Conformational changes of the HsDHODH N-terminal microdomain via DEER spectroscopy

The human enzyme dihydroorotate dehydrogenase (HsDHODH) has been studied for being a target for development of new antineoplasic and antiproliferative drugs. The synthetic peptide N-t(DH) represents the N-terminal microdomain of this enzyme, responsible for anchoring it to the inner mitochondrial membrane. Also, it is known to harbor quinones that are essential for enzyme catalysis. Here we report structural features of the peptide/membrane interactions obtained by using CD and DEER spectroscopic techniques, both in micelles and in lipid vesicles. The data revealed different peptide conformational states in micelles and liposomes, which could suggest that this microdomain acts in specific regions or areas of the mitochondria, which can be related with the control of the quinone access to the HsDHODH active site. This is the first study to report on conformational changes of the HsDHODH N-terminal microdomain through a combination of CD and DEER spectroscopic techniques.

Adverse Drug Events Leading Children to Hospital Emergency Care

To determine the incidence of adverse drug events (ADE) that resulted in the need for children's emergency care, a total of 23,286 pediatric emergency case notes were analyzed. They were selected on the basis of the ICD code indicating a possible ADE. ADEs were found in 13 case notes (0.06%), predominantly among girls and mainly in the 1 to 5 year age group. About half of the observed events occurred as a result of accidental ingestion, 27.3% were suicide attempts, and 27.3% arose due to the discontinuation of treatment. Antiepileptic drugs were those most often involved. Three (23%) were serious. The results suggest that children have easy access to medications and are involved in the majority of accidental occurrences. Using drugs involves risks, and drawing attention to such risks while prescribing and dispensing them fosters the sharing of responsibility and the empowerment of the users, measures necessary to health promotion.

Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis

Xylanases (EC 3.2.1.8 endo-1,4-glycosyl hydrolase) catalyze the hydrolysis of xylan, an abundant hemicellulose of plant cell walls. Access to the catalytic site of GH11 xylanases is regulated by movement of a short beta-hairpin, the so-called thumb region, which can adopt open or closed conformations. A crystallographic study has shown that the D11F/R122D mutant of the GH11 xylanase A from Bacillus subtilis (BsXA) displays a stable "open" conformation, and here we report a molecular dynamics simulation study comparing this mutant with the native enzyme over a range of temperatures. The mutant open conformation was stable at 300 and 328 K, however it showed a transition to the closed state at 338 K. Analysis of dihedral angles identified thumb region residues Y113 and T123 as key hinge points which determine the open-closed transition at 338 K. Although the D11F/R122D mutations result in a reduction in local inter-intramolecular hydrogen bonding, the global energies of the open and closed conformations in the native enzyme are equivalent, suggesting that the two conformations are equally accessible. These results indicate that the thumb region shows a broader degree of energetically permissible conformations which regulate the access to the active site region. The R122D mutation contributes to the stability of the open conformation, but is not essential for thumb dynamics, i.e., the wild type enzyme can also adapt to the open conformation.

Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

Background Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont’s contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. Results Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. Conclusion We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of experimental results. We uncovered the remarkable plasticity in essential amino acid biosynthesis pathway evolution in these protozoans, demonstrating heavy influence of horizontal gene transfer events, from Bacteria to trypanosomatid nuclei, in the evolution of these pathways.

Chemical and morphological characterization of sugarcane bagasse submitted to a delignification process for enhanced enzymatic digestibility

Abstract Background In recent years, biorefining of lignocellulosic biomass to produce multi-products such as ethanol and other biomaterials has become a dynamic research area. Pretreatment technologies that fractionate sugarcane bagasse are essential for the successful use of this feedstock in ethanol production. In this paper, we investigate modifications in the morphology and chemical composition of sugarcane bagasse submitted to a two-step treatment, using diluted acid followed by a delignification process with increasing sodium hydroxide concentrations. Detailed chemical and morphological characterization of the samples after each pretreatment condition, studied by high performance liquid chromatography, solid-state nuclear magnetic resonance, diffuse reflectance Fourier transformed infrared spectroscopy and scanning electron microscopy, is reported, together with sample crystallinity and enzymatic digestibility. Results Chemical composition analysis performed on samples obtained after different pretreatment conditions showed that up to 96% and 85% of hemicellulose and lignin fractions, respectively, were removed by this two-step method when sodium hydroxide concentrations of 1% (m/v) or higher were used. The efficient lignin removal resulted in an enhanced hydrolysis yield reaching values around 100%. Considering the cellulose loss due to the pretreatment (maximum of 30%, depending on the process), the total cellulose conversion increases significantly from 22.0% (value for the untreated bagasse) to 72.4%. The delignification process, with consequent increase in the cellulose to lignin ratio, is also clearly observed by nuclear magnetic resonance and diffuse reflectance Fourier transformed infrared spectroscopy experiments. We also demonstrated that the morphological changes contributing to this remarkable improvement occur as a consequence of lignin removal from the sample. Bagasse unstructuring is favored by the loss of cohesion between neighboring cell walls, as well as by changes in the inner cell wall structure, such as damaging, hole formation and loss of mechanical resistance, facilitating liquid and enzyme access to crystalline cellulose. Conclusions The results presented herewith show the efficiency of the proposed method for improving the enzymatic digestibility of sugarcane bagasse and provide understanding of the pretreatment action mechanism. Combining the different techniques applied in this work warranted thorough information about the undergoing morphological and chemical changes and was an efficient approach to understand the morphological effects resulting from sample delignification and its influence on the enhanced hydrolysis results.

Bringing results to fruition through publication: An analysis of a peer-reviewed, open access and context-focused journal's editorial practice

When it comes to helping to shape sustainable development, research is most useful when it bridges the science–implementation/management gap and when it brings development specialists and researchers into a dialogue (Hurni et al. 2004); can a peer-reviewed journal contribute to this aim? In the classical system for validation and dissemination of scientific knowledge, journals focus on knowledge exchange within the academic community and do not specifically address a ‘life-world audience’. Within a North-South context, another knowledge divide is added: the peer review process excludes a large proportion of scientists from the South from participating in the production of scientific knowledge (Karlsson et al. 2007). Mountain Research and Development (MRD) is a journal whose mission is based on an editorial strategy to build the bridge between research and development and ensure that authors from the global South have access to knowledge production, ultimately with a view to supporting sustainable development in mountains. In doing so, MRD faces a number of challenges that we would like to discuss with the td-net community, after having presented our experience and strategy as editors of this journal. MRD was launched in 1981 by mountain researchers who wanted mountains to be included in the 1992 Rio process. In the late 1990s, MRD realized that the journal needed to go beyond addressing only the scientific community. It therefore launched a new section addressing a broader audience in 2000, with the aim of disseminating insights into, and recommendations for, the implementation of sustainable development in mountains. In 2006, we conducted a survey among MRD’s authors, reviewers, and readers (Wymann et al. 2007): respondents confirmed that MRD had succeeded in bridging the gap between research and development. But we realized that MRD could become an even more efficient tool for sustainability if development knowledge were validated: in 2009, we began submitting ‘development’ papers (‘transformation knowledge’) to external peer review of a kind different from the scientific-only peer review (for ‘systems knowledge’). At the same time, the journal became open access in order to increase the permeability between science and society, and ensure greater access for readers and authors in the South. We are currently rethinking our review process for development papers, with a view to creating more space for communication between science and society, and enhancing the co-production of knowledge (Roux 2008). Hopefully, these efforts will also contribute to the urgent debate on the ‘publication culture’ needed in transdisciplinary research (Kueffer et al. 2007).

An introduction to low-level analysis methods of DNA microarray data

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of nucleic acid abundance in a set of tissues or cell populations for thousands of transcripts or loci simultaneously. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. This includes the design of probes, the experimental design, the image analysis of microarray scanned images, the normalization of fluorescence intensities, the assessment of the quality of microarray data and incorporation of quality information in subsequent analyses, the combination of information across arrays and across sets of experiments, the discovery and recognition of patterns in expression at the single gene and multiple gene levels, and the assessment of significance of these findings, considering the fact that there is a lot of noise and thus random features in the data. For all of these components, access to a flexible and efficient statistical computing environment is an essential aspect.

Public-health and individual approaches to antiretroviral therapy: township South Africa and Switzerland compared

BACKGROUND: The provision of highly active antiretroviral therapy (HAART) in resource-limited settings follows a public health approach, which is characterised by a limited number of regimens and the standardisation of clinical and laboratory monitoring. In industrialized countries doctors prescribe from the full range of available antiretroviral drugs, supported by resistance testing and frequent laboratory monitoring. We compared virologic response, changes to first-line regimens, and mortality in HIV-infected patients starting HAART in South Africa and Switzerland. METHODS AND FINDINGS: We analysed data from the Swiss HIV Cohort Study and two HAART programmes in townships of Cape Town, South Africa. We included treatment-naïve patients aged 16 y or older who had started treatment with at least three drugs since 2001, and excluded intravenous drug users. Data from a total of 2,348 patients from South Africa and 1,016 patients from the Swiss HIV Cohort Study were analysed. Median baseline CD4+ T cell counts were 80 cells/mul in South Africa and 204 cells/mul in Switzerland. In South Africa, patients started with one of four first-line regimens, which was subsequently changed in 514 patients (22%). In Switzerland, 36 first-line regimens were used initially, and these were changed in 539 patients (53%). In most patients HIV-1 RNA was suppressed to 500 copies/ml or less within one year: 96% (95% confidence interval [CI] 95%-97%) in South Africa and 96% (94%-97%) in Switzerland, and 26% (22%-29%) and 27% (24%-31%), respectively, developed viral rebound within two years. Mortality was higher in South Africa than in Switzerland during the first months of HAART: adjusted hazard ratios were 5.90 (95% CI 1.81-19.2) during months 1-3 and 1.77 (0.90-3.50) during months 4-24. CONCLUSIONS: Compared to the highly individualised approach in Switzerland, programmatic HAART in South Africa resulted in similar virologic outcomes, with relatively few changes to initial regimens. Further innovation and resources are required in South Africa to both achieve more timely access to HAART and improve the prognosis of patients who start HAART with advanced disease.

The Protection and Promotion of Cultural Diversity in a Digital Networked Environment : Mapping Possible Advances to Coherence

The present paper is the result of a four-year-long project examining the concept and the policies of cultural diversity and the impact of digital media upon the regulatory environment where the goal of cultural diversity is to be achieved. The focus of the project was primarily on the international level and in particular on the World Trade Organization (WTO) and the United Nations Educational Scientific and Cultural Organization (UNESCO), which also epitomise the often framed as opposing pair of trade and culture. In the broad context of the project, we sought to pinpoint the essential elements of an international trade-and-culture conducive framework that can also overcome the existing fragmentation in the field of international law and move towards more coherent solutions. In a narrower context, we sketched some possible improvements to the WTO law that can make it more suitable to the digital networked environment and to the objective of diverse media that some states aspire. . Our key messages are: (1) Neither the WTO nor UNESCO currently offers appropriate solutions to the trade and culture predicament and allows for efficient protection and promotion of cultural diversity; (2) The trade and culture discourse is overly politicised and due to the related path dependencies, a number of feasible solutions appears presently blocked; (3) The digital networked environment has profoundly changed the ways cultural content is created, distributed, accessed and consumed, and may thus offer good reasons to reassess and readjust the present models of governance; (4) Access to information appears to be the most appropriate focus of the discussions with view to protecting and promoting cultural diversity in the new digital media setting, both in local and global contexts; (5) This new focal point demands also broadening and interconnecting the policy discussions, which should go beyond the narrow scope of audiovisual media services, but cautiously account for the developments at the network and applications levels, as well as in other domains, such as most notably intellectual property rights protection; (6) There are various ways in which the WTO can be made more conducive to cultural policy considerations and these include, among others, improved and updated services classifications; enhanced legal certainty with regard to digitally transferred goods and services; incorporation of rules on subsidies for services and on competition.

Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration

INTRODUCTION HIV care and treatment programmes worldwide are transforming as they push to deliver universal access to essential prevention, care and treatment services to persons living with HIV and their communities. The characteristics and capacity of these HIV programmes affect patient outcomes and quality of care. Despite the importance of ensuring optimal outcomes, few studies have addressed the capacity of HIV programmes to deliver comprehensive care. We sought to describe such capacity in HIV programmes in seven regions worldwide. METHODS Staff from 128 sites in 41 countries participating in the International epidemiologic Databases to Evaluate AIDS completed a site survey from 2009 to 2010, including sites in the Asia-Pacific region (n=20), Latin America and the Caribbean (n=7), North America (n=7), Central Africa (n=12), East Africa (n=51), Southern Africa (n=16) and West Africa (n=15). We computed a measure of the comprehensiveness of care based on seven World Health Organization-recommended essential HIV services. RESULTS Most sites reported serving urban (61%; region range (rr): 33-100%) and both adult and paediatric populations (77%; rr: 29-96%). Only 45% of HIV clinics that reported treating children had paediatricians on staff. As for the seven essential services, survey respondents reported that CD4+ cell count testing was available to all but one site, while tuberculosis (TB) screening and community outreach services were available in 80 and 72%, respectively. The remaining four essential services - nutritional support (82%), combination antiretroviral therapy adherence support (88%), prevention of mother-to-child transmission (PMTCT) (94%) and other prevention and clinical management services (97%) - were uniformly available. Approximately half (46%) of sites reported offering all seven services. Newer sites and sites in settings with low rankings on the UN Human Development Index (HDI), especially those in the President's Emergency Plan for AIDS Relief focus countries, tended to offer a more comprehensive array of essential services. HIV care programme characteristics and comprehensiveness varied according to the number of years the site had been in operation and the HDI of the site setting, with more recently established clinics in low-HDI settings reporting a more comprehensive array of available services. Survey respondents frequently identified contact tracing of patients, patient outreach, nutritional counselling, onsite viral load testing, universal TB screening and the provision of isoniazid preventive therapy as unavailable services. CONCLUSIONS This study serves as a baseline for on-going monitoring of the evolution of care delivery over time and lays the groundwork for evaluating HIV treatment outcomes in relation to site capacity for comprehensive care.

What is the Need for Prostatic Biomarkers in Prostate Cancer Management?

Discriminating patients with a low risk of progression from those with lethal prostate cancer is one of the main challenges in prostate cancer management. Indeed, such discrimination is essential if we aim to avoid overtreatment in men with indolent disease and to improve survival in those men with lethal disease. We are reporting on the current literature on such prognostic tools that are now available, their clinical role and their limitations in individualizing care. There is an urgent need to incorporate such genomic tools into new platform-based clinical trial structures to further develop and validate prognostic and predictive biomarkers and provide prostate cancer patients with an effective and cost-efficient access to new drugs in the setting of personalized treatment.

Antibody-Drug Conjugates for Tumor Targeting-Novel Conjugation Chemistries and the Promise of non-IgG Binding Proteins

Antibody-drug conjugates (ADCs) have emerged as a promising class of anticancer agents, combining the specificity of antibodies for tumor targeting and the destructive potential of highly potent drugs as payload. An essential component of these immunoconjugates is a bifunctional linker capable of reacting with the antibody and the payload to assemble a functional entity. Linker design is fundamental, as it must provide high stability in the circulation to prevent premature drug release, but be capable of releasing the active drug inside the target cell upon receptor-mediated endocytosis. Although ADCs have demonstrated an increased therapeutic window, compared to conventional chemotherapy in recent clinical trials, therapeutic success rates are still far from optimal. To explore other regimes of half-life variation and drug conjugation stoichiometries, it is necessary to investigate additional binding proteins which offer access to a wide range of formats, all with molecularly defined drug conjugation. Here, we delineate recent progress with site-specific and biorthogonal conjugation chemistries, and discuss alternative, biophysically more stable protein scaffolds like Designed Ankyrin Repeat Proteins (DARPins), which may provide such additional engineering opportunities for drug conjugates with improved pharmacological performance.

The need for second-line antiretroviral therapy in adults in sub-Saharan Africa up to 2030: a mathematical modelling study.

BACKGROUND The number of patients in need of second-line antiretroviral drugs is increasing in sub-Saharan Africa. We aimed to project the need of second-line antiretroviral therapy in adults in sub-Saharan Africa up to 2030. METHODS We developed a simulation model for HIV and applied it to each sub-Saharan African country. We used the WHO country intelligence database to estimate the number of adult patients receiving antiretroviral therapy from 2005 to 2014. We fitted the number of adult patients receiving antiretroviral therapy to observed estimates, and predicted first-line and second-line needs between 2015 and 2030. We present results for sub-Saharan Africa, and eight selected countries. We present 18 scenarios, combining the availability of viral load monitoring, speed of antiretroviral scale-up, and rates of retention and switching to second-line. HIV transmission was not included. FINDINGS Depending on the scenario, 8·7-25·6 million people are expected to receive antiretroviral therapy in 2020, of whom 0·5-3·0 million will be receiving second-line antiretroviral therapy. The proportion of patients on treatment receiving second-line therapy was highest (15·6%) in the scenario with perfect retention and immediate switching, no further scale-up, and universal routine viral load monitoring. In 2030, the estimated range of patients receiving antiretroviral therapy will remain constant, but the number of patients receiving second-line antiretroviral therapy will increase to 0·8-4·6 million (6·6-19·6%). The need for second-line antiretroviral therapy was two to three times higher if routine viral load monitoring was implemented throughout the region, compared with a scenario of no further viral load monitoring scale-up. For each monitoring strategy, the future proportion of patients receiving second-line antiretroviral therapy differed only minimally between countries. INTERPRETATION Donors and countries in sub-Saharan Africa should prepare for a substantial increase in the need for second-line drugs during the next few years as access to viral load monitoring improves. An urgent need exists to decrease the costs of second-line drugs. FUNDING World Health Organization, Swiss National Science Foundation, National Institutes of Health.

Implementing the Global Plan of Action on workers' health: Components to protect health care workers

Health care workers are at risk for percutaneous injuries and infection with blood born pathogens due to needle stick injuries with contaminated needles. The most common pathogens transmitted are hepatitis B, and C and HIV/AIDS. According to the WHO Global Plan of Action (GPA) a large gap exist between and within countries with regards to the health status of workers and their exposure to occupational risk. Less than 15% of the world's work forces have access to occupational health services despite the availability of effective interventions that can prevent occupational hazards, or protect and promote health in the workplace. The 2006 World Health Report declared that there is a global crisis in the health care work force. 1 in 400 of the world's health care workers work in Sub-Saharan Africa. 1 in 3 work in the U.S or Canada. The shortage of health care workers is worst in Southeast Asia and Sub-Saharan Africa. These countries have the highest burden of exposure to contaminated sharps. They rarely, if ever monitor the exposure or health impact of occupational ailments and injuries on workers. Many injuries are unreported. Occupational health services in the developing world are virtually non existent. Many health care workers leave their home countries and go to work in other countries where the working conditions, occupational services included, are better. The inability of countries to provide the necessary numbers of health care workers to provide a high level of health coverage is a threat to national and international public health security. Immunizing health care workers against hepatitis B and providing them PEP, PPE, education and safety training is an essential part of increasing and maintaining the numbers of health care workers in the critical shortage areas. ^

The impact of parent acculturation on parental fruit and vegetable intake, child fruit and vegetable intake, and child perceived access and availability to fruits and vegetables in the home environment

The purpose of this thesis was to investigate the association between parent acculturation and parental fruit and vegetable intake, child fruit and vegetable intake, and child access and availability to fruits and vegetables. Secondary data analysis was performed on a convenience sample of low-income Hispanic-identifying parents (n = 177) and children from a baseline survey from the Sprouting Healthy Kids intervention. T tests were used to examine the association between parent acculturation status (acculturated or non-acculturated) and fruit intake, vegetable intake and combined fruit and vegetable intake of both the parent and the child. T tests were also used to determine the relationship between parent acculturation and child access and availability to fruits, vegetables, and combined fruits and vegetables. Statistical significance was set at a p level of 0.05. The mean FVI for the parents and children were 3.41 servings and 2.96 servings, respectively. Statistical significance was found for the relationships between parent acculturation and parent fruit intake and parent acculturation and child fruit access. Lower acculturation of the parent was significantly related to higher fruit intake. Counter to the hypothesis, higher acculturation was found to be associated with greater access to fruits for the child. These findings suggest the necessity for not only culturally specific nutrition interventions, but the need for interventions to target behaviors for specific levels of acculturation within a culture. ^