Wellcome Open Research最新文献

We present a genome assembly from an individual male Pachyrhinus lethierryi (weevil; Arthropoda; Insecta; Coleoptera; Curculionidae). The assembly contains two haplotypes with total lengths of 619.57 megabases and 512.45 megabases. Most of haplotype 1 (99.88%) is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 21.74 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.

We present a genome assembly from an individual male Chrysomela saliceti (leaf beetle; Arthropoda; Insecta; Coleoptera; Chrysomelidae). The assembly contains two haplotypes with total lengths of 738.63 megabases and 703.32 megabases. Most of haplotype 1 (98.68%) is scaffolded into 17 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 21.9 kilobases. Gene annotation of this assembly on Ensembl identified 14 722 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 the trio-binned, haplotype-resolved genome assemblies (released in 2020) of both haplotypes of an individual of the Danio rerio SAT strain, a cross between Tuebingen (maternal) and AB (paternal) strains (zebrafish; Chordata; Actinopteri; Cypriniformes; Cyprinidae). The genome sequence of the paternal haplotype (fDreABH1) is 1,354.1 megabases long, while the genome sequence of the maternal haplotype (fDreTuH) is 1,360.5 megabases long. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.6 kilobases in length.

We present a genome assembly from an individual female Eudonia murana (Moorland Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The assembly contains two haplotypes with total lengths of 729.58 megabases and 550.40 megabases. Most of haplotype 1 (98.55%) is scaffolded into 31 chromosomal pseudomolecules, including the W, Z ₁ and Z ₂ sex chromosomes. Most of haplotype 2 (95.39%) is scaffolded into 28 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.34 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.

We present a genome assembly from an individual Cepaea hortensis (white-lipped garden snail; Mollusca; Gastropoda; Stylommatophora; Helicidae). The genome sequence has a total length of 3 168.99 megabases. Most of the assembly (97.52%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.08 kilobases. Gene annotation of this assembly on Ensembl identified 17 974 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.

Background: The pandemic of antimicrobial resistance (AMR) will only be mitigated by policy action and innovation and importantly, supported by local and community action. Last year (2024) with the United Nations General Assembly high level meeting on AMR in September we decided to ascertain citizens' understanding of the issues and prioritisation for action.

Methods: Over the summer, while intergovernmental negotiations on the outcome document were taking place, we used Deliberative Polling ^®, a methodology founded on deliberative democratic theory, in six middle income countries across three continents to explore people's understanding and support for 45 policies that were likely to feature in the political declaration.

Results: In total 2419 participants were randomised to deliberation intervention (written and video information, facilitated online small group discussions, and expert plenary sessions) or control groups who only completed the pre- and post- deliberation surveys. Support increased significantly through deliberation for 3/4 of the proposals (>90% for 2/3), as well as on knowledge about AMR and internal political efficacy. Proposals relating to infection prevention were most heavily supported across all six countries. We found regional variation in support for proposals relating to informal antibiotic access and the use of antibiotics in food production, with less support for selected proposals from South America.

Conclusions: Deliberative polling is a powerful method of large scale community engagement and this is new for AMR helping us to understand the views of the public relating to policies that will require their support to enact.

We present a genome assembly from an individual male Cyclophora linearia (Clay Triple-lines; Arthropoda; Insecta; Lepidoptera; Geometridae). The assembly contains two haplotypes with total lengths of 280.22 megabases and 284.23 megabases. Most of haplotype 1 (99.9%) is scaffolded into 31 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 16.54 kilobases. Gene annotation of this assembly on Ensembl identified 11 742 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.

Background: Patient and public involvement and engagement (PPIE) in research is a collaboration between researchers, patients, and the public, enhancing research acceptability, relevance, and impact. There is a growing prevalence of PPIE in high-income country research; however, its integration in low- and middle-income countries (LMICs) remains poorly understood. Recognising this gap, the Ziauddin University Clinical Trials Unit in Karachi, Pakistan, launched a dedicated PPIE initiative in 2022. This study evaluates the engagement process and experiences of patient and public members and researchers to identify barriers and facilitators to participation within the PPIE group.

