Rooting a phylogenetic tree with nonreversible substitution models

BACKGROUND: We compared two methods of rooting a phylogenetic tree: the stationary and the nonstationary substitution processes. These methods do not require an outgroup. METHODS: Given a multiple alignment and an unrooted tree, the maximum likelihood estimates of branch lengths and substitution parameters for each associated rooted tree are found; rooted trees are compared using their likelihood values. Site variation in substitution rates is handled by assigning sites into several classes before the analysis. RESULTS: In three test datasets where the trees are small and the roots are assumed known, the nonstationary process gets the correct estimate significantly more often, and fits data much better, than the stationary process. Both processes give biologically plausible root placements in a set of nine primate mitochondrial DNA sequences. CONCLUSIONS: The nonstationary process is simple to use and is much better than the stationary process at inferring the root. It could be useful for situations where an outgroup is unavailable

Folding and Aggregation of Designed Proteins

Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory disorder Alzheimer's. Protein aggregation have traditionally been connected to either unfolded or native states. Inclusion body formation (disordered aggregation) has been assumed to arise from hydrophobic aggregation of the unfolded or denaturated states, while the amyloid fibrils (ordered aggregation) have been assumed to arise from native-like conformations in a process analogous to the polymerization of hemoglobin S. Making use of lattice-model simulations we find that both ordered and disordered aggregation arise from elementary structures which eventually build the folding nucleus of the heteropolymers, and takes place when some of the most strongly interacting amino acids establish their contacts leading to the formation of a specific subset of the native structure. These elementary structures can be viewed as the partially folded intermediates suggested to be involved in the aggregation of a number of proteins. These results have evolutionary implications, as the elementary structures forming the folding core of designed proteins contain the residues which are conserved among the members of homologous sequences.Comment: 10 pages, 2 colour ps figures and 1 b/w ps figur

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals ∼30–50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions

Building spaces for controversial public engagement – Exploring and challenging democratic deficits in NHS marketization

The Brighton Citizen's Health Services Survey (BCHSS) was developed to explore and potentially challenge how knowledge is used and by whom in the production of local health commissioning institutions and relations. Through the creation of an ‘animating set of questions’, it sought to open up spaces through which to make visible some of the ways of knowing and valuing the NHS and health services that had been minimised through the commensuration practices of post-2012 public engagement. In this way there was a clear agenda to facilitate a form of knowledge democratisation which opened up and validated different 'health publics’, in order to explore and broaden participative engagement opportunities. The paper provides an account of the project. It considers the theoretical and methodological underpinnings of this example of ‘evidence-based activism’, reflects on the impact of the project on local commissioning and considers the range of controversies that arose as a result of the work. It explores the way that research straddling the boundary between academic inquiry and political activism speaks to the many issues that are prevalent in the changing HE sector as well as NHS privatisation, health commissioning and public sector cuts

Service user involvement in pre-registration general nurse education: a systematic review

Aims and objectives: A systematic review of published studies on service user involvement in undergraduate, pre-registration general nursing education (excluding mental health-specific programmes). The objective is to examine how students are exposed to engagement with service users. Background: The requirement of service user involvement in all nurse education is policy expectation of health professional education providers, in response to the increased public and political expectations. Previous literature reviews have focused solely on mental health. Design: Systematic review using the PRISMA guidelines; timeframe 1997-2014; published in English. Methods: Search of CINAHL, Cochrane Review, Education Research Complete, Internurse, MEDLINE, PsychINFO, Scopus, SocINDEX and Web of Science yielded 229 citations; 11 studies met the review eligibility criteria. Results: Seven studies used qualitative methodology, two quantitative and two mixed methods. Studies from the United Kingdom dominated (n=9), the remainder from South Africa and Turkey. The results are described using four themes: benefits and limitations of service user involvement; nursing student selection; education delivery; practice-based learning and assessment. Most studies were small scale; nine had less than 30 participants. Overall the evidence suggests that student, lecturers and service users valued service user involvement in nurse education, to provide an authentic insight into the illness experience. Logistical considerations around support and student cohort size emerged. Conclusions: This is the first systematic review to focus on service user involvement in general nurse education. It reveals that service user involvement commenced later and is more limited in general programmes as compared to equivalent mental health education provision. Most of the evidence focuses on perceptions of the value of involvement. Further research is required to more clearly establish impact on learning and clinical practice. Relevance to clinical practice: service user involvement in nurse education is valued by stakeholders but preparation and support for those involved, including mentors is underestimated

Crop Updates 2003 - Geraldton

This session covers twenty eight papers from different authors Seasonal Outlook: What is in store for 2003, David Stephens, Department of Agriculture Examining The Management Options For Wheat Crops In The Coming Season, James Fisher, Department of Agriculture GMO’s – what do they offer? Ian Edwards, Grain Bio Tech Australia Pty Ltd The Big Gamble – Wheat prices for 2003, Dennis Wise, Profarmer Market outlook for other grains, Andrew Young, General Manager Agricorp Stripe rust – where to now for the WA wheat industry? Robert Loughman, Ciara Beard and Greg Shea, Department of Agriculture Baudin and Hamlin – new generation of malting barley developed in Western Australia, Blakely Paynter, Roslyn Jettner and Kevin Young, Department of Agriculture DBM in Canola, Kevin Walden, Department of Agriculture The latest on Lupin diseases, Geoff Thomas, Department of Agriculture Wheat variety performance in 2002 compared to the long term, Robin Wilson, Iain Barclay, Robyn McLean, Robert Loughman, Jenny Garlinge, Bill Lambe, Neil Venn and Peter Clarke, Department of Agriculture Do wide rows drought proof lupins on red loam? Martin Harries, Bob French, Wayne Parker and Murray Blyth, Department of Agriculture Do wide rows drought proof lupins on a sandy loam? Martin Harries, Bob French, Wayne Parker and Murray Blyth, Department of Agriculture Profit Proving Precision Agriculture, Peter Norris, Agronomy For Profit, Greg Lyle, CSIRO Land and Water, Yuna Farm Improvement Group Annual ryegrass seedbanks: the good, the bad, and the ugly, Kathryn Steadman, University of Western Australia, Amander Ellery, CSIRO Plant Industry, Sally C Peltzer, Department of Agriculture Wheat management packages for low rainfall areas, Kari-Lee Falconer, Department of Agriculture Ground water 1. Atrazine, Russell Speed, Department of Agriculture Groundwater 2. Current Trends, Russell Speed, Department of Agriculture Herbicide tolerance of wheat, lupins and pastures, Terry Piper and Harmohinder Dhammu, Department of Agriculture Farming with Tramlines, Bindi Webb, Paul Blackwell, Department of Agriculture, Phil Logue, Binnu, Nigel Moffat, Geraldton, Rohan Ford, Binnu, Miles Obst, Mingenew, The role of green manure crops in renovating poor performing paddocks: What’s it worth? Frances Hoyle, Leanne Schulz and Judith Devenish Department of Agriculture The looming threat of wild radish, Peter Newman, Department of Agriculture Does one ‘size’ fit all? Grant Morrow, Syngenta Crop Protection Climate Forecasts on the Internet, Ian Foster and David Stephens, Department of Agriculture Moisture delving = more reliable lupin establishment, Paul Blackwell, and Wayne Parker, Department of Agriculture Tramline Designs for better Weed control and Wheat value from non-spraying tramlines in a dry season, Paul Blackwell, Bindi Webb and Darshan Sharma, Department of Agriculture Biserrula Grazing Trial, Marnie Thomas, Department of Agriculture Performance of IT and TT canola varieties in the medium and high rainfall agzones of W.A., 2001-02, Graham Walton, Hasan Zaheer and Paul Carmody, Department of Agriculture Rapid Catchment Appraisal in Northern Agricultural Region, Mike Clarke, Paul Raper, Department of Agricultur