Dynamics of Gene Duplication in the Genomes of Chlorophyll d-Producing Cyanobacteria: Implications for the Ecological Niche

Gene duplication may be an important mechanism for the evolution of new functions and for the adaptive modulation of gene expression via dosage effects. Here, we analyzed the fate of gene duplicates for two strains of a novel group of cyanobacteria (genus Acaryochloris) that produces the far-red light absorbing chlorophyll d as its main photosynthetic pigment. The genomes of both strains contain an unusually high number of gene duplicates for bacteria. As has been observed for eukaryotic genomes, we find that the demography of gene duplicates can be well modeled by a birth–death process. Most duplicated Acaryochloris genes are of comparatively recent origin, are strain-specific, and tend to be located on different genetic elements. Analyses of selection on duplicates of different divergence classes suggest that a minority of paralogs exhibit near neutral evolutionary dynamics immediately following duplication but that most duplicate pairs (including those which have been retained for long periods) are under strong purifying selection against amino acid change. The likelihood of duplicate retention varied among gene functional classes, and the pronounced differences between strains in the pool of retained recent duplicates likely reflects differences in the nutrient status and other characteristics of their respective environments. We conclude that most duplicates are quickly purged from Acaryochloris genomes and that those which are retained likely make important contributions to organism ecology by conferring fitness benefits via gene dosage effects. The mechanism of enhanced duplication may involve homologous recombination between genetic elements mediated by paralogous copies of recA

Subglacial controls on dynamic thinning at Trinity-Wykeham Glacier, Prince of Wales Ice Field, Canadian Arctic

Mass loss from glaciers and ice caps represents the largest terrestrial component of current sea level rise. However, our understanding of how the processes governing mass loss will respond to climate warming remains incomplete. This study explores the relationship between surface elevation changes (dh/dt), glacier velocity changes (du/dt), and bedrock topography at the Trinity-Wykeham Glacier system (TWG), Canadian High Arctic, using a range of satellite and airborne datasets. We use measurements of dh/dt from ICESat (2003-2009) and CryoSat-2 (2010-2016) repeat observations to show that rates of surface lowering increased from 4 m yr-1 to 6 m yr-1 across the lowermost 10 km of the TWG. We show that surface flow rates at both Trinity Glacier and Wykeham Glacier doubled over 16 years, during which time the ice front retreated 4.45 km. The combination of thinning, acceleration and retreat of the TWG suggests that a dynamic thinning mechanism is responsible for the observed changes, and we suggest that both glaciers have transitioned from fully grounded to partially floating. Furthermore, by comparing the separate glacier troughs we suggest that the dynamic changes are modulated by both lateral friction from the valley sides and the complex geometry of the bed. Further, the presence of bedrock ridges induces crevassing on the surface and provides a direct link for surface meltwater to reach the bed. We observe supraglacial lakes that drain at the end of summer and are concurrent with a reduction in glacier velocity, suggesting hydrological connections between the surface and the bed significantly impact ice flow. The bedrock topography thus has a primary influence on the nature of the changes in ice dynamics observed over the last decade.</p

Development of a high-temperature diagnostics-while-drilling tool.

