http://www.dspace.cam.ac.uk:80/handle/1810/228588 Thu, 20 Jun 2013 01:39:46 GMT 2013-06-20T01:39:46Z http://www.dspace.cam.ac.uk:80/handle/1810/244683 Title: Effects of emotion recognition training on mood among individuals with high levels of depressive symptoms: study protocol for a randomised controlled trial Authors: Adams, Sally; Penton-Voak, Ian S; Harmer, Catherine J; Holmes, Emily A; Munafò, Marcus R Abstract: Abstract Background We have developed a new paradigm that targets the recognition of facial expression of emotions. Here we report the protocol of a randomised controlled trial of the effects of emotion recognition training on mood in a sample of individuals with depressive symptoms over a 6-week follow-up period. Methods/Design We will recruit 190 adults from the general population who report high levels of depressive symptoms (defined as a score ≥ 14 on the Beck Depression Inventory-II). Participants will attend a screening session and will be randomised to intervention or control procedures, repeated five times over consecutive days (Monday to Friday). A follow-up session will take place at end-of -treatment, 2-weeks and 6-weeks after training. Our primary study outcome will be depressive symptoms, Beck Depression Inventory- II (rated over the past two weeks). Our secondary outcomes are: depressive symptoms, Hamilton Rating Scale for Depression; anxiety symptoms, Beck Anxiety Inventory (rated over the past month); positive affect, Positive and Negative Affect Schedule (rated as ‘how you feel right now’); negative affect, Positive and Negative Affect Schedule (rated as ‘how you feel right now’); emotion sensitivity, Emotion Recognition Task (test phase); approach motivation and persistence, the Fishing Game; and depressive interpretation bias, Scrambled Sentences Test. Discussion This study is of a novel cognitive bias modification technique that targets biases in emotional processing characteristic of depression, and can be delivered automatically via computer, Internet or Smartphone. It therefore has potential to be a valuable cost-effective adjunctive treatment for depression which may be used together with more traditional psychotherapy, cognitive-behavioural therapy and pharmacotherapy. Trial registration Current Controlled Trials: ISRCTN17767674 Fri, 31 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244683 2013-05-31T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244681 Title: Depletion of polycistronic transcripts using short interfering RNAs: cDNA synthesis method affects levels of non-targeted genes determined by quantitative PCR Authors: Hanning, Jennifer E; Groves, Ian J; Pett, Mark R; Coleman, Nicholas Abstract: Abstract Background Short interfering RNAs (siRNAs) are often used to deplete viral polycistronic transcripts, such as those encoded by human papillomavirus (HPV). There are conflicting data in the literature concerning how siRNAs targeting one HPV gene can affect levels of other genes in the polycistronic transcripts. We hypothesised that the conflict might be partly explained by the method of cDNA synthesis used prior to transcript quantification. Findings We treated HPV16-positive cervical keratinocytes with siRNAs targeting the HPV16 E7 gene and used quantitative PCR to compare transcript levels of E7 with those of E6 and E2, viral genes located upstream and downstream of the target site respectively. We compared our findings from cDNA generated using oligo-dT primers alone with those from cDNA generated using a combination of random hexamer and oligo-dT primers. Our data show that when polycistronic transcripts are targeted by siRNAs, there is a period when untranslatable cleaved mRNA upstream of the siRNA binding site remains detectable by PCR, if cDNA is generated using random hexamer primers. Such false indications of mRNA abundance are avoided using oligo-dT primers. The period corresponds to the time taken for siRNA activity and degradation of the cleaved transcripts. Genes downstream of the siRNA binding site are detectable during this interval, regardless of how the cDNA is generated. Conclusions These data emphasise the importance of the cDNA synthesis method used when measuring transcript abundance following siRNA depletion of polycistronic transcripts. They provide a partial explanation for erroneous reports suggesting that siRNAs targeting HPV E7 can have gene-specific effects. Mon, 20 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244681 2013-05-20T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244680 Title: HIV mortality in urban slums of Nairobi, Kenya 2003¿2010: a period effect analysis Authors: Oti, Samuel O; Mutua, Michael; Mgomella, George S; Egondi, Thaddaeus; Ezeh, Alex; Kyobutungi, Catherine Abstract: Abstract Background It has been almost a decade since HIV was declared a national disaster in Kenya. Antiretroviral therapy (ART) provision has been a mainstay of HIV treatment efforts globally. In Kenya, the government started ART provision in 2003 with significantly scale-up after 2006. This study aims to demonstrate changes in population-level HIV mortality in two high HIV prevalence slums in Nairobi with respect to the initiation and subsequent scale-up of the national ART program. Methods We used data from 2070 deaths of people aged 15–54 years that occurred between 2003 and 2010 in a population of about 72,000 individuals living in two slums covered by the Nairobi Urban Health and Demographic Surveillance System. Only deaths for which verbal autopsy was conducted were included in the study. We divided the analysis into two time periods: the “early” period (2003–2006) which coincides with the initiation of ART program in Kenya, and the “late” period (2007–2010) which coincides with the scale up of the program nationally. We calculated the mortality rate per 1000 person years by gender and age for both periods. Poisson regression was used to predict the risk of HIV mortality in the two periods while controlling for age and gender. Results Overall, HIV mortality declined significantly from 2.5 per 1,000 person years in the early period to 1.7 per 1,000 person years in the late period. The risk of dying from HIV was 53 percent less in the late period compared to the period before, controlling for age and gender. Women experienced a decline in HIV mortality between the two periods that was more than double that of men. At the same time, the risk of non-HIV mortality did not change significantly between the two time periods. Conclusions Population-level HIV mortality in Nairobi’s slums was significantly lower in the approximate period coinciding with the scale-up of ART provision in Kenya. However, further studies that incorporate ART coverage data in mortality estimates are needed. Such information will enhance our understanding of the full impact of ART scale-up in reducing adult mortality among marginalized slum populations in Kenya. Sun, 16 Jun 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244680 2013-06-16T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244679 Title: Short and long-term genome stability analysis of prokaryotic genomes Authors: Brilli, Matteo; Liò, Pietro; Lacroix, Vincent; Sagot, Marie-France Abstract: Abstract Background Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. Results We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. Conclusion In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were able to explore genome organization stability at different time-scales and to find significant differences for pathogen and non-pathogen species. The output of our framework also allows to identify the conserved gene clusters and/or partial occurrences thereof, making possible to explore how gene clusters assembled during evolution. Tue, 07 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244679 2013-05-07T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244678 Title: Development and validation of a robust automated analysis of plasma phospholipid fatty acids for metabolic phenotyping of large epidemiological studies Authors: Wang, Laura Y; Summerhill, Keith; Rodriguez-Canas, Carmen; Mather, Ian; Patel, Pinal; Eiden, Michael; Young, Stephen; Forouhi, Nita G; Koulman, Albert Abstract: Abstract A fully automated, high-throughput method was developed to profile the fatty acids of phospholipids from human plasma samples for application to a large epidemiological sample set (n > 25,000). We report here on the data obtained for the quality-control materials used with the first 860 batches, and the validation process used. The method consists of two robotic systems combined with gas chromatography, performing lipid extraction, phospholipid isolation, hydrolysis and derivatization to fatty-acid methyl esters, and on-line analysis. This is the first report showing that fatty-acid profiling is an achievable strategy for metabolic phenotyping in very large epidemiological and genetic studies. Wed, 24 Apr 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244678 2013-04-24T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244675 Title: Campath, calcineurin inhibitor reduction and chronic allograft nephropathy (3C) study: background, rationale, and study protocol Authors: Haynes, Richard; Baigent, Colin; Harden, Paul; Landray, Martin; Akyol, Murat; Asderakis, Argiris; Baxter, Alex; Bhandari, Sunil; Chowdhury, Paramit; Clancy, Marc; Emberson, Jonathan; Gibbs, Paul; Hammad, Abdul; Herrington, Will; Jayne, Kathy; Jones, Gareth; Krishnan, Nithya; Lay, Michael; Lewis, David; Macdougall, Iain; Nathan, Chidambaram; Neuberger, James; Newstead, Chas; Pararajasingam, Ravi; Puliatti, Carmelo; Rigg, Keith; Rowe, Peter; Sharif, Adnan; Sheerin, Neil; Sinha, Sanjay; Watson, Chris; Friend, Peter; The 