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A project to identify the phenotypes of disruptive mutations in every zebrafish protein-coding gene has so far revealed potentially disruptive mutations in more than 38% of the protein-coding genes, and the phenotypic consequences of each allele can be assessed using a novel multi-allelic phenotyping scheme. The zebrafish genome The genome of the zebrafish — a key model organism for the study of development and human disease — has now been sequenced and published as a well-annotated reference genome. Zebrafish turns out to have the largest gene set of any vertebrate so far sequenced, and few pseudogenes. Importantly for disease studies, comparison between human and zebrafish sequences reveals that 70% of human genes have at least one obvious zebrafish orthologue. A second paper reports on an ongoing effort to identify and phenotype disruptive mutations in every zebrafish protein-coding gene. Using the reference genome sequence along with high-throughput sequencing and efficient chemical mutagenesis, the project's initial results — covering 38% of all known protein-coding genes — they describe phenotypic consequences of more than 1,000 alleles. The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. All mutant alleles and data are freely available at go.nature.com/en6mos . Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in model vertebrate organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches 1 , 2 , 3 and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes 3 , 4 , this number falls considerably short of the more than 22,000 mouse protein-coding genes 5 . Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning 6 , insertional mutagenesis 7 , 8 , 9 , antisense morpholino oligonucleotides 10 , targeted re-sequencing 11 , 12 , 13 , and zinc finger and TAL endonucleases 14 , 15 , 16 , 17 have made substantial contributions to our understanding of the biological activity of vertebrate genes, but again the number of genes studied falls well short of the more than 26,000 zebrafish protein-coding genes 18 . Importantly, for both mice and zebrafish, none of these strategies are particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Here we describe an active project that aims to identify and phenotype the disruptive mutations in every zebrafish protein-coding gene, using a well-annotated zebrafish reference genome sequence 18 , 19 , high-throughput sequencing and efficient chemical mutagenesis. So far we have identified potentially disruptive mutations in more than 38% of all known zebrafish protein-coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1,000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.

Background Insecticide-treated nets (ITNs) contributed significantly to the decline in malaria since 2000. Their protective efficacy depends not only on access, use, and net integrity, but also location of people within the home environment and mosquito biting profiles. Anopheline mosquito biting and human location data were integrated to identify potential gaps in protection and better understand malaria transmission dynamics in Busia County, western Kenya. Methods Direct observation of human activities and human landing catches (HLC) were performed hourly between 1700 to 0700 h. Household members were recorded as home or away; and, if at home, as indoors/outdoors, awake/asleep, and under a net or not. Aggregated data was analysed by weighting hourly anopheline biting activity with human location. Standard indicators of human-vector interaction were calculated using a Microsoft Excel template. Results There was no significant difference between indoor and outdoor biting for Anopheles gambiae sensu lato ( s.l. ) (RR = 0.82; 95% CI 0.65–1.03); significantly fewer Anopheles funestus were captured outdoors than indoors (RR = 0.41; 95% CI 0.25–0.66). Biting peaked before dawn and extended into early morning hours when people began to awake and perform routine activities, between 0400–0700 h for An. gambiae and 0300–0700 h for An. funestus . The study population away from home peaked at 1700–1800 h (58%), gradually decreased and remained constant at 10% throughout the night, before rising again to 40% by 0600–0700 h. When accounting for resident location, nearly all bites within the peri-domestic space (defined as inside household structures and surrounding outdoor spaces) occurred indoors for unprotected people (98%). Using an ITN while sleeping was estimated to prevent 79% and 82% of bites for An. gambiae and An. funestus, respectively. For an ITN user, most remaining exposure to bites occurred indoors in the hours before bed and early morning. Conclusion While use of an ITN was estimated to prevent most vector bites in this context, results suggest gaps in protection, particularly in the early hours of the morning when biting peaks and many people are awake and active. Assessment of additional human exposure points, including outside of the peri-domestic setting, are needed to guide supplementary interventions for transmission reduction.

