Salmon mortality investigation

On 1 March 2012, the New Zealand King Salmon Company (NZKS) notified MPI of a significant mortality event occurring in Chinook salmon (Oncorhynchus tshawytscha) at their sea farm in Waihinau Bay, outer Pelorus Sound

Does shade improve light interception efficiency? A comparison among seedlings from shade-tolerant and -intolerant temperate deciduous tree species

• Here, we tested two hypotheses: shading increases light interception efficiency (LIE) of broadleaved tree seedlings, and shade-tolerant species exhibit larger LIEs than do shade-intolerant ones. The impact of seedling size was taken into account to detect potential size-independent effects on LIE. LIE was defined as the ratio of mean light intercepted by leaves to light intercepted by a horizontal surface of equal area. • Seedlings from five species differing in shade tolerance (Acer saccharum, Betula alleghaniensis, A. pseudoplatanus, B. pendula, Fagus sylvatica) were grown under neutral shading nets providing 36, 16 and 4% of external irradiance. Seedlings (1- and 2-year-old) were three-dimensionally digitized, allowing calculation of LIE. • Shading induced dramatic reduction in total leaf area, which was lowest in shade-tolerant species in all irradiance regimes. Irradiance reduced LIE through increasing leaf overlap with increasing leaf area. There was very little evidence of significant size-independent plasticity of LIE. • No relationship was found between the known shade tolerance of species and LIE at equivalent size and irradiance

Access to Psychological Therapies - DCAQ in NHS Lothian: Phase 2 Report

EdinburghThe purpose of this document is to report on phase two of the Demand, Capacity, Activity & Queue (DCAQ) work carried out with Midlothian Psychological Therapies Service and East Lothian Psychological Therapies Service between April 2011 and March 2012. The overall project was broken down into two phases and this report is a summary of the work completed in phase two. The phase one report can be accessed at the following web address; http://www.qihub.scot.nhs.uk/media/220541/nhs%20lothian%20dcaq%20phase%201%20report%20vfinal2.doc The phase two report has two main purposes: To provide feedback on the work completed in phase two and to outline the additional service improvement opportunities that might be explored for each service participating; To provide a learning resource for other services interested in applying DCAQ.sch_occpub3131pu

Linking compact dwarf starburst galaxies in the resolve survey to downsized blue nuggets

Abstract We identify and characterize compact dwarf starburst (CDS) galaxies in the RESOLVE survey, a volume-limited census of galaxies in the local universe, to probe whether this population contains any residual “blue nuggets,” a class of intensely star-forming compact galaxies first identified at high redshift z. Our 50 low-z CDS galaxies are defined by dwarf masses (stellar mass M* < 109.5 M⊙), compact bulged-disk or spheroid-dominated morphologies (using a quantitative criterion, \mu _\Delta > 8.6), and specific star formation rates above the defining threshold for high-z blue nuggets (log SSFR [Gyr−1] > −0.5). Across redshifts, blue nuggets exhibit three defining properties: compactness relative to contemporaneous galaxies, abundant cold gas, and formation via compaction in mergers or colliding streams. Those with halo mass below Mhalo ∼ 1011.5 M⊙ may in theory evade permanent quenching and cyclically refuel until the present day. Selected only for compactness and starburst activity, our CDS galaxies generally have Mhalo ≲ 1011.5 M⊙ and gas-to-stellar mass ratio ≳1. Moreover, analysis of archival DECaLS photometry and new 3D spectroscopic observations for CDS galaxies reveals a high rate of photometric and kinematic disturbances suggestive of dwarf mergers. The SSFRs, surface mass densities, and number counts of CDS galaxies are compatible with theoretical and observational expectations for redshift evolution in blue nuggets. We argue that CDS galaxies represent a maximally-starbursting subset of traditional compact dwarf classes such as blue compact dwarfs and blue E/S0s. We conclude that CDS galaxies represent a low-z tail of the blue nugget phenomenon formed via a moderated compaction channel that leaves open the possibility of disk regrowth and evolution into normal disk galaxies

Ancestral bias in the Hras1 gene and distal Chromosome 7 among inbred mice

Inbred strains of mice vary in their frequency of liver tumors initiated by a mutation in the Hras1 (H-ras) proto-oncogene. We sequenced 4.5 kb of the Hras1 gene on distal Chr 7 in a diverse set of 12 commonly used laboratory inbred strains of mice and detected no sequence variation to account for strain-specific differences in Hras1 mutation prevalence. Furthermore, the Hras1 sequence is essentially monoallelic for an ancestral gene derived from the M. m. domesticus species. To determine if the monoallelism and associated low rate of polymorphism are unique to Hras1 or representative of the general chromosomal locale, we extended the sequence analysis to 12 genes in the final 8 Mb of distal Chr 7. A region of at least 2.5 Mb that encompasses several genes, including Hras1 and the H19/Igf2 loci, demonstrates virtually no sequence variation. The 12 inbred strains share one dominant haplotype derived from the M. m. domesticus allele. Chromosomal regions flanking the monoallelic segment exhibit a significantly higher rate of variation and multiple haplotypes, a majority of which are attributed to M. m. domesticus or M. m. musculus ancestry

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

Using a combination of whole-genome resequencing and high-density genotyping arrays, genome-wide haplotypes were reconstructed for two of the most important bulls in the history of the dairy cattle industry, Pawnee Farm Arlinda Chief (“Chief”) and his son Walkway Chief Mark (“Mark”), each accounting for ∼7% of all current genomes. We aligned 20.5 Gbp (∼7.3× coverage) and 37.9 Gbp (∼13.5× coverage) of the Chief and Mark genomic sequences, respectively. More than 1.3 million high-quality SNPs were detected in Chief and Mark sequences. The genome-wide haplotypes inherited by Mark from Chief were reconstructed using ∼1 million informative SNPs. Comparison of a set of 15,826 SNPs that overlapped in the sequence-based and BovineSNP50 SNPs showed the accuracy of the sequence-based haplotype reconstruction to be as high as 97%. By using the BovineSNP50 genotypes, the frequencies of Chief alleles on his two haplotypes then were determined in 1,149 of his descendants, and the distribution was compared with the frequencies that would be expected assuming no selection. We identified 49 chromosomal segments in which Chief alleles showed strong evidence of selection. Candidate polymorphisms for traits that have been under selection in the dairy cattle population then were identified by referencing Chief’s DNA sequence within these selected chromosome blocks. Eleven candidate genes were identified with functions related to milk-production, fertility, and disease-resistance traits. These data demonstrate that haplotype reconstruction of an ancestral proband by whole-genome resequencing in combination with high-density SNP genotyping of descendants can be used for rapid, genome-wide identification of the ancestor’s alleles that have been subjected to artificial selection

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin