Phenotypic and Genetic Consequences of Size Selection at the Larval Stage in the Pacific Oyster (Crassostrea gigas)

The life histories of oysters in the genus "Crassostrea", like those of most marine bivalves, are typified by high fecundity and low survival in nature. Rearing conditions in hatcheries however ensure optimized density, diet, and temperature. Hatcheries are becoming increasingly important for the production of juveniles in aquaculture, and their culture practices often include culling of slow growing larvae to reduce and synchronize the time taken to reach settlement. Because previous studies have found substantial genetic variation for early life developmental traits in "Crassostrea gigas", these culling practices are likely to cause highly different selective pressures in hatcheries from those in the natural environment. We studied the phenotypic and genetic impact of such culling practices in a factorial cross between 10 males and 3 females subjected to progressive culling of the smallest 50% of larvae, compared with a non-culled control. Measurements were made on larval growth, survival, time taken to attain pediveliger stage and settlement success. Culling had a larger effect on the variance of these larval traits than on their means. The larvae in culled cultures were approximately 10% larger than those in controls, whereas the coefficient of variation was reduced by 30 -40%. Culling also reduced the mean time to settlement by 12% and its variance by 55%. Using a multiplexed set of microsatellite markers to trace parentage, we also estimated the variance in reproductive success in a controlled experiment to quantify the consequences of intensive hatchery rearing practices. We also focused on changes in effective population size and genetic structure over time (and developmental stages). Our results show a loss of genetic diversity following removal of the smallest larvae by culling, as well as temporally varying genetic structure of the larval population. This supports the existence of genetic variability in early life developmental traits in C. gigas. Culling in hatcheries, like size-related selective pressures in the wild, are likely to have a significant genetic impact, through their effects on the timing of settlement

Filling the intervention gap: service evaluation of an intensive nonsurgical weight management programme for severe and complex obesity

Background: Weight management including formula total diet replacement (TDR) is emerging as an effective intervention for severe and complex obesity, particularly with respect to type 2 diabetes (T2DM). However, no prospective audit and service evaluation of such programmes have been reported. Methods: Following initial feasibility piloting, the Counterweight‐Plus programme was commissioned across a variety of healthcare providers. The programme includes: Screening, TDR (formula low energy diet), food reintroduction and weight loss maintenance, all delivered by staff with 8 h of training, in‐service mentoring, ongoing specialist support and access to medical consultant expertise. Anonymised data are returned centrally for clinical evaluation. Results: Up to December 2016, 288 patients commenced the programme. Mean (SD) baseline characteristics were: age 47.5 (12.7) years, weight 128.0 (32.0) kg, body mass index 45.7 (10.1) kg m−2, n = 76 (26.5%) were male and n = 99 (34.5%) had T2DM. On an intention‐to‐treat (ITT) basis, a loss of ≥15 kg at 12 months was achieved by 48 patients, representing 22.1% of all who started and 40% of those who maintained engagement. For complete cases, mean (95% confidence interval) weight loss was 13.3 (12.1–14.4) kg at 3 months, 16.0 (14.4–17.6) kg at 6 months and 14.2 (12.1–16.3) kg at 12 months (all P < 0.001), with losses to follow‐up of 10.8%, 29.3% and 44.2%, respectively. Mean loss at 12 months by ITT analyses was: single imputation –10.5 (9.5) kg, last observation carried forward –10.9 (11.6) kg and baseline observation carried forward –7.9 (11.1) kg. The presence of diabetes had no significant impact on weight change outcomes. Conclusions: This nonsurgical approach is effective for many individuals with severe and complex obesity, representing an option before considering surgery. The results are equally effective in terms of weight loss for people with T2DM

Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization

Arabidopsis and Medicago truncatula represent sister clades within the dicot subclass Rosidae. We used genetic map-based and bacterial artificial chromosome sequence-based approaches to estimate the level of synteny between the genomes of these model plant species. Mapping of 82 tentative orthologous gene pairs reveals a lack of extended macrosynteny between the two genomes, although marker collinearity is frequently observed over small genetic intervals. Divergence estimates based on non-synonymous nucleotide substitutions suggest that a majority of the genes under analysis have experienced duplication in Arabidopsis subsequent to divergence of the two genomes, potentially confounding synteny analysis. Moreover, in cases of localized synteny, genetically linked loci in M. truncatula often share multiple points of synteny with Arabidopsis; this latter observation is consistent with the large number of segmental duplications that compose the Arabidopsis genome. More detailed analysis, based on complete sequencing and annotation of three M. truncatula bacterial artificial chromosome contigs suggests that the two genomes are related by networks of microsynteny that are often highly degenerate. In some cases, the erosion of microsynteny could be ascribed to the selective gene loss from duplicated loci, whereas in other cases, it is due to the absence of close homologs of M. truncatula genes in Arabidopsis

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies

In the past few years, case-control studies of common diseases have shifted their focus from single genes to whole exomes. New sequencing technologies now routinely detect hundreds of thousands of sequence variants in a single study, many of which are rare or even novel. The limitation of classical single-marker association analysis for rare variants has been a challenge in such studies. A new generation of statistical methods for case-control association studies has been developed to meet this challenge. A common approach to association analysis of rare variants is the burden-style collapsing methods to combine rare variant data within individuals across or within genes. Here, we propose a new hybrid likelihood model that combines a burden test with a test of the position distribution of variants. In extensive simulations and on empirical data from the Dallas Heart Study, the new model demonstrates consistently good power, in particular when applied to a gene set (e.g., multiple candidate genes with shared biological function or pathway), when rare variants cluster in key functional regions of a gene, and when protective variants are present. When applied to data from an ongoing sequencing study of bipolar disorder (191 cases, 107 controls), the model identifies seven gene sets with nominal p-values<0.05, of which one MAPK signaling pathway (KEGG) reaches trend-level significance after correcting for multiple testing. © 2013 Chen et al

Clinicians' perspectives on supporting individuals with severe anorexia nervosa in specialist eating disorder intensive treatment settings

BACKGROUND: Admissions to intensive treatment (i.e., inpatient [IP] and/or day patient [DP]) for individuals with severe anorexia nervosa (AN) are common. Growing literature indicates potential risks and benefits of each intensive treatment approach; however, existing research has focused on patient and carer perspectives of these treatments. Also, there is scant empirical evidence available for guiding the parameters of intensive treatments for AN. We therefore explored clinicians' perspectives and experience of supporting adults with severe AN in intensive settings. METHODS: We conducted twenty one semi-structured interviews with clinicians who deliver intensive treatments (i.e., IP and/or DP) for individuals with severe AN across four specialist Eating Disorder Services in the United Kingdom between May 2020 and June 2021. We asked clinicians about their views and experiences of supporting individuals with severe AN in intensive treatment settings and the challenges and opportunities associated with IP and DP treatment. Data were analysed using reflexive thematic analysis supported by NVivo software. RESULTS: Five broad and interrelated themes were identified: (1) Intensive Support; (2) The Severity of Patients' Illnesses; (3) Hope and Recovery; (4) Which Treatment When; (5) Limited Resources; and (6) Carer Burden. We identified various similarities between the two intensive treatment approaches, including the value of intensive and multidisciplinary support and carer involvement, and the challenge of managing complex and unique needs in resource-limited intensive settings. We also found differences in the relationship of treatment to patients' home environments, the necessity of patient motivation, and the management of risk. CONCLUSIONS: Both intensive treatment settings are valued by clinicians; however, there are unique challenges and opportunities for supporting individuals with severe AN within each. Our findings suggest DP treatment may be used as an alternative to IP treatment for individuals with severe AN. However, clear questions remain over which intensive treatment setting is best suited to which patient when and should be the focus of future research