Background Over the past decade, food insecurity, connected to erratic rains and reduced agricultural outputs, has plagued Malawi. Many households are turning to fishing to seek additional sources of income and food. There is anecdotal evidence that insecticide-treated net (ITN) recipients in Malawi are using their nets for purposes other than sleeping, such as for fishing, protecting crops, and displaying merchandise, among others. The objective of this qualitative study was to explore the factors leading residents of waterside communities in Malawi to use ITNs for fishing. Methods This study used qualitative and observational methods. Five waterside communities were identified, two each in the North, Central and Southern regions, representing a mix of lakeside and riverside settings. Fifteen focus group discussions were conducted with a total of 146 participants, including men, women, and community leaders. Results Respondents stated that they knew that ITNs should be slept under to protect from malaria. Respondents discussed financial hardships their communities were facing due to droughts, poverty, food scarcity, unemployment, and devaluation of the Malawian currency, the kwacha . Many described selling household goods, including clothes and cooking pots, to generate short-term income for their family. Though no respondents admitted to selling an ITN themselves, the practice was commonly known. Participants said that food shortages were forcing them to make difficult choices. Fishing with ITNs was reported to be common in the study sites, as a response to food insecurity, and was widely understood to be harmful over the longer term. Respondents felt that it was everyone’s responsibility to cut down on this practice, but that efforts to confiscate or burn nets and boats of those caught fishing with ITNs were counter-productive since boats, especially, were a required resource for a productive livelihood. Respondents feared that if the health workers, government officials and donors continued to see ITNs being misused for fishing, the distribution of free ITNs would end, which would worsen malaria in their communities. Conclusions Faced with economic hardships and food security crises, participants reported being forced to look for alternative incomes to feed their families. This sometimes included selling or repurposing their belongings, including ITNs, for income. This issue is complex and will require a community-led multisectoral response to preserve health, fisheries, and livelihoods.

Background In response to reports of thrombosis with thrombocytopenia syndrome (TTS) post-vaccination, the Johnson & Johnson (J&J) vaccine was paused and then restarted in April 2021. Our objective was to assess whether this pause adversely impacted vaccine confidence. Methods Two large internet-based surveys were conducted in the US among adults to measure knowledge, attitudes and perceptions of the J&J vaccine pause and rates of vaccine hesitancy among unvaccinated persons before, during and after the pause. Results Among 66% of respondents aware of the pause, 44% identified blood clots as the reason for the pause without prompting. The impact of the pause on vaccine behavior among unvaccinated persons and perception of the vaccine safety system was mixed and modified by trust in the public health authorities. Those who were less willing to get vaccinated because of the pause were less inclined for all vaccines, not only the J&J product. Moreover, a notable proportion (22.1%) of the small number of persons (n = 30) vaccinated with the J&J vaccine after the pause reported not receiving information about the risk of TTS. The proportion of unvaccinated persons who were hesitant was increasing before and during the pause and then leveled off after the pause. Conclusions The J&J vaccine pause is unlikely to be a major barrier to vaccine uptake. Public attitudes about vaccines may be more resilient than appreciated, especially when safety issues are investigated with transparent communication. This paper has important implications for messaging and program administration with future vaccine-specific adverse events. Efforts may be warranted to ensure all persons being offered the J&J vaccine are made aware of the risk of TTS.

Health committees are a common strategy to foster community participation in health. Efforts to strengthen committees often focus on technical inputs to improve committee form (e.g. representative membership) and functioning (e.g. meeting procedures). However, porous and interconnected contextual spheres also mediate committee effectiveness. Using a framework for contextual analysis, we explored the contextual features that facilitated or hindered Village Health, Sanitation and Nutrition Committee (VHSNC) functionality in rural north India. We conducted interviews (n = 74), focus groups (n = 18) and observation over 1.5 years. Thematic content analysis enabled the identification and grouping of themes, and detailed exploration of sub-themes. While the intervention succeeded in strengthening committee form and functioning, participant accounts illuminated the different ways in which contextual influences impinged on VHSNC efficacy. Women and marginalized groups navigated social hierarchies that curtailed their ability to assert themselves in the presence of men and powerful local families. These dynamics were not static and unchanging, illustrated by pre-existing cross-caste problem solving, and the committee's creation of opportunities for the careful violation of social norms. Resource and capacity deficits in government services limited opportunities to build relationships between health system actors and committee members and engendered mistrust of government institutions. Fragmented administrative accountability left committee members bearing responsibility for improving local health without access to stakeholders who could support or respond to their efforts. The committee's narrow authority was at odds with widespread community needs, and committee members struggled to involve diverse government services across the health, sanitation, and nutrition sectors. Multiple parallel systems (political decentralization, media and other village groups) presented opportunities to create more enabling VHSNC contexts, although the potential to harness these opportunities was largely unmet. This study highlights the urgent need for supportive contexts in which people can not only participate in health committees, but also access the power and resources needed to bring about actual improvements to their health and wellbeing.

