Regional differences in recombination hotspots between two chicken populations

<p>Abstract</p> <p>Background</p> <p>Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs.</p> <p>Results</p> <p>The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross.</p> <p>Conclusions</p> <p>In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.</p

Engaging rural Australian communities in National Science Week helps increase visibility for women researchers

During a week-long celebration of science, run under the federally-supported National Science Week umbrella, the Catch a Rising Star: women in Queensland research (CaRS) program flew scientists who identify as women to regional and remote communities in the Australian State of Queensland. The aim of the project was twofold: first, to bring science to remote and regional communities in a large, economically diverse state; and second, to determine whether media and public engagement provide career advancement opportunities for women scientists. This paper focuses on the latter goal. The data show: 1) a substantial majority (> 80%) of researchers thought the training and experience provided by the program would help develop her career as a research scientist in the future; 2) the majority (65%) thought the program would help relate her research to end users, industry partners, or stakeholders in the future; and, 3) analytics can help create a compelling narrative around engagement metrics and help to quantify influence. During the weeklong project, scientists reached 600,000 impressions on one social media platform (Twitter) using a program hashtag. The breadth and depth of the project outcomes indicate funding bodies and employers could use similar data as an informative source of metrics to support hiring and promotion decisions. Although this project focused on researchers who identify as women, the lessons learned are applicable to researchers representing a diverse range of backgrounds. Future surveys will help determine whether the CaRS program provided long-term career advantages to participating scientists and communities

SNP and haplotype mapping for genetic analysis in the rat

The laboratory rat is one of the most extensively studied model organisms. Inbred laboratory rat strains originated from limited Rattus norvegicus founder populations, and the inherited genetic variation provides an excellent resource for the correlation of genotype to phenotype. Here, we report a survey of genetic variation based on almost 3 million newly identified SNPs. We obtained accurate and complete genotypes for a subset of 20,238 SNPs across 167 distinct inbred rat strains, two rat recombinant inbred panels and an F2 intercross. Using 81% of these SNPs, we constructed high-density genetic maps, creating a large dataset of fully characterized SNPs for disease gene mapping. Our data characterize the population structure and illustrate the degree of linkage disequilibrium. We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies.This work was supported by European Union grants LSGH-2004-005235 and LSHG-CT-2005-019015. D.G. is supported by a Wellcome Trust Senior Fellowship in Basic Biomedical Science (057733/Z/99/A). M.-T.B. and D.G. acknowledge support from the Wellcome Cardiovascular Functional Genomics Initiative (066780/Z/01/Z

A comparison of the CAPS-5 and PCL-5 to assess PTSD in military and veteran treatment-seeking samples

Background: This study was an examination of the puzzling finding that people assessed for symptoms of posttraumatic stress disorder (PTSD) consistently score higher on the self-report PTSD Checklist for DSM-5 (PCL-5) than the Clinician-Administered PTSD Scale for DSM-5 (CAPS-5). Both scales purportedly assess PTSD severity with the same number of items, scaling, and scoring range, but differences in scores between measures make outcomes difficult to decipher. Objective: The purpose of this study was to examine several possible psychometric reasons for the discrepancy in scores between interview and self-report. Method: Data were combined from four clinical trials to examine the baseline and posttreatment assessments of treatment-seeking active duty military personnel and veterans. Results: As in previous studies, total scores were higher on the PCL-5 compared to the CAPS-5 at baseline and posttreatment. At baseline, PCL-5 scores were higher on all 20 items, with small to large differences in effect size. At posttreatment, only three items were not significantly different. Distributions of item responses and wording of scale anchors and items were examined as possible explanations of the difference between measures. Participants were more likely to use the full range of responses on the PCL-5 compared to interviewers. Conclusions: Suggestions for improving the congruence between these two scales are discussed. Administration of interviews by trained assessors can be resource intensive, so it is important that those assessing PTSD severity are afforded confidence in the equivalence of their assessment of PTSD regardless of the assessment method used

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

Recent advances in molecular technologies have opened up unprecedented opportunities for molecular ecologists to better understand the molecular basis of traits of ecological and evolutionary importance in almost any organism. Nevertheless, reliable and systematic inference of functionally relevant information from these masses of data remains challenging. The aim of this review is to highlight how the Gene Ontology (GO) database can be of use in resolving this challenge. The GO provides a largely species-neutral source of information on the molecular function, biological role and cellular location of tens of thousands of gene products. As it is designed to be species-neutral, the GO is well suited for cross-species use, meaning that, functional annotation derived from model organisms can be transferred to inferred orthologues in newly sequenced species. In other words, the GO can provide gene annotation information for species with nonannotated genomes. In this review, we describe the GO database, how functional information is linked with genes/gene products in model organisms, and how molecular ecologists can utilize this information to annotate their own data. Then, we outline various applications of GO for enhancing the understanding of molecular basis of traits in ecologically relevant species. We also highlight potential pitfalls, provide step-by-step recommendations for conducting a sound study in nonmodel organisms, suggest avenues for future research and outline a strategy for maximizing the benefits of a more ecological and evolutionary genomics-oriented ontology by ensuring its compatibility with the GO

Facilitating technology adoption in the NHS : negotiating the organisational and policy context : a qualitative study

Background: Proven clinical effectiveness and patient safety are insufficient to ensure adoption and implementation of new clinical technologies. Despite current government policy, clinical technologies are not yet demand-led through commissioning. Hence, adoption and implementation relies on providers. Introducing new technologies initially raises providers’ costs as they necessitate training, alter patient pathways and change patient management, and may lead to reduced patient throughput in the short term. The current funding regime for providers – Payment by Results (PbR) – rewards activity. It is not surprising, therefore, that providers often see new technologies as risky. Objectives: This study investigated the organisational and policy context for the adoption and implementation of clinical technologies, because this context may present barriers that slow – or even prevent – uptake. The research focused on three clinical technologies: insulin pump therapy (IPT); breast lymph node assay (BLNA), a diagnostic tool for metastases; and ultrawide field retinal imaging (UFRI). The implementation of these technologies had been supported by NHS Technology Adoption Centre (NTAC). Methods: The research method was qualitative case studies of these three clinical technologies. The primary data collection technique was semistructured interviews of NTAC staff, clinicians, managers and commissioners, supplemented by documentary evidence, participant and non-participant observation of meetings and videos. For IPT, we also conducted a survey of clinicians and analysed anonymised e-mails from patients. Results: NHS providers did not perceive any central ‘push’ from the Department of Health or the National Institute for Health and Care Excellence (NICE) to adopt, implement or diffuse new clinical technologies. There is a ‘bottom-up’ adoption culture: any trust could choose to adopt any, all or none of the three clinical technologies we investigated. This is undesirable, as clinically efficacious technologies should be equally available to all patients. Where there is NICE guidance, this acted as an enabler for adoption, but some trusts still did not offer IPT despite this. We found that PbR could be a major obstacle to adoption. Our evidence also indicates that, contrary to its intention, commissioning practice is more of a barrier than an enabler of innovation. Protracted negotiations over funding between providers and commissioners delayed implementation of BLNA and IPT. Organisational power and politics between hospitals and community-based services was a significant barrier for adoption of UFRI. Clinicians outside of specialist ophthalmology centres did not understand the clinical utility of UFRI (e.g. its diagnostic potential or how and when to use it). Conclusions: NTAC was successful in assisting trusts over the generic organisational barriers outlined above, particularly with regard to taking responsibility for the logistics of implementation, negotiating new patient pathways and ways of working with relevant stakeholders, and using their skills in project management and stakeholder engagement to drive processes forward. Where there were major obstacles, however, the NTAC process stalled. ‘Bottom-up’ adoption at individual trusts needs to be linked into wider national processes that offer vision, some central direction, further assessment and evaluation, and the infrastructure to ensure diffusion to sites that have the capabilities and capacities to best utilise the clinical technology