Autopsy of a failed trial part 1: A qualitative investigation of clinician's views on and experiences of the implementation of the DAISIES trial in UK-based intensive eating disorder services

Objective: The DAISIES trial, comparing inpatient and stepped-care day patient treatment for adults with severe anorexia nervosa was prematurely terminated in March 2022 due to poor recruitment. This qualitative study seeks to understand the difficulties faced during the trial by investigating stakeholders' views on and experiences of its implementation. / Method: Semi-structured interview and focus group transcripts, and trial management and oversight group meeting minutes from May 2020-June 2022 were analysed using thematic analysis. Participants were 47 clinicians and co-investigators involved with the DAISIES trial. The Non-Adoption, Abandonment, Scale-up, Spread, and Sustainability (NASSS) framework was applied to the interpretive themes to classify barriers and facilitators to implementation. / Results: Five themes were identified: incompatible participation interests; changing standard practice; concerns around clinical management; systemic capacity and capability issues; and Covid-19 disrupting implementation. Applying the NASSS framework indicated the greatest implementation challenges to arise with the adopters (e.g. patients, clinicians), the organisational systems (e.g. service capacity), and the wider socio-political context (e.g. Covid-19 closing services). / Conclusions: Our findings emphasise the top-down impact of systemic-level research implementation challenges. The impact of the Covid-19 pandemic accentuated pre-existing organisational barriers to trial implementation within intensive eating disorder services, further limiting the capacity for research

Rapid isolation of cDNA by hybridization

The isolation of genes from a given genomic region can be a rate-limiting step in the discovery of disease genes. We describe an approach to the isolation of cDNAs that have sequences in common with large genomic clones such as bacterial artificial chromosomes. We applied this method to loci both amplified and deleted in cancer, illustrating its usage in the identification of both oncogenes and tumor suppressor genes, respectively. The method, called rapid isolation of cDNAs by hybridization (RICH), depends on solution hybridization, enzymatic modification, and amplification/selection of sequences present in both cDNA populations and the genomic clones. The method should facilitate the development of transcription maps for large genomic clones, possibly even yeast artificial chromosomes

Access to Artemisinin-Based Anti-Malarial Treatment and its Related Factors in Rural Tanzania.

Artemisinin-based combination treatment (ACT) has been widely adopted as one of the main malaria control strategies. However, its promise to save thousands of lives in sub-Saharan Africa depends on how effective the use of ACT is within the routine health system. The INESS platform evaluated effective coverage of ACT in several African countries. Timely access within 24 hours to an authorized ACT outlet is one of the determinants of effective coverage and was assessed for artemether-lumefantrine (Alu), in two district health systems in rural Tanzania. From October 2009 to June 2011we conducted continuous rolling household surveys in the Kilombero-Ulanga and the Rufiji Health and Demographic Surveillance Sites (HDSS). Surveys were linked to the routine HDSS update rounds. Members of randomly pre-selected households that had experienced a fever episode in the previous two weeks were eligible for a structured interview. Data on individual treatment seeking, access to treatment, timing, source of treatment and household costs per episode were collected. Data are presented on timely access from a total of 2,112 interviews in relation to demographics, seasonality, and socio economic status. In Kilombero-Ulanga, 41.8% (CI: 36.6-45.1) and in Rufiji 36.8% (33.7-40.1) of fever cases had access to an authorized ACT provider within 24 hours of fever onset. In neither of the HDSS site was age, sex, socio-economic status or seasonality of malaria found to be significantly correlated with timely access. Timely access to authorized ACT providers is below 50% despite interventions intended to improve access such as social marketing and accreditation of private dispensing outlets. To improve prompt diagnosis and treatment, access remains a major bottle neck and new more innovative interventions are needed to raise effective coverage of malaria treatment in Tanzania

Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data

Background: Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results: The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/ deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions: A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies