61,212 research outputs found

    Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics

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    Summary: The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens

    Comparison of Sequencing Methods for <i>De Novo </i>Plasmid Assembly - Data

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    The raw data and generated assemblies from Illumina MiSeq, Oxford Nanopore MinION, and Sanger Sequencing. </p

    Simplified Model of Vesicular Stomatitis Virus.

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    Visual representation of the simplified model used in this paper. Every molecule depicted has a degradation reaction associated with it that is not represented here.</p

    Model Reactions with Reactants and Products.

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    We present the first complete stochastic model of vesicular stomatitis virus (VSV) intracellular replication. Previous models developed to capture VSV’s intracellular replication have either been ODE-based or have not represented the complete replicative cycle, limiting our ability to understand the impact of the stochastic nature of early cellular infections on virion production between cells and how these dynamics change in response to mutations. Our model accurately predicts changes in mean virion production in gene-shuffled VSV variants and can capture the distribution of the number of viruses produced. This model has allowed us to enhance our understanding of intercellular variability in virion production, which appears to be influenced by the duration of the early phase of infection, and variation between variants, arising from balancing the time the genome spends in the active state, the speed of incorporating new genomes into virions, and the production of viral components. Being a stochastic model, we can also assess other effects of mutations beyond just the mean number of virions produced, including the probability of aborted infections and the standard deviation of the number of virions produced. Our model provides a biologically interpretable framework for studying the stochastic nature of VSV replication, shedding light on the mechanisms underlying variation in virion production. In the future, this model could enable the design of more complex viral phenotypes when attenuating VSV, moving beyond solely considering the mean number of virions produced.</div

    Socially promiscuous mobile phone pets

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    Virtual pets offer an abstracted version of animal ownership. Currently, most simulated creatures tend to be sequestered from the real world and so have little or no knowledge as to their whereabouts. This limits the scope of the possible interactions between the player and their simulated pet. Gophers are artificial pets designed to be carried by users on their mobile phone. They are socially promiscuous (like cats) and enjoy visiting the phones of other players without the permission of their 'owner'. During their lives, these artificial animals collect topological information regarding their movements, and semantic data related to their location via interactions with the humans they encounter. Future versions of the game will utilise this information to create a more contextually aware experience.</p

    Gene Shuffled Vesicular Stomatitis Virus Variants with Associated Statistics.

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    Gene Shuffled Vesicular Stomatitis Virus Variants with Associated Statistics.</p

    N and P gene position most strongly influence virion production in gene shuffled VSV variants.

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    (A) The average number of virions produced over time for all 120 variants. The trajectory of the wild-type variant is in red. (B-F) The average number of virions produced as a function of gene position (which determines the transcription rate) for genes (B) N, (C) P, (D) M, (E) G, and (F) L. The error bars represent the standard error of the mean, and the orange dots represent the individual variants.</p

    Total survey sample size.

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    Adolescents living in humanitarian settings are often at a higher risk of negative sexual and reproductive health outcomes, and yet, limited information is available on adolescents’ experiences and needs in these settings while available services do not always correspond to their needs. This study explored knowledge, attitudes, and behaviors relating to sexual and reproductive health among 12–17 year old refugees from Darfur currently living in two refugee camps in eastern Chad. The research team conducted a cross-sectional survey of 689 adolescent girls and boys, informed by participatory research activities, to explore key sexual and reproductive health topics. This study found that sexual and reproductive health knowledge among adolescents is low, with only 69.1% able to identify at least one modern contraceptive method. Early marriage was uncommon (5% of girls, 0.8% of boys), but 17.6% of adolescents had already had a romantic relationship. Few adolescents (11.4%) had ever had sex, but among these adolescents,18.4% reported using a condom the last time they had sex. No boys reported current modern contraceptive use, but 28.3% of girls, both married and unmarried, reported current use. These findings demonstrate the importance of making sexual and reproductive health services in humanitarian settings more adolescent-responsive and minimizing barriers to access, including addressing community stigma surrounding adolescents’ use of sexual and reproductive health services and increasing trust in the confidentiality of sexual and reproductive health services in the camps.</div

    I’m shutting them in, so it stays in the bucket”.

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    The Veivanua campaign is a menstrual health intervention for people with intellectual disabilities and their caregivers in Vanuatu’s humanitarian setting. The campaign was adapted from the Bishesta campaign delivered in Nepal’s development setting. This feasibility study is designed to assess the feasibility and acceptability of the Veivanua campaign to understand if efficacy testing is warranted. The Veivanua campaign was delivered to a preselected group of 30 young people (individuals with intellectual disabilities) and 35 caregivers (males and females). Data were collected through several qualitative tools to allow for methods triangulation: process monitoring, post-intervention in-depth interviews with caregivers and nine young people, observation of young persons, photovoice and ranking with two young people, campaign resource ranking, and key informant interviews with staff involved in the intervention. Data were analysed thematically using Nvivo 12. Results show that the Veivanua campaign is feasible. Male and female caregivers reported an increased ability to support young people’s menstrual health and greater preparedness for the next emergency. Young people understood the training and applied their learning. Key informants want to scale up the intervention in their humanitarian responses. Several changes were made to the adapted campaign, but similar outcomes were recorded in Nepal and Vanuatu. All target behaviours improved, and campaign resources were used, but many caregivers found the menstrual calendar confusing. The intervention was not delivered with fidelity but responded to the context. The campaign cost more than the Bishesta campaign because procurement was more expensive in Vanuatu. In conclusion, this is the first intervention globally, so it begins to fill a substantial gap, but more must be done. As the Veivanua campaign is feasible, it requires efficacy testing in Vanuatu. It should also be adapted to humanitarian crises in other countries to support the menstrual health of this previously excluded population.</div
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