The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page

Unique morphological characteristics of mitochondrial subtypes in the heart: the effect of ischemia and ischemic preconditioning.

RATIONALE: Three subsets of mitochondria have been described in adult cardiomyocytes - intermyofibrillar (IMF), subsarcolemmal (SSM), and perinuclear (PN). They have been shown to differ in physiology, but whether they also vary in morphological characteristics is unknown. Ischemic preconditioning (IPC) is known to prevent mitochondrial dysfunction induced by acute myocardial ischemia/reperfusion injury (IRI), but whether IPC can also modulate mitochondrial morphology is not known. AIMS: Morphological characteristics of three different subsets of adult cardiac mitochondria along with the effect of ischemia and IPC on mitochondrial morphology will be investigated. METHODS: Mouse hearts were subjected to the following treatments (N=6 for each group): stabilization only, IPC (3x5 min cycles of global ischemia and reperfusion), ischemia only (20 min global ischemia); and IPC and ischemia. Hearts were then processed for electron microscopy and mitochondrial morphology was assessed subsequently. RESULTS: In adult cardiomyocytes, IMF mitochondria were found to be more elongated and less spherical than PN and SSM mitochondria. PN mitochondria were smaller in size when compared to the other two subsets. SSM mitochondria had similar area to IMF mitochondria but their sphericity measures were similar to PN mitochondria. Ischemia was shown to increase the sphericity parameters of all 3 subsets of mitochondria; reduce the length of IMF mitochondria, and increase the size of PN mitochondria. IPC had no effect on mitochondrial morphology either at baseline or after ischemia. CONCLUSION: The three subsets of mitochondria in the adult heart are morphologically different. IPC does not appear to modulate mitochondrial morphology in adult cardiomyocytes

Use of the out-of-hours emergency dental service at two south-east London hospitals

<p>Abstract</p> <p>Background</p> <p>Prior to the introduction of the 2006 NHS dental contract in England and Wales, general dental practitioners (GDPs) were responsible for the provision of out-of-hours (OOH) emergency dental services (EDS); however there was great national variation in service provision. Under the contractual arrangements introduced 1^stApril 2006, local commissioning agencies became formally responsible for the provision of out-of-hours emergency dental services. This study aimed to examine patients' use of an out-of-hours emergency dental service and to determine whether the introduction of the 2006 national NHS dental contract had resulted in a change in service use, with a view to informing future planning and commissioning of care.</p> <p>Methods</p> <p>A questionnaire was administered to people attending the out-of-hours emergency dental service at two inner city London hospitals over two time periods; four weeks before and six months after the introduction of the dental contract in April 2006. The questionnaire explored: reasons for attending; dental registration status and attendance; method of access; knowledge and use of NHS Direct; satisfaction with the service; future preferences for access and use of out-of-hours dental services. Data were compared to determine any impact of the new contract on how and why people accessed the emergency dental service.</p> <p>Results</p> <p>The response rate was 73% of attendees with 981 respondents for the first time period and 546 for the second. There were no significant differences between the two time periods in the gender, age, ethnic distribution or main language of service users accessing the service. Overall, the main dental problem was toothache (72%) and the main reason for choosing this service was due to the inability to access another emergency dental service (42%). Significantly fewer service users attended the out-of-hours emergency dental service during the second period because they could not get an appointment with their own dentist (p = 0.002 from 28% to 20%) and significantly more service users in the second period felt the emergency dental service was easier to get to than their own dentist (P = 0.003 from 8% to 14%). Service users found out about the service from multiple sources, of which family and friends were the most common source (30%). In the second period fewer service users were obtaining information about the service from dental receptionists (P = 0.002 from 14% to 9%) and increased use of NHS Direct for a dental problem was reported (P = 0.002 from 16% to 22%) along with more service users being referred to the service by NHS Direct (P = 0.02 from 19% to 24%). The most common preference for future emergency dental care was face-to-face with a dentist (79%).</p> <p>Conclusion</p> <p>This study has provided an insight into how and why people use an out-of-hours emergency dental service and has helped to guide future commissioning of these services. Overall, the service was being used in much the same way both before and after the 2006 dental contract. Significantly more use was being made of NHS Direct after April 2006; however, informal information networks such as friends and family remain an important source of information about accessing emergency dental services.</p

Trends in the Discovery of New Marine Natural Products from Invertebrates over the Last Two Decades – Where and What Are We Bioprospecting?

