Targeted identification of genomic regions using TAGdb

Background: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. Results: We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome. Conclusions: The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly

Characteristics of Workplace Psychosocial Resources and Risk of Diabetes: A Prospective Cohort Study

OBJECTIVE: To examine whether characteristics of workplace psychosocial resources are associated with the risk of type 2 diabetes among employees. RESEARCH DESIGN AND METHODS: Participants were 49,835 employees (77% women, aged 40-65 years, and diabetes free at baseline) from the Finnish Public Sector cohort study. Characteristics of horizontal (culture of collaboration and support from colleagues) and vertical (leadership quality and organizational procedural justice) psychosocial resources were self-reported. Incident type 2 diabetes (n = 2,148) was ascertained through linkage to electronic health records from national registers. We used latent class modeling to assess the clustering of resource characteristics. Cox proportional hazards models were used to examine the relationship between the identified clusters and risk of type 2 diabetes during 10.9 years of follow-up, adjusting for age, sex, marital status, educational level, type of employment contract, comorbidity, and diagnosed mental disorders. RESULTS: We identified four patterns of workplace psychosocial resources: unfavorable, favorable vertical, favorable horizontal, and favorable vertical and horizontal. Compared with unfavorable, favorable vertical (hazard ratio 0.87 [95% CI 0.78; 0.97]), favorable horizontal (0.77 [0.67; 0.88]), and favorable vertical and horizontal (0.77 [0.68; 0.86]) resources were associated with a lower risk of type 2 diabetes, with the strongest associations seen in employees at age ≥55 years (Pinteraction = 0.03). These associations were robust to multivariable adjustments and were not explained by reverse causation. CONCLUSIONS: A favorable culture of collaboration, support from colleagues, leadership quality, and organizational procedural justice are associated with a lower risk of employees developing type 2 diabetes than in those without such favorable workplace psychosocial resources

Striatal dopamine D2/D3 receptor binding in pathological gambling is correlated with mood-related impulsivity

AbstractPathological gambling (PG) is a behavioural addiction associated with elevated impulsivity and suspected dopamine dysregulation. Reduced striatal dopamine D2/D3 receptor availability has been reported in drug addiction, and may constitute a premorbid vulnerability marker for addictive disorders. The aim of the present study was to assess striatal dopamine D2/D3 receptor availability in PG, and its association with trait impulsivity. Males with PG (n=9) and male healthy controls (n=9) underwent [11C]-raclopride positron emission tomography imaging and completed the UPPS-P impulsivity scale. There was no significant difference between groups in striatal dopamine D2/D3 receptor availability, in contrast to previous reports in drug addiction. However, mood-related impulsivity (‘Urgency’) was negatively correlated with [11C]-raclopride binding potentials in the PG group. The absence of a group difference in striatal dopamine binding implies a distinction between behavioural addictions and drug addictions. Nevertheless, our data indicate heterogeneity in dopamine receptor availability in disordered gambling, such that individuals with high mood-related impulsivity may show differential benefits from dopamine-based medications

Does daily consumption of vitamin K1 from cruciferous vegetables reach the circulation and the knee joint?

Irish Section Meeting, 20–22 June 2018, Targeted approaches to tackling current nutritional issue

Inorganic nitrate, hypoxia, and the regulation of cardiac mitochondrial respiration-probing the role of PPARα.

Dietary inorganic nitrate prevents aspects of cardiac mitochondrial dysfunction induced by hypoxia, although the mechanism is not completely understood. In both heart and skeletal muscle, nitrate increases fatty acid oxidation capacity, and in the latter case, this involves up-regulation of peroxisome proliferator-activated receptor (PPAR)α expression. Here, we investigated whether dietary nitrate modifies mitochondrial function in the hypoxic heart in a PPARα-dependent manner. Wild-type (WT) mice and mice without PPARα (Ppara-/-) were given water containing 0.7 mM NaCl (control) or 0.7 mM NaNO3 for 35 d. After 7 d, mice were exposed to normoxia or hypoxia (10% O2) for the remainder of the study. Mitochondrial respiratory function and metabolism were assessed in saponin-permeabilized cardiac muscle fibers. Environmental hypoxia suppressed mass-specific mitochondrial respiration and additionally lowered the proportion of respiration supported by fatty acid oxidation by 18% (P < 0.001). This switch away from fatty acid oxidation was reversed by nitrate treatment in hypoxic WT but not Ppara-/- mice, indicating a PPARα-dependent effect. Hypoxia increased hexokinase activity by 33% in all mice, whereas lactate dehydrogenase activity increased by 71% in hypoxic WT but not Ppara-/- mice. Our findings indicate that PPARα plays a key role in mediating cardiac metabolic remodeling in response to both hypoxia and dietary nitrate supplementation.-Horscroft, J. A., O'Brien, K. A., Clark, A. D., Lindsay, R. T., Steel, A. S., Procter, N. E. K., Devaux, J., Frenneaux, M., Harridge, S. D. R., Murray, A. J. Inorganic nitrate, hypoxia, and the regulation of cardiac mitochondrial respiration-probing the role of PPARα

