Novel Inducers of the Envelope Stress Response BaeSR in Salmonella Typhimurium: BaeR Is Critically Required for Tungstate Waste Disposal

The RpoE and CpxR regulated envelope stress responses are extremely important for SalmonellaTyphimurium to cause infection in a range of hosts. Until now the role for BaeSR in both the Salmonella Typhimurium response to stress and its contribution to infection have not been fully elucidated. Here we demonstrate stationary phase growth, iron and sodium tungstate as novel inducers of the BaeRregulon, with BaeR critically required for Salmonella resistance to sodium tungstate. We show that functional overlap between the resistance nodulation-cell division (RND) multidrug transporters, MdtA, AcrD and AcrB exists for the waste disposal of tungstate from the cell. We also point to a role for enterobactinsiderophores in the protection of enteric organisms from tungstate, akin to the scenario in nitrogen fixing bacteria. Surprisingly, BaeR is the first envelope stress response pathway investigated in S. Typhimurium that is not required for murine typhoid in either ityS or ityR mouse backgrounds. BaeR is therefore either required for survival in larger mammals such as pigs or calves, an avian host such as chickens, or survival out with the host altogether where Salmonella and related enterics must survive in soil and water

Psychology students’ perception of and engagement with feedback as a function of year of study

Undergraduate students’ perception of feedback and level of engagement with the feedback they receive have gained increasing attention in the educational literature recently to identify areas which require educators’ attention. However, research in this area has generally been based on limited self-selecting samples, and has not considered how students’ relationship with feedback may alter depending on their year of study. To address this, a survey measuring students’ views and practices regarding feedback was completed at a higher education institution by 447 first-, second- and third-year psychology students, representing 77% of the cohort. Findings revealed that third years responded more negatively in both areas than their first- and second-year counterparts, whose ratings on these aspects themselves were far from optimal. These findings highlight the need for early interventions to improve students’ perception of and engagement with feedback in the earlier years, and to prevent the recorded deterioration later on in the degree course

Fabrication of low-cost, large-area prototype Si(Li) detectors for the GAPS experiment

A Si(Li) detector fabrication procedure has been developed with the aim of satisfying the unique requirements of the GAPS (General Antiparticle Spectrometer) experiment. Si(Li) detectors are particularly well-suited to the GAPS detection scheme, in which several planes of detectors act as the target to slow and capture an incoming antiparticle into an exotic atom, as well as the spectrometer and tracker to measure the resulting decay X-rays and annihilation products. These detectors must provide the absorption depth, energy resolution, tracking efficiency, and active area necessary for this technique, all within the significant temperature, power, and cost constraints of an Antarctic long-duration balloon flight. We report here on the fabrication and performance of prototype 2"-diameter, 1-1.25 mm-thick, single-strip Si(Li) detectors that provide the necessary X-ray energy resolution of $\sim$4 keV for a cost per unit area that is far below that of previously-acquired commercial detectors. This fabrication procedure is currently being optimized for the 4"-diameter, 2.5 mm-thick, multi-strip geometry that will be used for the GAPS flight detectors.Comment: Accepted for publication at Nuclear Instrumentation and Methods A, 12 pages, 11 figure

Who Opens Alerts to Physicians? (And Who Doesn’t?)

Background: Electronic medical records (EMR) provide opportunities to implement systems of information flow, such as alerts to providers. Methods: Within a group practice with an EMR, we conducted a trial of automated alerts to the in-baskets of primary care physicians and staff when patients were discharged from hospital to home. We generated alerts for new medications or monitoring needs. Staff received alerts to schedule office visits. Using EMR “digital crumbs”, we tracked when alerts were viewed. We analyzed the impact of physician age, gender, department, and employment status (full-time, part-time) as well as patient conditions (age, gender, comorbidity, and number of office visits in the previous year) on timely opening. Results: Of 763 alerts to physicians, 616 (81%) were opened within one day. Characteristics associated with timely opening were age \u3c 50 (OR 1.7, 95% CI 1.1, 2.6) and full-time employment (OR 2.9, 95% CI 1.6, 5.2). Of 1928 alerts to staff, 1173 (61%) were opened within one day. Staff of male physicians were more likely to open the alerts within one day (OR 1.8, 95% CI 1.4, 2.4) as were working for the Family Medicine department (OR 1.9, 95% CI 1.3, 2.6) or a sub-specialty department (OR 16.6, 95% CI 2.3, 122.3). Staff of full-time physicians were less likely to open alerts (OR 0.64, 95% CI 0.47, 0.87). Adjusting for patient characteristics had no impact on results. Conclusion: Special efforts may be required to reach physicians working part-time and older physicians. Characteristics related to staff opening of alerts are specific to this group practice, but the high level of variability across physician types and departments is likely to be an issue in many settings. Design of a system directed at reaching staff quickly may require in-depth assessment of work flow and communication patterns in clinical department

TCR deep sequencing of transgenic RAG-1-deficient mice reveals endogenous TCR recombination: a cause for caution

The utility of T‐cell receptor (TCR) transgenic mice in medical research has been considerable, with applications ranging from basic biology all the way to translational and clinical investigations. Crossing of TCR transgenic mice with either recombination‐activating gene (RAG)‐1 or RAG‐2 knockouts is frequently used to generate mice with a monoclonal T‐cell repertoire. However, low level productive TCR rearrangement has been reported in RAG‐deficient mice expressing transgenic TCRs. Using deep sequencing, we set out to directly examine and quantify the presence of these endogenous TCRs. Our demonstration that functional nontransgenic TCRs are present in nonmanipulated mice has wide reaching ramifications worthy of critical consideration

Identification of furfural resistant strains of Saccharomyces cerevisiae and Saccharomyces paradoxus from a collection of environmental and industrial isolates

Background Fermentation of bioethanol using lignocellulosic biomass as a raw material provides a sustainable alternative to current biofuel production methods by utilising waste food streams as raw material. Before lignocellulose can be fermented it requires physical, chemical and enzymatic treatment in order to release monosaccharides, a process that causes the chemical transformation of glucose and xylose into the cyclic aldehydes furfural and hydroxyfurfural. These furan compounds are potent inhibitors of Saccharomyces fermentation, and consequently furfural tolerant strains of Saccharomyces are required for lignocellulosic fermentation. Results This study investigated yeast tolerance to furfural and hydroxyfurfural using a collection of 71 environmental and industrial isolates of the baker’s yeast Saccharomyces cerevisiae and its closest relative Saccharomyces paradoxus. The Saccharomyces strains were initially screened for growth on media containing 100 mM glucose and 1.5 mg ml-1 furfural. Five strains were identified that showed a significant tolerance to growth in the presence of furfural and these were then screened for growth and ethanol production in the presence of increasing amounts (0.1-4 mg ml-1) of furfural. Conclusions Of the five furfural tolerant strains S. cerevisiae NCYC 3451 displayed the greatest furfural resistance, and was able to grow in the presence of up to 3.0 mg ml-1 furfural. Furthermore, ethanol production in this strain did not appear to be inhibited by furfural, with the highest ethanol yield observed at 3.0 mg ml-1 furfural. Although furfural resistance was not found to be a trait specific to any one particular lineage or population, three of the strains were isolated from environments where they might be continually exposed to low levels of furfural through the on-going natural degradation of lignocelluloses, and would therefore develop elevated levels of resistance to these furan compounds. Thus these strains represent good candidates for future studies of genetic variation relevant to understanding and manipulating furfural resistance and in the development of tolerant ethanologenic yeast strains for use in bioethanol production from lignocellulose processing

Development and testing of a behavioural change intervention to increase physical activity, predominantly through walking, after stroke

Introduction Globally stroke remains the leading cause of adult disability. An aging population and a reduction in stroke case fatality has led to an increasing number of people living with stroke i.e. stroke survivors. The ability to perform important day-to-day activities, such as walking and housework, is frequently impaired in stroke survivors. Therefore, it has become essential to address the long-term needs of stroke survivors, prompting focussed research on life after stroke. A reduction in physical fitness after stroke may contribute to stroke related disability. It is possible to improve physical fitness by regular, structured physical activity. Improving physical fitness after stroke and increasing physical activity are aspects of life after stroke that are increasingly being researched. Although the evidence base for the benefits of physical fitness training is growing, research has indicated that benefits gained are not always maintained at follow-up. To facilitate the uptake and maintenance of physical activity after stroke, it is essential to understand why many stroke survivors do not undertake regular physical activity. Understanding this difficult concept will enable the tailoring of behaviour change interventions to promote and maintain physical activity after stroke. However, there has been limited work in developing theory driven behaviour change interventions to increase physical activity in stroke survivors. Therefore, the aim of this thesis was to develop and test a behaviour change intervention to increase physical activity after stroke. Methods In order to address the above aim, six interlinking studies were conducted within the development and feasibility stages of the MRC framework for the development of complex interventions. A systematic review (study one) examined barriers and facilitators to physical activity perceived by stroke survivors. This study showed a lack of literature in this area, and that the already published studies had limited generalisability to the UK stroke population. Therefore, it was deemed appropriate to conduct a qualitative study (study two) to examine the perceived barriers and facilitators to physical activity in the local stroke population. Both studies one and two highlighted the influence of self-efficacy towards increasing physical activity. As part of earlier work conducted prior to this PhD, there was previously unanalysed data on perceived barriers and facilitators to physical activity after stroke. These quantitative data encompassed specific questions exploring self-efficacy and intention to physical activity post stroke. In light of the evidence it was deemed necessary to analyse these data (study three). It was envisaged that the behaviour change intervention would incorporate a feedback device, so participants could clearly see how much daily physical activity they were undertaking. An opportunity arose to collaborate with a team at Newcastle University who had developed an accelerometer that incorporated an immediate feedback screen. Therefore, a device validation study was conducted as study four. Results from studies one to four were combined, with the use of the Theoretical Domains Framework, and the behaviour change intervention was developed. Two uncontrolled pilot studies (studies five and six) were conducted to determine the feasibility and acceptability of the behaviour change intervention to the stroke population. Results The systematic review included six articles, providing data on 174 stroke survivors. Commonly reported barriers were environmental factors, health concerns and stroke impairments. Commonly reported facilitators were social support and the need to be able to perform daily tasks. Qualitative interviews were conducted with 13 stroke survivors, at which point data saturation was reached. The most commonly reported TDF domains were ‘beliefs about capabilities’, ‘environmental context and resources’ and ‘social influence’. The quantitative study provided data from 50 stroke survivors. Intention and self-efficacy were high, with self-efficacy graded as either 4 or 5 (highly confident) on a five-point scale by [34 (68%)] participants, whilst 42 (84%) participants “strongly agreed” or “agreed” that they intended to increase their walking after their stroke. Ten participants were recruited to validate the new accelerometer. Mean time since stroke was 29 days (SD =27.9 days). The 10 participants walked a mean distance of 245 meters (SD=129m) and their mean walking speed was 0.79ms-1 (SD=0.34ms-1). The Culture Lab were unable to develop the accelerometer in the necessary time frame and therefore no accelerometer was available for trialling the behaviour change intervention. Therefore, pedometers were used to record step count during the behaviour change intervention. A total of four participants took part in the 12 week behaviour change intervention, over two study periods. All participants managed to increase their step counts during this time. The studies had problems both with recruitment and retention of participants. These issues have been discussed. Conclusions This work has enhanced the understanding of the barriers and facilitators perceived by stroke survivors to increase physical activity. This work has allowed the development of a theoretically driven, complex behaviour change intervention that was successfully trialled with a small group of stroke survivors. Areas of further research have been discussed

Is chlamydia screening and testing in Britain reaching young adults at risk of infection? Findings from the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3).

BACKGROUND: In the context of widespread opportunistic chlamydia screening among young adults, we aimed to quantify chlamydia testing and diagnosis among 16-24 year olds in Britain in relation to risk factors for prevalent chlamydia infection. METHODS: Using data from sexually experienced (≥1 lifetime sexual partner) 16-year-old to 24-year-old participants in Britain's third National Survey of Sexual Attitudes and Lifestyles (conducted 2010-2012), we explored socio-demographic and behavioural factors associated with prevalent chlamydia infection (detected in urine; n=1832), self-reported testing and self-reported diagnosis in the last year (both n=3115). RESULTS: Chlamydia prevalence was 3.1% (95% CI 2.2% to 4.3%) in women and 2.3% (1.5% to 3.4%) in men. A total of 12.3% of women and 5.3% men had a previous chlamydia diagnosis. Factors associated with prevalent infection were also associated with testing and diagnosis (eg, increasing numbers of sexual partners), with some exceptions. For example, chlamydia prevalence was higher in women living in more deprived areas, whereas testing was not. In men, prevalence was higher in 20-24 than 16-19 year olds but testing was lower. Thirty per cent of women and 53.7% of men with ≥2 new sexual partners in the last year had not recently tested. CONCLUSIONS: In 2010-2012 in Britain, the proportion of young adults reporting chlamydia testing was generally higher in those reporting factors associated with chlamydia. However, many of those with risk factors had not been recently tested, leaving potential for undiagnosed infections. Greater screening and prevention efforts among individuals in deprived areas and those reporting risk factors for chlamydia may reduce undiagnosed prevalence and transmission

Resolving the contributions of the membrane-bound and periplasmic nitrate reductase systems to nitric oxide and nitrous oxide production in Salmonella enterica serovar Typhimurium

The production of cytotoxic nitric oxide (NO) and conversion into the neuropharmacological agent and potent greenhouse gas nitrous oxide (N2O) is linked with anoxic nitrate catabolism by Salmonella enterica serovar Typhimurium. Salmonella can synthesize two types of nitrate reductase: a membrane-bound form (Nar) and a periplasmic form (Nap). Nitrate catabolism was studied under nitrate-rich and nitrate-limited conditions in chemostat cultures following transition from oxic to anoxic conditions. Intracellular NO production was reported qualitatively by assessing transcription of the NO-regulated genes encoding flavohaemoglobin (Hmp), flavorubredoxin (NorV) and hybrid cluster protein (Hcp). A more quantitative analysis of the extent of NO formation was gained by measuring production of N2O, the end-product of anoxic NO-detoxification. Under nitrate-rich conditions, the nar, nap, hmp, norV and hcp genes were all induced following transition from the oxic to anoxic state, and 20% of nitrate consumed in steady-state was released as N2O when nitrite had accumulated to millimolar levels. The kinetics of nitrate consumption, nitrite accumulation and N2O production were similar to those of wild-type in nitrate-sufficient cultures of a nap mutant. In contrast, in a narG mutant, the steady-state rate of N2O production was ~30-fold lower than that of the wild-type. Under nitrate-limited conditions, nap, but not nar, was up-regulated following transition from oxic to anoxic metabolism and very little N2O production was observed. Thus a combination of nitrate-sufficiency, nitrite accumulation and an active Nar-type nitrate reductase leads to NO and thence N2O production, and this can account for up to 20% of the nitrate catabolized