Background Malaria transmission in Africa significantly declined between 2005 and 2015 due to widespread distribution of insecticide-treated nets (ITNs). However, since 2015, transmission has increased due to insecticide resistance and biting at times when people are not using ITNs. Spatial repellents (SRs) may help address these challenges. A double-blinded cluster-randomized controlled trial (cRCT) in Busia County, Kenya, reported that Mosquito Shield™, a transfluthrin-based SR, reduced malaria infections by 33.4% during interim analysis and 32.7% by the end of the study, among children aged 6 months to 10 years. Understanding community responses to SRs is critical for their successful deployment and long-term use. This paper reports the initial community response to MosquitoShield™ as part of the Advancing Evidence for the Global Implementation of Spatial Repellents (AEGIS) project. Methods Longitudinal qualitative data were collected from 30 households participating in the cRCT, using modified trials of improved practices (TIPs) to assess participants’ perceptions of MosquitoShield’s utility, efficacy, appearance, and user experience with monthly product replacement. This analysis focuses on initial responses recorded one week and two months post-installation. The data were analysed using thematic coding, with researchers blinded to trial arm assignment. Results The participants reported a positive initial response to the SR, with a significant perceived reduction in mosquito density and activity. Some also reported concerns about the product’s effectiveness over time and its comparison with existing mosquito control methods, particularly after first replacement. Participants highlighted their perception that the SR provided continuous protection in contrast with the situational protection offered by ITNs. Improvement suggestions included modified installation methods plus a longer-lasting product that protected more space. Conclusion MosquitoShield™ shows potential as a promising malaria prevention tool among communities in Busia County, Kenya. Incorporating user feedback and addressing concerns about product installation, duration, and coverage are crucial for successful implementation. Future research exploring community perceptions, cultural factors and behavioural responses related to long-term acceptability and the impact of SRs on malaria transmission will be crucial to ensure effective SR implementation.

Ribosome biogenesis is a ubiquitous and essential process in cells. Defects in ribosome biogenesis and function result in a group of human disorders, collectively known as ribosomopathies. In this study, we describe a zebrafish mutant with a loss-of-function mutation in nol9, a gene that encodes a non-ribosomal protein involved in rRNA processing. nol9sa1022/sa1022 mutants have a defect in 28S rRNA processing. The nol9sa1022/sa1022 larvae display hypoplastic pancreas, liver and intestine and have decreased numbers of hematopoietic stem and progenitor cells (HSPCs), as well as definitive erythrocytes and lymphocytes. In addition, ultrastructural analysis revealed signs of pathological processes occurring in endothelial cells of the caudal vein, emphasizing the complexity of the phenotype observed in nol9sa1022/sa1022 larvae. We further show that both the pancreatic and hematopoietic deficiencies in nol9sa1022/sa1022 embryos were due to impaired cell proliferation of respective progenitor cells. Interestingly, genetic loss of Tp53 rescued the HSPCs but not the pancreatic defects. In contrast, activation of mRNA translation via the mTOR pathway by L-Leucine treatment did not revert the erythroid or pancreatic defects. Together, we present the nol9sa1022/sa1022 mutant, a novel zebrafish ribosomopathy model, which recapitulates key human disease characteristics. The use of this genetically tractable model will enhance our understanding of the tissue-specific mechanisms following impaired ribosome biogenesis in the context of an intact vertebrate.

During embryonic development, signalling molecules known as morphogens act in a concentration-dependent manner to provide positional information to responding tissues. In the early zebrafish embryo, graded signalling by members of the nodal family induces the formation of mesoderm and endoderm, thereby patterning the embryo into three germ layers. Nodal signalling has also been implicated in the establishment of the dorso-ventral axis of the embryo. Although one can infer the existence of nodal gradients by comparing gene expression patterns in wild-type embryos and embryos in which nodal signalling is diminished or augmented, real understanding can only come from directly observing the gradients. One approach is to determine local ligand concentrations in the embryo, but this is technically challenging, and the presence of inhibitors might cause the effective concentration of a ligand to differ from its actual concentration. We have therefore taken two approaches to visualise a direct response to nodal signalling. In the first, we have used transgenic embryos to study the nuclear accumulation of a Smad2-Venus fusion protein, and in the second we have used bimolecular fluorescence complementation to visualise the formation of a complex between Smad2 and Smad4. This has allowed us to visualise, in living embryos, the formation of a graded distribution of nodal signalling activity. We have quantified the formation of the gradient in time and space, and our results not only confirm that nodal signalling patterns the embryo into three germ layers, but also shed light on its role in patterning the dorso-ventral axis and highlight unexpected complexities of mesodermal patterning.

To identify factors contributing to low uptake of intermittent preventive treatment of malaria in pregnancy with sulfadoxine-pyrimethamine (IPTp-SP) in rural Mali. We conducted secondary data analysis on Mali's 2012-2013 Demographic and Health Survey (DHS) to determine the proportion of women who failed to take IPTp-SP due to ineligibility or non-attendance at antenatal care (ANC). We also identified the proportion who reported taking other or unknown medications to prevent malaria in pregnancy and those who did not know if they took any medication to prevent malaria in pregnancy. We conducted qualitative interviews, focus groups and ANC observations in six rural sites in Mali's Sikasso and Koulikoro regions to identify reasons for missed opportunities. Our secondary data analysis found that reported IPTp-SP coverage estimates are misleading due to their dependence on a variable (\"source of IPTp\") that is missing 62% of its data points. Among all women who gave birth in the two years prior to the survey, 56.2% reported taking at least one dose of IPTp-SP. Another 5.2% reported taking chloroquine, 1.9% taking another drug to prevent malaria in pregnancy, 4.4% not knowing what drug they took to prevent malaria, and 1.1% not knowing if they took any drug to prevent malaria. The majority of women who did not receive IPTp-SP were women who also did not attend ANC. Our qualitative data revealed that many health centers neither administer IPTp-SP by directly observed therapy, nor give IPTp-SP at one month intervals through the second and third trimesters, nor provide IPTp-SP free of charge. Women generally reported IPTp-SP as available and tolerable, but frequently could not identify its name or purpose, potentially affecting accuracy of responses in household surveys. We estimate IPTp-SP uptake to be significantly higher than stated in Mali's 2012-13 DHS report. Increasing ANC attendance should be the first priority for increasing IPTp-SP coverage. Reducing cost and access barriers, ensuring that providers follow up-to-date guidelines, and improving patient counseling on IPTp-SP would also facilitate optimal uptake.

Background Participatory health initiatives ideally support progressive social change and stronger collective agency for marginalized groups. However, this empowering potential is often limited by inequalities within communities and between communities and outside actors (i.e. government officials, policymakers). We examined how the participatory initiative of Village Health, Sanitation, and Nutrition Committees (VHSNCs) can enable and hinder the renegotiation of power in rural north India. Methods Over 18 months, we conducted 74 interviews and 18 focus groups with VHSNC members (including female community health workers and local government officials), non-VHSNC community members, NGO staff, and higher-level functionaries. We observed 54 VHSNC-related events (such as trainings and meetings). Initial thematic network analysis supported further examination of power relations, gendered “social spaces,” and the “discourses of responsibility” that affected collective agency. Results VHSNCs supported some re-negotiation of intra-community inequalities, for example by enabling some women to speak in front of men and perform assertive public roles. However, the extent to which these new gender dynamics transformed relations beyond the VHSNC was limited. Furthermore, inequalities between the community and outside stakeholders were re-entrenched through a “discourse of responsibility”: The comparatively powerful outside stakeholders emphasized community responsibility for improving health without acknowledging or correcting barriers to effective VHSNC action. In response, some community members blamed peers for not taking up this responsibility, reinforcing a negative collective identity where participation was futile because no one would work for the greater good. Others resisted this discourse, arguing that the VHSNC alone was not responsible for taking action: Government must also intervene. This counter-narrative also positioned VHSNC participation as futile. Conclusions Interventions to strengthen participation in health systems can engender social transformation. However they must consider how changing power relations can be sustained outside participatory spaces, and how discourse frames the rationale for community participation.