might cause LV hypertrophy). Numerous excellent reviews and consensus documents provide a wealth of additional background.1–8 HCM is the leading cause of sudden death in young people and leads to significant disability in survivors. It is caused by mutations in genes that encode components of the sarcomere. Cardiomyocyte and cardiac hypertrophy, myocyte disarray, interstitial and replacement fibrosis, and dysplastic intramyocardial arterioles characterize the pathology of HCM. Clinical manifestations include impaired diastolic function, heart failure, tachyarrhythmia (both atrial and ventricular), and sudden death. At present, there is a lack of understanding of how the mutations in genes encoding sarcomere proteins lead to the phenotypes described above. Current therapeutic approaches have focused on the prevention of sudden death, with implantable cardioverter defibrillator placement in high-risk patients. But medical therapies have largely focused on alleviating symptoms of the disease, not on altering its natural history. The present Working Group of the National Heart, Lung, and Blood Institute brought together clinical, translational, and basic scientists with the overarching goal of identifying novel strategies to prevent the phenotypic expression of disease. Herein, we identify research initiatives that we hope will lead to novel therapeutic approaches for patients with HCM

STROBE-X: A probe-class mission for x-ray spectroscopy and timing on timescales from microseconds to years

We describe the Spectroscopic Time-Resolving Observatory for Broadband Energy X-rays (STROBE-X), a probeclass mission concept that will provide an unprecedented view of the X-ray sky, performing timing and spectroscopy over both a broad energy band (0.2-30 keV) and a wide range of timescales from microseconds to years. STROBE-X comprises two narrow-field instruments and a wide field monitor. The soft or low-energy band (0.2-12 keV) is covered by an array of lightweight optics (3-m focal length) that concentrate incident photons onto small solid-state detectors with CCD-level (85-175 eV) energy resolution, 100 ns time resolution, and low background rates. This technology has been fully developed for NICER and will be scaled up to take advantage of the longer focal length of STROBE-X. The higher-energy band (2-30 keV) is covered by large-area, collimated silicon drift detectors that were developed for the European LOFT mission concept. Each instrument will provide an order of magnitude improvement in effective area over its predecessor (NICER in the soft band and RXTE in the hard band). Finally, STROBE-X offers a sensitive wide-field monitor (WFM), both to act as a trigger for pointed observations of X-ray transients and also to provide high duty-cycle, high time-resolution, and high spectral-resolution monitoring of the variable X-ray sky. The WFM will boast approximately 20 times the sensitivity of the RXTE All-Sky Monitor, enabling multi-wavelength and multi-messenger investigations with a large instantaneous field of view. This mission concept will be presented to the 2020 Decadal Survey for consideration

Alzheimer's disease biomarker discovery using SOMAscan multiplexed protein technology

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