Current challenges in de novo plant genome sequencing and assembly

ABSTRACT: Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community

Enhanced Oxygen Ion Conductivity and Mechanistic Understanding in Ba3Nb1-xVxMoO8.5

Funding Sources This research was supported by the Leverhulme trust and the University of Aberdeen. ACKNOWLEDGMENT We also acknowledge STFC-GB for provision of beamtime at ISIS.Peer reviewedPostprin

The suppression of CMR in Nd(Mn1−xCox)AsO0.95F0.05

This research is supported by the EPSRC (research grant EP/L002493/1). We also acknowledge the UK Science and Technology Facilities Council (STFC) for provision of beam time at ISIS.Peer reviewedPostprin

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available, and we used this for sequencing the Saccharomyces cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr specifically for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5-50 kbp) at such high error rates (between approximately 5% and 40% error). With this new method, we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: The contig N50 length is more than ten times greater than an Illumina-only assembly (678 kb versus 59.9 kbp) and has >99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly

The Relationship between the Crystal Structure and Electrical Properties of Oxide Ion Conducting Ba3W1.2Nb0.8O8.6

This research was supported by the University of Aberdeen and EPSRC (research grant EP/L002493/1). We also acknowledge the UK Science and Technology Facilities Council (STFC) for provision of beamtime at ISIS and the ILL.Peer reviewedPostprintPostprin

The crystal structure and electrical properties of the oxide ion conductor Ba3WNbO8.5

This research was supported by the Northern Research Partnership and the University of Aberdeen. We also acknowledge Science and Technology Facilities Council (STFC) for provision of beamtime at ISIS.Peer reviewedPostprin

Type 2 diabetes remission: economic evaluation of the DiRECT/Counterweight‐Plus weight management programme within a primary care randomized controlled trial

Aim: The Counterweight‐Plus weight management programme achieved 46% remission of Type 2 diabetes at 1 year in the DiRECT trial. We estimated the implementation costs of the Counterweight‐Plus programme and its 1‐year cost‐effectiveness in terms of diabetes remission, compared with usual care, from the UK National Health Service (NHS) perspective. Methods: Within‐trial total costs included programme set‐up and running costs (practitioner appointment visits, low‐energy formula diet sachets and training), oral anti‐diabetes and anti‐hypertensive medications, and healthcare contacts. Total costs were calculated for aggregated resource use for each participant and 95% confidence intervals (CI) were based on 1000 non‐parametric bootstrap iterations. Results: One‐year programme costs under trial conditions were estimated at £1137 per participant (95% CI £1071, £1205). The intervention led to a significant cost‐saving of £120 (95% CI £78, £163) for the oral anti‐diabetes drugs and £14 (95% CI £7.9, £22) for anti‐hypertensive medications compared with the control. Deducting the cost‐savings of all healthcare contacts from the intervention cost resulted an incremental cost of £982 (95% CI £732, £1258). Cost per 1 year of diabetes remission was £2359 (95% CI £1668, £3250). Conclusions: Remission of Type 2 diabetes within 1‐year can be achieved at a cost below the annual cost of diabetes (including complications). Providing a reasonable proportion of remissions can be maintained over time, with multiple medical gains expected, as well as immediate social benefits, there is a case for shifting resources within diabetes care budgets to offer support for people with Type 2 diabetes to attempt remission. (Clinical Trial Registry No.: ISRCTN03267836)

The Diabetes Remission Clinical Trial (DiRECT): protocol for a cluster randomised trial

Background: Despite improving evidence-based practice following clinical guidelines to optimise drug therapy, Type 2 diabetes (T2DM) still exerts a devastating toll from vascular complications and premature death. Biochemical remission of T2DM has been demonstrated with weight loss around 15kg following bariatric surgery and in several small studies of non-surgical energy-restriction treatments. The non-surgical Counterweight-Plus programme, running in Primary Care where obesity and T2DM are routinely managed, produces >15 kg weight loss in 33 % of all enrolled patients. The Diabetes UK-funded Counterpoint study suggested that this should be sufficient to reverse T2DM by removing ectopic fat in liver and pancreas, restoring first-phase insulin secretion. The Diabetes Remission Clinical Trial (DiRECT) was designed to determine whether a structured, intensive, weight management programme, delivered in a routine Primary Care setting, is a viable treatment for achieving durable normoglycaemia. Other aims are to understand the mechanistic basis of remission and to identify psychological predictors of response. Methods/Design: Cluster-randomised design with GP practice as the unit of randomisation: 280 participants from around 30 practices in Scotland and England will be allocated either to continue usual guideline-based care or to add the Counterweight-Plus weight management programme, which includes primary care nurse or dietitian delivery of 12-20weeks low calorie diet replacement, food reintroduction, and long-term weight loss maintenance. Main inclusion criteria: men and women aged 20-65years, all ethnicities, T2DM 0-6years duration, BMI 27-45 kg/m2. Tyneside participants will undergo Magnetic Resonance (MR) studies of pancreatic and hepatic fat, and metabolic studies to determine mechanisms underlying T2DM remission. Co-primary endpoints: weight reduction ≥ 15 kg and HbA1c <48 mmol/mol at one year. Further follow-up at 2 years. Discussion: This study will establish whether a structured weight management programme, delivered in Primary Care by practice nurses or dietitians, is a viable treatment to achieve T2DM remission. Results, available from 2018 onwards, will inform future service strategy

Within-trial cost and 1-year cost-effectiveness of the DiRECT/Counterweight-Plus weight-management programme to achieve remission of type 2 diabetes

No abstract available