The Genetics of Adaptation for Eight Microvirid Bacteriophages

Theories of adaptive molecular evolution have recently experienced significant expansion, and their predictions and assumptions have begun to be subjected to rigorous empirical testing. However, these theories focus largely on predicting the first event in adaptive evolution, the fixation of a single beneficial mutation. To address long-term adaptation it is necessary to include new assumptions, but empirical data are needed for guidance. To empirically characterize the general properties of adaptive walks, eight recently isolated relatives of the single-stranded DNA (ssDNA) bacteriophage φX174 (family Microviridae) were adapted to identical selective conditions. Three of the eight genotypes were adapted in replicate, for a total of 11 adaptive walks. We measured fitness improvement and identified the genetic changes underlying the observed adaptation. Nearly all phages were evolvable; nine of the 11 lineages showed a significant increase in fitness. However, fitness plateaued quickly, and adaptation was achieved through only three substitutions on average. Parallel evolution was rampant, both across replicates of the same genotype as well as across different genotypes, yet adaptation of replicates never proceeded through the exact same set of mutations. Despite this, final fitnesses did not vary significantly among replicates. Final fitnesses did vary significantly across genotypes but not across phylogenetic groupings of genotypes. A positive correlation was found between the number of substitutions in an adaptive walk and the magnitude of fitness improvement, but no correlation was found between starting and ending fitness. These results provide an empirical framework for future adaptation theory

Achieving Consensus in the Development of an Online Intervention Designed to Effectively Support Midwives in Work-Related Psychological Distress: Protocol for a Delphi Study

BACKGROUND: The development of an online intervention designed to effectively support midwives in work-related psychological distress will be challenging due to the ethical, practical, and therapeutic issues surrounding its design. Related literature suggests that midwives may require an anonymous, confidential, and therapeutic platform that facilitates amnesty and nonpunitive approaches to remedy ill health. However, it is unclear which requirements may be most salient to midwifery populations. OBJECTIVE: The objective of this paper is to describe the design of a Delphi study, intended to achieve expert consensus on the needs of midwives in work-related psychological distress who may be supported via an online intervention. This protocol may also serve as a research framework for similar studies to be modeled upon. METHODS: A heterogeneous sample of at least thirty experts on psychological well-being and distress associated with midwifery work will be recruited. Their opinions regarding the development of an online intervention designed to support midwives in work-related psychological distress will be collected through 2 rounds of questioning, via the Delphi Technique. When 60% (≥18, assuming the minimum is 30) of panelists score within 2 adjacent points on a 7-point scale, consensus will be acknowledged. This Delphi study protocol will invite both qualitative and quantitative outcomes. RESULTS: This study is currently in development. It is financially supported by a full-time scholarship at the Centre for Technology Enabled Health Research at Coventry University (Coventry, UK). The implementation of this Delphi study is anticipated to occur during the autumn of 2015. CONCLUSIONS: The results of this study will direct the development of an online intervention designed to support midwives in work-related psychological distress, summarize expert driven consensus, and direct future research

The SABRTooth feasibility trial protocol: a study to determine the feasibility and acceptability of conducting a phase III randomised controlled trial comparing stereotactic ablative radiotherapy (SABR) with surgery in patients with peripheral stage I non-small cell lung cancer (NSCLC) considered to be at higher risk of complications from surgical resection.

Background Stage I non-small cell lung cancer (NSCLC) is potentially curable, and surgery is considered to be the standard of care for patients with good performance status and minimal co-morbidity. However, a significant proportion of patients with stage I NSCLC have a poorer performance status and significant medical co-morbidity that make them at higher risk of morbidity and mortality from surgery. Stereotactic ablative radiotherapy (SABR), which uses modern radiotherapeutic techniques to deliver large doses of radiation, has shown superiority over conventional radiotherapy in terms of local control and toxicity and is a standard of care for patients with stage I NSCLC who are at too high risk for surgery. However, it is not known whether surgery or SABR is the most effective in patients with stage I NSCLC who are suitable for surgery but are less fit and at higher risk surgical complications. Previous randomised studies have failed to recruit in this setting, and therefore, a feasibility study is required to see whether a full randomised control trial would be possible. Methods/design SABRTooth is a UK-based, multi-centre, open-label, two-group individually (1:1) randomised controlled feasibility study in patients with peripheral stage I NSCLC considered to be at higher risk from surgical resection. The study will assess the feasibility of conducting a definitive large-scale phase III trial. The primary objective is to assess recruitment rates to provide evidence that, when scaled up, recruitment to a large phase III trial would be possible; the target recruitment being 54 patients in total, over a 21-month period. There are multiple secondary and exploratory objectives designed to explore the optimum recruitment and data collection strategies to help optimise the design of a future phase III trial. Discussion To know whether SABR is a better, equivalent or inferior alternative to surgery for higher risk patients is a key question in lung cancer. Other studies comparing SABR to surgery have closed early due to poor recruitment, and therefore, the SABRTooth feasibility study has been designed around the UK National Health Service (NHS) cancer pathway incorporating many design features in order to maximise recruitment for a future definitive phase III trial

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA

The Ubiquitin Proteasome System Is a Key Regulator of Pluripotent Stem Cell Survival and Motor Neuron Differentiation

The ubiquitin proteasome system (UPS) plays an important role in regulating numerous cellular processes, and a dysfunctional UPS is thought to contribute to motor neuron disease. Consequently, we sought to map the changing ubiquitome in human iPSCs during their pluripotent stage and following differentiation to motor neurons. Ubiquitinomics analysis identified that spliceosomal and ribosomal proteins were more ubiquitylated in pluripotent stem cells, whilst proteins involved in fatty acid metabolism and the cytoskeleton were specifically ubiquitylated in the motor neurons. The UPS regulator, ubiquitin-like modifier activating enzyme 1 (UBA1), was increased 36-fold in the ubiquitome of motor neurons compared to pluripotent stem cells. Thus, we further investigated the functional consequences of inhibiting the UPS and UBA1 on motor neurons. The proteasome inhibitor MG132, or the UBA1-specific inhibitor PYR41, significantly decreased the viability of motor neurons. Consistent with a role of the UPS in maintaining the cytoskeleton and regulating motor neuron differentiation, UBA1 inhibition also reduced neurite length. Pluripotent stem cells were extremely sensitive to MG132, showing toxicity at nanomolar concentrations. The motor neurons were more resilient to MG132 than pluripotent stem cells but demonstrated higher sensitivity than fibroblasts. Together, this data highlights the important regulatory role of the UPS in pluripotent stem cell survival and motor neuron differentiation

Preparation, structured deliberate practice and decision making in elite level football: The case study of Gary Neville (Manchester United FC and England)

Decision making in elite level sporting competition is often regarded as distinguishing success from failure. As an intricate brain-based process it is unlike other physical processes because it is invisible and is typically only evidenced after the event. This case study shows how an individual achieved great success in elite level professional football through consistent positive decision making on and off the field of play. Through prolonged interviewing, Gary Neville, a player from Manchester United Football Club, explored personal behaviours, the structure and activities of deliberate practice and his professional choices in match preparation. His career-long devotion to purposeful organised practice was focused on cognition, physical preparation, context-relative physical action and refined repetition to optimise his mental comfort while enhancing his match day performances. This approach was underpinned by diligent personal and collective organisation and by concerted action. Results provide an insight into the categorical nature of his deliberate practice, sport-specific information processing and match-based decision making. At the operational level, his process was mediated by a complex mental representation of ongoing and anticipated game situations; these representations were continuously updated during each match. Allowing for the limitations of the design, implications are provided for developmental and educational coaching, match preparation, deliberate practice activity and improved use of the performance analysis software packages in professional football