The envisioned benefits of Diagnostics-While-Drilling (DWD) are based on the principle that high-speed, real-time information from the downhole environment will promote better control of the drilling process. Although in practice a DWD system could provide information related to any aspect of exploration and production of subsurface resources, the current DWD system provides data on drilling dynamics. This particular set of new tools provided by DWD will allow quicker detection of problems, reduce drilling flat-time and facilitate more efficient drilling (drilling optimization) with the overarching result of decreased drilling costs. In addition to providing the driller with an improved, real-time picture of the drilling conditions downhole, data generated from DWD systems provides researchers with valuable, high fidelity data sets necessary for developing and validating enhanced understanding of the drilling process. Toward this end, the availability of DWD creates a synergy with other Sandia Geothermal programs, such as the hard-rock bit program, where the introduction of alternative rock-reduction technologies are contingent on the reduction or elimination of damaging dynamic effects. More detailed descriptions of the rationale for the program and early development efforts are described in more detail by others [SAND2003-2069 and SAND2000-0239]. A first-generation low-temperature (LT) DWD system was fielded in a series of proof-of-concept tests (POC) to validate functionality. Using the LT system, DWD was subsequently used to support a single-laboratory/multiple-partner CRADA (Cooperative Research and Development Agreement) entitled Advanced Drag Bits for Hard-Rock Drilling. The drag-bit CRADA was established between Sandia and four bit companies, and involved testing of a PDC bit from each company [Wise, et al., 2003, 2004] in the same lithologic interval at the Gas Technology Institute (GTI) test facility near Catoosa, OK. In addition, the LT DWD system has been fielded in cost-sharing efforts with an industrial partner to support the development of new generation hard-rock drag bits. Following the demonstrated success of the POC DWD system, efforts were initiated in FY05 to design, fabricate and test a high-temperature (HT) capable version of the DWD system. The design temperature for the HT DWD system was 225 C. Programmatic requirements dictated that a HT DWD tool be developed during FY05 and that a working system be demonstrated before the end of FY05. During initial design discussions regarding a high-temperature system it was decided that, to the extent possible, the HT DWD system would maintain functionality similar to the low temperature system, that is, the HT DWD system would also be designed to provide the driller with real-time information on bit and bottom-hole-assembly (BHA) dynamics while drilling. Additionally, because of time and fiscal constraints associated with the HT system development, the design of the HT DWD tool would follow that of the LT tool. The downhole electronics package would be contained in a concentrically located pressure barrel and the use of externally applied strain gages with thru-tool connectors would also be used in the new design. Also, in order to maximize the potential wells available for the HT DWD system and to allow better comparison with the low-temperature design, the diameter of the tool was maintained at 7-inches. This report discusses the efforts associated with the development of a DWD system capable of sustained operation at 225 C. This report documents work performed in the second phase of the Diagnostics-While-Drilling (DWD) project in which a high-temperature (HT) version of the phase 1 low-temperature (LT) proof-of-concept (POC) DWD tool was built and tested. Descriptions of the design, fabrication and field testing of the HT tool are provided. Background on prior phases of the project can be found in SAND2003-2069 and SAND2000-0239

Development of Rapid Detection and Genetic Characterization of Salmonella in Poultry Breeder Feeds

Salmonella is a leading cause of foodborne illness in the United States, with poultry and poultry products being a primary source of infection to humans. Poultry may carry some Salmonella serovars without any signs or symptoms of disease and without causing any adverse effects to the health of the bird. Salmonella may be introduced to a flock by multiple environmental sources, but poultry feed is suspected to be a leading source. Detecting Salmonella in feed can be challenging because low levels of the bacteria may not be recovered using traditional culturing techniques. Numerous detection methodologies have been examined over the years for quantifying Salmonella in feeds and many have proven to be effective for Salmonella isolation and detection in a variety of feeds. However, given the potential need for increased detection sensitivity, molecular detection technologies may the best candidate for developing rapid sensitive methods for identifying small numbers of Salmonella in the background of large volumes of feed. Several studies have been done using polymerase chain reaction (PCR) assays and commercial kits to detect Salmonella spp. in a wide variety of feed sources. In addition, DNA array technology has recently been utilized to track the dissemination of a specific Salmonella serotype in feed mills. This review will discuss the processing of feeds and potential points in the process that may introduce Salmonella contamination to the feed. Detection methods currently used and the need for advances in these methods also will be discussed. Finally, implementation of rapid detection for optimizing control methods to prevent and remove any Salmonella contamination of feeds will be considered

Hepatic P450 Enzyme Activity, Tissue Morphology and Histology of Mink (Mustela vison) Exposed to Polychlorinated Dibenzofurans

Dose- and time-dependent effects of environmentally relevant concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin equivalents (TEQ) of 2,3,7,8-tetrachlorodibenzofuran (TCDF), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF), or a mixture of these two congeners on hepatic P450 enzyme activity and tissue morphology, including jaw histology, of adult ranch mink were determined under controlled conditions. Adult female ranch mink were fed either TCDF (0.98, 3.8, or 20 ng TEQTCDF/kg bw/day) or PeCDF (0.62, 2.2, or 9.5 ng TEQPeCDF/kg bw/day), or a mixture of TCDF and PeCDF (4.1 ng TEQTCDF/kg bw/day and 2.8 ng TEQPeCDF/kg bw/day, respectively) for 180 days. Doses used in this study were approximately eight times greater than those reported in a parallel field study. Activities of the cytochrome P450 1A enzymes, ethoxyresorufin O-deethylase (EROD) and methoxyresorufin O-deethylase (MROD) were significantly greater in livers of mink exposed to TCDF, PeCDF, and a mixture of the two congeners; however, there were no significant histological or morphological effects observed. It was determined that EROD and MROD activity can be used as sensitive biomarkers of exposure to PeCDF and TCDF in adult female mink; however, under the conditions of this study, the response of EROD/MROD induction occurred at doses that were less than those required to cause histological or morphological changes

2009 Focused Updates: ACC/AHA Guidelines for the Management of Patients With ST-Elevation Myocardial Infarction (Updating the 2004 Guideline and 2007 Focused Update) and ACC/AHA/SCAI Guidelines on Percutaneous Coronary Intervention (Updating the 2005 Guideline and 2007 Focused Update)

Late-breaking clinical trials presented at the 2007 and 2008 annual scientific meetings of the ACC, AHA, Transcatheter Cardiovascular Therapeutics, the European Society of Cardiology, and the 2009 annual scientific sessions of the ACC were reviewed by the standing guideline writing committee along with the parent Task Force and other experts to identify those trials and other key data that may impact guideline recommendations. On the basis of the criteria/considerations noted above, recent trial data and other clinical information were considered important enough to prompt a focused update of the ACC/AHA 2004 Guidelines for the Management of Patients With ST-Elevation Myocardial Infarction and the ACC/AHA 2005 Guidelines for Percutaneous Coronary Intervention, inclusive of their respective 2007 focused updates (2–5)

Evaluation of metabolomics profiles of grain from maize hybrids derived from near-isogenic GM positive and negative segregant inbreds demonstrates that observed differences cannot be attributed unequivocally to the GM trait

Introduction: Past studies on plant metabolomes have highlighted the influence of growing environments and varietal differences in variation of levels of metabolites yet there remains continued interest in evaluating the effect of genetic modification (GM). Objectives: Here we test the hypothesis that metabolomics differences in grain from maize hybrids derived from a series of GM (NK603, herbicide tolerance) inbreds and corresponding negative segregants can arise from residual genetic variation associated with backcrossing and that the effect of insertion of the GM trait is negligible. Methods: Four NK603-positive and negative segregant inbred males were crossed with two different females (testers). The resultant hybrids, as well as conventional comparator hybrids, were then grown at three replicated field sites in Illinois, Minnesota, and Nebraska during the 2013 season. Metabolomics data acquisition using gas chromatography–time of flight-mass spectrometry (GC–TOF-MS) allowed the measurement of 367 unique metabolite features in harvested grain, of which 153 were identified with small molecule standards. Multivariate analyses of these data included multi-block principal component analysis and ANOVA-simultaneous component analysis. Univariate analyses of all 153 identified metabolites was conducted based on significance testing (α = 0.05), effect size evaluation (assessing magnitudes of differences), and variance component analysis. Results: Results demonstrated that the largest effects on metabolomic variation were associated with different growing locations and the female tester. They further demonstrated that differences observed between GM and non-GM comparators, even in stringent tests utilizing near-isogenic positive and negative segregants, can simply reflect minor genomic differences associated with conventional back-crossing practices. Conclusion: The effect of GM on metabolomics variation was determined to be negligible and supports that there is no scientific rationale for prioritizing GM as a source of variation.</p