A Sarcoptes scabiei specific isothermal amplification assay for detection of this important ectoparasite of wombats and other animals

Background The globally distributed epidermal ectoparasite, Sarcoptes scabiei, is a serious health and welfare burden to at-risk human and animal populations. Rapid and sensitive detection of S. scabiei infestation is critical for intervention strategies. While direct microscopy of skin scrapings is a widely utilised diagnostic method, it has low sensitivity. PCR, alternatively, has been shown to readily detect mite DNA even in microscopy-negative skin scrapings. However, a limitation to the latter method is the requirements for specialised equipment and reagents. Such resources may not be readily available in regional or remote clinical settings and are an important consideration in diagnosis of this parasitic disease. Methodology A Loop Mediated Isothermal Amplification (LAMP) assay targeting the ITS-2 gene for S. scabiei was developed and evaluated on clinical samples from various hosts, previously screened with conventional S. scabies-specific PCR. Species specificity of the newly developed LAMP assay was tested against a range of DNA samples from other arthropods. The LAMP assays were performed on a real-time fluorometer as well as thermal cycler to evaluate an end-point of detection. Using skin scrapings, a rapid sample processing method was assessed to eliminate extensive processing times involved with DNA extractions prior to diagnostic assays, including LAMP. Results The S. scabiei LAMP assay was demonstrated to be species-specific and able to detect DNA extracted from a single mite within a skin scraping in under 30 minutes. Application of this assay to DNA extracts from skin scrapings taken from a range of hosts revealed 92.3% congruence (with 92.50% specificity and 100% sensitivity) to the conventional PCR detection of S. scabiei. Preliminary results have indicated that diagnostic outcome from rapidly processed dry skin scrapings using our newly developed LAMP is possible in approximately 40 minutes. Discussion We have developed a novel, rapid and robust molecular assay for detecting S. scabiei infesting humans and animals. Based on these findings, we anticipate that this assay will serve an important role as an ancillary diagnostic tool at the point-of-care, complementing existing diagnostic protocols for S. scabiei

The evolution of agro-urbanism: A case study from Angkor, Cambodia

16 pages. Published in "Journal of Anthropological Archaeology" by Elsevier: A.K. Carter, S. Klassen, M.T. Stark, M. Polkinghorne, P. Heng, D.H. Evans, R. Chhay; The evolution of agro-urbanism: a case study from Angkor, Cambodia; J. Anthropol. Archaeol., 63 (2021), Article 101323The vast agro-urban settlements that developed in the humid tropics of Mesoamerica and Asia contained both elite civic-ceremonial spaces and sprawling metropolitan areas. Recent studies have suggested that both local autonomy and elite policies facilitated the development of these settlements; however, studies have been limited by a lack of detail in considering how, when, and why these factors contributed to the evolution of these sites. In this paper, we use a fine-grained diachronic analysis of Angkor’s landscape to identify both the state-level policies and infrastructure and bottom-up organization that spurred the growth of Angkor as the world’s most extensive pre-industrial settlement complex. This degree of diachronic detail is unique for the ancient world. We observe that Angkor’s low-density metropolitan area and higher-density civic-ceremonial center grew at different rates and independently of one another. While local historical factors contributed to these developments, we argue that future comparative studies might identify similar patterns.The Authors thank the APSARA National Authority for their permission to conduct remote sensing and field investigations. Thanks also to Roland Fletcher for his support. Thank you to Terry and Eileen Lustig for their comments and suggestions on aspects of economic geography and Michael E. Smith for reading and offering comments on an earlier draft of this paper. Thanks to Malay So and Maryne Dana for administrative support. Research, planning, and writing of this manuscript was undertaken with the support of the University of Oregon Global Oregon Faculty Collaboration Fund supported by the Global Studies Institute in the UO Office of International Affairs. Data collection for parts of the research in this study have been funded by: the National Geographic Society Committee for Research and Exploration under Grant 9602-14; Dumbarton Oaks under a Project Grant in Garden and Landscape Studies; the Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship; the National Science Foundation Doctoral Dissertation Research Improvement Awards (#1638137); Australian Research Council Discovery Early Career Researcher Award (DE150100756) and Council Discovery Grant (DP170102574); and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements 639828 and 866454)

The cascading pathogenic consequences of Sarcoptes scabiei infection that manifest in host disease

Sarcoptic mange, caused by the parasitic mite Sarcoptes scabiei, causes a substantive burden of disease to humans, domestic animals and wildlife, globally. There are many effects of S. scabiei infection, culminating in the disease which hosts suffer. However, major knowledge gaps remain on the pathogenic impacts of this infection. Here, we focus on the bare-nosed wombat host (Vombatus ursinus) to investigate the effects of mange on: (i) host heat loss and thermoregulation, (ii) field metabolic rates, (iii) foraging and resting behaviour across full circadian cycles, and (iv) fatty acid composition in host adipose, bone marrow, brain and muscle tissues. Our findings indicate that mange-infected V. ursinus lose more heat to the environment from alopeciaaffected body regions than healthy individuals. Additionally, mange-infected individuals have higher metabolic rates in the wild. However, these metabolic demands are difficult to meet, because infected individuals spend less time foraging and more time inactive relative to their healthy counterparts, despite being outside of the burrow for longer

The spin dependence of high energy proton scattering

Motivated by the need for an absolute polarimeter to determine the beam polarization for the forthcoming RHIC spin program, we study the spin dependence of the proton-proton elastic scattering amplitudes at high energy and small momentum transfer.We examine experimental evidence for the existence of an asymptotic part of the helicity-flip amplitude phi_5 which is not negligible relative to the largely imaginary average non-flip amplitude phi_+. We discuss theoretical estimates of r_5, essentially the ratio of phi_5 to phi_+, based upon extrapolation of low and medium energy Regge phenomenological results to high energies, models based on a hybrid of perturbative QCD and non-relativistic quark models, and models based on eikonalization techniques. We also apply the model-independent methods of analyticity and unitarity.The preponderence of evidence at available energy indicates that r_5 is small, probably less than 10%. The best available experimental limit comes from Fermilab E704:those data indicate that |r_5|<15%. These bounds are important because rigorous methods allow much larger values. In contradiction to a widely-held prejudice that r_5 decreases with energy, general principles allow it to grow as fast as ln(s) asymptotically, and some models show an even faster growth in the RHIC range. One needs a more precise measurement of r_5 or to bound it to be smaller than 5% in order to use the classical Coulomb-nuclear interference technique for RHIC polarimetry. As part of this study, we demonstrate the surprising result that proton-proton elastic scattering is self-analysing, in the sense that all the helicity amplitudes can, in principle, be determined experimentally at small momentum transfer without a knowledge of the magnitude of the beam and target polarization

Clinical disorders affecting mesopic vision

Vision in the mesopic range is affected by a number of inherited and acquired clinical disorders. We review these conditions and summarize the historical background, describing the clinical characteristics alongside the genetic basis and molecular biological mechanisms giving rise to rod and cone dysfunction relevant to twilight vision. The current diagnostic gold standards for each disease are discussed and curative and symptomatic treatment strategies are summarized

Identification, characterisation and expression analysis of natural killer receptor genes in Chlamydia pecorum infected koalas (Phascolarctos cinereus)

BACKGROUND: Koalas (Phascolarctos cinereus), an iconic Australian marsupial, are being heavily impacted by the spread of Chlamydia pecorum, an obligate intracellular bacterial pathogen. Koalas vary in their response to this pathogen, with some showing no symptoms, while others suffer severe symptoms leading to infertility, blindness or death. Little is known about the pathology of this disease and the immune response against it in this host. Studies have demonstrated that natural killer (NK) cells, key components of the innate immune system, are involved in the immune response to chlamydial infections in humans. These cells can directly lyse cells infected by intracellular pathogens and their ability to recognise these infected cells is mediated through NK receptors on their surface. These are encoded in two regions of the genome, the leukocyte receptor complex (LRC) and the natural killer complex (NKC). These two families evolve rapidly and different repertoires of genes, which have evolved by gene duplication, are seen in different species. METHODS: In this study we aimed to characterise genes belonging to the NK receptor clusters in the koala by searching available koala transcriptomes using a combination of search methods. We developed a qPCR assay to quantify relative expression of four genes, two encoded within the NK receptor cluster (CLEC1B, CLEC4E) and two known to play a role in NK response to Chalmydia in humans (NCR3, PRF1). RESULTS: We found that the NK receptor repertoire of the koala closely resembles that of the Tasmanian devil, with minimal genes in the NKC, but with lineage specific expansions in the LRC. Additional genes important for NK cell activity, NCR3 and PRF1, were also identified and characterised. In a preliminary study to investigate whether these genes are involved in the koala immune response to infection by its chlamydial pathogen, C. pecorum, we investigated the expression of four genes in koalas with active chlamydia infection, those with past infection and those without infection using qPCR. This analysis revealed that one of these four, CLEC4E, may be upregulated in response to chlamydia infection. CONCLUSION: We have characterised genes of the NKC and LRC in koalas and have discovered evidence that one of these genes may be upregulated in koalas with chlamydia, suggesting that these receptors may play a role in the immune response of koalas to chlamydia infection

Exploring women’s experiences: embodied pathways and influences for exercise participation

It has been well-documented that women face pressures to conform to a slim, toned, and athletic body, becoming “tyrannised” by beauty ideals. Under these contemporary ideologies of perfectionism, women are placed under constant surveillance, evaluation and, objectification and are thus reduced to “being” their bodies. However, there is little known about the potential relationships between different types of exercise, body image, and exercise motivation. With this in mind, this paper contributes towards a small but developing body of research that utilises feminist phenomenology to reveal twelve women’s early embodied motivations for exercising and draws upon material gathered from a three-year ethnography into the embodied experiences of women in fitness cultures. This paper delves into the influences on their continued participation over time and explores how these experiences shape their understandings of the embodied self and the broader constructions of the gendered body. The discussion provided illuminates how early influences on exercise participation and how pressures on women to conform to dominant notions of the “feminine” body are imposed by structural, cultural, historical, and localised forces in ways that affect and shape future physical activity participation, and the physical cultures where these tensions are played out

Diachronic modeling of the population within the medieval Greater Angkor Region settlement complex

9 pagesAngkor is one of the world’s largest premodern settlement complexes (9th to 15th centuries CE), but to date, no comprehensive demographic study has been completed, and key aspects of its population and demographic history remain unknown. Here, we combine lidar, archaeological excavation data, radiocarbon dates, and machine learning algorithms to create maps that model the development of the city and its population growth through time. We conclude that the Greater Angkor Region was home to approximately 700,000 to 900,000 inhabitants at its apogee in the 13th century CE. This granular, diachronic, paleodemographic model of the Angkor complex can be applied to any ancient civilization.We wish to thank the APSARA National Authority for permission to conduct remote sensing and collaborative field investigations. We thank M. So and M. Dana for administrative support. We thank E. Lustig and T. Lustig for comments and suggestions on aspects of economic geography and M. E. Smith and C. Isendahl for reading and offering comments on an earlier draft of this paper. Funding: Much of the work on research, planning, and writing of this manuscript was undertaken with the support of the University of Oregon Global Oregon Faculty Collaboration Fund, supported by the Global Studies Institute in the UO Office of International Affairs. Parts of this research have been funded by the Rust Family Foundation, the Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship, the National Science Foundation Doctoral Dissertation Research Improvement Awards (no. 1638137), the ACLS-Robert H. N. Ho Family Foundation Program in Buddhist Studies, Australian Research Council Discovery Grant DP1092663, Australian Research Council Discovery Early Career Researcher Award DE150100756, Australian Research Council Discovery Grant DP170102574, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement nos. 639828 and 866454). Author contributions: S.K. and A.K.C. contributed to the planning of this research. S.K., A.K.C., M.H., and S.O. drafted the manuscript. S.K., A.K.C., D.E., M.T.S., M.P., G.P.M., R.F., and P.H. edited the manuscript. S.K., A.A.L., M.H., J.N.-W., D.E., P.W., and S.O. contributed to the analysis. S.K., A.K.C., P.H., and M.P. compiled the data. S.K., A.K.C., P.H., G.P.M., R.F., D.E., C.P., and M.P. contributed data. S.K., M.H., and A.A.L. designed the figures. All authors discussed the results and commented on the manuscript. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper maybe requested from the authors

Broken biosecurity?: veterinarians’ framing of biosecurity on dairy farms in England

There is seen to be a need for better biosecurity – the control of disease spread on and off farm – in the dairy sector. Veterinarians play a key role in communicating and implementing biosecurity measures on farm, and little research has been carried out on how veterinarians see their own and farmers’ roles in improving biosecurity. In order to help address this gap, qualitative interviews were carried out with 28 veterinarians from Royal College of Veterinary Surgeon farm accredited practices in England. The results were analysed using a social ecology framework and frame analysis to explore not only what barriers vets identified, but also how vets saw the problem of inadequate biosecurity as being located. Veterinarians’ frames of biosecurity were analysed at the individual, interpersonal and contextual scales, following the social ecology framework, which see the problem in different ways with different solutions. Farmers and veterinarians were both framed by veterinarians as individualised groups lacking consistency. This means that best practice is not spread and veterinarians are finding it difficult to work as a group to move towards a “predict and prevent” model of veterinary intervention. But diversity and individualism were also framed as positive and necessary among veterinarians to the extent that they can tailor advice to individual farmers. Veterinarians saw their role in educating the farmer as not only being about giving advice to farmers, but trying to convince the farmer of their perspective and values on disease problems. Vets felt they were meeting with limited success because vets and farmers may be emphasising different framings of biosecurity. Vets emphasise the individual and interpersonal frames that disease problems are a problem on farm that can and should be controlled by individual farmers working with vets. According to vets, farmers may emphasise the contextual frame that biosecurity is largely outside of their control on dairy farms because of logistical, economic and geographical factors, and so some level of disease on dairy farms is not entirely unexpected or controllable. There needs to be a step back within the vet-farmer relationship to realise that there may be different perspectives at play, and within the wider debate to explore the question of what a biosecure dairy sector would look like within a rapidly changing agricultural landscape