Integrating modelling and phenotyping approaches to identify and screen complex traits: transpiration efficiency in cereals.

Following advances in genetics, genomics, and phenotyping, trait selection in breeding is limited by our ability to understand interactions within the plant and with the environment, and to identify traits of most relevance to the target population of environments. We propose an integrated approach that combines insights from crop modelling, physiology, genetics, and breeding to characterize traits valuable for yield gain in the target population of environments, develop relevant high-throughput phenotyping platforms, and identify genetic controls and their value in production environments. This paper uses transpiration efficiency (biomass produced per unit of water used) as an example of a complex trait of interest to illustrate how the approach can guide modelling, phenotyping, and selection in a breeding programme. We believe that this approach, by integrating insights from diverse disciplines, can increase the resource use efficiency of breeding programmes for improving yield gains in target populations of environments.

Mindfulness-based stress reduction in Parkinson's disease: a systematic review.

BACKGROUND: Mindfulness based stress reduction (MBSR) is increasingly being used to improve outcomes such as stress and depression in a range of long-term conditions (LTCs). While systematic reviews on MBSR have taken place for a number of conditions there remains limited information on its impact on individuals with Parkinson's disease (PD). METHODS: Medline, Central, Embase, Amed, CINAHAL were searched in March 2016. These databases were searched using a combination of MeSH subject headings where available and keywords in the title and abstracts. We also searched the reference lists of related reviews. Study quality was assessed based on questions from the Cochrane Collaboration risk of bias tool. RESULTS: Two interventions and three papers with a total of 66 participants were included. The interventions were undertaken in Belgium (n = 27) and the USA (n = 39). One study reported significantly increased grey matter density (GMD) in the brains of the MBSR group compared to the usual care group. Significant improvements were reported in one study for a number of outcomes including PD outcomes, depression, mindfulness, and quality of life indicators. Only one intervention was of reasonable quality and both interventions failed to control for potential confounders in the analysis. Adverse events and reasons for drop-outs were not reported. There was also no reporting on the costs/benefits of the intervention or how they affected health service utilisation. CONCLUSION: This systematic review found limited and inconclusive evidence of the effectiveness of MBSR for PD patients. Both of the included interventions claimed positive effects for PD patients but significant outcomes were often contradicted by other results. Further trials with larger sample sizes, control groups and longer follow-ups are needed before the evidence for MBSR in PD can be conclusively judged.

A case of popliteal artery stenosis: masquerading as an infective foot ulcer in a young male traveller.

Here, we present a case report of a young male who had been travelling in Thailand. The patient sustained a relatively minor trauma to the soft tissue under his left third metatarsal head on a piece of coral reef. He subsequently developed an infected ulcer, which did not heal despite appropriate antibiotic therapy and surgical debridement. Unfortunately, the patient required amputation of the left third toe and metatarsal head due to osteomyelitic destruction. It later transpired that the ulcer was initially ischaemic in nature due to previously undiagnosed and asymptomatic popliteal artery stenosis.

What is associated with being active in arthritis? Analysis from the Obstacles to Action study.

BACKGROUND: Many adults with arthritis do not achieve physical activity levels recommended for good health. This study aimed to identify factors associated with physical activity participation in people with arthritis. METHODS: 1106 out of 8163 adults with self-reported arthritis were identified from the 2003 Obstacles to Action study. Participants were classified as active if they reported 30 min of moderate activity > or = 5 days a week or 20 min of vigorous activity > or = 3 days a week (n = 613), or insufficiently active if they did not (n = 438). Sociodemographic factors, attitudes, self-efficacy, motivators and barriers to being active were analysed. RESULTS: Active people with arthritis had a lower burden of chronic disease than insufficiently active people (18% with three or more chronic medical conditions vs 33%, P < 0.0001). Active participants believed more strongly in the benefits of physical activity, reported higher levels of encouragement from others and had greater overall levels of self-efficacy when compared with the less active participants (P for all <0.0001). Arthritis, fatigue and discomfort were ranked by both groups as the top three barriers. However, the active participants reported lower impact scores for these barriers than the inactive group (P for all <0.0001). These findings persisted after adjusting for occupational status, body mass index and comorbidities. CONCLUSION: Active adults with arthritis have lower levels of chronic disease, greater self-efficacy and fewer psychosocial barriers. Recognition of such barriers and motivators may be useful when designing intervention programmes to help people with arthritis initiate or intensify physical activity participation.

Optoelectronic retinal prosthesis: system design and performance.

The design of high-resolution retinal prostheses presents many unique engineering and biological challenges. Ever smaller electrodes must inject enough charge to stimulate nerve cells, within electrochemically safe voltage limits. Stimulation sites should be placed within an electrode diameter from the target cells to prevent 'blurring' and minimize current. Signals must be delivered wirelessly from an external source to a large number of electrodes, and visual information should, ideally, maintain its natural link to eye movements. Finally, a good system must have a wide range of stimulation currents, external control of image processing and the option of either anodic-first or cathodic-first pulses. This paper discusses these challenges and presents solutions to them for a system based on a photodiode array implant. Video frames are processed and imaged onto the retinal implant by a head-mounted near-to-eye projection system operating at near-infrared wavelengths. Photodiodes convert light into pulsed electric current, with charge injection maximized by applying a common biphasic bias waveform. The resulting prosthesis will provide stimulation with a frame rate of up to 50 Hz in a central 10 degrees visual field, with a full 30 degrees field accessible via eye movements. Pixel sizes are scalable from 100 to 25 microm, corresponding to 640-10,000 pixels on an implant 3 mm in diameter.

Deprivation and quality of primary care services: evidence for persistence of the inverse care law from the UK Quality and Outcomes Framework.

OBJECTIVE: To examine whether the quality of primary care measured by the 2004 contract varies with socioeconomic deprivation. DESIGN: Retrospective analysis of publicly available data, comparing quality indicators used for payment that allow exclusion of patients (payment quality) and indicators based on the care delivered to all patients (delivered quality). SETTING AND PARTICIPANTS: 1024 general practices in Scotland. MAIN OUTCOME MEASURES: Regression coefficients summarising the relationships between deprivation and payment and delivered quality. RESULTS: Little systematic association is found between payment quality and deprivation but, for 17 of the 33 indicators examined, delivered quality falls with increasing deprivation. Absolute differences in delivered quality are small for most simpler process measures, such as recording of smoking status or blood pressure. Greater inequalities are seen for more complex process measures such as diagnostic procedures, some intermediate outcome measures such as glycaemic control in diabetes and measures of treatment such as influenza immunisation. CONCLUSIONS: The exclusions system succeeds in not penalising practices financially for the characteristics of the population they serve, but does not reward the additional work required in deprived areas and contributes to a continuation of the inverse care law. The contract data collected prevent examination of most complex process or treatment measures and this analysis is likely to underestimate the extent of continuing inequalities in care. Broader lessons cannot be drawn on the effect on inequalities of this new set of incentives until changes are made to the way contract data are collected and analysed.

A review of the use of routine data on CHD in general practice research in Scotland.

BACKGROUND: The primary aim of the Platform Project is to maximise the use of routine data for primary care research in Scotland. AIMS: To assess the extent to which routine data is available and has been used in studies on CHD in General Practice research in Scotland. To assess the advantages and limitations of using routine data in this setting. METHODS: Literature review using a variety of databases catalogues and websites, bibliographies of articles retrieved and searching through journals by hand not available electronically. RESULTS: This review has found that the use of routine data in CHD studies in General Practice research in Scotland remains small. There has been little work undertaken which has combined the use of routine data with other research methods. Limitations with routine data exist particularly with regard to risk factors and ethnicity. However, despite such limitations there exists an increasingly extensive range of data, which exists to help explain tends in CHD, which so far has been largely underused.

Biased immunoglobulin G (IgG) subclass production in a case of hyper-IgM syndrome.

Hyper-immunoglobulin M (IgM) syndrome (HIGM) is a rare heterogeneous primary immune deficiency. We describe a patient with HIGM characterized by skewed production of serum IgG subclasses and normal somatic hypermutation. This case may represent a subgroup of HIGM type 4 that is characterized by a biased switching to the V-region proximal constant regions.

The Steve Biko affair: a case study in medical ethics.

Steve Biko died in detention in South Africa in 1977. Critical ethical issues are raised both by the conduct of the doctors responsible for Biko's care and by the subsequent response of the medical profession as a whole. Because those issues are relevant to all healthcare professionals everywhere, the Biko affair provides a useful case study in medical ethics. We discuss the case in this article, describing how we use it in our teaching.

Response of patients and families to lengthening of the facial bones by extraoral distraction osteogenesis: a review of 14 patients.

Fourteen patients or their immediate family were interviewed about their experiences of having either unilateral or bilateral external distraction osteogenesis of the mandible. The patients showed a high level of co-operation with treatment. Six of the 14 patients required repeat distractions, and had been informed and accepted that this was a possibility before the initial distraction. However, patients or their parents expressed some reservations about the extraoral distractors, which prevented them from practising their favourite sport and made them vulnerable to bullying by their friends and colleagues. Patients had moderate pain when the appliances were removed. They all expressed their satisfaction with the results and would recommend this treatment to others. Problems, including speech, eating, pain, and sleeping difficulties, were encountered by patients at all stages of treatment. Of considerable concern was the disruption of education when the child was treated during the school term.

Decreased focal adhesion kinase suppresses papilloma formation during experimental mouse skin carcinogenesis.

Although focal adhesion kinase (FAK) is elevated in epithelial cancers, it is not known whether FAK expression influences tumor development in vivo. We found that fak +/- heterozygous mice display reduced 7,12-dimethylbenz[a]anthracene-induced papilloma formation that correlates with reduced FAK protein expression in the skin. However, the frequency of malignant conversion of papillomas into carcinomas is indistinguishable in fak +/- mice and their wild-type fak +/+ littermates, most likely because papilloma FAK protein expression is elevated to wild-type levels. We also found that keratinocyte FAK protein expression is important for cellular responses downstream of ras in vitro (monitored by extracellular signal-regulated kinase activation after integrin engagement). Because 7,12-dimethylbenz[a]anthracene induces an activating mutation of H-ras, this provides one possible explanation for suppression of papilloma formation when FAK protein is limiting.

The protrusive phase and full development of integrin-dependent adhesions in colon epithelial cells require FAK- and ERK-mediated actin spike formation: deregulation in cancer cells.

Integrins play an important role in tumour progression by influencing cellular responses and matrix-dependent adhesion. However, the regulation of matrix-dependent adhesion assembly in epithelial cells is poorly understood. We have investigated the integrin and signalling requirements of cell-matrix adhesion assembly in colon carcinoma cells after plating on fibronectin. Adhesion assembly in these, and in the adenoma cells from which they were derived, was largely dependent on alpha v beta 6 integrin and required phosphorylation of FAK on tyrosine-397. The rate of fibronectin-induced adhesion assembly and the expression of both alpha v beta 6 integrin and FAK were increased during the adenoma-to-carcinoma transition. The matrix-dependent adhesion assembly process, particularly the final stages of complex protrusion that is required for optimal cell spreading, required the activity of extracellular signal-regulated kinase (ERK). Furthermore, phosphorylated ERK was targeted to newly forming cell--matrix adhesions in the carcinoma cells but not the adenoma cells, and inhibition of FAK--tyrosine-397 phosphorylation or MEK suppressed the appearance of phosphorylated ERK at peripheral sites. In addition, inhibition of MEK--ERK activation blocked the formation of peripheral actin microspikes that were necessary for the protrusive phase of cell-matrix adhesion assembly. Thus, MEK--ERK--dependent peripheral actin re-organization is required for the full development of integrin-induced adhesions and this pathway is stimulated in an in vitro model of colon cancer progression.

v-Src induces tyrosine phosphorylation of focal adhesion kinase independently of tyrosine 397 and formation of a complex with Src.

The non-receptor tyrosine kinase FAK plays a key role at sites of cellular adhesion. It is subject to regulatory tyrosine phosphorylation in response to a variety of stimuli, including integrin engagement after attachment to extracellular matrix, oncogene activation, and growth factor stimulation. Here we use an antibody that specifically recognizes the phosphorylated form of the putative FAK autophosphorylation site, Tyr(397). We demonstrate that FAK phosphorylation induced by integrins during focal adhesion assembly differs from that induced by activation of a temperature-sensitive v-Src, which is associated with focal adhesion turnover and transformation. Specifically, although v-Src induces tyrosine phosphorylation of FAK, there is no detectable phosphorylation of Tyr(397). Moreover, activation of v-Src results in a net decrease in fibronectin-stimulated phosphorylation of Tyr(397), suggesting possible antagonism between v-Src and integrin-induced phosphorylation. Our mutational analysis further indicates that the binding of v-Src to Tyr(397) of FAK in its phosphorylated form, which is normally mediated, at least in part, by the SH2 domain of Src, is not essential for v-Src-induced cell transformation. We conclude that different stimuli can induce phosphorylation of FAK on distinct tyrosine residues, linking specific phosphorylation events to ensuing biological responses.

The catalytic activity of the Src family kinases is required to disrupt cadherin-dependent cell-cell contacts.

Despite the importance of epithelial cell contacts in determining cell behavior, we still lack a detailed understanding of the assembly and disassembly of intercellular contacts. Here we examined the role of the catalytic activity of the Src family kinases at epithelial cell contacts in vitro. Like E- and P-cadherin, Ca(2+) treatment of normal and tumor-derived human keratinocytes resulted in c-Yes (and c-Src and Fyn), as well as their putative substrate p120(CTN), being recruited to cell-cell contacts. A tyrosine kinase inhibitor with selectivity against the Src family kinases, PD162531, and a dominant-inhibitory c-Src protein that interferes with the catalytic function of the endogenous Src kinases induced cell-cell contact and E-cadherin redistribution, even in low Ca(2+), which does not normally support stable cell-cell adhesion. Time-lapse microscopy demonstrated that Src kinase inhibition induced stabilization of transiently formed intercellular contacts in low Ca(2+). Furthermore, a combination of E- and P-cadherin-specific antibodies suppressed cell-cell contact, indicating cadherin involvement. As a consequence of contact stabilization, normal cells were unable to dissociate from an epithelial sheet formed at high density and repair a wound in vitro, although individual cells were still motile. Thus, cadherin-dependent contacts can be stabilized both by high Ca(2+) and by inhibiting Src activity in low (0.03 mM) Ca(2+) in vitro.

Human and murine immunoglobulin expression vector cassettes.

We describe the construction of new immunoglobulin (Ig) expression vectors and their use in the production of recombinant chimeric Ig molecules in transfected mammalian cells. The vectors contain the cDNA encoding the constant regions of human (mu, alpha1, gammal, gamma2, gamma3, gamma4, kappa) and murine (mu, gamma2a, kappa) Ig heavy and light chains. Unique restriction sites flanking the Ig variable region allow for replacement of variable regions generated by PCR. The CMV promoter allows for the transfection and expression of Ig in non-lymphoid cells. Distinct drug selection markers for heavy chain and light chain expression vectors allows for sequential or co-transfection of the vectors. We show that secretion of recombinant Ig can reach 1.2 microg/ml per million cells per day for transfected B cells. Replacement of the variable region results in the production of functional Ig retaining antigen specificity.