Methods: The evaluation uses an explanatory sequential mixed-method design. First, the Public and Patient Engagement Evaluation Tool (PPEET) questionnaire will be administered online to group members, coordinators, and senior institutional leads. Insights from questionnaires will be further explored during semi-structured interviews, with questions guided by the Patient Engagement in Research (PEIR) framework, supplemented with analysis of project documentation. Study activities will be conducted in both English and Urdu. The study has been co-designed with PPIE members and is co-led with a public partner. Findings will highlight areas for improvement, inform best practices, and guide the development of more effective engagement strategies.

Outcome: Although focused on a single group, this evaluation lays the groundwork for understanding PPIE practices in LMIC contexts. It provides valuable insights into developing equitable partnerships and improving patient-centred research. This study contributes to a growing body of knowledge, offering practical guidance for implementing PPIE in settings with unique socioeconomic challenges and cultural realities. The findings are expected to benefit the local research community and similar initiatives globally, particularly in regions with comparable challenges.

Trypanosoma brucei is an extracellular eukaryotic parasite that causes sleeping sickness in humans and Nagana, Surra and Dourine in livestock, game animals and horses. The parasite displays an extensive immune evasion mechanism, utilising the expression and ability to switch antigenically distinct variant surface glycoprotein (VSG) coats. VSG encoding genes account for ~10% of the T. brucei genome, and mosaic VSGs, assembled from distinct incomplete VSG gene copies, can be produced from this VSG library, generating an almost infinite VSG repertoire, which enables chronic infections. Each parasite expresses just one VSG at a time, but within a host, many VSGs can be expressed simultaneously. Understanding patterns of VSG expression is therefore central to studying parasite dynamics, tissue tropism, and infection persistence. VSGSeq is an amplicon sequencing approach that enables surveillance of the population-wide diversity and abundance of expressed VSGs. We present vsgseq2, an updated and fully reproducible workflow for analysing VSGSeq data. Implemented in Nextflow, vsgseq2 integrates modern tools for transcript assembly and quantification, improves computational efficiency. Benchmarking against defined T. brucei VSG expression datasets demonstrated that vsgseq2 accurately reconstructs population-wide VSG repertoires and better recapitulates VSG expression proportions. Analyses of in vivo infection data further confirmed that vsgseq2 enhances reproducibility and improves data utilisation, and improves computational efficiency. vsgseq2 enables researchers to efficiently and reproducibly analyse complex VSG expression data and the mechanisms driving immune evasion in T. brucei.

Background: Learning platforms can strengthen primary healthcare (PHC) by integrating community knowledge with system decision-making, but evidence on how they work in low-resource settings is limited. This study presents a realist evaluation of the Verbal Autopsy with Participatory Action Research (VAPAR) learning platform in rural Mpumalanga, South Africa (2015-25). VAPAR aimed to embed participatory evidence generation and shared learning within routine district processes to support more equitable, community-linked PHC.

Methods: A realist design was used to synthesise data from five action-learning cycles (2017-23), a preceding pilot (2015-16), and an engagement and uptake phase (2023-25). Data included cycle reports, participatory outputs, verbal autopsy (VA) analyses, 22 endline interviews, policy, strategy and planning documents. Using a co-developed theory of change, qualitative data were coded to examine context-mechanism-outcome patterns. Mechanisms were identified and refined through cross-cycle comparison, triangulation, and stakeholder validation.

Results: VAPAR was contextually responsive, adapting to shocks such as COVID-19 and progressively embedding within the district health system. Through regular dialogue, the platform activated generative mechanisms of trust-building, role clarity and recognition, collective sense-making, and strengthened agency, particularly among Community Health Workers (CHWs), whose skills, confidence and legitimacy expanded. These mechanisms operated within an enabling structural context shaped by PHC reforms that strengthened the District Health System and Ward-Based Primary Health Care Outreach Teams, alongside trade-union action for CHW absorption into public service. Institutionalisation followed through Mpumalanga's revitalised Health Promotion Programme, with adaptation to additional provinces and for outbreak response and emergency obstetric care. Outcomes were interpreted through context-mechanism-outcome patterns, illustrating how participatory learning becomes embedded in decentralised health systems.

Conclusions: Over a decade, VAPAR demonstrated how structured, participatory learning can reshape relationships, strengthen community-linked PHC, and support institutionalisation of routine, evidence-informed practice in decentralised health systems. The findings offer transferable lessons for sustaining learning platforms in resource-constrained settings.