MULE DEER (ODOCOILEUS HEMIONUS) REPRODUCTION, FAWN SURVIVAL, AND EXPOSURE OF FAWNS TO INFECTIOUS AGENTS IN A CHRONIC WASTING DISEASE ENDEMIC AREA OF SOUTHERN SASKATCHEWAN

As a part of an ongoing study of the geographic spread and long term population effects of chronic wasting disease (CWD) in southwestern Saskatchewan, we captured and radio-collared female mule deer (Odocoileus hemionus) in the winter of 2009, 2010 and 2011 and, in the subsequent spring, we captured their newborn fawns. Fawns were blood sampled, radio-collared and ear tagged, released and then continuously monitored for survival status until the following February or March. During the winter capture we also sampled blood, tonsils and feces from juvenile mule deer which were approximately 8 months old. Our primary objectives were to 1) estimate female reproductive indices and evaluate fawn survival rates within the first 8 months of life and 2) detect exposure to selected infectious agents in neonates and 8-month old juveniles. Pregnancy rate, as determined by ultrasound in 2010 and 2011 winter was 100% (n=84); the overall average number of fetuses per doe was 1.99 ± SD 0.33 (167 fetuses, 84 does) with a predominance of twins. Mean birth rate was 1.29 ± SD 0.72 fawns per doe (139 neonates, 108 does). During the 3 capture years, we captured and radio-collared 118 neonates (n=38 in 2009, n=41 in 2010, n=39 in 2011). Probability of fawn survival was 0.334 ± SD 0.047 for the first 8 months of life from 2009 to 2011 and did not differ among capture years (P = 0.411). The most common known cause of mortality was predation. Having a longer body length at birth reduced the risk of fawn death for 0 - 7 day postpartum period. Members of larger litters had a higher risk of death during 8 – 30 day postpartum period. However, subclinical CWD status of dam was a poor predictor of fawn survival during the first 8 months of life. We performed various laboratory tests on feces, blood and tonsils of 8-month-old deer to detect prevalence of parasitic agents shed in feces, CWD in tonsils, mule deer lymphotropic herpes virus (mule deer-LHV) in buffy coat and presence of antibody titers in serum to bovine viral diarrhoea virus (BVDV), bovine herpes virus-1 (BHV-1), parainfluenza 3 virus (PI3), and the protozoan parasite Neospora caninum. Fecal analysis revealed a high prevalence for Orthostrongylus sp.: 86% (80/93), and moderate prevalence for Moniezia: 29% (27/93) and Thysanasoma: 29% (27/93). Seroprevalence for BHV-1, BVDV, PI3 virus and Neospora caninum was 3% (3/92), 20% (19/93), 22% (20/93), and 3% (3/91) respectively. Prevalence of mule deer-LHV was 15% (13/85). In 2010 and 2011, we detected subclinical CWD infection in 2 and 1 juveniles, respectively, with an overall prevalence of 3% (3/95). Serology on neonate blood revealed 12% (13/106) were seropositive for N. caninum and all dams that were seropositive for Neospora gave birth to at least one fawn. Mule deer in the Antelope Creek area of southwestern Saskatchewan have low fawn survival rates which may, in combination with high adult mortality due to hunting or CWD, result in population declines. Given the long incubation of CWD, even a low prevalence of CWD in 8 month old fawns suggests high infection pressure on resident deer. The high prevalence of gastrointestinal parasites and moderate seroprevalence for BVDV and PI3 virus at 8 months of age indicates frequent exposure to pathogens spread via the environment and by direct transmission. Because these are routes of transmission shared by CWD, this moderate to high prevalence of exposure to infectious agents also supports the hypothesis that fawns are potentially exposed to CWD at a young age. To understand factors responsible for the observed annual variability in exposure to Orthostrongylus, BVDV, and PI3 virus requires investigation of these infectious agents in sympatric species including livestock in the area

Validation and use of novel techniques to study the impacts of large-scale environmental changes on the health of wild waterfowl

Wild animals are experiencing an increasing number and magnitude of stressors associated with the rapidly changing world. Repeated or prolonged stressors can trigger sustained elevations of glucocorticoids, resulting in detrimental effects on health and reproduction, with potential impacts on populations. This Ph.D. research validated the use of two novel techniques to investigate stress responses in wild birds: feather corticosterone and nuclear magnetic resonance spectrometry (NMR)- based metabolomics, and then used these approaches in field-based studies to investigate the impacts of a changing environment on stress responses or increased energetic demands on free-ranging migratory birds. Feather corticosterone (CORTf) is increasingly used to measure cumulative stress responses experienced during feather growth. CORTf is potentially a very useful tool as it is a non-invasive approach to investigate stress responses or energetic demands that a bird may have experienced during the previous moulting period and may provide historical information on responses to environmental changes over time if archived or museum specimens are available. However, a major criticism of the technique has been the limited support for the assumption that it reflects blood corticosterone levels during the period of feather growth. In Chapter 2, captive lesser scaup (Aythya affinis) were surgically implanted with CORT or placebo pellets during the natural moult period to test this assumption. Additionally, I used deuterium-labelled CORT (2H-CORT) pellets to evaluate the relative deposition of exogenous and endogenous CORT into growing feathers. I measured CORT in serum before, during, and after the active period of the implants, and in corresponding feather sections of the tail, wing (secondary coverts), and back feathers. Our results confirm that a) CORT deposited in feathers is primarily derived from serum CORT; b) a considerable amount of feather development (and hence CORT deposition) occurs within the follicle before the feather emerges from the surface of the skin and c) CORT is deposited throughout the length of the feather until that feather is no longer growing, and no longer has a blood supply. This research provides critical evidence to support a central assumption associated with the use of CORTf and offers new insight into the deposition of CORT into feathers. In Chapter 3, I validated the use of metabolomics, using NMR, to identify alterations in metabolite profiles related to energy metabolism resulting from prolonged stress. The energy required for maintenance or other important functions in a bird’s annual cycle may be re-routed towards coping with stressors, ultimately resulting in fluctuations in metabolite levels associated with energy metabolism. Environmental metabolomics is a discipline that assesses an organism's interactions with its environment, which includes responses to endogenous and exogenous stressors. However, the use of metabolomics to study stress in wild birds is still in its infancy. Serum samples collected during the experimental trial performed for Chapter 2 on captive lesser scaup were extracted and subjected to 1D 1H-NMR spectrometry. Quantitative targeted metabolite analysis revealed that metabolites related to energy metabolism: glucose, formate, lactate, glutamine, 3-hydroxybutyrate, ethanolamine, indole-3- acetate, and threonine differentiated ducks with higher circulatory CORT from controls on the second day post-implant. These metabolites function as substrates or intermediates in metabolic pathways related to energy production affected by elevated serum CORT. The use of metabolomics shows promise as a novel tool to identify and characterize physiological responses to stressors in wild birds and can also be used to link responses to environmental changes with downstream impacts on reproduction and survival. Variations in climate are occurring more rapidly in polar regions, and temperatures in the Arctic have increased at more than three times the global average rate over the last five decades. Climate change also affects mercury (Hg) cycles and impacts distribution and quality of prey. Given that future climate change models are predicting that Arctic ecosystems will continue to undergo significant environmental changes in years to come, it is critical to take a multi-stressor approach to examine impacts of a rapidly changing environment on Arctic wildlife health. In Chapter 4, using feather samples collected from frozen or archived museum specimens sampled over 119 years (1893-2012), I used multiple feather-based measures to assess temporal trends and impacts of rising temperatures, exposure to Hg, and variation in diet (as measured by stable isotopes of nitrogen (δ15N) and carbon (δ13C)) on stress responses or energetic demands in all four subspecies of common eider (Somateria mollissima; COEI) that breed in North America (S. m. borealis, S. m. dresseri, S. m. sedentaria, and S. m. v-nigra). All COEI subspecies are experiencing increased temperatures within their respective geographic ranges, and energetic costs experienced by COEI (as measured by CORTf) are progressively increasing over time. Rising temperatures for all three Northern COEI subspecies result in increased energetic costs, which have been shown to have significant carry-over effects on reproduction and survival in this species. In the southern S. m. dresseri, CORTf was negatively associated with climate, suggesting reduced energetic costs in relation to rising temperatures. In addition to rising temperatures over time, common eiders are experiencing an increase in other concurrent stressors over time, including increases in Hg exposure (S. m. borealis), a progressive reduction in δ15N in their diets suggesting lower trophic position diets over time (S. m. sedentaria and S. m. dresseri), and decreases in feather δ13C levels over time, suggesting changes in feeding ecology or locations (S. m. v-nigra). Results demonstrate that COEI are facing an increase in multiple concurrent stressors over time in response to largescale environmental changes and illustrate how energetic demands of distinct subspecies adapted to different climates or geographic ranges can be differentially affected by multiple stressors. Findings in Chapter 4 highlight the value of using non-invasive feather-based approaches to examine historical trends over time and over a large geographic range, to investigate relationships among climate, Hg exposure, trophic position, and how they impact stress responses or energetic demands, which have the potential to impact fitness, and lead to population-level impacts. In Appendix A, we used NMR-based metabolomics to differentiate wild arctic-nesting COEI (S. m. borealis) in relation to energetic demands experienced during moult (CORTf), pre-breeding body condition, arrival date, and nest-initiation date, all of which are indicators of breeding success in this subspecies. Metabolite profiles could differentiate free-living COEI with higher CORTf from those that had lower CORTf. To my knowledge, this is the first study that has investigated the use of NMR-based metabolomics to investigate stress responses in a wild marine duck population. These results link feather CORT variation (representing energetic demands experienced during the previous moult in August-September) with metabolite variation related to energy metabolism (representing energy metabolism at the time of sampling in early June) for the first time in any avian species. NMR-based metabolomics shows promise as a novel tool to link stress physiology and responses of wild avian species to environmental changes. Overall findings of this research contribute substantially to the current understanding of avian stress physiology as well as the application of novel techniques to study the causes and consequences of stress responses in wild bird species

Discipline in Sri Lanka, punish in Pakistan:neoliberalism, governance, and housing compared

In discussions of urban infrastructure and land, neoliberalism is often presented as a hegemonic economic model with, seemingly, identical outcomes across a range of historical and political circumstances. For instance, in large cities of the Global South, a combination of speculative capitalism, and increased privatisation in the provision of public services, has been blamed for structural dispossession and the pushing out of working-class and vulnerable groups from urban centres. However, little has been said about how these processes interact with more contextual specificities—longer histories of state provision, existing inequalities, local political dynamics and legislative structures. Through comparative work on urban infrastructure projects in Lahore and Colombo, this article tells a story in which historical differences in state policy on housing and governance have impacted the ways in which dispossession is meted out, experienced and contested. Contributing to calls for studies of ‘actually existing neoliberalism’ (Wacquant 2012), we illustrate the importance of closely examining the relationship between neoliberal policies and dispossession on the ground through a historical perspective

Multiple pathways to scaling up and sustainability: an exploration of digital health solutions in South Africa

Background With the aim to support further understanding of scaling up and sustaining digital health, we explore digital health solutions that have or are anticipated to reach national scale in South Africa: the Perinatal Problem Identification Programme (PPIP) and Child Healthcare Problem Identification Programme (Child PIP) (mortality audit reporting and visualisation tools), MomConnect (a direct to consumer maternal messaging and feedback service) and CommCare (a community health worker data capture and decision-support application). Results A framework integrating complexity and scaling up processes was used to conceptually orient the study. Findings are presented by case in four domains: value proposition, actors, technology and organisational context. The scale and use of PPIP and Child PIP were driven by ‘champions’; clinicians who developed technically simple tools to digitise clinical audit data. Top-down political will at the national level drove the scaling of MomConnect, supported by ongoing financial and technical support from donors and technical partners. Donor preferences played a significant role in the selection of CommCare as the platform to digitise community health worker service information, with a focus on HIV and TB. A key driver of scale across cases is leadership that recognises and advocates for the value of the digital health solution. The technology need not be complex but must navigate the complexity of operating within an overburdened and fragmented South African health system. Inadequate and unsustained investment from donors and government, particularly in human resource capacity and robust monitioring and evaluation, continue to threaten the sustainability of digital health solutions. Conclusions There is no single pathway to achieving scale up or sustainability, and there will be successes and challenges regardless of the configuration of the domains of value proposition, technology, actors and organisational context. While scaling and sustaining digital solutions has its technological challenges, perhaps more complex are the idiosyncratic factors and nature of the relationships between actors involved. Scaling up and sustaining digital solutions need to account for the interplay of the various technical and social dimensions involved in supporting digital solutions to succeed, particularly in health systems that are themselves social and political dynamic systems

A comprehensive assessment of lymphatic filariasis in Sri Lanka six years after cessation of mass drug administration

The Sri Lankan Anti-Filariasis Campaign conducted 5 rounds of mass drug administration (MDA) with diethycarbamazine plus albendazole between 2002 and 2006. We now report results of a comprehensive surveillance program that assessed the lymphatic filariasis (LF) situation in Sri Lanka 6 years after cessation of MDA.Transmission assessment surveys (TAS) were performed per WHO guidelines in primary school children in 11 evaluation units (EUs) in all 8 formerly endemic districts. All EUs easily satisfied WHO criteria for stopping MDA. Comprehensive surveillance was performed in 19 Public Health Inspector (PHI) areas (subdistrict health administrative units). The surveillance package included cross-sectional community surveys for microfilaremia (Mf) and circulating filarial antigenemia (CFA), school surveys for CFA and anti-filarial antibodies, and collection of Culex mosquitoes with gravid traps for detection of filarial DNA (molecular xenomonitoring, MX). Provisional target rates for interruption of LF transmission were community CFA <2%, antibody in school children <2%, and filarial DNA in mosquitoes <0.25%. Community Mf and CFA prevalence rates ranged from 0-0.9% and 0-3.4%, respectively. Infection rates were significantly higher in males and lower in people who denied prior treatment. Antibody rates in school children exceeded 2% in 10 study sites; the area that had the highest community and school CFA rates also had the highest school antibody rate (6.9%). Filarial DNA rates in mosquitoes exceeded 0.25% in 10 PHI areas.Comprehensive surveillance is feasible for some national filariasis elimination programs. Low-level persistence of LF was present in all study sites; several sites failed to meet provisional endpoint criteria for LF elimination, and follow-up testing will be needed in these areas. TAS was not sensitive for detecting low-level persistence of filariasis in Sri Lanka. We recommend use of antibody and MX testing as tools to complement TAS for post-MDA surveillance

ABL1, Overexpressed in Hepatocellular Carcinomas, Regulates Expression of NOTCH1 and Promotes Development of Liver Tumors in Mice

Background & Aims We investigated whether ABL proto-oncogene 1, non-receptor tyrosine kinase (ABL1) is involved in development of hepatocellular carcinoma (HCC). Methods We analyzed clinical and gene expression data from The Cancer Genome Atlas. Albumin-Cre (HepWT) mice and mice with hepatocyte-specific disruption of Abl1 (HepAbl–/– mice) were given hydrodynamic injections of plasmids encoding the Sleeping Beauty transposase and transposons with the MET gene and a catenin β1 gene with an N-terminal truncation, which induces development of liver tumors. Some mice were then gavaged with the ABL1 inhibitor nilotinib or vehicle (control) daily for 4 weeks. We knocked down ABL1 with short hairpin RNAs in Hep3B and Huh7 HCC cells and analyzed their proliferation and growth as xenograft tumors in mice. We performed RNA sequencing and gene set enrichment analysis of tumors. We knocked down or overexpressed NOTCH1 and MYC in HCC cells and analyzed proliferation. We measured levels of phosphorylated ABL1, MYC, and NOTCH1 by immunohistochemical analysis of an HCC tissue microarray. Results HCC tissues had higher levels of ABL1 than non-tumor liver tissues, which correlated with shorter survival times of patients. HepWT mice with the MET and catenin β1 transposons developed liver tumors and survived a median 64 days; HepAbl–/– mice with these transposons developed tumors that were 50% smaller and survived a median 81 days. Knockdown of ABL1 in human HCC cells reduced proliferation, growth as xenograft tumors in mice, and expression of MYC, which reduced expression of NOTCH1. Knockdown of NOTCH1 or MYC in HCC cells significantly reduced cell growth. NOTCH1 or MYC overexpression in human HCC cells promoted proliferation and rescued the phenotype caused by ABL1 knockdown. The level of phosphorylated (activated) ABL1 correlated with levels of MYC and NOTCH1 in human HCC specimens. Nilotinib decreased expression of MYC and NOTCH1 in HCC cell lines, reduced the growth of xenograft tumors in mice, and slowed growth of liver tumors in mice with MET and catenin β1 transposons, reducing tumor levels of MYC and NOTCH1. Conclusions HCC samples have increased levels of ABL1 compared with nontumor liver tissues, and increased levels of ABL1 correlate with shorter survival times of patients. Loss or inhibition of ABL1 reduces proliferation of HCC cells and slows growth of liver tumors in mice. Inhibitors of ABL1 might be used for treatment of HCC

Fungal diversity notes 929–1035: taxonomic and phylogenetic contributions on genera and species of fungi

This article is the ninth in the series of Fungal Diversity Notes, where 107 taxa distributed in three phyla, nine classes, 31 orders and 57 families are described and illustrated. Taxa described in the present study include 12 new genera, 74 new species, three new combinations, two reference specimens, a re-circumscription of the epitype, and 15 records of sexualasexual morph connections, new hosts and new geographical distributions. Twelve new genera comprise Brunneofusispora, Brunneomurispora, Liua, Lonicericola, Neoeutypella, Paratrimmatostroma, Parazalerion, Proliferophorum, Pseudoastrosphaeriellopsis, Septomelanconiella, Velebitea and Vicosamyces. Seventy-four new species are Agaricus memnonius, A. langensis, Aleurodiscus patagonicus, Amanita flavoalba, A. subtropicana, Amphisphaeria mangrovei, Baorangia major, Bartalinia kunmingensis, Brunneofusispora sinensis, Brunneomurispora lonicerae, Capronia camelliaeyunnanensis, Clavulina thindii, Coniochaeta simbalensis, Conlarium thailandense, Coprinus trigonosporus, Liua muriformis, Cyphellophora filicis, Cytospora ulmicola, Dacrymyces invisibilis, Dictyocheirospora metroxylonis, Distoseptispora thysanolaenae, Emericellopsis koreana, Galiicola baoshanensis, Hygrocybe lucida, Hypoxylon teeravasati, Hyweljonesia indica, Keissleriella caraganae, Lactarius olivaceopallidus, Lactifluus midnapurensis, Lembosia brigadeirensis, Leptosphaeria urticae, Lonicericola hyaloseptispora, Lophiotrema mucilaginosis, Marasmiellus bicoloripes, Marasmius indojasminodorus, Micropeltis phetchaburiensis, Mucor orantomantidis, Murilentithecium lonicerae, Neobambusicola brunnea, Neoeutypella baoshanensis, Neoroussoella heveae, Neosetophoma lonicerae, Ophiobolus malleolus, Parabambusicola thysanolaenae, Paratrimmatostroma kunmingensis, Parazalerion indica, Penicillium dokdoense, Peroneutypa mangrovei, Phaeosphaeria cycadis, Phanerochaete australosanguinea, Plectosphaerella kunmingensis, Plenodomus artemisiae, P. lijiangensis, Proliferophorum thailandicum, Pseudoastrosphaeriellopsis kaveriana, Pseudohelicomyces menglunicus, Pseudoplagiostoma mangiferae, Robillarda mangiferae, Roussoella elaeicola, Russula choptae, R. uttarakhandia, Septomelanconiella thailandica, Spencermartinsia acericola, Sphaerellopsis isthmospora, Thozetella lithocarpi, Trechispora echinospora, Tremellochaete atlantica, Trichoderma koreanum, T. pinicola, T. rugulosum, Velebitea chrysotexta, Vicosamyces venturisporus, Wojnowiciella kunmingensis and Zopfiella indica. Three new combinations are Baorangia rufomaculata, Lanmaoa pallidorosea and Wojnowiciella rosicola. The reference specimens of Canalisporium kenyense and Tamsiniella labiosa are designated. The epitype of Sarcopeziza sicula is re-circumscribed based on cyto- and histochemical analyses. The sexual-asexual morph connection of Plenodomus sinensis is reported from ferns and Cirsium for the first time. In addition, the new host records and country records are Amanita altipes, A. melleialba, Amarenomyces dactylidis, Chaetosphaeria panamensis, Coniella vitis, Coprinopsis kubickae, Dothiorella sarmentorum, Leptobacillium leptobactrum var. calidus, Muyocopron lithocarpi, Neoroussoella solani, Periconia cortaderiae, Phragmocamarosporium hederae, Sphaerellopsis paraphysata and Sphaeropsis eucalypticola

Climate Change Impacts on Rice Farming Systems in Northwestern Sri Lanka

Sri Lanka has achieved tremendous progress since 1950 in crop production and food availability. Yields grew at an impressive rate until leveling off in the mid-eighties. Sri Lanka's population is anticipated to grow in the coming decades, creating an ever-greater demand for food security on the household, sub-district, regional, and national scales.The agricultural sector in Sri Lanka is vulnerable to climate shocks. An unusual succession of droughts and floods from 2008 to 2014 has led to both booms and busts in agricultural production, which were reflected in food prices. In both instances, the majority of farmers and consumers were adversely affected.At present the rice-farming systems are under stress due to inadequate returns for the farmers and difficulty in coping with shocks due to climate, pests, and diseases, and prices for produce. There are government price-support mechanisms, fertilizer-subsidy schemes, and crop insurance schemes, but the levels of the supports are modest and often do not effectively reach the farmers

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment