109 research outputs found

    SLIDR and SLOPPR : flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

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    Acknowledgements The authors thank Bernadette Connolly for helpful discussions and Andreea Marin, David MacLeod and Lucrezia Piccicacchi for testing the pipelines. The authors acknowledge the support of the Maxwell and MacLeod computer clusters funded by the University of Aberdeen. Funding This work was supported by the Biotechnology and Biological Sciences Research Council [BB/J007137/1 to JP and BM, and BB/T002859/1 to BM and JP]. The funding body had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.Peer reviewedPublisher PD

    An in vivo genetic screen for genes involved in spliced leader trans-splicing indicates a crucial role for continuous de novo spliced leader RNP assembly

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    ACKNOWLEDGEMENTS Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). We would also like to thank Prof. Shohei Mitani,at the National Bioresource Project for the Experimental Animal ‘Nematode C. elegans’, Japan, for FX3079. We are grateful to Prof. Tom Blumenthal (University of Colorado, Boulder) for suggestions and support of this work; and to Kathrine Wood for her contribution to the initial stages of part of this work. Author contributions. L.P., G.P., R.F., N.H., J.P. and B.M. performed experiments; B.M., J.P. and B.C. designed and lead the study; B.M. and J.P. drafted the manuscript. All authors reviewed the manuscript. FUNDING Biotechnology and Biological Sciences Research Council (BBSRC) [Project grant BB/J007137/1]; Medical Research Council (MRC) Confidence in Concept 2014 - University of Aberdeen Award(MC PC 14114v.2); University of Aberdeen Elphinstone Scholarship (to R.F.) and TET Fund support through Adekunle Ajasin University, Nigeria (to R.F.). Funding for open access charge: Biotechnology and Biological Sciences Research Council and Medical Research Council.Peer reviewedPublisher PD

    A systematic review protocol to identify the key benefits and associated program characteristics of community gardening for vulnerable populations

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    Gardening has long been a popular pastime. There is a growing evidence base for the health and well-being benefits of gardening. Community gardening brings a social aspect to gardening, thereby increasing the potential benefits to include addressing social inclusion and poor community health through sharing of values, support of others, and building networks. This systematic review protocol aims to determine the characteristics of community gardening that could lead to beneficial outcomes such as connection with the community and development of new skills. Thirteen academic databases will be searched for studies looking at the benefits of community gardening, with a focus on vulnerable populations. Data will be extracted from all studies meeting the inclusion criteria and summarized to provide an overview of the current literature. This systematic review aims to provide a comprehensive investigation into community gardening, its benefits, and how they are achieved for the target population. By gathering and synthesizing this information, the review should allow policy makers and practitioners to work more effectively to address health and social inequities, by highlighting areas of need and enabling optimization of future interventions

    Identifying key benefits and characteristics of community gardening for vulnerable populations : a systematic review

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    Vulnerable communities (including people from refugee, Indigenous, culturally and linguistically diverse, and low socioeconomic backgrounds) represent the most at-risk populations facing inequities and negative health, economic, and social outcomes. Te recent COVID-19 pandemic both highlighted and fuelled these disparities. Community gardening has emerged as a communitybased solution to address these inequities, yet the research literature has largely considered outcomes for the general population rather than those with the most need. Tis paper represents the frst systematic review to summarise the evidence on the broad impact of community gardening on outcomes for vulnerable populations. A systematic search of 13 databases (PubMed, Medline, Scopus, ScienceDirect, Cumulative Index to Nursing and Allied Health Literature, PsycINFO, Web of Science, Academic Search Complete, Education Source, Education Resources Information Center, Psychology and Behavioral Science Collection, SocINDEX, and Allied Health and Complementary Medicine Database) for English language articles from 1985 to 2022 was conducted. Tere were 33 studies identifed where females were substantially overrepresented in the studies compared to males, and the main criteria for vulnerability included low socioeconomic-status and culturally diverse populations. Findings revealed that community gardening provides a wide range of benefts for vulnerable populations, with social connection, health, education, and nutrition being the more commonly cited. A relative emphasis on benefts of social connections, education, and nutrition is apparent for vulnerable populations in comparison to reviews considering the general population. Te quality of studies was evaluated as moderate with little information provided about program characteristics. Tese shortcomings reduce the understanding of what characteristics are most likely to result in improvements and limit the capacity of practitioners to translate research into policy and practice for vulnerable communities

    TES-1/Tes and ZYX-1/Zyxin protect junctional actin networks under tension during epidermal morphogenesis in the C. elegans embryo

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    Acknowledgments cDNA clones for hmr-1, ajm-1, zyx-1, zoo-1, hmp-1, and tes-1 (yk collection) were provided by Yuji Kohara (National Institute of Genetics). A.M.L., Y.Z., B.G.L., S.C.T.M., and J.H. were supported by NIH grant R01GM058038 and NIH MIRA R35GM145312 awarded to J.H.; S.C.T.M. was supported by a Gilliam Fellowship from the Howard Hughes Medical Institute and by an Advanced Opportunities Fellowship and a COVID-19 dissertation completion fellowship from the University of Wisconsin-Madison; S.B. and A.A. were supported by NIH MIRA R35GM134865 awarded to A.A.; J.D.W. was supported by NIH grant F32GM122372 and by NIH grant R01GM104032 and the Army Research Office Multidisciplinary University Research Initiative W911NF1410403 awarded to M.L.G.; and B.G. and M.M.S. were supported by NIH MIRA R35GM134838 awarded to B.G. and NIH grant F32GM119348 awarded to M.M.S. Some strains were provided by the Caenorhabditis Genetics Center (CGC; https://cbs.umn.edu/cgc/home), which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440).Peer reviewedPostprin

    A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs

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    Acknowledgements We thank Maheshika Kurukulasuriya for her assistance with immunoprecipitations from embryo extracts. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). Sequencing was performed by the Centre for Genome-Enabled Biology and Medicine of the University of Aberdeen, and proteomics analysis by the Aberdeen proteomics facility. We thank Kate Burgoyne and Craig Pattinson (Aberdeen Proteomics) for technical support. We thank WormBase for providing the community resource that facilitated the interrogation of C. elegans molecular genetics used in this work . Author contribution: P.E., M.A., E.S.-M., R.F., M.W., B.M. and J.P. contributed experiments. J.P. and B.M. conceived the research and managed and coordinated the research activity; J.P. and B.M. acquired funding for the project; D.S. guided the proteomics analysis, M.W., B.M. and J.P. designed and implemented the computational analysis; M.W., B.M. and J.P. wrote the manuscript and prepared figures and tables.Peer reviewe

    CMTr mediated 2`-O-ribose methylation status of cap adjacent-nucleotides across animals

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    ACKNOWLEDGMENTS We thank Mark Carrington and Nancy Standard for T. brucei total RNA, Jane Nimmo for honeybees, Caroline Chadwick for mouse tissue, Pawel Grzechnik for HEK293T cells, Roland Arnold for HCT116 cells, Rupert Fray for plasmids, and the National BioResource Project, Tokyo, Japan for the C. elegans CMTr2 strain. M.S. acknowledges funding from the Leverhulme Trust and the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/R002932/1), J.P. and B.M. from BBSRC (BB/T002859/1), and F.M. from the Wellcome Trust (106955/Z/15/Z).Peer reviewedPublisher PD
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