Genomic variations associated with attenuation in Mycobacterium avium subsp paratuberculosis vaccine strains

BACKGROUND: Mycobacterium avium subspecies paratuberculosis (MAP) whole cell vaccines have been widely used tools in the control of Johne's disease in animals despite being unable to provide complete protection. Current vaccine strains derive from stocks created many decades ago; however their genotypes, underlying mechanisms and relative degree of their attenuation are largely unknown. RESULTS: Using mouse virulence studies we confirm that MAP vaccine strains 316 F, II and 2e have diverse but clearly attenuated survival and persistence characteristics compared with wild type strains. Using a pan genomic microarray we characterise the genomic variations in a panel of vaccine strains sourced from stocks spanning over 40 years of maintenance. We describe multiple genomic variations specific for individual vaccine stocks in both deletion (26-32 Kbp) and tandem duplicated (11-40 Kbp) large variable genomic islands and insertion sequence copy numbers. We show individual differences suitable for diagnostic differentiation between vaccine and wild type genotypes and provide evidence for functionality of some of the deleted MAP-specific genes and their possible relation to attenuation. CONCLUSIONS: This study shows how culture environments have influenced MAP genome diversity resulting in large tandem genomic duplications, deletions and transposable element activity. In combination with classical selective systematic subculture this has led to fixation of specific MAP genomic alterations in some vaccine strain lineages which link the resulting attenuated phenotypes with deficiencies in high reactive oxygen species handling

Clinical features of colorectal cancer before diagnosis: a population-based case-control study

This is the final version of the article. Available from the publisher via the DOI in this record.Most colorectal cancers are diagnosed after the onset of symptoms. However, the risk of colorectal cancer posed by particular symptoms is largely unknown, especially in unselected populations like primary care. This was a population-based case-control study in all 21 general practices in Exeter, Devon, UK, aiming to identify and quantify the prediagnostic features of colorectal cancer. In total, 349 patients with colorectal cancer, aged 40 years or more, and 1744 controls, matched by age, sex and general practice, were studied. The full medical record for 2 years before diagnosis was coded using the International Classification of Primary Care-2. We calculated odds ratios for variables independently associated with cancer, using multivariable conditional logistic regressions, and then calculated the positive predictive values of these variables, both individually and in combination. In total, 10 features were associated with colorectal cancer before diagnosis. The positive predictive values (95% confidence interval) of these were rectal bleeding 2.4% (1.9, 3.2); weight loss 1.2% (0.91, 1.6); abdominal pain 1.1% (0.86, 1.3); diarrhoea 0.94% (0.73, 1.1); constipation 0.42% (0.34, 0.52); abnormal rectal examination 4.0% (2.4, 7.4); abdominal tenderness 1.1% (0.77, 1.5); haemoglobin 10 mmol l(-1) 0.78% (0.51, 1.1): all P < 0.001. Earlier diagnosis of colorectal cancer may be possible using the predictive values for single or multiple symptoms, physical signs or test results.Project funding from the Department of Health. The funding source had no role in study design, data collection, analysis or writing of the report. All authors had full access to all data, and take final responsibility for publication. WH was funded through his research practice (Barnfield Hill, Exeter) and RCGP/BUPA and NHS Fellowships. The views expressed in the publication are those of the authors and not necessarily those of the Department of Health. We wish to thank all 21 general practices in Exeter, the Dendrite personnel, and the Patients and Practitioners Service Authority, without which this project would not have been successful

Risk of ovarian cancer in women with symptoms in primary care: population based case-control study.

addresses: NIHR School for Primary Care Research, Department of Community Based Medicine, University of Bristol, Bristol BS8 2AA, UK. [email protected]: PMCID: PMC2731836types: Journal Article; Multicenter Study; Research Support, Non-U.S. Gov'tCopyright © 2009 by the BMJ Publishing Group Ltd. This articles was first published in: BMJ, 2009, Vol. 339, pp. b2998 -To identify and quantify symptoms of ovarian cancer in women in primary care

Encounters of culture, heritage and development: exploring global connection in Sierra Leone

This thesis examines the relationships emerging between culture, heritage and development in Sierra Leone. The concept of ‘culture for development’ is increasingly influential as a framework for intervention in both development and heritage work. However, it has so far received limited critical attention. Using a multi-­‐sited ethnographic approach, this research traces the complexities and contradictions that transpire as Sierra Leone’s cultural sector attempts to establish its position within the country’s future. ‘Culture for development’ emerges from a recognition that intervention has historically failed to respond to local contexts. This thesis proposes that in Sierra Leone, such an agenda is obscured by wider political, professional and personal concerns over the role of the past within a context of aspirational change and transformation

