Insertion site preference of Mu, Tn5, and Tn7 transposons

<p>Abstract</p> <p>Background</p> <p>Transposons, segments of DNA that can mobilize to other locations in a genome, are often used for insertion mutagenesis or to generate priming sites for sequencing of large DNA molecules. For both of these uses, a transposon with minimal insertion bias is desired to allow complete coverage with minimal oversampling.</p> <p>Findings</p> <p>Three transposons, Mu, Tn5, and Tn7, were used to generate insertions in the same set of fosmids containing <it>Candida glabrata </it>genomic DNA. Tn7 demonstrates markedly less insertion bias than either Mu or Tn5, with both Mu and Tn5 biased toward sequences containing guanosine (G) and cytidine (C). This preference of Mu and Tn5 yields less uniform spacing of insertions than for Tn7, in the adenosine (A) and thymidine (T) rich genome of <it>C. glabrata </it>(39% GC).</p> <p>Conclusions</p> <p>In light of its more uniform distribution of insertions, Tn7 should be considered for applications in which insertion bias is deleterious.</p

INPOP08, a 4-D planetary ephemeris: From asteroid and time-scale computations to ESA Mars Express and Venus Express contributions

The latest version of the planetary ephemerides developed at the Paris Observatory and at the Besancon Observatory is presented here. INPOP08 is a 4-dimension ephemeris since it provides to users positions and velocities of planets and the relation between TT and TDB. Investigations leading to improve the modeling of asteroids are described as well as the new sets of observations used for the fit of INPOP08. New observations provided by the European Space Agency (ESA) deduced from the tracking of the Mars Express (MEX) and Venus Express (VEX) missions are presented as well as the normal point deduced from the Cassini mission. We show the huge impact brought by these observations in the fit of INPOP08, especially in terms of Venus, Saturn and Earth-Moon barycenter orbits.Comment: 14 pages. submitted to A&A. accepted in A&

Did Ebola emerge in West Africa by a policy-driven phase change in agroecology? Ebola's social context

SCOPUS: no.jinfo:eu-repo/semantics/publishe

Surfaces: An interdisciplinary project to understand and enhance health in the vulnerable rainforests of Papua New Guinea

Background New Guinea has the third largest tropical rainforest on Earth. However, one quarter of the forests of Papua New Guinea (PNG, New Guinea’s eastern half) have been cleared or degraded, nearly half through commercial logging.Sustainable development requires supporting good health (Sustainable Development Goal [SDG] 3) and protecting life on land (SDG 15). To remote communities in PNG with low levels of health provision, these goals can seem in conflict. Logging companies’ offer of roads and income can partly extinguish the remoteness that bars access to health services, making desire for health a driver for forest destruction and erosion of health related ecosystem services. Conservation success thus requires synergies be developed with delivery of other SDGs, particularly those pertaining to health. We aim to provide a model of integrated health and conservation in PNGs rainforests. Methods We are mapping and piloting biological, anthropological, and medical methods to address SDGs on health and biodiversity, focusing first on scabies and fungal diseases. At Wanang, team members have a long term collaboration with nine clans with unmet health needs who collectively chose to preserve their 10,000 hectare forest whilst surrounding communities allowed logging. Similar collaborations are being developed along an altitudinal transect on Mt.Wilheim (4,509m). Stage 1 of Surfaces will (i) systematically map evidence on integrated conservation and health programmes, (ii) conduct clinical examinations and rapid anthropological assessments to understand medical needs, and survey skin disease, and (iii) produce a case study of the Wanang agreement, based on interviews with participants. This will lay the foundation for a multi-year health intervention and interdisciplinary study. Findings We are in the projects’ early stages (so do not yet have findings), and would appreciate advice and suggestions of collaboration from others in the Planetary Health community. Funding Sussex Sustainability Research Programme, University of Sussex, UK. Contributions All authors have commented on multiple drafts and approved the final version of the abstract for publication. Conflicts of interest We declare we have no conflicts of interest. Acknowledgments We thank the projects partner communities; New Guinea Binatang Research Centre; and our advisory group

Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae

Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.Jennifer R. Bellon, Frank Schmid, Dimitra L. Capone, Barbara L. Dunn, Paul J. Chamber

Financial crises and the attainment of the SDGs: an adjusted multidimensional poverty approach

This paper analyses the impact of financial crises on the Sustainable Development Goal of eradicating poverty. To do so, we develop an adjusted Multidimensional Poverty Framework (MPF) that includes 15 indicators that span across key poverty aspects related to income, basic needs, health, education and the environment. We then use an econometric model that allows us to examine the impact of financial crises on these indicators in 150 countries over the period 1980–2015. Our analysis produces new estimates on the impact of financial crises on poverty’s multiple social, economic and environmental aspects and equally important captures dynamic linkages between these aspects. Thus, we offer a better understanding of the potential impact of current debt dynamics on Multidimensional Poverty and demonstrate the need to move beyond the boundaries of SDG1, if we are to meet the target of eradicating poverty. Our results indicate that the current financial distress experienced by many low-income countries may reverse the progress that has been made hitherto in reducing poverty. We find that financial crises are associated with an approximately 10% increase of extreme poor in low-income countries. The impact is even stronger in some other poverty aspects. For instance, crises are associated with an average decrease of government spending in education by 17.72% in low-income countries. The dynamic linkages between most of the Multidimensional Poverty indicators, warn of a negative domino effect on a number of SDGs related to poverty, if there is a financial crisis shock. To pre-empt such a domino effect, the specific SDG target 17.4 on attaining long-term debt sustainability through coordinated policies plays a key role and requires urgent attention by the international community

Towards a synthesized critique of neoliberal biodiversity conservation

During the last three decades, the arena of biodiversity conservation has largely aligned itself with the globally dominant political ideology of neoliberalism and associated governmentalities. Schemes such as payments for ecological services are promoted to reach the multiple ‘wins’ so desired: improved biodiversity conservation, economic development, (international) cooperation and poverty alleviation, amongst others. While critical scholarship with respect to understanding the linkages between neoliberalism, capitalism and the environment has a long tradition, a synthesized critique of neoliberal conservation - the ideology (and related practices) that the salvation of nature requires capitalist expansion - remains lacking. This paper aims to provide such a critique. We commence with the assertion that there has been a conflation between ‘economics’ and neoliberal ideology in conservation thinking and implementation. As a result, we argue, it becomes easier to distinguish the main problems that neoliberal win-win models pose for biodiversity conservation. These are framed around three points: the stimulation of contradictions; appropriation and misrepresentation and the disciplining of dissent. Inspired by Bruno Latour’s recent ‘compositionist manifesto’, the conclusion outlines some ideas for moving beyond critique

Health service needs and perspectives of remote forest communities in Papua New Guinea: study protocol for combined clinical and rapid anthropological assessments with parallel treatment of urgent cases

Introduction Our project follows community requests for health service incorporation into conservation collaborations in the rainforests of Papua New Guinea (PNG). This protocol is for health needs assessments, our first step in coplanning medical provision in communities with no existing health data. Methods and analysis The study includes clinical assessments and rapid anthropological assessment procedures (RAP) exploring the health needs and perspectives of partner communities in two areas, conducted over 6 weeks fieldwork. First, in Wanang village (population c.200), which is set in lowland rainforest. Second, in six communities (population c.3000) along an altitudinal transect up the highest mountain in PNG, Mount Wilhelm. Individual primary care assessments incorporate physical examinations and questioning (providing qualitative and quantitative data) while RAP includes focus groups, interviews and field observations (providing qualitative data). Given absence of in-community primary care, treatments are offered alongside research activity but will not form part of the study. Data are collected by a research fellow, primary care clinician and two PNG research technicians. After quantitative and qualitative analyses, we will report: ethnoclassifications of disease, causes, symptoms and perceived appropriate treatment; community rankings of disease importance and service needs; attitudes regarding health service provision; disease burdens and associations with altitudinal-related variables and cultural practices. To aid wider use study tools are in online supplemental file, and paper and ODK versions are available free from the corresponding author. Ethics and dissemination Challenges include supporting informed consent in communities with low literacy and diverse cultures, moral duties to provide treatment alongside research in medically underserved areas while minimising risks of therapeutic misconception and inappropriate inducement, and PNG research capacity building. Brighton and Sussex Medical School (UK), PNG Institute of Medical Research and PNG Medical Research Advisory Committee have approved the study. Dissemination will be via journals, village meetings and plain language summaries

'Rumours' and clinical trials: a retrospective examination of a paediatric malnutrition study in Zambia, southern Africa

BACKGROUND: Many public health researchers conducting studies in resource-constrained settings have experienced negative 'rumours' about their work; in some cases they have been reported to create serious challenges and derail studies. However, what may appear superficially as 'gossip' or 'rumours' can also be regarded and understood as metaphors which represent local concerns. For researchers unaccustomed to having concerns expressed from participants in this manner, possible reactions can be to be unduly perturbed or conversely dismissive.This paper represents a retrospective examination of a malnutrition study conducted by an international team of researchers in Zambia, Southern Africa. The fears of mothers whose children were involved in the study and some of the concerns which were expressed as rumours are also presented. This paper argues that there is an underlying logic to these anxieties and to dismiss them simply as 'rumours' or 'gossip' would be to overlook the historic and socio-economic factors which have contributed to their production. METHODS: Qualitative interviews were conducted with the mothers whose children were involved in the study and with the research nurses. Twenty five face-to-face interviews and 2 focus group discussions (FGDs) were conducted with mothers. In addition, face-to-face interviews were conducted with research nurses participating in the trial. RESULTS: A prominent anxiety expressed as rumours by the mothers whose children were involved in the study was that recruitment into the trial was an indicator that the child was HIV-infected. Other anxieties included that the trial was a disguise for witchcraft or Satanism and that the children's body parts would be removed and sold. In addition, the liquid, milk-based food given to the children to improve their nutrition was suspected of being insufficiently nutritious, thus worsening their condition.The form which these anxieties took, such as rumours related to the stealing of body parts and other anxieties about a stigmatised condition, provide an insight into the historical, socio-economic and cultural influences in such settings. CONCLUSIONS: Employing strategies to understand local concerns should accompany research aims to achieve optimal success. The concerns raised by the participants we interviewed are not unique to this study. They are produced in countries where the historic, socio-economic and cultural settings communicate anxieties in this format. By examining this study we have shown that by contextualizing these 'rumours', the concerns they express can be constructively addressed and in turn result in the successful conduct of research aims