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Interactions between environmental factors and complex life‐history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype–environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster. [ABSTRACT FROM AUTHOR]

Infectious salmon anaemia (ISA) is a viral disease that affects farmed Atlantic salmon (Salmo salar L.), often leading to mass mortalities. A quick detection of the ISA virus (ISAV) is crucial for decision‐making and can prevent the occurrence of future outbreaks. Screening done by Canada's National Aquatic Animal Health Laboratory System (NAAHLS) uses quantitative reverse transcription PCR (RT‐qPCR) followed by sequencing of PCR amplicons. As neither technique provides information regarding the infectivity of the virus, suspected virulent strains are subsequently tested using viral isolation. However, this stepwise process can require significant time to deliver results. To speed up this delivery, we have improved on these pre‐existing techniques by combining the use of cell culture with RT‐qPCR to detect replicative virus in as little as 5 days. Preliminary assays enabled the establishment of a minimal shift in Ct values over time, which is representative of viral replication in cultured cells. Subsequent blind panel analyses allowed the establishment of the optimal sampling days, as well as diagnostic sensitivity (DSe) and specificity (DSp) estimates. This method could be adopted not only by laboratories conducting diagnostic analyses for ISAV, but also for other slow‐replicating viral agents that replicate through a budding mechanism. [ABSTRACT FROM AUTHOR]

The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that coprecipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often coprecipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant-rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in-house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing. Our open-source MoLSC protocol provides a cost-effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant-rich samples. [ABSTRACT FROM AUTHOR]

5-Lipoxygenase (5-LO) is the essential enzyme for the biosynthesis of leukotrienes, important mediators of inflammation. This study investigated whether variants of 5-LO exist in human leukocytes. 5-LO mRNA isoforms that are consistent with alternative splicing were identified by RT-PCR in a cell line or cell type-specific pattern. All evaluated cells expressed mRNA containing all 14 exons of 5-LO with the expected splicing sites. Individual isoforms that retained intron 10 (α-10), lacked exon 13 (Δ-13), and lacked exons 10 and 13 (Δ-10,13) or that lacked the first 96 base pairs of exon 10 (Δ-p10) were identified. Immunoreactive bands coeluting with the cloned α-10 and Δ-13 isoforms were measured in primary neutrophils and in Raji cells. When expressed in HEK293 cells, alternative proteins were without catalytic activity. However, when coexpressed with the active full-length 5-LO, alternative isoforms significantly decreased the biosynthesis of 5-LO products by up to 44%, as assessed by reverse-phase HPLC analysis. Additionally, in stimulated neutrophils the full-length active 5-LO was detected by immunoblot in both nuclear and non-nuclear compartments, while the Δ-13 isoform was only detected in the nuclear fraction. These alternative 5-LO isoforms may represent a new mechanism for the regulation of the 5-LO pathway and lipid mediator biosynthesis. [ABSTRACT FROM AUTHOR]

Most green algal taxa have circular-mapping mitochondrial genomes, whereas some have linear genome- or subgenomic-sized mitochondrial DNAs (mtDNA). It is not clear, however, if the circular-mapping genomes represent genome-sized circular molecules, if such circular molecules and the linear forms are the predominant in vivo mtDNA structures, or if the linear forms arose only once or multiple times among extant green algal lineages. We therefore examined the DNA components detected with homologous mtDNA probes after pulsed-field gel electrophoresis of total cellular DNA from the chlorophycean basal bodies displaced clockwise(CW)-group taxa Chlamydomonas reinhardtii and Chlamydomonas moewusii. For C. reinhardtii , the 15.8-kb linear mtDNA was the only DNA component detected, and there was no evidence of circular or large linear precursors of this DNA. In the case of C. moewusii , which is known to have a circular-mapping 22.9-kb mitochondrial genome, three DNA components were detected; these appeared to be circular (relaxed and supercoiled) and genome-sized linear DNA molecules, the latter of which likely resulted from random double-strand breaks in the circular forms during DNA isolation. In further studies, DNA from additional CW-group taxa was examined using conventional gel electrophoresis and DNA-filter blot analysis with C. reinhardtii and C. moewusii mtDNA probes. We conclude that all taxa from the “Volvox clade” (sensu Nakayama et al. 1996 of the CW-group have genome- or subgenomic-sized linear mtDNAs as their predominant mtDNA form and that these arose from a genome-sized circular form in an ancestor that existed near the base of this clade. [ABSTRACT FROM AUTHOR]

