The extraordinary evolutionary history of the reticuloendotheliosis viruses

The reticuloendotheliosis viruses (REVs) comprise several closely related amphotropic retroviruses isolated from birds. These viruses exhibit several highly unusual characteristics that have not so far been adequately explained, including their extremely close relationship to mammalian retroviruses, and their presence as endogenous sequences within the genomes of certain large DNA viruses. We present evidence for an iatrogenic origin of REVs that accounts for these phenomena. Firstly, we identify endogenous retroviral fossils in mammalian genomes that share a unique recombinant structure with REVs—unequivocally demonstrating that REVs derive directly from mammalian retroviruses. Secondly, through sequencing of archived REV isolates, we confirm that contaminated Plasmodium lophurae stocks have been the source of multiple REV outbreaks in experimentally infected birds. Finally, we show that both phylogenetic and historical evidence support a scenario wherein REVs originated as mammalian retroviruses that were accidentally introduced into avian hosts in the late 1930s, during experimental studies of P. lophurae, and subsequently integrated into the fowlpox virus (FWPV) and gallid herpesvirus type 2 (GHV-2) genomes, generating recombinant DNA viruses that now circulate in wild birds and poultry. Our findings provide a novel perspective on the origin and evolution of REV, and indicate that horizontal gene transfer between virus families can expand the impact of iatrogenic transmission events

Finding a Concrete Utopia in the Dystopia of a 'Sub-City'

This article examines a ten-year long series of annual short-term interventions with young people living in Dharavi (India) that has led to a number of public theatre events. The partnership offers a unique training experience to students from the UK in theatre facilitation, and a regular opportunity to participate in theatre for young people in Dharavi. It brings together students from The Royal Central School of Speech and Drama (University of London), working collaboratively with an Indian theatre practitioner, an NGO based in Mumbai, and young people who live in Dharavi. In the article, I explore the role theatre plays in the precarious lives of those who live in Dharavi, and the potential of this on-going partnership to develop a theatre of change in a community and site affected by extreme poverty. Focusing on the longevity of this applied theatre project and drawing on the writing of Paul Ricoeur on utopia, I argue that this on-going exchange can be understood both as a form of cultural invasion and, at the same time, a utopian community theatre practice. Whilst the project continues to raise troubling questions about cultural colonisation and power, the integrated investment of partners and participants over time has generated a resilient sense of optimism as well as, to a more limited degree, evidence of long-term positive change

“Without a mother”: caregivers and community members’ views about the impacts of maternal mortality on families in KwaZulu-Natal, South Africa.

BACKGROUND: Maternal mortality in South Africa is high and a cause for concern especially because the bulk of deaths from maternal causes are preventable. One of the proposed reasons for persistently high maternal mortality is HIV which causes death both indirectly and directly. While there is some evidence for the impact of maternal death on children and families in South Africa, few studies have explored the impacts of maternal mortality on the well-being of the surviving infants, older children and family. This study provides qualitative insight into the consequences of maternal mortality for child and family well-being throughout the life-course. METHODS: This qualitative study was conducted in rural and peri-urban communities in Vulindlela, KwaZulu-Natal. The sample included 22 families directly affected by maternal mortality, 15 community stakeholders and 7 community focus group discussions. These provided unique and diverse perspectives about the causes, experiences and impacts of maternal mortality. RESULTS AND DISCUSSION: Children left behind were primarily cared for by female family members, even where a father was alive and involved. The financial burden for care and children’s basic needs were largely met through government grants (direct and indirectly targeted at children) and/or through an obligation for the father or his family to assist. The repercussions of losing a mother were felt more by older children for whom it was harder for caregivers to provide educational supervision and emotional or psychological support. Respondents expressed concerns about adolescent’s educational attainment, general behaviour and particularly girl’s sexual risk. CONCLUSION: These results illuminate the high costs to surviving children and their families of failing to reduce maternal mortality in South Africa. Ensuring social protection and community support is important for remaining children and families. Additional qualitative evidence is needed to explore differential effects for children by gender and to guide future research and inform policies and programs aimed at supporting maternal orphans and other vulnerable children throughout their development.Web of Scienc

The application of sediment fingerprinting to floodplain and lake sediment cores: assumptions and uncertainties evaluated through case studies in the Nene Basin, UK

Purpose: Fine sediment has been shown to be a major cause of the degradation of lakes and rivers and, as a result, research has been directed towards the understanding of fine sediment dynamics and the minimisation of sediment inputs. The use of tracers within a sediment fingerprinting framework has become a heavily used technique to investigate the sources of fine sediment pressures. When combined with the use of historically deposited sediment, the technique provides the opportunity to reconstruct past changes to the environment. However, alterations to tracer signatures during sediment transport and storage are a major potential source of uncertainty associated with tracer use. At present, few studies have quantified the uncertainties associated with tracer use. Materials and methods: This paper investigated uncertainty by determining the differences between sediment provenance predictions obtained using lithogenic radionuclide, geochemical and mineral magnetic signatures when fingerprinting lake and floodplain sedimentary deposits. It also investigated the potential causes of the observed differences. Results and discussion: A reservoir core was fingerprinted with the least uncertainty, with tracer group predictions ∼28 % apart and a consistent down-core trend in changing sediment provenance produced. When fingerprinting an on-line lake core and four floodplain cores, differences between tracer group predictions were as large as 100 %; the down-core trends in changing sediment provenance were also different. The differences between tracer group predictions could be attributed to the organic matter content and particle size of the sediment. There was also evidence of the in-growth of bacterially derived magnetite and chemical dissolution affecting the preservation of tracer signatures. Simple data corrections for sediment organic matter content and particle size did not result in significantly greater agreement between the predictions of the different tracer groups. Likewise, the inclusions of weightings for tracer discriminatory efficiency and within-source variability had minimal effects on the fingerprinting results. Conclusions: This paper highlights the importance of tracer selection and the consideration of recognising tracer non-conservatism when using lake and floodplain sediment deposits to reconstruct anthropogenic changes to the environment and changing sediment dynamics. It was recommended that future research focus on the assessment of uncertainty using the artificial mixing of sediment source samples, the limitation of the fingerprinting to narrow particle size fractions and the development of specific particle size and organic matter correction factors for each tracer

Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations

Visna/Maedi, or ovine progressive pneumonia (OPP) as it is known in the United States, is an incurable slow-acting disease of sheep caused by persistent lentivirus infection. This disease affects multiple tissues, including those of the respiratory and central nervous systems. Our aim was to identify ovine genetic risk factors for lentivirus infection. Sixty-nine matched pairs of infected cases and uninfected controls were identified among 736 naturally exposed sheep older than five years of age. These pairs were used in a genome-wide association study with 50,614 markers. A single SNP was identified in the ovine transmembrane protein (TMEM154) that exceeded genome-wide significance (unadjusted p-value 3×10−9). Sanger sequencing of the ovine TMEM154 coding region identified six missense and two frameshift deletion mutations in the predicted signal peptide and extracellular domain. Two TMEM154 haplotypes encoding glutamate (E) at position 35 were associated with infection while a third haplotype with lysine (K) at position 35 was not. Haplotypes encoding full-length E35 isoforms were analyzed together as genetic risk factors in a multi-breed, matched case-control design, with 61 pairs of 4-year-old ewes. The odds of infection for ewes with one copy of a full-length TMEM154 E35 allele were 28 times greater than the odds for those without (p-value<0.0001, 95% CI 5–1,100). In a combined analysis of nine cohorts with 2,705 sheep from Nebraska, Idaho, and Iowa, the relative risk of infection was 2.85 times greater for sheep with a full-length TMEM154 E35 allele (p-value<0.0001, 95% CI 2.36–3.43). Although rare, some sheep were homozygous for TMEM154 deletion mutations and remained uninfected despite a lifetime of significant exposure. Together, these findings indicate that TMEM154 may play a central role in ovine lentivirus infection and removing sheep with the most susceptible genotypes may help eradicate OPP and protect flocks from reinfection

Sediment source fingerprinting: benchmarking recent outputs, remaining challenges and emerging themes

Abstract: Purpose: This review of sediment source fingerprinting assesses the current state-of-the-art, remaining challenges and emerging themes. It combines inputs from international scientists either with track records in the approach or with expertise relevant to progressing the science. Methods: Web of Science and Google Scholar were used to review published papers spanning the period 2013–2019, inclusive, to confirm publication trends in quantities of papers by study area country and the types of tracers used. The most recent (2018–2019, inclusive) papers were also benchmarked using a methodological decision-tree published in 2017. Scope: Areas requiring further research and international consensus on methodological detail are reviewed, and these comprise spatial variability in tracers and corresponding sampling implications for end-members, temporal variability in tracers and sampling implications for end-members and target sediment, tracer conservation and knowledge-based pre-selection, the physico-chemical basis for source discrimination and dissemination of fingerprinting results to stakeholders. Emerging themes are also discussed: novel tracers, concentration-dependence for biomarkers, combining sediment fingerprinting and age-dating, applications to sediment-bound pollutants, incorporation of supportive spatial information to augment discrimination and modelling, aeolian sediment source fingerprinting, integration with process-based models and development of open-access software tools for data processing. Conclusions: The popularity of sediment source fingerprinting continues on an upward trend globally, but with this growth comes issues surrounding lack of standardisation and procedural diversity. Nonetheless, the last 2 years have also evidenced growing uptake of critical requirements for robust applications and this review is intended to signpost investigators, both old and new, towards these benchmarks and remaining research challenges for, and emerging options for different applications of, the fingerprinting approach

Addressing the variability in soil hydraulic properties : is 'scaling' the answer ? a Northern Territory perspective

Made available by the Northern Territory Library via the Publications (Legal Deposit) Act 2004 (NT).Date:199

Assessment and parameterisation of ceres-maize-sat for the Australian semi arid tropics

Made available by the Northern Territory Library via the Publications (Legal Deposit) Act 2004 (NT).Date:1995-1