The use of AFLP to determine if a slimes-tolerant indigenous species shows local adaptation to slimes dam soils

Student Number : 9903228W - MSc dissertation - School of Molecular and Cell Biology - Faculty of SciencePlant populations show an ability to survive and adapt under varying environmental conditions. Adaptation to heavy metal contaminated soils usually results in a decrease in genetic variation. Slimes dams consist of the pulverized rock slurry left after the extraction of gold or uranium. High toxicity levels mean that these wastes often remain uncolonised and are therefore easily eroded through wind or water. Plant populations that will be viable for long-term vegetation of slimes dams will prevent erosion, and stabilise and improve the quality of the soil. Indigenous, locally adapted species are the most likely to be successful candidates for vegetation. Indigenous, slimes-tolerant species Indigofera adenoides and Indigofera zeyheri were therefore studied. The aim was to determine if plant populations show local adaptation to the adverse substrate conditions emanating from slimes dams, by investigating genetic and morphological variation between adjacent populations growing at different distances in relation to slimes dams. The AFLP technique was used to analyse genetic variation as it produces rapid results, is inexpensive, reproducible, and capable of screening the entire genome. Lower genetic diversity was observed in those areas of the dams with higher levels of slimes-associated contamination. This difference was observed in both species, and for all measures of genetic diversity (Shannon’s information index, Nei’s gene diversity, percentage of loci polymorphic). This may be due to a founder effect following colonisation, natural selection, flowering time differences, or a combination of these factors. Reduced morphological variation was observed in those areas of the dams with higher levels of slimes-associated contamination. Significant morphological differences were observed between groups of plants from different areas, some of which appear to have the capability to assist the plants in a slimes-contaminated environment. Some degree of adaptation to slimes-contaminated soil therefore seems to have occurred, with this being more pronounced in Indigofera adenoides, although it cannot be determined whether this is purely phenotypic, or a combination of phenotypic and genetic. These species therefore seem suitable as candidates for vegetation of slimes dams, although further work must be done to fully understand the effect of slimes-associated toxicity

Core information sets for informed consent to surgical interventions:baseline information of importance to patients and clinicians

BackgroundConsent remains a crucial, yet challenging, cornerstone of clinical practice. The ethical, legal and professional understandings of this construct have evolved away from a doctor-centred act to a patient-centred process that encompasses the patient’s values, beliefs and goals. This alignment of consent with the philosophy of shared decision-making was affirmed in a recent high-profile Supreme Court ruling in England. The communication of information is central to this model of health care delivery but it can be difficult for doctors to gauge the information needs of the individual patient. The aim of this paper is to describe ‘core information sets’ which are defined as a minimum set of consensus-derived information about a given procedure to be discussed with all patients. Importantly, they are intended to catalyse discussion of subjective importance to individuals.Main bodyThe model described in this paper applies health services research and Delphi consensus-building methods to an idea orginally proposed 30 years ago. The hypothesis is that, first, large amounts of potentially-important information are distilled down to discrete information domains. These are then, secondly, rated by key stakeholders in multiple iterations, so that core information of agreed importance can be defined. We argue that this scientific approach is key to identifying information important to all stakeholders, which may otherwise be communicated poorly or omitted from discussions entirely. Our methods apply systematic review, qualitative, survey and consensus-building techniques to define this ‘core information’. We propose that such information addresses the ‘reasonable patient’ standard for information disclosure but, more importantly, can serve as a spring board for high-value discussion of importance to the individual patient.ConclusionThe application of established research methods can define information of core importance to informed consent. Further work will establish how best to incorporate this model in routine practice

Core information sets for informed consent to surgical interventions:baseline information of importance to patients and clinicians

Abstract Background Consent remains a crucial, yet challenging, cornerstone of clinical practice. The ethical, legal and professional understandings of this construct have evolved away from a doctor-centred act to a patient-centred process that encompasses the patient’s values, beliefs and goals. This alignment of consent with the philosophy of shared decision-making was affirmed in a recent high-profile Supreme Court ruling in England. The communication of information is central to this model of health care delivery but it can be difficult for doctors to gauge the information needs of the individual patient. The aim of this paper is to describe ‘core information sets’ which are defined as a minimum set of consensus-derived information about a given procedure to be discussed with all patients. Importantly, they are intended to catalyse discussion of subjective importance to individuals. Main body The model described in this paper applies health services research and Delphi consensus-building methods to an idea orginally proposed 30 years ago. The hypothesis is that, first, large amounts of potentially-important information are distilled down to discrete information domains. These are then, secondly, rated by key stakeholders in multiple iterations, so that core information of agreed importance can be defined. We argue that this scientific approach is key to identifying information important to all stakeholders, which may otherwise be communicated poorly or omitted from discussions entirely. Our methods apply systematic review, qualitative, survey and consensus-building techniques to define this ‘core information’. We propose that such information addresses the ‘reasonable patient’ standard for information disclosure but, more importantly, can serve as a spring board for high-value discussion of importance to the individual patient. Conclusion The application of established research methods can define information of core importance to informed consent. Further work will establish how best to incorporate this model in routine practice

Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen.

Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L50 = 5; N50 = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. This genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control

'Trial Exegesis': Methods for Synthesizing Clinical and Patient Reported Outcome (PRO) Data in Trials to Inform Clinical Practice:A Systematic Review

PURPOSE:The CONSORT extension for patient reported outcomes (PROs) aims to improve reporting, but guidance on the optimal integration with clinical data is lacking. This study examines in detail the reporting of PROs and clinical data from randomized controlled trials (RCTs) in gastro-intestinal cancer to inform design and reporting of combined PRO and clinical data from trials to improve the 'take home' message for clinicians to use in practice. MATERIALS AND METHODS:The case study was undertaken in gastro-intestinal cancer trials. Well-conducted RCTs reporting PROs with validated instruments were identified and categorized into those combining PRO and clinical data in a single paper, or those separating data into linked primary and supplemental papers. Qualitative methods were developed to examine reporting of the critical interpretation of the trial results (trial exegesis) in the papers in relation of the PRO and clinical outcomes and applied to each publication category. Results were used to inform recommendations for practice. RESULTS:From 1917 screened abstracts, 49 high quality RCTs were identified reported in 36 combined and 15 linked primary and supplemental papers. In-depth analysis of manuscript text identified three categories for understanding trial exegesis: where authors reported a "detailed", "general", or absent PRO rationale and integrated interpretation of clinical and PRO results. A total of 11 (30%) and 6 (16%) combined papers reported "detailed" PRO rationale and integrated interpretation of results although only 2 (14%) and 1 (7%) primary papers achieved the same standard respectively. Supplemental papers provide better information with 11 (73%) and 3 (20%) achieving "detailed" rationale and integrated interpretation of results. Supplemental papers, however, were published a median of 20 months after the primary RCT data in lower impact factor journals (median 16.8 versus 5.2). CONCLUSION:It is recommended that single papers, with detailed PRO rationale and integrated PRO and clinical data are published to optimize trial exegesis. Further work to examine whether this improves the use of PRO data to inform practice is needed

Three nested randomized controlled trials of peer only or multiple stakeholder group feedback within Delphi surveys during core outcome and information set development

Top 10 items rated essential in round 1. (DOCX 17 kb

Assessing, quantifying and valuing the ecosystem services of coastal lagoons

The natural conservation of coastal lagoons is important not only for their ecological importance, but also because of the valuable ecosystem services they provide for human welfare and wellbeing. Coastal lagoons are shallow semi-enclosed systems that support important habitats such as wetlands, mangroves, salt-marshes and seagrass meadows, as well as a rich biodiversity. Coastal lagoons are also complex social-ecological systems with ecosystem services that provide livelihoods, wellbeing and welfare to humans. This study assessed, quantified and valued the ecosystem services of 32 coastal lagoons. The main findings of the study are: (i) the definitions of ecosystem services are still not generally accepted; (ii) the quantification of ecosystem services is made in many different ways, using different units; (iii) the evaluation in monetary terms of some ecosystem service is problematic, often relying on non-monetary evaluation methods; (iv) when ecosystem services are valued in monetary terms, this may represent very different human benefits; and, (v) different aspects of climate change, including increasing temperature, sea-level rise and changes in rainfall patterns threaten the valuable ecosystem services of coastal lagoons.DEVOTES project, from the European Union's Seventh Framework Programme for research, technological development and demonstration [308392]; networks and communities of Eurolag; Future Earth Coasts; SCOR; Fundacao para a Ciencia e a Tecnologia (FCT) Investigador Programme [IF/00331/2013]; Fundacao para a Ciencia e a Tecnologia [UID/MAR/04292/2013]; CESAM by FCT/MEC national funds (PIDDAC) [UID/AMB/50017/2013 - POCI-01-0145-FEDER-007638]; FEDER; European Commission, under the 7th Framework Programme through the collaborative research project LAGOONS [283157]; FCT [SFRH/BPD/107823/2015, SFRH/BPD/91494/2012

Life (evaluation), HIV/AIDS, and Death in Africa

We use data from the Gallup World Poll and from the Demographic and Health Surveys to investigate how subjective wellbeing (SWB) is affected by mortality in sub-Saharan Africa, including mortality from HIV/AIDS. The Gallup data provide direct evidence on Africans' own emotional and evaluative responses to high levels of infection and of mortality. By comparing the effect of mortality on SWB with the effect of income on SWB, we can attach monetary values to mortality to illuminate the often controversial question of how to value life in Africa. Large fractions of the respondents in the World Poll report the mortality of an immediate family member in the last twelve months, with malaria typically more important than AIDS, and deaths of women in childbirth more important than deaths from AIDS in many countries. A life evaluation measure (Cantril's ladder of life) is relatively insensitive to the deaths of immediate family, which suggests a low value of life. There are much larger effects on experiential measures, such as sadness and depression, which suggest much larger values of life. It is not clear whether either of these results is correct, yet our results demonstrate that experiential and evaluative measures are not the same thing, and that they cannot be used interchangeably as measures of "happiness" in welfare economics.

Towards an understanding of the role of sociocultural learning in family firm longevity.

Sociocultural learning occurs when social interaction takes place and is influenced by the prevailing values and beliefs of the particular group. The focus of this research is the family firm which is defined in general terms as a business owned and managed by members of a single family. Family firms form an important part of the Cumbrian economy and those that have survived to a third generation of family ownership, growing to medium or large companies in the process, are of particular significance. This research examines two such firms from the perspective of sociocultural learning, focusing particularly on situated learning and community of practice theory. Communities of practice are an integral part of daily life; in the context of this research, they refer to the workplace. This study examines two aspects: firstly, the nature of learning between the family members and their staff, and that occurring between experienced staff and newcomers to the company. Secondly, it investigates the impact of power relations on learning within the organizations. Using a constructivist interpretivist approach, a case study method was adopted, and interviews were conducted with family directors in two companies and members of management in one of them. The research found that practices in both companies were consistent with situated learning theory. Shared learning was not only key to innovation and adaptability but also contributed to the maintenance of the culture passed down from the previous generations. It was further identified that the potential for learning in the two organizations was facilitated or impeded by the way management power was exercised. The study concludes that people, values, and learning and adaptability are important aspects of family firm success and, depending on the way in which they are managed, may contribute to the firm’s longevity