The effect of Me2_{2}SO overexposure during cryopreservation on HOS TE85 and hMSC viability, growth and quality

With the cell therapy industry continuing to grow, the ability to preserve clinical grade cells, including mesenchymal stem cells (MSCs), whilst retaining cell viability and function remains critical for the generation of off-the-shelf therapies. Cryopreservation of MSCs, using slow freezing, is an established process at lab scale. However, the cytotoxicity of cryoprotectants, like Me$_{2}$SO, raises questions about the impact of prolonged cell exposure to cryoprotectant at temperatures >0 °C during processing of large cell batches for allogenic therapies prior to rapid cooling in a controlled rate freezer or in the clinic prior to administration. Here we show that exposure of human bone marrow derived MSCs to Me$_{2}$SO for ≥1 h before freezing, or after thawing, degrades membrane integrity, short-term cell attachment efficiency and alters cell immunophenotype. After 2 h's exposure to Me$_{2}$SO at 37 °C post-thaw, membrane integrity dropped to ∼70% and only ∼50% of cells retained the ability to adhere to tissue culture plastic. Furthermore, only 70% of the recovered MSCs retained an immunophenotype consistent with the ISCT minimal criteria after exposure. We also saw a similar loss of membrane integrity and attachment efficiency after exposing osteoblast (HOS TE85) cells to Me$_{2}$SO before, and after, cryopreservation. Overall, these results show that freezing medium exposure is a critical determinant of product quality as process scale increases. Defining and reporting cell sensitivity to freezing medium exposure, both before and after cryopreservation, enables a fair judgement of how scalable a particular cryopreservation process can be, and consequently whether the therapy has commercial feasibility.The authors would like to acknowledge the Engineering and Physical Sciences Research Council (EPSRC; UK, EP/F500491/1) and Bioprocessing Research Industry Club (BBSRC/BRIC; UK, BB/I017602/1) for their support and funding

The risk of colorectal cancer with symptoms at different ages and between the sexes: a case-control study

© 2009 Hamilton et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Colorectal cancer is generally diagnosed following a symptomatic presentation to primary care. Although the presenting features of the cancer are well described, the risks they convey are less well known. This study aimed to quantify the risk of cancer for different symptoms, across age groups and in both sexes

Sedentary time and markers of inflammation in people with newly diagnosed type 2 diabetes

This is the final version. Available on open access from Elsevier via the DOI in this recordBACKGROUND AND AIMS: We investigated whether objectively measured sedentary time was associated with markers of inflammation in adults with newly diagnosed type 2 diabetes. METHODS AND RESULTS: We studied 285 adults (184 men, 101 women, mean age 59.0 ± 9.7) who had been recruited to the Early ACTivity in Diabetes (Early ACTID) randomised controlled trial. C-reactive protein (CRP), adiponectin, soluble intracellular adhesion molecule-1 (sICAM-1), interleukin-6 (IL-6), and accelerometer-determined sedentary time and moderate-vigorous physical activity (MVPA) were measured at baseline and after six-months. Linear regression analysis was used to investigate the independent cross-sectional and longitudinal associations of sedentary time with markers of inflammation. At baseline, associations between sedentary time and IL-6 were observed in men and women, an association that was attenuated following adjustment for waist circumference. After 6 months of follow-up, sedentary time was reduced by 0.4 ± 1.2 h per day in women, with the change in sedentary time predicting CRP at follow-up. Every hour decrease in sedentary time between baseline and six-months was associated with 24% (1, 48) lower CRP. No changes in sedentary time between baseline and 6 months were seen in men. CONCLUSIONS: Higher sedentary time is associated with IL-6 in men and women with type 2 diabetes, and reducing sedentary time is associated with improved levels of CRP in women. Interventions to reduce sedentary time may help to reduce inflammation in women with type 2 diabetes.National Institute for Health Research (NIHR

Mendelian randomization study of B-type natriuretic peptide and type 2 diabetes: evidence of causal association from population studies

&lt;p&gt;Background: Genetic and epidemiological evidence suggests an inverse association between B-type natriuretic peptide (BNP) levels in blood and risk of type 2 diabetes (T2D), but the prospective association of BNP with T2D is uncertain, and it is unclear whether the association is confounded.&lt;/p&gt; &lt;p&gt;Methods and Findings: We analysed the association between levels of the N-terminal fragment of pro-BNP (NT-pro-BNP) in blood and risk of incident T2D in a prospective case-cohort study and genotyped the variant rs198389 within the BNP locus in three T2D case-control studies. We combined our results with existing data in a meta-analysis of 11 case-control studies. Using a Mendelian randomization approach, we compared the observed association between rs198389 and T2D to that expected from the NT-pro-BNP level to T2D association and the NT-pro-BNP difference per C allele of rs198389. In participants of our case-cohort study who were free of T2D and cardiovascular disease at baseline, we observed a 21% (95% CI 3%-36%) decreased risk of incident T2D per one standard deviation (SD) higher log-transformed NT-pro-BNP levels in analysis adjusted for age, sex, body mass index, systolic blood pressure, smoking, family history of T2D, history of hypertension, and levels of triglycerides, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol. The association between rs198389 and T2D observed in case-control studies (odds ratio = 0.94 per C allele, 95% CI 0.91-0.97) was similar to that expected (0.96, 0.93-0.98) based on the pooled estimate for the log-NT-pro-BNP level to T2D association derived from a meta-analysis of our study and published data (hazard ratio = 0.82 per SD, 0.74-0.90) and the difference in NT-pro-BNP levels (0.22 SD, 0.15-0.29) per C allele of rs198389. No significant associations were observed between the rs198389 genotype and potential confounders.&lt;/p&gt; &lt;p&gt;Conclusions: Our results provide evidence for a potential causal role of the BNP system in the aetiology of T2D. Further studies are needed to investigate the mechanisms underlying this association and possibilities for preventive interventions.&lt;/p&gt

The risk of colorectal cancer with symptoms at different ages and between the sexes: a case-control study

BACKGROUND: Colorectal cancer is generally diagnosed following a symptomatic presentation to primary care. Although the presenting features of the cancer are well described, the risks they convey are less well known. This study aimed to quantify the risk of cancer for different symptoms, across age groups and in both sexes. METHODS: This was a case-control study using pre-existing records in a large electronic primary care database. Cases were patients aged 30 years or older with a diagnosis of colorectal cancer between January 2001 and July 2006, matched to seven controls by age, sex and practice. All features of colorectal cancer recorded in the 2 years before diagnosis were identified. Features independently associated with cancer were identified using multivariable conditional logistic regression, and their risk of cancer quantified. RESULTS: We identified 5477 cases, with 38,314 age, sex and practice-matched controls. Six symptoms and two abnormal investigations (anaemia and microcytosis) were independently associated with colorectal cancer. The positive predictive values of symptoms were: rectal bleeding, positive predictive value for a male aged ≥ 80 years 4.5% (95% confidence interval 3.5, 5.9); change in bowel habit 3.9% (2.8, 5.5); weight loss 0.8% (0.5, 1.3); abdominal pain 1.2% (1.0, 1.4); diarrhoea 1.2% (1.0, 1.5) and constipation 0.7% (0.6, 0.8). Positive predictive values were lower in females and younger patients. Only 27% of patients had reported either of the two higher risk symptoms. CONCLUSION: Most symptomatic colorectal cancers present with only a low-risk symptom. There is a need to find a method of identifying those at highest risk of cancer from the large number presenting with such symptoms

Financing methods for small-scale hardwood plantations in Queensland, Australia

Under Vision 2020, a target was set in 1997 for trebling the plantation area in Australia by the year 2020. Government subsidies and extension for plantation establishment have largely disappeared, hence forestry expansion is highly dependent on access to private finance. In the state of Queensland, plantation expansion has occurred predominantly through managed investment schemes and the joint venture scheme managed by Forestry Plantations Queensland, a government-owned corporation. Most of these plantings are relatively small-scale hardwood plantations, which are designed to replace the hardwood timber from the native forests that will be protected from further logging after 2024 under the South-East Queensland Regional Forestry Agreement. Views on financing methods for forestry expansion in Queensland were investigated through by an email survey of 12 forestry and finance professionals, followed by in-depth personal interviews of the same group of key informants. Some of the issues identified include lack of transparent information, inequitable taxation system between Managed Investment Scheme (MIS) companies and small-scale forest operators, the need for further R&D on all aspects of the industry, the potential impacts of carbon credit schemes on the industry, and the design of a strategic model for forestry investors. Participants took the view that adoption of a strategic alliance model would encourage further investment in small-scale forestry, arguing that this model could protect the interest of all the stakeholders through reducing investment risk and creating competitive advantage. The potential introduction of a carbon trading scheme also attracted interest from investors, who look for recognisable structures that may alleviate the risk of investing in an industry with which they are unfamiliar. The participants considered that further R&D should be the main focus for government participation in small-scale forestry