3C Study Collaborative Group Abstract: Abstract Background Kidney transplantation is the best treatment for patients with end-stage renal failure, but uncertainty remains about the best immunosuppression strategy. Long-term graft survival has not improved substantially, and one possible explanation is calcineurin inhibitor (CNI) nephrotoxicity. CNI exposure could be minimized by using more potent induction therapy or alternative maintenance therapy to remove CNIs completely. However, the safety and efficacy of such strategies are unknown. Methods/Design The Campath, Calcineurin inhibitor reduction and Chronic allograft nephropathy (3C) Study is a multicentre, open-label, randomized controlled trial with 852 participants which is addressing two important questions in kidney transplantation. The first question is whether a Campath (alemtuzumab)-based induction therapy strategy is superior to basiliximab-based therapy, and the second is whether, from 6 months after transplantation, a sirolimus-based maintenance therapy strategy is superior to tacrolimus-based therapy. Recruitment is complete, and follow-up will continue for around 5 years post-transplant. The primary endpoint for the induction therapy comparison is biopsy-proven acute rejection by 6 months, and the primary endpoint for the maintenance therapy comparison is change in estimated glomerular filtration rate from baseline to 2 years after transplantation. The study is sponsored by the University of Oxford and endorsed by the British Transplantation Society, and 18 centers for adult kidney transplant are participating. Discussion Late graft failure is a major issue for kidney-transplant recipients. If our hypothesis that minimizing CNI exposure with Campath-based induction therapy and/or an elective conversion to sirolimus-based maintenance therapy can improve long-term graft function and survival is correct, then patients should experience better graft function for longer. A positive outcome could change clinical practice in kidney transplantation. Trial registration ClinicalTrials.gov, NCT01120028 and ISRCTN88894088 Sun, 05 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244675 2013-05-05T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244674 Title: Applications of the InChI in cheminformatics with the CDK and Bioclipse Authors: Spjuth, Ola; Berg, Arvid; Adams, Samuel; Willighagen, Egon L Abstract: Abstract Background The InChI algorithms are written in C++ and not available as Java library. Integration into software written in Java therefore requires a bridge between C and Java libraries, provided by the Java Native Interface (JNI) technology. Results We here describe how the InChI library is used in the Bioclipse workbench and the Chemistry Development Kit (CDK) cheminformatics library. To make this possible, a JNI bridge to the InChI library was developed, JNI-InChI, allowing Java software to access the InChI algorithms. By using this bridge, the CDK project packages the InChI binaries in a module and offers easy access from Java using the CDK API. The Bioclipse project packages and offers InChI as a dynamic OSGi bundle that can easily be used by any OSGi-compliant software, in addition to the regular Java Archive and Maven bundles. Bioclipse itself uses the InChI as a key component and calculates it on the fly when visualizing and editing chemical structures. We demonstrate the utility of InChI with various applications in CDK and Bioclipse, such as decision support for chemical liability assessment, tautomer generation, and for knowledge aggregation using a linked data approach. Conclusions These results show that the InChI library can be used in a variety of Java library dependency solutions, making the functionality easily accessible by Java software, such as in the CDK. The applications show various ways the InChI has been used in Bioclipse, to enrich its functionality. Wed, 13 Mar 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244674 2013-03-13T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244673 Title: Evidence for new targets and synergistic effect of metronomic celecoxib/fluvastatin combination in pilocytic astrocytoma Authors: Mercurio, Sandy; Padovani, Laetitia; Colin, Carole; Carré, Manon; Tchoghandjian, Aurélie; Scavarda, Didier; Lambert, Sally; Baeza-Kallee, Nathalie; Fernandez, Carla; Chappé, Céline; André, Nicolas; Figarella-Branger, Dominique Abstract: Abstract Background Pilocytic astrocytomas occur predominantly in childhood. In contrast to the posterior fossa location, hypothalamo-chiasmatic pilocytic astrocytomas display a worse prognosis often leading to multiple surgical procedures and/or several lines of chemotherapy and radiotherapy to achieve long-term control. Hypothalamo-chiasmatic pilocytic astrocytomas and cerebellar pilocytic astrocytomas have a distinctive gene signature and several differential expressed genes (ICAM1, CRK, CD36, and IQGAP1) are targets for available drugs: fluvastatin and/or celecoxib. Results Quantification by RT-Q-PCR of the expression of these genes was performed in a series of 51 pilocytic astrocytomas and 10 glioblastomas: they were all significantly overexpressed in hypothalamo-chiasmatic pilocytic astrocytomas relative to cerebellar pilocytic astrocytomas, and CRK and ICAM1 were significantly overexpressed in pilocytic astrocytomas versus glioblastomas.We used two commercially available glioblastoma cell lines and three pilocytic astrocytoma explant cultures to investigate the effect of celecoxib/fluvastatin alone or in combination. Glioblastoma cell lines were sensitive to both drugs and a combination of 100 μM celecoxib and 240 μM fluvastatin was the most synergistic. This synergistic combination was used on the explant cultures and led to massive cell death of pilocytic astrocytoma cells.As a proof of concept, a patient with a refractory multifocal pilocytic astrocytoma was successfully treated with the fluvastatin/celecoxib combination used for 18 months. It was well tolerated and led to a partial tumor response. Conclusion This study reports evidence for new targets and synergistic effect of celecoxib/fluvastatin combination in pilocytic astrocytoma. Because it is non-toxic, this new strategy offers hope for the treatment of patients with refractory pilocytic astrocytoma. Sun, 19 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244673 2013-05-19T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244672 Title: Predictors of change differ for moderate and vigorous intensity physical activity and for weekdays and weekends: a longitudinal analysis Authors: Corder, Kirsten; Craggs, Christopher; Jones, Andrew P; Ekelund, Ulf; Griffin, Simon J; van Sluijs, Esther MF Abstract: Abstract Background Predictors of physical activity (PA) change are rarely investigated separately for different PA intensities and for weekdays/weekends. We investigated whether individual-level predictors of one-year change in objectively-measured physical activity differ for moderate PA (MPA) and vigorous PA (VPA) and for weekends and weekdays. Methods Accelerometer-assessed PA (mins) was obtained at baseline and +1 year (n = 875, 41.5% male, Mean ± SD baseline age: 9.8 ± 0.4 years-old). Potential predictors (n = 38) were assessed at baseline from psychological (e.g. self-efficacy), socio-cultural (e.g. parent support) and environmental domains (e.g. land use). Associations between predictors and change in MPA (2000–3999 counts/minute (cpm)) and VPA (≥4000 cpm) separately for weekdays and weekends were studied using multi-level linear regression. Analyses were adjusted for school clustering, sex and baseline PA. Results Weekend PA declined (MPA decline 4.6 ± 21.8 mins/day; VPA decline: 2.1 ± 20.1 mins/day; both p < 0.001) whereas weekday PA did not significantly change. Higher baseline PA and being a girl were associated with greater PA declines in all four outcomes; remaining predictors differed for MPA and VPA and/or weekdays and weekends. Family logistic support was associated with less of a decline in weekend MPA (CI 95%) 0.15 (0.05, 0.25) and VPA 0.19 (0.09, 0.29), and peer support with less of a decline in weekday MPA 0.18 (0.02, 0.34) and VPA 0.22 (0.06, 0.38). Conclusions Results highlight the relevance of investigating predictors of PA change separately for different PA intensities and for weekdays/weekends. In addition to continued focus on school PA promotion, more effort to target interventions during weekends, such as in the family and community appears important. Encouraging peer support to increase weekday PA and targeting parent support for weekend PA may be health promotion priorities. Mon, 27 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244672 2013-05-27T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244671 Title: DSM-5: the debate continues Authors: Buxbaum, Joseph D; Baron-Cohen, Simon Abstract: Abstract We are fortunate to have invited commentaries from the laboratories of Dr Cathy Lord and Dr Fred Volkmar offering their perspectives on the new Diagnostic and Statistical Manual of Mental Disorders (DSM)-5 criteria for the autism spectrum. Both commentaries note how DSM-5 collapses the earlier diagnostic categories of the pervasive developmental disorders into a single category of autism spectrum disorder. In addition, DSM-5 collapses social and communication domains into a single combined domain. The commentaries go on to discuss the positive aspects of these changes and raise some areas of potential concern. We support the evidence-based changes to autism diagnosis found in DSM-5, and look forward to further studies on the autism phenotype as this has implications for diagnosis and treatment. As our mechanistic understanding of autism improves, diagnoses based on behavioral parameters will continue to provide opportunities for interventions targeting the behaviors, while etiological diagnoses will provide opportunities for interventions tailored to etiology. Tue, 14 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244671 2013-05-14T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244661 Title: Reversed argininosuccinate lyase activity in fumarate hydratase-deficient cancer cells Authors: Zheng, Liang; MacKenzie, Elaine D; Karim, Saadia A; Hedley, Ann; Blyth, Karen; Kalna, Gabriela; Watson, David G; Szlosarek, Peter; Frezza, Christian; Gottlieb, Eyal Abstract: Abstract Background Loss of function of fumarate hydratase (FH), the mitochondrial tumor suppressor and tricarboxylic acid (TCA) cycle enzyme, is associated with a highly malignant form of papillary and collecting duct renal cell cancer. The accumulation of fumarate in these cells has been linked to the tumorigenic process. However, little is known about the overall effects of the loss of FH on cellular metabolism. Methods We performed comprehensive metabolomic analyses of urine from Fh1-deficient mice and stable isotopologue tracing from human and mouse FH-deficient cell lines to investigate the biochemical signature of the loss of FH. Results The metabolomics analysis revealed that the urea cycle metabolite argininosuccinate is a common metabolic biomarker of FH deficiency. Argininosuccinate was found to be produced from arginine and fumarate by the reverse activity of the urea cycle enzyme argininosuccinate lyase (ASL), making these cells auxotrophic for arginine. Depleting arginine from the growth media by the addition of pegylated arginine deiminase (ADI-PEG 20) decreased the production of argininosuccinate in FH-deficient cells and reduced cell survival and proliferation. Conclusions These results unravel a previously unidentified correlation between fumarate accumulation and the urea cycle enzyme ASL in FH-deficient cells. The finding that FH-deficient cells become auxotrophic for arginine opens a new therapeutic perspective for the cure of hereditary leiomyomatosis and renal cell cancer (HLRCC). Thu, 21 Mar 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244661 2013-03-21T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244633 Title: An automated graphics tool for comparative genomics: the Coulson plot generator Authors: Field, Helen I; Coulson, Richard MR; Field, Mark C Abstract: Abstract Background Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. Results We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. Conclusions CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes. Availability CPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html Fri, 26 Apr 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244633 2013-04-26T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244630 Title: A structural role for the PHP domain in E. coli DNA polymerase III Authors: Barros, Tiago; Guenther, Joel; Kelch, Brian; Anaya, Jordan; Prabhakar, Arjun; O’Donnell, Mike; Kuriyan, John; Lamers, Meindert H Abstract: Abstract Background In addition to the core catalytic machinery, bacterial replicative DNA polymerases contain a Polymerase and Histidinol Phosphatase (PHP) domain whose function is not entirely understood. The PHP domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. In E. coli DNA polymerase III, however, the PHP domain has lost several metal-coordinating residues and is likely to be catalytically inactive. Results Genomic searches show that the loss of metal-coordinating residues in polymerase PHP domains is likely to have coevolved with the presence of a separate proofreading exonuclease that works with the polymerase. Although the E. coli Pol III PHP domain has lost metal-coordinating residues, the structure of the domain has been conserved to a remarkable degree when compared to that of metal-binding PHP domains. This is demonstrated by our ability to restore metal binding with only three point mutations, as confirmed by the metal-bound crystal structure of this mutant determined at 2.9 Å resolution. We also show that Pol III, a large multi-domain protein, unfolds cooperatively and that mutations in the degenerate metal-binding site of the PHP domain decrease the overall stability of Pol III and reduce its activity. Conclusions While the presence of a PHP domain in replicative bacterial polymerases is strictly conserved, its ability to coordinate metals and to perform proofreading exonuclease activity is not, suggesting additional non-enzymatic roles for the domain. Our results show that the PHP domain is a major structural element in Pol III and its integrity modulates both the stability and activity of the polymerase. Mon, 13 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244630 2013-05-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244612 Title: Walking and cycling to work despite reporting an unsupportive environment: insights from a mixed-method exploration of counterintuitive findings Authors: Guell, Cornelia; Panter, Jenna; Ogilvie, David Abstract: Abstract Background Perceptions of the environment appear to be associated with walking and cycling. We investigated the reasons for walking and cycling to or from work despite reporting an unsupportive route environment in a sample of commuters. Methods This mixed-method analysis used data collected as part of the Commuting and Health in Cambridge study. 