Comparative Genomics of Gossypium spp. through GBS and Candidate Genes – Delving into the Controlling Factors behind Photoperiodic Flowering

Cotton has been a world-wide economic staple in textiles and oil production. There has been a concerted effort for cotton improvement to increase yield and quality to compete with non-natural man-made fibers. Unfortunately, cultivated cotton has limited genetic diversity; therefore finding new marketable traits within cultivated cotton has reached a plateau. To alleviate this problem, traditional breeding programs have been attempting to incorporate practical traits from wild relatives into cultivated lines. This incorporation has presented a new problem: uncultivated cotton hampered by photoperiodism. Traditionally, due to differing floral times, wild and cultivated cotton species were unable to be bred together in many commercial production areas world-wide. This worldwide breeding problem has inhibited new trait incorporation. Before favorable traits from undomesticated cotton could be integrated into cultivated elite lines using marker-assisted selection breeding, the markers associated with photoperiod independence needed to be discovered. In order to increase information about this debilitating trait, we set out to identify informative markers associated with photoperiodism. This study was segmented into four areas. First, we reviewed the history of cotton to highlight current problems in production. Next, we explored cotton’s floral development through a study of floral transition candidate genes. The third area was an in-depth analysis of Phytochrome C (previously linked to photoperiod independence in other crops). In the final area of study, we used Genotype-By-Sequencing (GBS), in a segregating population, was used to determine photoperiod independence associated with single nucleotide polymorphisms (SNPs). In short, this research reported SNP differences in thirty-eight candidate gene homologs within the flowering time network, including photoreceptors, light dependent transcripts, circadian clock regulators, and floral integrators. Also, our research linked other discrete SNP differences, in addition to those contained within candidate genes, to photoperiodicity within cotton. In conclusion, the SNP markers that our study found may be used in future marker assisted selection (MAS) breeding schemas to incorporate desirable traits into elite lines without the introgression of photoperiod sensitivity

Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.)

<p>Abstract</p> <p>Background</p> <p>Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (<it>Gossypium </it>spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (<it>G. herbaceum</it>, <it>G. raimondii</it>) or allotetraploid (<it>G. hirsutum</it>, <it>G. barbadense</it>) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton.</p> <p>Results</p> <p>We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs) for members of the <it>PHYA</it>, <it>PHYB/D</it>, <it>PHYC </it>and <it>PHYE </it>gene sub-families from A- and D-genome diploid and AD-genome allotetraploid <it>Gossypium </it>species. We identified two paralogous <it>PHYA </it>genes (designated <it>PHYA1 </it>and <it>PHYA2</it>) in diploid cottons, the result of a Malvaceae-specific <it>PHYA </it>gene duplication that occurred approximately 14 million years ago (MYA), before the divergence of the A- and D-genome ancestors. We identified a single gene copy of <it>PHYB</it>, <it>PHYC</it>, and <it>PHYE </it>in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four <it>PHYA </it>genes and two genes encoding <it>PHYB</it>, <it>PHYC </it>and <it>PHYE </it>in the AD-genomes. We did not identify a <it>PHYD </it>gene in any cotton genomes examined.</p> <p>Conclusions</p> <p>Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for cotton improvement via modern marker-assisted selection strategies.</p

Non-pharmacological interventions for ADHD in school settings: an overarching synthesis of systematic reviews

OBJECTIVE: This overarching synthesis brings together the findings of four systematic reviews including 138 studies focused on non-pharmacological interventions for ADHD used in school settings. These reviews considered the effectiveness of school-based interventions for ADHD, attitudes toward and experience of school-based interventions for ADHD, and the experience of ADHD in school settings. METHOD: We developed novel methods to compare the findings across these reviews inductively and deductively. RESULTS: Key contextual issues that may influence the effectiveness and implementation of interventions include the relationships that pupils with ADHD have with their teachers and peers, the attributions individuals make about the etiology of ADHD, and stigma related to ADHD or intervention attendance. CONCLUSION: Although we found some positive effects for some outcomes and intervention categories, heterogeneity in effect size estimates and research evidence suggests a range of diverse contextual factors potentially moderate the implementation and effectiveness of school-based interventions for ADHD.National Institute for Health Research Health Technology Assessment (NIHR HTA) programNIHR Collaboration for Leadership in Applied HealthResearch and Care South West Peninsula (PenCLAHRC

Interventions to improve continence for children and young people with neurodisability: a national survey of practitioner and family perspectives and experiences.

Objective Describe families’ experiences of interventions to improve continence in children and young people with neurodisability, and health professionals’ and school and social care staff’s perspectives regarding factors affecting intervention use. Design Four online surveys were developed and advertised to parent carers, young people with neurodisability, health professionals and school and social care staff, via societies, charities, professional contacts, schools, local authorities, and national parent carer and family forums, who shared invitations with their networks. Survey questions explored: difficulties helping children and young people use interventions; acceptability of interventions and waiting times; ease of use and availability of interventions, and facilitators and barriers to improving continence. Results 1028 parent carers, 26 young people, 352 health professionals and 202 school and social care staff registered to participate. Completed surveys were received from 579 (56.3%) parent carers, 20 (77%) young people, 193 (54.8%) health professionals, and 119 (58.9%) school and social care staff. Common parent carer-reported difficulties in using interventions to help their children and young people to learn to use the toilet included their child’s lack of understanding about what was required (reported by 337 of 556 (60.6%) parent carers who completed question) and their child’s lack of willingness (343 of 556, 61.7%). Almost all (142 of 156, 91%) health professionals reported lack of funding and resources as barriers to provision of continence services. Many young people (14 of 19, 74%) were unhappy using toilet facilities while out and about. Conclusions Perceptions that children lack understanding and willingness, and inadequate facilities impact the implementation of toileting interventions for children and young people with neurodisability. Greater understanding is needed for children to learn developmentally appropriate toileting skills. Further research is recommended around availability and acceptability of interventions to ensure quality of life is unaffected

Development of an evidence-based complex intervention for community rehabilitation of patients with hip fracture using realist review, survey and focus groups

Objectives To develop an evidence and theory-based complex intervention for improving outcomes in elderly patients following hip fracture. Design Complex-intervention development (Medical Research Council (MRC) framework phase I) using realist literature review, surveys and focus groups of patients and rehabilitation teams. Setting North Wales. Participants Surveys of therapy managers (n=13), community and hospital-based physiotherapists (n=129) and occupational therapists (n=68) throughout the UK. Focus groups with patients (n=13), their carers (n=4) and members of the multidisciplinary rehabilitation teams in North Wales (n=13). Results The realist review provided understanding of how rehabilitation interventions work in the realworld context and three programme theories were developed: improving patient engagement by tailoring the intervention to individual needs; reducing fear of falling and improving self-efficacy to exercise and perform activities of daily living; and coordination of rehabilitation delivery. The survey provided context about usual rehabilitation practice; focus groups provided data on the experience, acceptability and feasibility of rehabilitation interventions. An intervention to enhance usual rehabilitation was developed to target these theory areas comprising: a physical component consisting of six additional therapy sessions; and a psychological component consisting of a workbook to enhance self-efficacy and a patient-held goal-setting diary for self-monitoring. Conclusions A realist approach may have advantages in the development of evidence-based interventions and can be used in conjunction with other established methods to contribute to the development of potentially more effective interventions. A rehabilitation intervention was developed which can be tested in a future randomised controlled trial (MRC framework phases II and III)

Evaluating the successful implementation of evidence into practice using the PARiHS framework : theoretical and practical challenges

Background The PARiHS framework (Promoting Action on Research Implementation in Health Services) has proved to be a useful practical and conceptual heuristic for many researchers and practitioners in framing their research or knowledge translation endeavours. However, as a conceptual framework it still remains untested and therefore its contribution to the overall development and testing of theory in the field of implementation science is largely unquantified. Discussion This being the case, the paper provides an integrated summary of our conceptual and theoretical thinking so far and introduces a typology (derived from social policy analysis) used to distinguish between the terms conceptual framework, theory and model – important definitional and conceptual issues in trying to refine theoretical and methodological approaches to knowledge translation. Secondly, the paper describes the next phase of our work, in particular concentrating on the conceptual thinking and mapping that has led to the generation of the hypothesis that the PARiHS framework is best utilised as a two-stage process: as a preliminary (diagnostic and evaluative) measure of the elements and sub-elements of evidence (E) and context (C), and then using the aggregated data from these measures to determine the most appropriate facilitation method. The exact nature of the intervention is thus determined by the specific actors in the specific context at a specific time and place. In the process of refining this next phase of our work, we have had to consider the wider issues around the use of theories to inform and shape our research activity; the ongoing challenges of developing robust and sensitive measures; facilitation as an intervention for getting research into practice; and finally to note how the current debates around evidence into practice are adopting wider notions that fit innovations more generally. Summary The paper concludes by suggesting that the future direction of the work on the PARiHS framework is to develop a two-stage diagnostic and evaluative approach, where the intervention is shaped and moulded by the information gathered about the specific situation and from participating stakeholders. In order to expedite the generation of new evidence and testing of emerging theories, we suggest the formation of an international research implementation science collaborative that can systematically collect and analyse experiences of using and testing the PARiHS framework and similar conceptual and theoretical approaches. We also recommend further refinement of the definitions around conceptual framework, theory, and model, suggesting a wider discussion that embraces multiple epistemological and ontological perspectives

An implementation research agenda.

In October 2006, the Chief Medical Officer (CMO) of England asked Professor Sir John Tooke to chair a High Level Group on Clinical Effectiveness in response to the chapter 'Waste not, want not' in the CMOs 2005 annual report 'On the State of the Public Health'. The high level group made recommendations to the CMO to address possible ways forward to improve clinical effectiveness in the UK National Health Service (NHS) and promote clinical engagement to deliver this. The report contained a short section on research needs that emerged from the process of writing the report, but in order to more fully identify the relevant research agenda Professor Sir John Tooke asked Professor Martin Eccles to convene an expert group - the Clinical Effectiveness Research Agenda Group (CERAG) - to define the research agenda. The CERAG's terms of reference were 'to further elaborate the research agenda in relation to pursuing clinically effective practice within the (UK) National Health Service'. This editorial presents the summary of the CERAG report and recommendations