Workplace psychosocial resources and risk of cardiovascular disease among employees : a multi-cohort study of 135 669 participants

Objective In terms of prevention, it is important to determine effects on cardiovascular disease (CVD) when some workplace psychosocial resources are high while others are low. The aim of the study was to assess the prospective relationship between clustering of workplace psychosocial resources and risk of CVD among employees.Methods We pooled data from three cohort studies of 135 669 employees (65% women, age 18-65 years and free of CVD) from Denmark, Finland and Sweden. Baseline horizontal resources (culture of collaboration and support from colleagues) and vertical resources (leadership quality and procedural justice) were measured using standard questionnaire items. Incident CVD, including coronary heart and cerebrovascular disease, was ascertained using linked electronic health records. We used latent class analysis to assess clustering (latent classes) of workplace psychosocial resources. Cox proportional hazard models were used to examine the association between these clusters and risk of CVD, adjusting for demographic and employment-related factors and pre-existing physical and mental disorders.Results We identified five clusters of workplace psychosocial resources from low on both vertical and horizontal resources (13%) to generally high resources (28%). High horizontal resources were combined with either intermediate [hazard ratio (HR) 0.84, 95% confidence interval (CI) 0.74-0.95] or high (HR 0.88, 95% CI 0.78-1.00) vertical resources were associated with lower risks of CVD compared to those with generally low resources. The association was most prominent for cerebrovascular disease (eg, general high resources: HR 0.80, 95% CI 0.67-0.96).Conclusions Individuals with high levels of workplace psychosocial resources across horizontal and vertical dimensions have a lower risk of CVD, particularly cerebrovascular disease.Peer reviewe

Deweyan tools for inquiry and the epistemological context of critical pedagogy

This article develops the notion of resistance as articulated in the literature of critical pedagogy as being both culturally sponsored and cognitively manifested. To do so, the authors draw upon John Dewey\u27s conception of tools for inquiry. Dewey provides a way to conceptualize student resistance not as a form of willful disputation, but instead as a function of socialization into cultural models of thought that actively truncate inquiry. In other words, resistance can be construed as the cognitive and emotive dimensions of the ongoing failure of institutions to provide ideas that help individuals both recognize social problems and imagine possible solutions. Focusing on Dewey\u27s epistemological framework, specifically tools for inquiry, provides a way to grasp this problem. It also affords some innovative solutions; for instance, it helps conceive of possible links between the regular curriculum and the study of specific social justice issues, a relationship that is often under-examined. The aims of critical pedagogy depend upon students developing dexterity with the conceptual tools they use to make meaning of the evidence they confront; these are background skills that the regular curriculum can be made to serve even outside social justice-focused curricula. Furthermore, the article concludes that because such inquiry involves the exploration and potential revision of students\u27 world-ordering beliefs, developing flexibility in how one thinks may be better achieved within academic subjects and topics that are not so intimately connected to students\u27 current social lives, especially where students may be directly implicated

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

© 2017 The Authors. Published by OUP. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1093/nar/gkx1070The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and functional reusability. New features of the PDBe Web site are discussed, including a context dependent menu providing links to raw experimental data and improved presentation of structures solved by hybrid methods. The paper also summarizes the features of the LiteMol suite, which is a set of services enabling fast and interactive 3D visualization of structures, with associated experimental maps, annotations and quality assessment information. We introduce a library of Web components which can be easily reused to port data and functionality available at PDBe to other services. We also introduce updates to the SIFTS resource which maps PDB data to other bioinformatics resources, and the PDBe REST API.Wellcome Trust [104948]; UK Biotechnology and Biological Sciences Research Council [BB/M011674/1, BB/N019172/1, BB/M020347/1]; European Union [284209]; European Molecular Biology Laboratory (EMBL). Funding for open access charge: EMBL.Published versio

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured