DIRECT AND INDIRECT EFFECTS OF ANTHROPOGENIC LAND USE ON BOBCATS (Lynx rufus) IN NEW ENGLAND

Bobcats (Lynx rufus) are the most widely distributed wild felids in North America, ranging across the contiguous United States, southern Canada, and northern Mexico. In the New England region (NER) bobcat populations endured nearly two centuries of intense harvest pressure and land use change that nearly led to their extirpation in parts of the region. However, they are currently experiencing a population resurgence despite large-scale increases of anthropogenic impacts on the landscape in the last 60 years. In this dissertation, I sought to understand the resurgence of bobcats in the NER by studying several aspects of bobcat ecology in relation to human land use. Bobcats present a unique system in which to study anthropogenic impacts on wildlife. The NER is near the northern edge of their range. Combined with their history of fluctuating abundance, this provides a dynamic demographic landscape. They are reclusive, typically avoiding human contact, but are also highly adaptable to varied habitats including human-dominated areas. Their habitat preferences can widely vary based on local conditions and biological factors. They are a wide-ranging and charismatic species with great public appeal, which makes them an ideal umbrella or flagship species for regional conservation efforts and provides ample opportunity for engagement with public stakeholders. Chapter 1 of this dissertation explores genetic patterns across the NER over the past 60 years. I compare genetic structure, diversity, effective population size, and gene flow between a historic (1952-1964) and a contemporary (2009-2017) time period. My results suggest that bobcat populations in the region are robust, but development and edge-of-range dynamics play a significant role in population structure. Chapter 2 compares the diet of bobcats in the NER between the same time periods. I found that historically, bobcats were highly dependent on lagomorphs but their diet diversified in the contemporary time period. In Chapter 3, I explore the effect of land use on bobcat stress levels using hair cortisol as an indicator of stress. Anthropogenic land use was a better predictor of cortisol levels in bobcats than their preferred undeveloped land cover types. Finally in Chapter 4, I integrate data from the first three chapters to explore how the genetic structure, diet, and stress physiology of bobcats in the NER interact with one another and with the landscape, particularly anthropogenic land use. I also developed a framework for further study to elucidate precise mechanisms that explain those interactions

Carbon and nitrogen dynamics: Greenhouse gases in groundwater beneath a constructed wetland treating municipal wastewater

Conference oral presentationConstructed wetlands (CW) act as nitrogen (N) sinks and reactors facilitating a number of physical, chemical and biological processes. The N removal efficiency of through-flowing water in such systems when used to treat municipal wastewater is variable. Their overall removal efficiencies do not specifically explain which N species have been removed by physical attenuation, and by biological assimilation or transformation to other forms. A wider understanding of how N removal occurs would help elucidate how losses of N and associated gases from CW impact on water and air quality. The objective of this study is to investigate the C and N cycling processes in the porewater of soils immediately adjacent, up-gradient and down- gradient to helophyte —vegetated CW cells

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer

The authors would like to acknowledge the support of The University of Cambridge, Cancer Research UK (CRUK SEB-Institute Group Award A ref10182; CRUK Senior fellowship C10112/A11388 to AEKI) and Hutchison Whampoa Limited. The Human Research Tissue Bank is supported by the NIHR Cambridge Biomedical Research Centre. FF is a ULB Professor funded by grants from the F.N.R.S. and Télévie, the IUAP P7/03 programme, the ARC (AUWB-2010-2015 ULB-No 7), the WB Health program and the Fonds Gaston Ithier. Data access: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=jpwzvsowiyuamzs&acc=GSE47592Background : The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which tumours can arise. Results : Here, we show that colorectal tumours and cancer cells express Ten-Eleven-Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. Conclusions : Together our results indicate that promoters that acquire 5hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5hmC in tumours. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.Publisher PDFPeer reviewe

Correction:Microwave gallium-68 radiochemistry for kinetically stable bis(thiosemicarbazone) complexes: Structural investigations and cellular uptake under hypoxia (Dalton Transactions (2016) 45 (144-155))

We report the microwave synthesis of several bis(thiosemicarbazones) and the rapid gallium-68 incorporation to give the corresponding metal complexes. These proved kinetically stable under ‘cold’ and ‘hot’ biological assays and were investigated using laser scanning confocal microscopy, flow cytometry and radioactive cell retention studies under normoxia and hypoxia. (68)Ga complex retention was found to be 34% higher in hypoxic cells than in normoxic cells over 30 min, further increasing to 53% at 120 min. Our data suggests that this class of gallium complexes show hypoxia selectivity suitable for imaging in living cells and in vivo tests by microPET in nude athymic mice showed that they are excreted within 1 h of their administration

Postexposure prophylaxis with rVSV-ZEBOV following exposure to a patient with Ebola virus disease relapse in the United Kingdom: an operational, safety, and immunogenicity report

Background: In October 2015, 65 people came into direct contact with a healthcare worker presenting with a late reactivation of Ebola virus disease (EVD) in the UK. Vaccination was offered to 45 individuals with an initial assessment of high exposure risk. Methods: Approval for rapid expanded access to the recombinant vesicular stomatitis virus–Zaire Ebola virus vaccine (rVSV-ZEBOV) as an unlicensed emergency medicine was obtained from the relevant authorities. An observational follow-up study was carried out for 1 year following vaccination. Results: 26/45 individuals elected to receive vaccination between October 10th and 11th 2015 following written informed consent. By day 14, 39% had seroconverted, rising to 87% by day 28 and 100% by 3 months, although these responses were not always sustained. Neutralising antibody responses were detectable in 36% by day 14 and 73% at 12 months. Common side effects included fatigue, myalgia, headache, arthralgia and fever. These were positively associated with glycoprotein (GP)-specific T-cell but not IgM or IgG antibody responses. No severe vaccine-related adverse events were reported. No-one exposed to the virus became infected. Conclusions: This paper reports the use of the rVSV-ZEBOV vaccine given as an emergency intervention to individuals exposed to a patient presenting with a late reactivation of EVD. The vaccine was relatively well tolerated but a high percentage developed a fever ≥37.5oC necessitating urgent screening for Ebola virus and a small number developed persistent arthralgia

Progesterone receptor modulates ERα action in breast cancer.

Progesterone receptor (PR) expression is used as a biomarker of oestrogen receptor-α (ERα) function and breast cancer prognosis. Here we show that PR is not merely an ERα-induced gene target, but is also an ERα-associated protein that modulates its behaviour. In the presence of agonist ligands, PR associates with ERα to direct ERα chromatin binding events within breast cancer cells, resulting in a unique gene expression programme that is associated with good clinical outcome. Progesterone inhibited oestrogen-mediated growth of ERα(+) cell line xenografts and primary ERα(+) breast tumour explants, and had increased anti-proliferative effects when coupled with an ERα antagonist. Copy number loss of PGR, the gene coding for PR, is a common feature in ERα(+) breast cancers, explaining lower PR levels in a subset of cases. Our findings indicate that PR functions as a molecular rheostat to control ERα chromatin binding and transcriptional activity, which has important implications for prognosis and therapeutic interventions.We would like to acknowledge the support of the University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited. Research reported in this manuscript was supported by the National Cancer Institute of the National Institutes of Health under award number 5P30CA142543 (to UT Southwestern) and Department of Defense grants W81XWH-12-1-0288-03 (GVR). W.D.T. is supported by grants from the National Health and Medical Research Council of Australia (ID 1008349; ID 1084416) and Cancer Australia (ID 627229) T.E.H held a Fellowship Award from the US Department of Defense Breast Cancer Research Program (BCRP; #W81XWH-11-1-0592) and currently is supported by a Florey Fellowship from the Royal Adelaide Hospital Research Foundation. J.S.C is supported by an ERC starting grant and an EMBO Young investigator award.This is the accepted manuscript. The final version is available at www.nature.com/nature/journal/v523/n7560/full/nature14583.htm

Genome-Scale Validation of Deep-Sequencing Libraries

Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing

Cortisol levels and suicidal behavior: a meta-analysis

Suicide is a major cause of death worldwide, responsible for 1.5% of all mortality. The causes of suicidal behavior are not fully understood. Dysregulated hypothalamic-pituitary-adrenal (HPA) axis activity, as measured by cortisol levels, is one potential risk factor. This meta-analytic review aimed i) to estimate the strength and variability of the association between naturally fluctuating cortisol levels and suicidal behavior and ii) to identify moderators of this relationship. A systematic literature search identified 27 studies (N = 2226; 779 suicide attempters & 1447 non-attempters) that met the study eligibility criteria from a total of 417 unique records initially examined. Estimates of effect sizes (r) obtained from these studies were analysed using Comprehensive Meta-Analysis. In these analyses, we compared participants identified as having a past history of suicide attempt(s) to those with no such history. Study quality, mean age of sample and percentage of male participants were examined as potential moderators. Overall, there was no significant effect of suicide group on cortisol. However, significant associations between cortisol and suicide attempts were observed as a function of age. In studies where the mean age of the sample was below 40 years the association was positive (i.e., higher cortisol was associated with suicide attempts; r = .234, p < .001), and where the mean age was 40 or above the association was negative (i.e., lower cortisol was associated with suicide attempts; r = - .129, p < .001). These findings confirm that HPA axis activity, as indicated by age-dependent variations in cortisol levels, is associated with suicidal behavior. The challenge for theory and clinical practice is to explain the complete reversal of the association with age and to identify its clinical implications

Implementation fidelity of a nurse-led falls prevention program in acute hospitals during the 6-PACK trial

Background: When tested in a randomized controlled trial (RCT) of 31,411 patients, the nurse-led 6-PACK falls prevention program did not reduce falls. Poor implementation fidelity (i.e., program not implemented as intended) may explain this result. Despite repeated calls for the examination of implementation fidelity as an essential component of evaluating interventions designed to improve the delivery of care, it has been neglected in prior falls prevention studies. This study examined implementation fidelity of the 6-PACK program during a large multi-site RCT. Methods: Based on the 6-PACK implementation framework and intervention description, implementation fidelity was examined by quantifying adherence to program components and organizational support. Adherence indicators were: 1) falls-risk tool completion; and for patients classified as high-risk, provision of 2) a ‘Falls alert’ sign; and 3) at least one additional 6-PACK intervention. Organizational support indicators were: 1) provision of resources (executive sponsorship, site clinical leaders and equipment); 2) implementation activities (modification of patient care plans; training; implementation tailoring; audits, reminders and feedback; and provision of data); and 3) program acceptability. Data were collected from daily bedside observation, medical records, resource utilization diaries and nurse surveys. Results: All seven intervention components were delivered on the 12 intervention wards. Program adherence data were collected from 103,398 observations and medical record audits. The falls-risk tool was completed each day for 75% of patients. Of the 38% of patients classified as high-risk, 79% had a ‘Falls alert’ sign and 63% were provided with at least one additional 6-PACK intervention, as recommended. All hospitals provided the recommended resources and undertook the nine outlined program implementation activities. Most of the nurses surveyed considered program components important for falls prevention. Conclusions: While implementation fidelity was variable across wards, overall it was found to be acceptable during the RCT. Implementation failure is unlikely to be a key factor for the observed lack of program effectiveness in the 6-PACK trial. Trial registration: The 6-PACK cluster RCT is registered with the Australian New Zealand Clinical Trials Registry, number ACTRN12611000332921 (29 March 2011)