De novo Assembly and Analysis of the Northern Leopard Frog Rana pipiens Transcriptome

The northern leopard frog Rana (Lithobates) pipiens is an important animal model, being used extensively in cancer, neurology, physiology, and biomechanical studies. R. pipiens is a native North American frog whose range extends from northern Canada to southwest United States, but over the past few decades its populations have declined significantly and is now considered uncommon in large portions of the United States and Canada. To aid in the study and conservation of R. pipiens, this paper describes the first R. pipiens transcriptome. The R. pipiens transcriptome was annotated using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Eukaryotic Orthologous Groups (KOG). Differential expression analysis revealed universal and tissue specific genes, and endocrine-related genes were identified. Transcriptome assemblies and other sequence data are available for download

Estimating Bacterial diversity in scirtothrips dorsalis (thysanoptera: thripidae) Via Next generation sequencing

The last 2 decades have produced a better understanding of insect-microbial associations and yielded some important opportunities for insect control. However, most of our knowledge comes from model systems. Thrips (Thysanoptera: Thripidae) have been understudied despite their global importance as invasive species, plant pests and disease vectors. Using a culture and primer independent next-generation sequencing and metagenomics pipeline, we surveyed the bacteria of the globally important pest, Scirtothrips dorsalis Hood. The most abundant bacterial phyla identified were Actinobacteria and Proteobacteria and the most abundant genera were Propionibacterium, Stenotrophomonas, and Pseudomonas. A total of 189 genera of bacteria were identified. The absence of any vertically transferred symbiont taxa commonly found in insects is consistent with other studies suggesting that thrips primarilly acquire resident microbes from their environment. This does not preclude a possible beneficial/intimate association between S. dorsalis and the dominant taxa identified and future work should determine the nature of these associations

Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids

<p>Abstract</p> <p>Background</p> <p>Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like testosterone and estrogens. This represents a challenge when performing selection against androstenone in breeding programs, without simultaneously decreasing levels of other steroids. The aim of this study was to use high-density genome wide association (GWA) in combination with linkage disequilibrium-linkage analysis (LDLA) to identify quantitative trait loci (QTL) associated with boar taint compounds and related sex steroids in commercial Landrace (n = 1,251) and Duroc (n = 918) breeds.</p> <p>Results</p> <p>Altogether, 14 genome wide significant (GWS) QTL regions for androstenone in subcutaneous fat were obtained from the LDLA study in Landrace and 14 GWS QTL regions in Duroc. LDLA analysis revealed that 7 of these QTL regions, located on SSC 1, 2, 3, 7 and 15, were obtained in both breeds. All 14 GWS androstenone QTLs in Landrace are also affecting the estrogens at chromosome wise significance (CWS) or GWS levels, while in Duroc, 3 of the 14 QTLs affect androstenone without affecting any of the estrogens. For skatole, 10 and 4 QTLs were GWS in the LDLA analysis for Landrace and Duroc respectively, with 4 of these detected in both breeds. The GWS QTLs for skatole obtained by LDLA are located at SSC 1, 5, 6, 7, 10, 11, 13 and 14.</p> <p>Conclusion</p> <p>This is the first report applying the Porcine 60 K SNP array for simultaneous analysis of boar taint compounds and related sex hormones, using both GWA and LDLA approaches. Several QTLs are involved in regulation of androstenone and skatole, and most of the QTLs for androstenone are also affecting the levels of estrogens. Seven QTLs for androstenone were detected in one breed and confirmed in the other, i.e. in an independent sample, although the majority of QTLs are breed specific. Most QTLs for skatole do not negatively affect other sex hormones and should be easier to implement into the breeding scheme.</p

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p 10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10−392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group

Vertebral Arteriovenous Fistula: An Unwelcome Thrill

Cervical vertebral AV fistulae are uncommon vascular lesions involving abnormal communication between the extradural vertebral artery and surrounding venous structures. We examine the case of a female evaluated in the emergency department with a vertebral AV fistula presenting classically as pulsatile tinnitus and later successfully treated with standard endovascular techniques. A discussion on the etiology, pathophysiology, and management of vertebral AV fistulae follows

β‑Lactone Synthetase Found in the Olefin Biosynthesis Pathway

The first β-lactone synthetase enzyme is reported, creating an unexpected link between the biosynthesis of olefinic hydrocarbons and highly functionalized natural products. The enzyme OleC, involved in the microbial biosynthesis of long-chain olefinic hydrocarbons, reacts with <i>syn</i>- and <i>anti</i>-β-hydroxy acid substrates to yield <i>cis-</i> and <i>trans</i>-β-lactones, respectively. Protein sequence comparisons reveal that enzymes homologous to OleC are encoded in natural product gene clusters that generate β-lactone rings, suggesting a common mechanism of biosynthesis

Long-Term Integrated Studies Show Complex and Surprising Effects of Climate Change in the Northern Hardwood Forest

Evaluations of the local effects of global change are often confounded by the interactions of natural and anthropogenic factors that overshadow the effects of climate changes on ecosystems. Long-term watershed and natural elevation gradient studies at the Hubbard Brook Experimental Forest and in the surrounding region show surprising results demonstrating the effects of climate change on hydrologic variables (e.g., evapotranspiration, streamflow, soil moisture); the importance of changes in phenology on water, carbon, and nitrogen fluxes during critical seasonal transition periods; winter climate change effects on plant and animal community composition and ecosystem services; and the effects of anthropogenic disturbances and land-use history on plant community composition. These studies highlight the value of long-term integrated research for assessments of the subtle effects of changing climate on complex ecosystem

Long-Term Integrated Studies Show Complex and Surprising Effects of Climate Change in the Northern Hardwood Forest

Evaluations of the local effects of global change are often confounded by the interactions of natural and anthropogenic factors that overshadow the effects of climate changes on ecosystems. Long-term watershed and natural elevation gradient studies at the Hubbard Brook Experimental Forest and in the surrounding region show surprising results demonstrating the effects of climate change on hydrologic variables (e.g., evapotranspiration, streamflow, soil moisture); the importance of changes in phenology on water, carbon, and nitrogen fluxes during critical seasonal transition periods; winter climate change effects on plant and animal community composition and ecosystem services; and the effects of anthropogenic disturbances and land-use history on plant community composition. These studies highlight the value of long-term integrated research for assessments of the subtle effects of changing climate on complex ecosystem