Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections.

Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are known to infect both mammals and snakes. Arenaviruses package a large (L) and small (S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes can be generated through mutation, recombination, and reassortment. Although it is believed that an ancient recombination event led to the emergence of a new lineage of mammalian arenaviruses, neither recombination nor reassortment has been definitively documented in natural arenavirus infections. Here, we used metagenomic sequencing to survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected animals, we determined the complete or near complete sequence of 210 genome segments that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected, with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes, and a particular S segment genotype dominated in individual animals and at a population level. We corroborated sequencing results by qRT-PCR and virus isolation, and isolates replicated as ensembles in culture. Numerous instances of recombination and reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication and transmission despite their atypical structures. Overall, this represents intrahost diversity of an extent and form that goes well beyond what has been observed for arenaviruses or for viruses in general. This diversity can be plausibly attributed to the captive intermingling of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique opportunity to study arenavirus evolution and adaptation, these findings allow the investigation of unintended anthropogenic impacts on viral ecology, diversity, and disease potential

Land cover change in marginalised landscapes of South Africa (1984–2014): Insights into the influence of socio-economic and political factors

Rural landscapes in South Africa experience high conversion rates due to intense land use; however, the changes are site specific and depend on the socio-economic and political history of the area. Land cover change (LCC) was assessed in response to socio-economic and political factors in uThukela Municipal District, KwaZulu-Natal, using Landsat imagery from 1984 to 2014, while making comparisons to other studies in South Africa. Socio-economic/political data were used to gain insights into the observed LCC patterns. Land cover was classified using a random forest classifier, and accuracies ranging from 87% to 92% were achieved. Systematic and intensity analysis methods were used to describe patterns, rates, and transitions of LCC in Imbabazane (ILM) and Okhahlamba (OLM) local municipalities. The results showed a reduced rate of change intensity from 3.4% to 0.9% in ILM and from 3.1% to 1.1% in OLM between 1984 and 2014. Grassland was persistent, covering over 70% in both local municipalities between 1984 and 2014. Although persistent, grassland experienced respective losses of 3.7% and 14.3% in both observation periods in ILM and of 10.2% and 13.3% in OLM. During the analysis period, settlements and cropland gained actively in both local municipalities. The changes represent a degree of population, local authority, and people’s perception as influencers of land use and LCC. It is therefore argued that socio-economic and political changes can potentially influence land use and LCC; however, natural ecosystems can persist under those conditions, and this requires more research efforts. Significance: This study contributes towards a growing knowledge and understanding of land cover change studies in marginalised landscapes in South Africa. The findings enforce the notion that natural vegetation systems can be altered by human-induced land use such as expansion of settlement and commercial agricultural. We show that in recent times there has been a decline in the overall rate of land cover conversion, and a high persistence of grassland amid global change, although the quality of the vegetation needs further research. We argue that the changes observed in marginalised landscapes are potentially driven by socio-economic and political dynamics

Disparities in risk perception of thyroid cancer recurrence and death

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154276/1/cncr32670.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154276/2/cncr32670_am.pd

A complete classification of epistatic two-locus models

Background: The study of epistasis is of great importance in statistical genetics in fields such as linkage and association analysis and QTL mapping. In an effort to classify the types of epistasis in the case of two biallelic loci Li and Reich listed and described all models in the simplest case of 0/ 1 penetrance values. However, they left open the problem of finding a classification of two-locus models with continuous penetrance values. Results: We provide a complete classification of biallelic two-locus models. In addition to solving the classification problem for dichotomous trait disease models, our results apply to any instance where real numbers are assigned to genotypes, and provide a complete framework for studying epistasis in QTL data. Our approach is geometric and we show that there are 387 distinct types of two-locus models, which can be reduced to 69 when symmetry between loci and alleles is accounted for. The model types are defined by 86 circuits, which are linear combinations of genotype values, each of which measures a fundamental unit of interaction. Conclusion: The circuits provide information on epistasis beyond that contained in the additive × additive, additive × dominance, and dominance × dominance interaction terms. We discuss th

Cathepsin K in lymphangioleiomyomatosis: LAM cell-fibroblast Interactions enhance protease activity by extracellular acidification

Lymphangioleiomyomatosis (LAM) is a rare disease in which clonal ‘LAM’ cells infiltrate the lungs and lymphatics. In association with recruited fibroblasts, LAM cells form nodules adjacent to lung cysts. It is assumed LAM nodule derived proteases lead to cyst formation although, this is uncertain. We profiled protease gene expression in whole lung tissue and observed cathepsin K was 40 fold over-expressed in LAM compared with control lungs (p≤0.0001). Immunohistochemistry confirmed cathepsin K protein in LAM nodules but not control lungs. Cathepsin K gene expression, protein and protease activity was detected in LAM associated fibroblasts but not the LAM cell line 621-101. In lung nodules, cathepsin K immune reactivity was predominantly co-localised with LAM associated fibroblasts. In vitro, extra-cellular cathepsin K activity was minimal at pH 7.5 but significantly enhanced in fibroblast cultures at pH 7 and 6. 621-101 cells reduced extracellular pH by 0.5 units over 24 hours. Acidification was dependent upon 621-101 cell mTOR activity and net hydrogen ion transporters, particularly sodium/bicarbonate co-transporters and carbonic anhydrases which were also expressed in LAM lung tissue. In LAM cell/fibroblast co-cultures, acidification paralleled cathepsin K activity and both were inhibited by sodium bicarbonate co-transporter (p≤0.0001) and carbonic anhydrase inhibitors (p=0.0021). Our findings suggest cathepsin K activity is dependent on LAM cell/fibroblast interactions and inhibitors of extracellular acidification may be potential therapies for LAM

Crop Updates 1999 - Lupins

This article contains twenty three papers 1998 LUPIN HIGHLIGHTS LUPIN ANTHRACNOSE 1. Anthracnose overview, Greg Shea, Geoff Thomas and Mark Sweetingham, Agriculture Western Australia 2. Anthracnose – Critical seed infection levels for resistant and susceptible varieties, Geoff Thomas, Mark Sweetingham, Bill O\u27Neill and Greg Shea, Agriculture Western Australia 3. Fungicide seed treatment for anthracnose and brown spot control in lupin, G. Thomas and M. Sweetingham, Agriculture Western Australia LUPIN BREEDING AND AGRONOMY 4. Anthracnose resistance in lupins – an innovative Australian research effort 1996-1998, Wallace Cowling1\u272, Bevan Buirchell1,2 Mark Sweetinqham1,2, Hua\u27an Yang2, Geoff Thomas 1, David Luckett3, Allan Brown4 and John Hamblin2, 1 Agriculture Western Australia, 2 Centre for Legumes in Mediterranean Agriculture, University of Western Australia, 3 NSW Agriculture, Agricultural Institute, Wagga Wagga, NSW, 4 Consultant, 16 Rochester Way, Dianella, WA 5. Gene transfer to pulses: Challenges through 1989-99. Joanne E. Barton, Centre for Legumes in Mediterranean Agriculture, University of Western Australia 6. Can we select for restricted branching in narrow-leafed lupin (Lupinus angustifolius) Kedar Adhikari1, Nick Galwey1and Miles Dracup2, 1Plant Sciences, Faculty of Agriculture, The University of Western Australia,2 Agriculture Western Australia 7. Getting the beat out of new lupin varieties, Dr Bob French, Grain Legume Agronomist, Agriculture Western Australia 8. Starter nitrogen on lupins, Dr Bob French, Grain Legume Agronomist, Agriculture Western Australia APHIDS AND VIRUS CONTROL 9. Forecasting aphid and virus risk in lupins, Debbie Thackray and Roger Jones, CRC for Legumes in Mediterranean Agriculture and Agriculture Western Australia 10. Screening for resistance to cucumber mosaic virus in lupins, Roger Jones, Brenda Coutts, Narelle Reeve, Wallace Cowling and Bevan Buirchell, Agriculture Western Australia and CRC for Legumes in Mediterranean Agriculture 11. The non-necrotic strain of bean yellow mosaic virus spreads faster than the necrotic strain in lupins, Y. Cheng 1 and R.A.C. Jones 1•2, 1 Cooperative Research Centre for Legumes in Mediterranean Agriculture, 2 Agriculture Western Australia 12. Spraying to control aphid feeding damage increases yields of some lupin varieties and faba bean, Francoise Berlandier and Linnet Cartwright, Entomology, Agriculture Western Australia LUPIN NUTRITION 13. Calculated lime requirements for rotations, James Fisher1, Art Diggle 1•2 and Bill Bowden 1•2, 1 Centre for Legumes in Mediterranean Agriculture, 2 Agriculture Western Australia 14. What does lime do to acidic soils – lupin nutrition, Chris Gazey, Research Officer, Agriculture Western Australia 15. Effect of application method of manganese fertiliser and manganese concentration of seed source on seed yield of lupins grown in the West Midlands, Luigi Moreschi, CSBP Area Manager HERBICIDE TOLERANCE AND WEED CONTROL 16. Herbicide tolerance of lupins, Terry Piper, Weed Science Group, Agriculture Western Australia 17. Weed control in Wodjil yellow lupins, Terry Piper, Weed Science Group, Agriculture Western Australia 18. Herbicide tolerance of new lupin varieties, Peter Newman, Agronomist, Elders Mingenew 19. Control of volunteer canola in lupins, Terry Piper and Dave Nicholson, Weed Science Group, Agriculture Western Australia LUPIN ESTABLISHMENT 20. A new seed pressing system for healthy lupin establishment and productivity, Mohammad Amjad, Glen Riethmuller and Ron Jarvis, Agriculture Western Australia 21. Encouragement for controlled traffic farming in the Northern Wheatbelt, Paul Blackwell, Agriculture Western Australia LUPIN HARVESTING 22. Improved lupin harvesting efficiency with different knife guard extensions, Glen Riethmuller, Agriculture Western Australia LUPIN AND PULSE UTILISATION 23. The value of pulse grains for sheep, C.L. White, CSIRO Division of Animal Productio

Are Happiness and Life Satisfaction Different Across Religious groups? Exploring Determinants of Happiness and Life Satisfaction

This study explores whether different religions experience different levels of happiness and life satisfaction and in case this is affected by country economic and cultural environment. Using World Value Survey (from 1981 to 2014), this study found that individual religiosity and country level of development play a significant role in shaping people’s subjective well-being (SWB). Protestants, Buddhists and Roman Catholic were happier and most satisfied with their lives compared to other religious groups. Orthodox has the lowest SWB. Health status, household’s financial satisfaction and freedom of choice are means by which religious groups and governments across the globe can improve the SWB of their citizens. Keywords: happiness; life satisfaction; religion; religious differences; cultur

A qualitative study exploring midlife women’s stages of change from domestic violence towards freedom

Gold OABackground Domestic Violence (DV) remains a significant global health problem for women in contemporary society. Existing literature on midlife women’s experiences of domestic violence is limited and focuses on health implications. Leaving a violent relationship is a dynamic process that often requires multiple attempts and separations prior to final termination. The aim of this study was to explore the process of leaving a violent relationship for midlife women. Methods This qualitative study involved fifteen women aged between 40–55 who had accessed residential and non-residential community support services for domestic violence within the UK. Community-based support agencies provided these women with access to letters of invitation and participant information sheet explaining the study. The women notified agency staff who contacted the research team to arrange a mutually convenient time to meet within a safe place for both the women and researchers. It was stressed to all potential participants that no identifiable information would be shared with the agency staff. Women were considered survivors of DV if they defined themselves as such. Data were gathered through semi structured interviews, transcribed verbatim and thematically analysed. Results Midlife women appear to differ from younger women by transitioning quickly though the stages of change, moving rapidly through the breaking free onto the maintenance stage. This rapid transition is the resultant effect of living with long-term violence causing a shift in the women’s perception towards the violent partner, with an associated reclamation of power from within the violent relationship. A realisation that rapid departure from the violence may be critical in terms of personal safety, and the realisation that there was something ‘wrong’ within the relationship, a ‘day of dawning’ that had not been apparent previously appears to positively affect the trajectory of leaving. Conclusions Midlife women appeared to navigate through the stages of change in a rapid linear process, forging ahead and exiting the relationship with certainty and without considering options. Whilst these findings appear to differ from younger women’s process of leaving, further research is needed to explore and understand the optimum time for intervention and support to maximise midlife women’s opportunities to escape an abusive partner, before being reflected appropriately in policy and practice.This study received funding from The Research and Knowledge Transfer Office, The University of Chester, and from the Western Australian Health Promotion Foundation – ‘Healthway

Identification of PLCL1 Gene for Hip Bone Size Variation in Females in a Genome-Wide Association Study

Osteoporosis, the most prevalent metabolic bone disease among older people, increases risk for low trauma hip fractures (HF) that are associated with high morbidity and mortality. Hip bone size (BS) has been identified as one of the key measurable risk factors for HF. Although hip BS is highly genetically determined, genetic factors underlying the trait are still poorly defined. Here, we performed the first genome-wide association study (GWAS) of hip BS interrogating ∼380,000 SNPs on the Affymetrix platform in 1,000 homogeneous unrelated Caucasian subjects, including 501 females and 499 males. We identified a gene, PLCL1 (phospholipase c-like 1), that had four SNPs associated with hip BS at, or approaching, a genome-wide significance level in our female subjects; the most significant SNP, rs7595412, achieved a p value of 3.72×10−7. The gene's importance to hip BS was replicated using the Illumina genotyping platform in an independent UK cohort containing 1,216 Caucasian females. Two SNPs of the PLCL1 gene, rs892515 and rs9789480, surrounded by the four SNPs identified in our GWAS, achieved p values of 8.62×10−3 and 2.44×10−3, respectively, for association with hip BS. Imputation analyses on our GWAS and the UK samples further confirmed the replication signals; eight SNPs of the gene achieved combined imputed p values<10−5 in the two samples. The PLCL1 gene's relevance to HF was also observed in a Chinese sample containing 403 females, including 266 with HF and 177 control subjects. A SNP of the PLCL1 gene, rs3771362 that is only ∼0.6 kb apart from the most significant SNP detected in our GWAS (rs7595412), achieved a p value of 7.66×10−3 (odds ratio = 0.26) for association with HF. Additional biological support for the role of PLCL1 in BS comes from previous demonstrations that the PLCL1 protein inhibits IP3 (inositol 1,4,5-trisphosphate)-mediated calcium signaling, an important pathway regulating mechanical sensing of bone cells. Our findings suggest that PLCL1 is a novel gene associated with variation in hip BS, and provide new insights into the pathogenesis of HF

Crop Updates 2002 - Cereals

This session covers thirty one papers from different authors: VARIETIES AND BREEDING 1. Agronomic evaluation of wheat and barley in the central wheatbelt of Western Australia, Peter Burgess1and Gary Fawell2, 1Agritech and 2Farmanco Management 2. Evaluating stress tolerance to terminal drought by Western Australian wheats, Dean Diepeveen and Dr Tim Setter, Department of Agriculture 3. Broadscale wheat variety comparisons featuring Wyalkatchem, Jeff Russell, Department of Agriculture 4. Australian crop accreditation system variety selector, Tony Seymour, Australian Crop Accreditation System 5. Future wheat varieties, Robin Wilson, Iain Barclay,Robyn McLean, Robert Loughman, Jenny Garlinge, Bill Lambe, Neil Venn and Peter Clarke, Department of Agriculture AGRONOMY 6. Beware of wheat variety interactions with row spacing and seed rate, Mohammad Amjad and Wal Anderson, Department of Agriculture 7. Yield and falling numbers of wheat varieties on the South Coast, Mohammad Amjad and Wal Anderson, Department of Agriculture 8. Maximising wheat variety performance through agronomic management, Wal Anderson, Raffaele Del Cima, James Bee, Darshan Sharma, Sheena Lyon, Melaine Kupsch, Mohammad Amjad, Pam Burgess, Veronika Reck, Brenda Shackley, Ray Tugwell, BindiWebb and Steve Penny Jr, Department of Agriculture 9. High impact of soil type and seasonal rainfall on optimum wheat seed rate , Raffaele Del Cima and Wal Anderson Department of Agriculture 10. 101 seasons in one day: Using the ‘WA Wheat’ database to predict wheat yield, James Fisher1, Bill Bowden1, Craig Scanlan1, Senthold Asseng2and Michael Robertson2 1Department of Agriculture, 2CSIRO 11. Economics of improving compact soils, M.A. Hamza1, G. McConnell2and W.K. Anderson1, 1Department of Agriculture, 2Planfarm 12. Reducing the risks in producing durum wheat in Western Australia, Md Shahajahan Miyan and Wal Anderson, Department of Agriculture 13. Taking the Why out of Wyalkatchem – the new widely adopted wheat variety, Steve Penny, Department of Agriculture 14. Influence of nutrition and environmental factors on seed vigour in wheat, Darshan Sharma, Wal Anderson and Daya Patabendige, Department of Agriculture NUTRITION 15. N and K are important for oat yield and quality, Patrick Gethin, Stephen Loss, Tim O’Dea, Ryan Guthrie and Lisa Leaver, CSBP Futurefarm 16. Effects of nitrogen and phosphorus on the grain yield and quality of noodle wheat, Tyrone Henning1, Lionel Martin1and Wal Anderson2 1Muresk Institute of Agriculture, 2Department of Agriculture 17. Assessment of a high input fertiliser regime on the yield and quality of Gairdner barley, Narelle Hill1, Simon Wallwork2and Laurence Carslake2 1Department of Agriculture, 2Wesfarmers Landmark 18. The use of Flexi-N to achieve high yielding, high protein wheat, Darren Hughes1, Lionel Martin1, Wal Anderson2and Stephen Loss3 1Muresk Institute of Agriculture, 2Department of Agriculture, 3CSBP Futurefarm 19. Are liquid phosphorus fertilisers more efficient than solid fertilisers in Western Australia?Stephen Loss, Lisa Leaver, Ryan Guthrie, Patrick Gethin and Tim O’Dea, CSBP Futurefarm 20. Oats respond to phosphorus and potassium, Glenn McDonald, Department of Agriculture PESTS AND DISEASES 21. Cereal disease diagnostics and rust monitoring, Nichole Burges and Dominie Wright, Department of Agriculture 22. Distribution and incidence of aphids and barley yellow dwarf virus in over-summering grasses in the Western Australian wheatbelt, Jenny Hawkes and Roger Jones, Centre for Legumes in Mediterranean Agriculture and Department of Agriculture 23. Spring sprays for powdery mildew control in cereals, Kith Jayasena1, Kazue Tanaka1, Vanessa Johnson1, Robert Loughman1and Josh Jury2 1Department of Agriculture, 2Wesfarmers Landmark 24. Impact of root lesion nematodes on wheat and triticale in Western Australia, Sean Kelly and Shashi Sharma, Department of Agriculture 25. Cropping options for the management of root lesion nematodes in Western Australia, Sean Kelly, Shashi Sharma and Robert Loughman, Department of Agriculture 26. Cereal rust update 2002 – new stem rust on Camm wheat, Robert Loughman1and Robert Park2 1Department of Agriculture, 2University of Sydney 27. Cereal aphids and direct feeding damage to cereals, Phil Michael, Department of Agriculture 28. A decision support system for control of aphids and BYDV in cereal crops, Debbie Thackray, Jenny Hawkes and Roger Jones, Department of Agriculture and Centre for Legumes in Mediterranean Agriculture STORAGE 29. Aeration – opportunity for profit, Christopher Newman, Department of Agriculture CLIMATE 30. Financial impact of frost on the Western Australian grains industry, Garren Knell and Kim Povey, ConsultAg 31. Summary of 2001 weather and seasonal prospects for 2002, David Stephens, Department of Agricultur