It is acknowledged that marine invertebrates produce bioactive natural products that may be useful for developing new drugs. By exploring untapped geographical sources and/or novel groups of organisms one can maximize the search for new marine drugs to treat human diseases. The goal of this paper is to analyse the trends associated with the discovery of new marine natural products from invertebrates (NMNPI) over the last two decades. The analysis considers different taxonomical levels and geographical approaches of bioprospected species. Additionally, this research is also directed to provide new insights into less bioprospected taxa and world regions. In order to gather the information available on NMNPI, the yearly-published reviews of Marine Natural Products covering 1990–2009 were surveyed. Information on source organisms, specifically taxonomical information and collection sites, was assembled together with additional geographical information collected from the articles originally describing the new natural product. Almost 10000 NMNPI were discovered since 1990, with a pronounced increase between decades. Porifera and Cnidaria were the two dominant sources of NMNPI worldwide. The exception was polar regions where Echinodermata dominated. The majority of species that yielded the new natural products belong to only one class of each Porifera and Cnidaria phyla (Demospongiae and Anthozoa, respectively). Increased bioprospecting efforts were observed in the Pacific Ocean, particularly in Asian countries that are associated with the Japan Biodiversity Hotspot and the Kuroshio Current. Although results show comparably less NMNPI from polar regions, the number of new natural products per species is similar to that recorded for other regions. The present study provides information to future bioprospecting efforts addressing previously unexplored taxonomic groups and/or regions. We also highlight how marine invertebrates, which in some cases have no commercial value, may become highly valuable in the ongoing search for new drugs from the sea

Parasitic pneumonia in roe deer (Capreolus capreolus) in Cornwall, Great Britain, caused by Varestrongylus capreoli (Protostrongylidae)

Abstract Background Roe deer (Capreolus capreolus) became extinct over large areas of Britain during the post mediaeval period but following re-introductions from Europe during the 1800s and early 1900s the population started to recover and in recent decades there has been a spectacular increase. Many roe deer are shot in Britain each year but despite this there is little published information on the diseases and causes of mortality of roe deer in Great Britain. Case presentation The lungs of two hunter-shot roe deer in Cornwall showed multiple, raised, nodular lesions associated with numerous protostrongylid-type nematode eggs and first stage larvae. There was a pronounced inflammatory cell response (mostly macrophages, eosinophils and multinucleate giant cells) and smooth muscle hypertrophy of the smaller bronchioles. The morphology of the larvae was consistent with that of a Varestrongylus species and sequencing of an internal transcribed spacer-2 fragment confirmed 100% identity with a published Norwegian Varestrongylus cf. capreoli sequence. To the best of the authors’ knowledge this is the first confirmed record of V. capreoli in Great Britain. Co-infection with an adult protostrongylid, identified by DNA sequencing as Varestrongylus sagittatus, was also demonstrated in one case. Conclusions Parasitic pneumonia is regarded as a common cause of mortality in roe deer and is typically attributed to infection with Dictyocaulus sp. This study has shown that Varestrongylus capreoli also has the capability to cause significant lung pathology in roe deer and heavy infection could be of clinical significance

Foreword to ‘Quantitative and analytical relations in biochemistry’—a special issue in honour of Donald J. Winzor’s 80th birthday

The purpose of this special issue is to honour Professor Donald J. Winzor’s long career as a researcher and scientific mentor, and to celebrate the milestone of his 80th birthday. Throughout his career, Don has been renowned for his development of clever approximations to difficult quantitative relations governing a range of biophysical measurements. The theme of this special issue, ‘Quantitative and analytical relations in biochemistry’, was chosen to reflect this aspect of Don’s scientific approach

Predicting language diversity with complex network

Evolution and propagation of the world's languages is a complex phenomenon, driven, to a large extent, by social interactions. Multilingual society can be seen as a system of interacting agents, where the interaction leads to a modification of the language spoken by the individuals. Two people can reach the state of full linguistic compatibility due to the positive interactions, like transfer of loanwords. But, on the other hand, if they speak entirely different languages, they will separate from each other. These simple observations make the network science the most suitable framework to describe and analyze dynamics of language change. Although many mechanisms have been explained, we lack a qualitative description of the scaling behavior for different sizes of a population. Here we address the issue of the language diversity in societies of different sizes, and we show that local interactions are crucial to capture characteristics of the empirical data. We propose a model of social interactions, extending the idea from, that explains the growth of the language diversity with the size of a population of country or society. We argue that high clustering and network disintegration are the most important characteristics of models properly describing empirical data. Furthermore, we cancel the contradiction between previous models and the Solomon Islands case. Our results demonstrate the importance of the topology of the network, and the rewiring mechanism in the process of language change

Rapid global fitting of large fluorescence lifetime imaging microscopy datasets

Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell homo-FRET data. A software package implementing this algorithm, FLIMfit, is available under an open source licence through the Open Microscopy Environment

Brain science and early years policy: Hopeful ethos or ‘cruel optimism’?

Ideas that the quality of parental nurturing and attachment in the first years of a child’s life is formative, hard-wiring their brains for success or failure, are reflected in policy reports from across the political spectrum and in targeted services delivering early intervention. In this article we draw on our research into ‘Brain science and early intervention’, using reviews of key policy literature and interviews with influential advocates of early intervention and with early years practitioners, to critically assess the ramifications and implications of these claims. Rather than upholding the ‘hopeful ethos’ proffered by advocates of the progressive nature of brain science and early intervention, we show that brain claims are justifying gendered, raced and social inequalities, positioning poor mothers as architects of their children’s deprivation

Not All Are Lost: Interrupted Laboratory Monitoring, Early Death, and Loss to Follow-Up (LTFU) in a Large South African Treatment Program

Background: Many HIV treatment programs in resource-limited settings are plagued by high rates of loss to follow-up (LTFU). Most studies have not distinguished between those who briefly interrupt, but return to care, and those more chronically lost to follow-up. Methods: We conducted a retrospective cohort study of 11,397 adults initiating antiretroviral therapy (ART) in 71 Southern African Catholic Bishops Conference/Catholic Relief Services HIV treatment clinics between January 2004 and December 2008. We distinguished among patients with early death, within the first 7 months on ART; patients with interruptions in laboratory monitoring (ILM), defined as missing visits in the first 7 months on ART, but returning to care by 12 months; and those LTFU, defined as missing all follow-up visits in the first 12 months on ART. We used multilevel logistic regression models to determine patient and clinic-level characteristics associated with these outcomes. Results: In the first year on ART, 60% of patients remained in care, 30% missed laboratory visits, and 10% suffered early death. Of the 3,194 patients who missed laboratory visits, 40% had ILM, resuming care by 12 months. After 12 months on ART, patients with ILM had a 30% increase in detectable viremia compared to those who remained in care. Risk of LTFU decreased with increasing enrollment year, and was lowest for patients who enrolled in 2008 compared to 2004 [OR 0.49, 95%CI 0.39–0.62]. Conclusions: In a large community-based cohort in South Africa, nearly 30% of patients miss follow-up visits for CD4 monitoring in the first year after starting ART. Of those, 40% have ILM but return to clinic with worse virologic outcomes than those who remain in care. The risk of chronic LTFU decreased with enrollment year. As ART availability increases, interruptions in care may become more common, and should be accounted for in addressing program LTFU