Most green algal taxa have circular-mapping mitochondrial genomes, whereas some have linear genome- or subgenomic-sized mitochondrial DNAs (mtDNA). It is not clear, however, if the circular-mapping genomes represent genome-sized circular molecules, if such circular molecules and the linear forms are the predominant in vivo mtDNA structures, or if the linear forms arose only once or multiple times among extant green algal lineages. We therefore examined the DNA components detected with homologous mtDNA probes after pulsed-field gel electrophoresis of total cellular DNA from the chlorophycean basal bodies displaced clockwise(CW)-group taxa Chlamydomonas reinhardtii and Chlamydomonas moewusii. For C. reinhardtii , the 15.8-kb linear mtDNA was the only DNA component detected, and there was no evidence of circular or large linear precursors of this DNA. In the case of C. moewusii , which is known to have a circular-mapping 22.9-kb mitochondrial genome, three DNA components were detected; these appeared to be circular (relaxed and supercoiled) and genome-sized linear DNA molecules, the latter of which likely resulted from random double-strand breaks in the circular forms during DNA isolation. In further studies, DNA from additional CW-group taxa was examined using conventional gel electrophoresis and DNA-filter blot analysis with C. reinhardtii and C. moewusii mtDNA probes. We conclude that all taxa from the “Volvox clade” (sensu Nakayama et al. 1996 of the CW-group have genome- or subgenomic-sized linear mtDNAs as their predominant mtDNA form and that these arose from a genome-sized circular form in an ancestor that existed near the base of this clade. [ABSTRACT FROM AUTHOR]

Our understanding of gene function and gene interactions has changed dramatically with the development of high-throughput systems. It now seems clear that any given gene interacts with a number of different partners, and in a number of different molecular pathways. Traditionally, gene function has been studied using animal knockout systems or naturally occurring mutants. RNA-based gene suppression systems for example, RNA interference or ribozymes, offer a number of advantages over the traditional systems, including ease of use, high specificity, and efficacy in nearly any biological system, and the ability to perform large-scale screens. Since their advent in the mid-1990s, DNA microarrays have been the choice for genome-wide expression analysis. The synergistic effect from the combined use of RNA-based gene suppression and molecular profiling is providing researchers with vast amounts of data. As a result, we are rapidly gaining an understanding of gene interactions and function. This review will focus primarily on gene inactivation systems that have been proven worthy of use in molecular pathway analysis when combined with microarray analysis.

Surgeons typically document operative events using dictation services. Dictated reports are frequently incomplete or delayed. Electronic note templates could potentially improve this process. Using a study design of alternating four week blocks, we compared the timeliness and comprehensiveness of operative notes created through the use of electronic templates versus dictation services for five surgical procedures. Templates resulted in dramatically faster times to the presence of a verified operative report in the medical record compared to dictation services (mean 28 v. 22,440 minutes). Templates increased overall compliance with national standards for operative note documentation and avoided transcription costs. Documentation with templates took slightly more time than dictation (mean 6.77 v. 5.96 minutes; P=0.036), not including the additional time necessary to subsequently verify dictated reports. We conclude that electronic note templates can improve the timeliness and comprehensiveness of operative documentation, while decreasing transcription costs and requiring minimal additional effort on the part of surgeons.

This paper describes the comparative evaluation of an experimental automated text summarization system, Centrifuser and three conventional search engines - Google, Yahoo and About.com. Centrifuser provides information to patients and families relevant to their questions about specific health conditions. It then produces a multidocument summary of articles retrieved by a standard search engine, tailored to the user's question. Subjects, consisting of friends or family of hospitalized patients, were asked to "think aloud" as they interacted with the four systems. The evaluation involved audio- and video recording of subject interactions with the interfaces in situ at a hospital. Results of the evaluation show that subjects found Centrifuser's summarization capability useful and easy to understand. In comparing Centrifuser to the three search engines, subjects' ratings varied; however, specific interface features were deemed useful across interfaces. We conclude with a discussion of the implications for engineering Web-based retrieval systems.