Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Raising the profile of pilot and feasibility studies in relation to the development, evaluation and implementation of patient-reported outcome measures.

This editorial introduces a new special series on the pilot and feasibility testing of patient-reported outcome measures (PROMs) in the on-line open access journal Pilot and Feasibility Studies. Pilot and feasibility studies are typically implemented to address issues of uncertainty before undertaking a larger definitive study such as a randomised controlled trial or large scale survey. This editorial considers the role that such pilot and feasibility testing plays in relation to the development, evaluation and implementation of PROMs. This is often an essential element of PROM research but is typically overlooked-especially within current methodological guidance, reporting space and also debate. This editorial aims to open up a dialogue about the role of pilot and feasibility testing in relation to PROMs. It highlights some of the areas in PROMs research where these types of studies have been carried out and discusses the ways in which the PROM community may be better supported and encouraged to integrate this element of the research process into their PROM-based work

Responsiveness of SF-36 Health Survey and Patient Generated Index in people with chronic knee pain commenced on oral analgesia: analysis of data from a randomised controlled clinical trial

Purpose. (1) to assess the responsiveness of the Short Form 36 Health Survey (SF-36) and Patient Generated Index (PGI) in people with knee pain who were given oral analgesics; and (2) to perform content analysis of the SF-36 and PGI aiming to identify differences between the instruments and causes of different responsiveness. Methods. An observational study nested within a randomised controlled trial comparing oral paracetamol, ibuprofen or a combination of the two in 884 community-derived people with chronic knee pain. Each participant was given the SF-36 and PGI questionnaires to fill out at baseline, day 10, week 7 and week 13 after commencement on analgesia. Responsiveness was measured as a standardised response mean from baseline and contents of the instruments were analysed. Results. The PGI showed the greater responsiveness to analgesics than the SF-36 throughout the study period. Only the Bodily Pain Score of the SF-36 showed comparable responsiveness to the PGI. The standardised response mean of the PGI at 13 weeks was 0.61 (95% confidence interval 0.51 to 0.72), and that of the Bodily Pain Score of the SF-36 was 0.49 (95% confidence interval 0.39 to 0.58). Content analysis of the PGI identified multiple areas which are not represented in the SF-36 which may help explain its performance. Conclusions. Overall the PGI is more responsive than the SF-36 to commonly used oral analgesics taken for knee pain. The PGI is able to elicit areas of individualised health related quality of life which are not captured by the SF-36

Evaluating the Impact of a ‘Virtual Clinic’ on Patient Experience, Personal and Provider Costs of Care in Urinary Incontinence: A Randomised Controlled Trial.

Objective: To evaluate the impact of using a ‘virtual clinic’ on patient experience and cost in the care of women with urinary incontinence. Materials and Methods: Women, aged > 18 years referred to a urogynaecology unit were randomised to either (1) A Standard Clinic or (2) A Virtual Clinic. Both groups completed a validated, web-based interactive, patient-reported outome measure (ePAQ-Pelvic Floor), in advance of their appointment followed by either a telephone consultation (Virtual Clinic) or face-to-face consultation (Standard Care). The primary outcome was the mean ‘short-term outcome scale’ score on the Patient Experience Questionnaire (PEQ). Secondary Outcome Measures included the other domains of the PEQ (Communications, Emotions and Barriers), Client Satisfaction Questionnaire (CSQ), Short-Form 12 (SF-12), personal, societal and NHS costs. Results: 195 women were randomised: 98 received the intervention and 97 received standard care. The primary outcome showed a non-significant difference between the two study arms. No significant differences were also observed on the CSQ and SF-12. However, the intervention group showed significantly higher PEQ domain scores for Communications, Emotions and Barriers (including following adjustment for age and parity). Whilst standard care was overall more cost-effective, this was minimal (£38.04). The virtual clinic also significantly reduced consultation time (10.94 minutes, compared with a mean duration of 25.9 minutes respectively) and consultation costs compared to usual care (£31.75 versus £72.17 respectively), thus presenting potential cost-savings in out-patient management. Conclusions: The virtual clinical had no impact on the short-term dimension of the PEQ and overall was not as cost-effective as standard care, due to greater clinic re-attendances in this group. In the virtual clinic group, consultation times were briefer, communication experience was enhanced and personal costs lower. For medical conditions of a sensitive or intimate nature, a virtual clinic has potential to support patients to communicate with health professionals about their condition

Active learning and optimal climate policy

This paper develops a climate-economy model with uncertainty, irreversibility, and active learning. Whereas previous papers assume learning from one observation per period, or experiment with control variables to gain additional information, this paper considers active learning from investment in monitoring, specifically in improved observations of the global mean temperature. We find that the decision maker invests a significant amount of money in climate research, far more than the current level, in order to increase the rate of learning about climate change. This helps the decision maker make improved decisions. The level of uncertainty decreases more rapidly in the active learning model than in the passive learning model with only temperature observations. As the uncertainty about climate change is smaller, active learning reduces the optimal carbon tax. The greater the risk, the larger is the effect of learning. The method proposed here is applicable to any dynamic control problem where the quality of monitoring is a choice variable, for instance, the precision at which we observe GDP, unemployment, or the quality of education

Genetic variability and ontogeny predict microbiome structure in a disease-challenged montane amphibian

Amphibian populations worldwide are at risk of extinction from infectious diseases, including chytridiomycosis caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Amphibian cutaneous microbiomes interact with Bd and can confer protective benefits to the host. The composition of the microbiome itself is influenced by many environment- and host-related factors. However, little is known about the interacting effects of host population structure, genetic variation and developmental stage on microbiome composition and Bd prevalence across multiple sites. Here we explore these questions in Amietia hymenopus, a disease-affected frog in southern Africa. We use microsatellite genotyping and 16S amplicon sequencing to show that the microbiome associated with tadpole mouthparts is structured spatially, and is influenced by host genotype and developmental stage. We observed strong genetic structure in host populations based on rivers and geographic distances, but this did not correspond to spatial patterns in microbiome composition. These results indicate that demographic and host genetic factors affect microbiome composition within sites, but different factors are responsible for host population structure and microbiome structure at the between-site level. Our results help to elucidate complex within- and among- population drivers of microbiome structure in amphibian populations. That there is a genetic basis to microbiome composition in amphibians could help to inform amphibian conservation efforts against infectious diseases

Religious perspectives on human suffering: Implications for medicine and bioethics

The prevention and relief of suffering has long been a core medical concern. But while this is a laudable goal, some question whether medicine can, or should, aim for a world without pain, sadness, anxiety, despair or uncertainty. To explore these issues, we invited experts from six of the world’s major faith traditions to address the following question. Is there value in suffering? And is something lost in the prevention and/or relief of suffering? While each of the perspectives provided maintains that suffering should be alleviated and that medicine’s proper role is to prevent and relieve suffering by ethical means, it is also apparent that questions regarding the meaning and value of suffering are beyond the realm of medicine. These perspectives suggest that medicine and bioethics has much to gain from respectful consideration of religious discourse surrounding suffering. Keywords Suffering; religion; medicine; bioethic

Religious perspectives on human suffering: Implications for medicine and bioethics

The prevention and relief of suffering has long been a core medical concern. But while this is a laudable goal, some question whether medicine can, or should, aim for a world without pain, sadness, anxiety, despair or uncertainty. To explore these issues, we invited experts from six of the world’s major faith traditions to address the following question. Is there value in suffering? And is something lost in the prevention and/or relief of suffering? While each of the perspectives provided maintains that suffering should be alleviated and that medicine’s proper role is to prevent and relieve suffering by ethical means, it is also apparent that questions regarding the meaning and value of suffering are beyond the realm of medicine. These perspectives suggest that medicine and bioethics has much to gain from respectful consideration of religious discourse surrounding suffering. Keywords Suffering; religion; medicine; bioethic