1164 participants completed questionnaires which assessed the travel modes used and time spent on the commute and the perceived environmental conditions on the route to work. A subset of 50 also completed qualitative interviews in which they discussed their experiences of commuting. Participants were included in this analysis if they reported unsupportive conditions for walking or cycling on their route (e.g. heavy traffic) in questionnaires, walked or cycled all or part of the journey to work, and completed qualitative interviews. Using content analysis of these interviews, we investigated their reasons for walking or cycling. Results 340 participants reported walking or cycling on the journey to work despite unsupportive conditions, of whom 15 also completed qualitative interviews. From these, three potential explanations emerged. First, some commuters found strategies for coping with unsupportive conditions. Participants described knowledge of the locality and opportunities for alternative routes more conducive to active commuting, as well as their cycling experience and acquired confidence to cycle in heavy traffic. Second, some commuters had other reasons for being reliant on or preferring active commuting despite adverse environments, such as childcare arrangements, enjoyment, having more control over their journey time, employers’ restrictions on car parking, or the cost of petrol or parking. Finally, some survey respondents appeared to have reported not their own environmental perceptions but those of others such as family members or ‘the public’, partly to make a political statement regarding the adversity of active commuting in their setting. Conclusions Participants report walking and cycling to work despite adverse environmental conditions. Understanding this resilience might be just as important as investigating ‘barriers’ to cycling. These findings suggest that developing knowledge of safe walking and cycling routes, improving cycling confidence and restricting workplace parking may help to encourage walking and cycling to and from work. Thu, 23 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244612 2013-05-23T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244608 Title: Functional modelling of planar cell polarity: an approach for identifying molecular function Authors: Hazelwood, Lee D; Hancock, John M Abstract: Abstract Background Cells in some tissues acquire a polarisation in the plane of the tissue in addition to apical-basal polarity. This polarisation is commonly known as planar cell polarity and has been found to be important in developmental processes, as planar polarity is required to define the in-plane tissue coordinate system at the cellular level. Results We have built an in-silico functional model of cellular polarisation that includes cellular asymmetry, cell-cell signalling and a response to a global cue. The model has been validated and parameterised against domineering non-autonomous wing hair phenotypes in Drosophila. Conclusions We have carried out a systematic comparison of in-silico polarity phenotypes with patterns observed in vivo under different genetic manipulations in the wing. This has allowed us to classify the specific functional roles of proteins involved in generating cell polarity, providing new hypotheses about their specific functions, in particular for Pk and Dsh. The predictions from the model allow direct assignment of functional roles of genes from genetic mosaic analysis of Drosophila wings. Mon, 13 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244608 2013-05-13T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244606 Title: Lignin biosynthesis perturbations affect secondary cell wall composition and saccharification yield in Arabidopsis thaliana Authors: Van Acker, Rebecca; Vanholme, Ruben; Storme, Véronique; Mortimer, Jennifer C; Dupree, Paul; Boerjan, Wout Abstract: Abstract Background Second-generation biofuels are generally produced from the polysaccharides in the lignocellulosic plant biomass, mainly cellulose. However, because cellulose is embedded in a matrix of other polysaccharides and lignin, its hydrolysis into the fermentable glucose is hampered. The senesced inflorescence stems of a set of 20 Arabidopsis thaliana mutants in 10 different genes of