Wellcome Open Research最新文献

We present a genome assembly from a specimen of Danio rerio (zebra danio; Chordata; Actinopteri; Cypriniformes; Danionidae). The genome sequence has a total length of 1 413.66 megabases. Most of the assembly (99.85%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome was also assembled, with a length of 16.6 kilobases.

We present a genome assembly from an individual Chelidonichthys lucerna (tub gurnard; Chordata; Actinopteri; Perciformes; Triglidae). The assembly contains two haplotypes with total lengths of 649.07 megabases and 651.58 megabases. Most of haplotype 1 (96.66%) is scaffolded into 24 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.52 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Background: The 7-1-7 metrics with ≤7 days for detection, ≤1 day for notification, ≤7 days to complete early response actions during public health outbreaks, enable early detection, notification, and rapid response. We evaluated the adoption, use of 7-1-7 metrics, and the bottlenecks and enablers for achieving the metrics in the public health sector of Cambodia.

Methods: A sequential explanatory mixed-methods design was used. A cross-sectional study using a structured checklist was employed to assess the level of adoption (26 participants) and a cohort design to assess use of 7-1-7 metrics for the public health events reported between Jan'23 and Jul'2025. A qualitative descriptive study using 6 focus group discussions and 22 key informant interviews was conducted to explore the bottlenecks and enablers in 7-1-7 adoption and implementation.

Results: Adoption of 7-1-7 metrics was achieved at national level and is in progress at the subnational level. Health system readiness, intersectoral coordination, capacity building, budget and resources, and digital data collection were major themes that influence adoption. Among 58 events, 26 were respiratory illnesses. The median (range) time was 6(<1-149) days for detection, with 36(62%) events meeting the target; less than 24 hours(0-4) for notification with 51(88%) events meeting the target; 1(1-101) day for early response with 50(86%) events meeting the target. Overall, 28(48%) events met all targets. Among 168 bottlenecks identified, 86(62%) were for detection, and among the 226 enablers identified, 94(42%) were related to early responses. Key bottlenecks included delayed care-seeking, low awareness among private health workers, and lack of community knowledge. Significant enablers included strong reporting lines and rapid coordinated response mechanisms.

Conclusion: Cambodia has made substantial progress in adopting and implementing the 7-1-7 metrics. Delays in detection remain a key challenge; addressing this through enhanced risk communication, stronger private sector engagement, and improved surveillance capacity will strengthen Cambodia's overall outbreak preparedness.

We present a genome assembly from an individual Biomphalaria glabrata NIMR strain (bloodfluke planorb; Mollusca; Gastropoda; Planorbidae). The genome sequence spans 850.60 megabases. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 13.67 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,327 protein-coding genes.

Background: Children who are HIV-exposed and uninfected (HEU) are at risk of neurodevelopmental delays, potentially via prenatal immune dysregulation. We investigated whether maternal and child peripheral blood immune markers relate to early brain metabolite profiles in children with and without HIV exposure from a South African birth cohort.

Methods: Within the Drakenstein Child Health Study, a neuroimaging subgroup of children underwent single-voxel magnetic resonance spectroscopy at 2-3 years (n=156; 66 HEU, 90 HIV-unexposed). A panel of eighteen immune markers was quantified in blood serum of pregnant women and in their children at 7 weeks and 2 years follow-up. Neurometabolite ratios to creatine were quantified in midline parietal grey matter and left and right parietal white matter. Cross-sectional associations between immune markers and neurometabolite ratios were tested using linear models with robust standard errors, adjusting for age at scan, sex, and voxel tissue composition, and controlling for false discovery rate.

Results: In children who were HEU, higher concentrations of maternal pro-inflammatory cytokines IL-5 (β=0.79, p=0.005) and IL-8 (β=0.64, p=0.02) were positively associated with myo-inositol ratios in midline parietal grey and right parietal white matter regions, respectively. At two years, higher child serum MMP-9 was positively associated with myo-inositol ratios in midline parietal grey matter (β=1.30, p=0.03). Maternal IL-13 was positively associated with glutamate ratios in the midline parietal grey matter of HIV-unexposed peers (β=0.42, p<0.0001), with no association in children who are HEU.

Conclusions: In this South African cohort, HIV exposure-specific associations were observed between certain mother and child immune markers and child neurometabolite ratios at 2-3 years. Larger, longitudinal neuroimaging studies integrating neurodevelopmental outcomes are needed to clarify mechanisms and clinical implications.

Introduction: Metabolomics is the study of measured metabolites and low-molecular weight molecules in a biological specimen, collectively known as the metabolome. Measuring the metabolome in populations is useful for investigating complex, polygenic and multifactorial traits as it can give insight into cellular metabolism and its perturbations in various states of health and disease. Here we present a description of metabolomics data generated using an untargeted mass-spectrometry approach in two studies: (1) the Avon Longitudinal Study of Parents and Children (ALSPAC) - a healthy, general population; and (2) the By-Band-Sleeve trial (BBS) - a pragmatic randomised controlled trial (RCT) of metabolic and bariatric surgery (MBS) plus a non-randomised observational sub-study.

Methods: Samples for this work were collected from ALSPAC participants at 30 years of age. Two sample collection efforts were made within BBS - firstly, from the RCT comparing the effectiveness of three types of MBS: the Roux-en-Y gastric bypass ("bypass"), laparoscopic adjustable gastric band ("band") and the sleeve gastrectomy ("sleeve"), and secondly from the non-randomised (observational) study of MBS. In both instances, samples were collected from patients before and after surgery. In total, 2128 samples were sent for mass-spectrometry (MS) metabolomics analysis by Metabolon (Discovery HD4 platform). Data underwent quality control (QC) via a standard pipeline using the R package metaboprep.

Results: After QC, the combined dataset consists of semi-quantitative data for 1176 features in 517 ALSPAC participants and 1062 BBS participants (1018 from the RCT and 44 from the non-randomised study) (1013 pre-surgery samples and 421 post-surgery samples).

Conclusion: Overall, we have provided a summary of MS data produced across two different study populations, described the QC procedures undertaken and provided some data validation analyses. Bringing together samples from these two studies in a single experiment offers a novel study design able to explore the biological implications of weight and intentional weight loss.

The objectives of this integrative systematic review were to describe how community researchers (CRs) in low-and middle-income country (LMIC) settings are recruited, trained and supported in research projects, to identify facilitators, challenges and impacts of involving CRs, and to explore CRs' own experiences of conducting research. This area has not previously been synthesised across studies, thereby offering an original contribution to the evidence base. Primary research studies, of any study design and in any language, that provided insights into the review objectives in LMICs were included in the review. Search strategies included database searches and backward and forward chaining. Seven databases were searched on 5th November 2024 without date or language limits: Medline, Embase, CINAHL, PsycINFO, SocINDEX, Web of Science and Global Index Medicus. Quality assessment of included studies was conducted using the Mixed-Methods Appraisal Tool (MMAT). Qualitative synthesis of the findings was undertaken using a reflexive thematic approach. Overall, 39 papers reporting 27 studies were included in the review, with only seven papers scoring under 80% on the MMAT. Findings were synthesised over four themes: (1) recruitment, engagement and support; (2) benefits and challenges to the community researchers and communities; (3) benefits and challenges to the research; (4) ethics of engagement. Engaging CRs offers clear benefits, including improved access to marginalised groups, reduced power imbalances, and richer, culturally informed data. However, this review also highlights ethical concerns, emotional strain, and inequitable compensation, particularly in LMIC contexts where there are structural inequalities, limited resources, and sociocultural challenges. These findings highlight the need for research teams to adopt more ethical and inclusive approaches to CR involvement. Priorities include attribute-based recruitment processes, comprehensive training and ongoing support, fair remuneration, and structures that protect CRs' wellbeing. Strengthening these practices is essential to minimise harm, enhance data quality, and ensure community-engaged research delivers meaningful and equitable benefits.

We present a genome assembly from an individual female Dryobotodes eremita (the Brindled Green; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 709.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,706 protein coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

We present a genome assembly from a male specimen of Limenitis populi (Poplar Admiral; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 342.08 megabases and 341.73 megabases. Most of haplotype 1 (99.97%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.22 kilobases. Gene annotation of this assembly on Ensembl identified 11 495 protein-coding genes. This work is part of Project Psyche, a collaborative programme generating genomes for European butterflies and moths.

We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria ( Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales ( Candidatus Poriferisodalaceae), among others.