Quantum Transition State Theory for proton transfer reactions in enzymes

We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of kinetic isotope effects for two classes of enzymes which have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction due to the environment is weak and only slightly modifies the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental degrees of freedom with frequencies much less than 1000 cm$^{-1}$ do not have a significant effect on quantum corrections to the reaction rate.Comment: Aspects of the article are discussed at condensedconcepts.blogspot.co

Ab Initio Molecular Dynamics on the Electronic Boltzmann Equilibrium Distribution

We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In addition, these molecular dynamics do not need to assume that the electrons immediately follow the nuclear motion (in contrast to any adiabatic approach), and do not present problems in the presence of crossing points between different potential energy surfaces (conical intersections or spin-crossings). A practical application of this molecular dynamics to study the effect of temperature in molecular systems presenting (nearly) degenerate states - such as the avoided crossing in the ring-closure process of ozone - is presented.Comment: published in New J. Phy

Development of the OPgun™ for bombardment of animal tissues

A simple and inexpensive particle-bombardment device, the OPgun™, was constructed for the delivery of DNA into animal tissues. This device is based on the particle-inflow gun first described for plant-cell transfection. The delivery of tungsten particles into the epidermis of the mouse ear, without the use of vacuum and without causing damage to the tissue, was demonstrated. The system was also shown to be capable of inducing antibodies to a foreign gene in mice.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat X Pro was used to OCR the text and also for the merging and conversion to the final presentation PDF-format

HIV pre-exposure prophylaxis and early antiretroviral treatment among female sex workers in South Africa: Results from a prospective observational demonstration project.

BACKGROUND: Operational research is required to design delivery of pre-exposure prophylaxis (PrEP) and early antiretroviral treatment (ART). This paper presents the primary analysis of programmatic data, as well as demographic, behavioural, and clinical data, from the TAPS Demonstration Project, which offered both interventions to female sex workers (FSWs) at 2 urban clinic sites in South Africa. METHODS AND FINDINGS: The TAPS study was conducted between 30 March 2015 and 30 June 2017, with the enrolment period ending on 31 July 2016. TAPS was a prospective observational cohort study with 2 groups receiving interventions delivered in existing service settings: (1) PrEP as part of combination prevention for HIV-negative FSWs and (2) early ART for HIV-positive FSWs. The main outcome was programme retention at 12 months of follow-up. Of the 947 FSWs initially seen in clinic, 692 were HIV tested. HIV prevalence was 49%. Among those returning to clinic after HIV testing and clinical screening, 93% of the women who were HIV-negative were confirmed as clinically eligible for PrEP (n = 224/241), and 41% (n = 110/270) of the women who were HIV-positive had CD4 counts within National Department of Health ART initiation guidelines at assessment. Of the remaining women who were HIV-positive, 93% were eligible for early ART (n = 148/160). From those eligible, 98% (n = 219/224) and 94% (n = 139/148) took up PrEP and early ART, respectively. At baseline, a substantial fraction of women had a steady partner, worked in brothels, and were born in Zimbabwe. Of those enrolled, 22% on PrEP (n = 49/219) and 60% on early ART (n = 83/139) were seen at 12 months; we observed high rates of loss to follow-up: 71% (n = 156/219) and 30% (n = 42/139) in the PrEP and early ART groups, respectively. Little change over time was reported in consistent condom use or the number of sexual partners in the last 7 days, with high levels of consistent condom use with clients and low use with steady partners in both study groups. There were no seroconversions on PrEP and 7 virological failures on early ART among women remaining in the study. Reported adherence to PrEP varied over time between 70% and 85%, whereas over 90% of participants reported taking pills daily while on early ART. Data on provider-side costs were also collected and analysed. The total cost of service delivery was approximately US$126 for PrEP and US$406 for early ART per person-year. The main limitations of this study include the lack of a control group, which was not included due to ethical considerations; clinical study requirements imposed when PrEP was not approved through the regulatory system, which could have affected uptake; and the timing of the implementation of a national sex worker HIV programme, which could have also affected uptake and retention. CONCLUSIONS: PrEP and early ART services can be implemented within FSW routine services in high prevalence, urban settings. We observed good uptake for both PrEP and early ART; however, retention rates for PrEP were low. Retention rates for early ART were similar to retention rates for the current standard of care. While the cost of the interventions was higher than previously published, there is potential for cost reduction at scale. The TAPS Demonstration Project results provided the basis for the first government PrEP and early ART guidelines and the rollout of the national sex worker HIV programme in South Africa

Land beneficiaries as game farmers: conservation, land reform and the invention of the 'community game farm' in KwaZulu-Natal

Scholarship on post-apartheid land reform includes research on land claims made to formal protected areas, such as national parks and state game reserves. Little attention has however, been paid to the question of land restitution claims on private lands, on which a range of nominally ‘conservation-friendly’ land-uses (including commercial hunting) have taken place. This article traces the emergence of the ‘community game farm’ as a product of land reform processes affecting freehold land in the midlands of KwaZulu-Natal province, South Africa. Two groups of land beneficiaries who were granted title to former privately owned game farms used for leisure hunting are studied in detail. The article shows that a range of state and private actors, as well as traditional authorities, have worked to ensure the continuation of the land under conservation or game farming after transfer. The central argument is that in this process, a generic narrative is imposed which works to conflate or deny the distinct historical identities of the beneficiary groups. The article raises questions about the real efficacy of land restitution in this context, as well as the appropriateness of a community-based conservation narrative when applied in the context of small farms such as those considered here.International Bibliography of Social Science

Influence of dietary lipid sources on sensory characteristics of broiler meat

________________________________________________________________________________ Abstract A study was conducted to determine the influence of different dietary lipid sources and inclusion levels on sensory characteristics of chicken breast meat. Eight isoenergetic (15.1 MJ AME/kg DM) and isonitrogenous (223 g CP/kg DM) diets were formulated, using high oleic sunflower oil (HOSO), sunflower oil (SO), fish oil (FO) and tallow (T) at 30 g/kg and 60 g/kg inclusion levels. Eight hundred, day-old Ross 788 broiler males were randomly allocated to the eight treatments (n = 100) and further subdivided into four replicates/treatment (n = 25). All birds receive a commercial starter diet for the first 14 days, where-after the experimental diets were fed for 28 days. At 42 days of age, three birds/replicate (n = 12/treatment) were randomly selected, weighed and slaughtered at a commercial abattoir. Breast muscles were removed from the chilled carcasses (4 °C) and de-skinned. Meat samples were wrapped in aluminium foil and steamed (200 °C) before cutting into smaller pieces (2.5 cm 3 ) and served to the respondents (n = 75) of a consumer panel. Each respondent tasted eight meat samples while completing a nine-point hedonic scale questionnaire. Meat samples of the HOSO treatment were preferred, while FO samples were the least acceptable to the respondents. These results suggested that dietary lipid sources could be used to manipulate sensory characteristics of broiler breast meat according to consumer preferences. _______________________________________________________________________________

A hypothetico-deductive approach to assessing the social function of chemical signalling in a non-territorial solitary carnivore

The function of chemical signalling in non-territorial solitary carnivores is still relatively unclear. Studies on territorial solitary and social carnivores have highlighted odour capability and utility, however the social function of chemical signalling in wild carnivore populations operating dominance hierarchy social systems has received little attention. We monitored scent marking and investigatory behaviour of wild brown bears Ursus arctos, to test multiple hypotheses relating to the social function of chemical signalling. Camera traps were stationed facing bear ‘marking trees’ to document behaviour by different age sex classes in different seasons. We found evidence to support the hypothesis that adult males utilise chemical signalling to communicate dominance to other males throughout the non-denning period. Adult females did not appear to utilise marking trees to advertise oestrous state during the breeding season. The function of marking by subadult bears is somewhat unclear, but may be related to the behaviour of adult males. Subadults investigated trees more often than they scent marked during the breeding season, which could be a result of an increased risk from adult males. Females with young showed an increase in marking and investigation of trees outside of the breeding season. We propose the hypothesis that females engage their dependent young with marking trees from a young age, at a relatively ‘safe’ time of year. Memory, experience, and learning at a young age, may all contribute towards odour capabilities in adult bears

Supported: supporting, enabling, and sustaining homecare workers to deliver end-of-life care: a qualitative study protocol

Background Homecare workers provide essential care at home for people at end-of-life but are often poorly trained and supported. Aim To explore the experiences and needs of homecare workers and the views of homecare clients and carers, and other community-based health and social care staff about the homecare worker role, including identification of good practice. Methods In this qualitative exploratory study, we will conduct 150 semi-structured interviews with homecare workers within three geographic English localities chosen for maximum socio-demographic variation. Eligible participants will be consenting adults providing care services (workers [n = 45], managers [n = 15] community practitioners [n = 30]), receiving care (clients thought to be in the last 6 months of life [n = 30], family carers [n = 15], or commissioners of homecare services supporting end-of-life care [n = 15]. Interviews may adopt a Pictor-guided or standard semi-structured approach according to their preference. Managers and commissioners can contribute to an online focus group if preferred. A range of recruitment strategies will be used, including through homecare agencies, local authorities, local NHS services, charities, voluntary sector groups and social media. Interviews and focus groups will be recorded, transcribed, anonymised, and analysed adopting a case-based approach for each geographic area within-case and then comparison across cases using reflexive thematic analysis. The design and analysis will be informed by Bronfenbrenner’s Adapted Ecological Systems theory. This study is registered on the Research Registry (No.8613). Contribution We will provide evidence on ways to improve the experiences and address the needs of homecare workers in relation to caring for people nearing end-of-life. It will offer insight into good practice around supporting homecare workers including responding to their training and development needs. Findings will inform subsequent stages of an evaluation-phase study of a training resource for homecare workers

An Advanced Method to Assess the Diet of Free-Ranging Large Carnivores Based on Scats

<div><h3>Background</h3><p>The diet of free-ranging carnivores is an important part of their ecology. It is often determined from prey remains in scats. In many cases, scat analyses are the most efficient method but they require correction for potential biases. When the diet is expressed as proportions of consumed mass of each prey species, the consumed prey mass to excrete one scat needs to be determined and corrected for prey body mass because the proportion of digestible to indigestible matter increases with prey body mass. Prey body mass can be corrected for by conducting feeding experiments using prey of various body masses and fitting a regression between consumed prey mass to excrete one scat and prey body mass (correction factor 1). When the diet is expressed as proportions of consumed individuals of each prey species and includes prey animals not completely consumed, the actual mass of each prey consumed by the carnivore needs to be controlled for (correction factor 2). No previous study controlled for this second bias.</p> <h3>Methodology/Principal Findings</h3><p>Here we use an extended series of feeding experiments on a large carnivore, the cheetah (<em>Acinonyx jubatus</em>), to establish both correction factors. In contrast to previous studies which fitted a linear regression for correction factor 1, we fitted a biologically more meaningful exponential regression model where the consumed prey mass to excrete one scat reaches an asymptote at large prey sizes. Using our protocol, we also derive correction factor 1 and 2 for other carnivore species and apply them to published studies. We show that the new method increases the number and proportion of consumed individuals in the diet for large prey animals compared to the conventional method.</p> <h3>Conclusion/Significance</h3><p>Our results have important implications for the interpretation of scat-based studies in feeding ecology and the resolution of human-wildlife conflicts for the conservation of large carnivores.</p> </div