the lignin biosynthetic pathway were analyzed for cell wall composition and saccharification yield. Saccharification models were built to elucidate which cell wall parameters played a role in cell wall recalcitrance. Results Although lignin is a key polymer providing the strength necessary for the plant’s ability to grow upward, a reduction in lignin content down to 64% of the wild-type level in Arabidopsis was tolerated without any obvious growth penalty. In contrast to common perception, we found that a reduction in lignin was not compensated for by an increase in cellulose, but rather by an increase in matrix polysaccharides. In most lignin mutants, the saccharification yield was improved by up to 88% cellulose conversion for the cinnamoyl-coenzyme A reductase1 mutants under pretreatment conditions, whereas the wild-type cellulose conversion only reached 18%. The saccharification models and Pearson correlation matrix revealed that the lignin content was the main factor determining the saccharification yield. However, also lignin composition, matrix polysaccharide content and composition, and, especially, the xylose, galactose, and arabinose contents influenced the saccharification yield. Strikingly, cellulose content did not significantly affect saccharification yield. Conclusions Although the lignin content had the main effect on saccharification, also other cell wall factors could be engineered to potentially increase the cell wall processability, such as the galactose content. Our results contribute to a better understanding of the effect of lignin perturbations on plant cell wall composition and its influence on saccharification yield, and provide new potential targets for genetic improvement. Thu, 25 Apr 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244606 2013-04-25T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244603 Title: The histone deacetylase inhibitor sodium valproate causes limited transcriptional change in mouse embryonic stem cells but selectively overrides Polycomb-mediated Hoxb silencing Authors: Boudadi, Elsa; Stower, Hannah; Halsall, John A; Rutledge, Charlotte E; Leeb, Martin; Wutz, Anton; O’Neill, Laura P; Nightingale, Karl P; Turner, Bryan M Abstract: Abstract Background Histone deacetylase inhibitors (HDACi) cause histone hyperacetylation and H3K4 hypermethylation in various cell types. They find clinical application as anti-epileptics and chemotherapeutic agents, but the pathways through which they operate remain unclear. Surprisingly, changes in gene expression caused by HDACi are often limited in extent and can be positive or negative. Here we have explored the ability of the clinically important HDACi valproic acid (VPA) to alter histone modification and gene expression, both globally and at specific genes, in mouse embryonic stem (ES) cells. Results Microarray expression analysis of ES cells exposed to VPA (1 mM, 8 h), showed that only 2.4% of genes showed a significant, >1.5-fold transcriptional change. Of these, 33% were down-regulated. There was no correlation between gene expression and VPA-induced changes in histone acetylation or H3K4 methylation at gene promoters, which were usually minimal. In contrast, all Hoxb genes showed increased levels of H3K9ac after exposure to VPA, but much less change in other modifications showing bulk increases. VPA-induced changes were lost within 24 h of inhibitor removal. VPA significantly increased the low transcription of Hoxb4 and Hoxb7, but not other Hoxb genes. Expression of Hoxb genes increased in ES cells lacking functional Polycomb silencing complexes PRC1 and PRC2. Surprisingly, VPA caused no further increase in Hoxb transcription in these cells, except for Hoxb1, whose expression increased several fold. Retinoic acid (RA) increased transcription of all Hoxb genes in differentiating ES cells within 24 h, but thereafter transcription remained the same, increased progressively or fell progressively in a locus-specific manner. Conclusions Hoxb genes in ES cells are unusual in being sensitive to VPA, with effects on both cluster-wide and locus-specific processes. VPA increases H3K9ac at all Hoxb loci but significantly overrides PRC-mediated silencing only at Hoxb4 and Hoxb7. Hoxb1 is the only Hoxb gene that is further up-regulated by VPA in PRC-deficient cells. Our results demonstrate that VPA can exert both cluster-wide and locus-specific effects on Hoxb regulation. Tue, 30 Apr 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244603 2013-04-30T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244600 Title: A metadata-aware application for remote scoring and exchange of tissue microarray images Authors: Morris, Lorna; Tsui, Andrew; Crichton, Charles; Harris, Steve; Maccallum, Peter H; Howat, William J; Davies, Jim; Brenton, James D; Caldas, Carlos Abstract: Abstract Background The use of tissue microarrays (TMA) and advances in digital scanning microscopy has enabled the collection of thousands of tissue images. There is a need for software tools to annotate, query and share this data amongst researchers in different physical locations. Results We have developed an open source web-based application for remote scoring of TMA images, which exploits the value of Microsoft Silverlight Deep Zoom to provide a intuitive interface for zooming and panning around digital images. We use and extend existing XML-based standards to ensure that the data collected can be archived and that our system is interoperable with other standards-compliant systems. Conclusion The application has been used for multi-centre scoring of TMA slides composed of tissues from several Phase III breast cancer trials and ten different studies participating in the International Breast Cancer Association Consortium (BCAC). The system has enabled researchers to simultaneously score large collections of TMA and export the standardised data to integrate with pathological and clinical outcome data, thereby facilitating biomarker discovery. Tue, 30 Apr 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244600 2013-04-30T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244597 Title: A combination of mutations in AKR1D1 and SKIV2L in a family with severe infantile liver disease Authors: Morgan, Neil V; Hartley, Jane L; Setchell, Kenneth DR; Simpson, Michael A; Brown, Rachel; Tee, Louise; Kirkham, Sian; Pasha, Shanaz; Trembath, Richard C; Maher, Eamonn R; Gissen, Paul; Kelly, Deirdre A Abstract: Abstract Infantile cholestatic diseases can be caused by mutations in a number of genes involved in different hepatocyte molecular pathways. Whilst some of the essential pathways have a well understood function, such as bile biosynthesis and transport, the role of the others is not known. Here we report the findings of a clinical, biochemical and molecular study of a family with three patients affected with a severe infantile cholestatic disease. A novel homozygous frameshift germline mutation (c.587delG) in the AKR1D1 gene; which encodes the enzyme Δ 4-3-oxosteroid 5β–reductase that is required for synthesis of primary bile acids and is crucial for establishment of normal bile flow, was found in all 3 patients. Although the initial bile acid analysis was inconclusive, subsequent testing confirmed the diagnosis of a bile acid biogenesis disorder. An additional novel homozygous frameshift mutation (c.3391delC) was detected in SKIV2L in one of the patients. SKIV2L encodes a homologue of a yeast ski2 protein proposed to be involved in RNA processing and mutations in SKIV2L were recently described in patients with Tricohepatoenteric syndrome (THES). A combination of autozygosity mapping and whole-exome-sequencing allowed the identification of causal mutations in this family with a complex liver phenotype. Although the initial 2 affected cousins died in the first year of life, accurate diagnosis and management of the youngest patient led to successful treatment of the liver disease and disease-free survival. Wed, 15 May 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244597 2013-05-15T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244596 Title: Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution Authors: Hardcastle, Thomas J; Kelly, Krystyna A Abstract: Abstract Background Pairing of samples arises naturally in many genomic experiments; for example, gene expression in tumour and normal tissue from the same patients. Methods for analysing high-throughput sequencing data from such experiments are required to identify differential expression, both within paired samples and between pairs under different experimental conditions. Results We develop an empirical Bayesian method based on the beta-binomial distribution to model paired data from high-throughput sequencing experiments. We examine the performance of this method on simulated and real data in a variety of scenarios. Our methods are implemented as part of the RbaySeq package (versions 1.11.6 and greater) available from Bioconductor (http://www.bioconductor.org). Conclusions We compare our approach to alternatives based on generalised linear modelling approaches and show that our method offers significant gains in performance on simulated data. In testing on real data from oral squamous cell carcinoma patients, we discover greater enrichment of previously identified head and neck squamous cell carcinoma associated gene sets than has previously been achieved through a generalised linear modelling approach, suggesting that similar gains in performance may be found in real data. Our methods thus show real and substantial improvements in analyses of high-throughput sequencing data from paired samples. Mon, 22 Apr 2013 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244596 2013-04-22T23:00:00Z