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  1. Article ; Online: An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond.

    Williams, Jason J / Tractenberg, Rochelle E / Batut, Bérénice / Becker, Erin A / Brown, Anne M / Burke, Melissa L / Busby, Ben / Cooch, Nisha K / Dillman, Allissa A / Donovan, Samuel S / Doyle, Maria A / van Gelder, Celia W G / Hall, Christina R / Hertweck, Kate L / Jordan, Kari L / Jungck, John R / Latour, Ainsley R / Lindvall, Jessica M / Lloret-Llinares, Marta /
    McDowell, Gary S / Morris, Rana / Mourad, Teresa / Nisselle, Amy / Ordóñez, Patricia / Paladin, Lisanna / Palagi, Patricia M / Sukhai, Mahadeo A / Teal, Tracy K / Woodley, Louise

    PloS one

    2023  Volume 18, Issue 11, Page(s) e0293879

    Abstract: Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and ... ...

    Abstract Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit SFT's effectiveness and inclusiveness. Education researchers, students in SFT courses, and organizations have called for research and strategies that can strengthen SFT in terms of effectiveness, inclusiveness, and accessibility across multiple dimensions. This paper describes the project that resulted in a consensus set of 14 actionable recommendations to systematically strengthen SFT. A diverse international group of 30 experts in education, accessibility, and life sciences came together from 10 countries to develop recommendations that can help strengthen SFT globally. Participants, including representation from some of the largest life science training programs globally, assembled findings in the educational sciences and encompassed the experiences of several of the largest life science SFT programs. The 14 recommendations were derived through a Delphi method, where consensus was achieved in real time as the group completed a series of meetings and tasks designed to elicit specific recommendations. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned with a purpose-built framework-"The Bicycle Principles"-that prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT.
    MeSH term(s) Humans ; Consensus ; Students ; Technology ; Engineering
    Language English
    Publishing date 2023-11-09
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0293879
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Regulation of alternative pre-mRNA splicing.

    Woodley, Louise / Valcárcel, Juan

    Briefings in functional genomics & proteomics

    2004  Volume 1, Issue 3, Page(s) 266–277

    Abstract: The first wave of bioinformatic studies that followed genome and complementary DNA sequencing projects revealed that alternative splicing of messenger RNA precursors (pre-mRNAs) contributes substantially to transcriptome complexity in higher eukaryotes. ... ...

    Abstract The first wave of bioinformatic studies that followed genome and complementary DNA sequencing projects revealed that alternative splicing of messenger RNA precursors (pre-mRNAs) contributes substantially to transcriptome complexity in higher eukaryotes. Together with the realisation of the impact of the process on cell differentiation, development and disease, these studies portray alternative splicing as a fundamental component of gene regulation. Both detailed mechanistic studies and genome-wide analyses will be necessary to unravel the molecular basis for cell type-specific splice site selection. This paper will highlight some recent progress and future challenges for functional genomics and bioinformatics in this rapidly developing area.
    MeSH term(s) Alternative Splicing ; RNA Precursors/genetics ; RNA, Messenger/chemistry ; RNA, Messenger/genetics
    Chemical Substances RNA Precursors ; RNA, Messenger
    Language English
    Publishing date 2004-05-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2138368-6
    ISSN 1477-4062 ; 1473-9550
    ISSN (online) 1477-4062
    ISSN 1473-9550
    DOI 10.1093/bfgp/1.3.266
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia.

    Williamson, Neil R / Fineran, Peter C / Ogawa, Wakano / Woodley, Louise R / Salmond, George P C

    Environmental microbiology

    2008  Volume 10, Issue 5, Page(s) 1202–1217

    Abstract: Serratia sp. ATCC 39006 (Serratia 39006) is a Gram-negative bacterium which produces the secondary metabolite antibiotics, prodigiosin and 1-carbapen-2-em-3-carboxylic acid and secretes plant cell wall degrading enzymes. In this study we have identified ... ...

    Abstract Serratia sp. ATCC 39006 (Serratia 39006) is a Gram-negative bacterium which produces the secondary metabolite antibiotics, prodigiosin and 1-carbapen-2-em-3-carboxylic acid and secretes plant cell wall degrading enzymes. In this study we have identified mutations in the genes, pigX, rap and rsmA, which caused increased production of a previously unidentified surfactant and flagella-dependent swarming phenotype in Serratia 39006. Analysis of both the biosynthesis and regulation of surfactant production and swarming, revealed FlhC, quorum sensing, a GGDEF/EAL domain protein (PigX), a GacAS two-component system, an Rsm system and Rap as key regulators. In addition, surfactant biosynthesis required a protein similar to RhlA, involved in rhamnolipid synthesis in Pseudomonas aeruginosa. Homologues of RhlA have not previously been identified in members of the Enterobacteriaceae. Furthermore, we provide evidence that the surfactant may be responsible for dispersal of the antimicrobial pigment, prodigiosin. This study demonstrates the complex regulatory inputs into the coordinated multicellular swarming phenotype in Serratia.
    MeSH term(s) Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Flagella/metabolism ; Gene Expression Regulation, Bacterial ; Movement ; Mutation ; Prodigiosin/metabolism ; Quorum Sensing ; Serratia/genetics ; Serratia/growth & development ; Serratia/metabolism ; Serratia/physiology ; Signal Transduction ; Surface-Active Agents/metabolism ; Transcription, Genetic
    Chemical Substances Bacterial Proteins ; Surface-Active Agents ; Prodigiosin (OL369FU7CJ)
    Language English
    Publishing date 2008-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/j.1462-2920.2007.01536.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia

    Williamson, Neil R / Fineran, Peter C / Ogawa, Wakano / Woodley, Louise R / Salmond, George P.C

    Environmental microbiology. 2008 May, v. 10, no. 5

    2008  

    Abstract: Serratia sp. ATCC 39006 (Serratia 39006) is a Gram-negative bacterium which produces the secondary metabolite antibiotics, prodigiosin and 1-carbapen-2-em-3-carboxylic acid and secretes plant cell wall degrading enzymes. In this study we have identified ... ...

    Abstract Serratia sp. ATCC 39006 (Serratia 39006) is a Gram-negative bacterium which produces the secondary metabolite antibiotics, prodigiosin and 1-carbapen-2-em-3-carboxylic acid and secretes plant cell wall degrading enzymes. In this study we have identified mutations in the genes, pigX, rap and rsmA, which caused increased production of a previously unidentified surfactant and flagella-dependent swarming phenotype in Serratia 39006. Analysis of both the biosynthesis and regulation of surfactant production and swarming, revealed FlhC, quorum sensing, a GGDEF/EAL domain protein (PigX), a GacAS two-component system, an Rsm system and Rap as key regulators. In addition, surfactant biosynthesis required a protein similar to RhlA, involved in rhamnolipid synthesis in Pseudomonas aeruginosa. Homologues of RhlA have not previously been identified in members of the Enterobacteriaceae. Furthermore, we provide evidence that the surfactant may be responsible for dispersal of the antimicrobial pigment, prodigiosin. This study demonstrates the complex regulatory inputs into the coordinated multicellular swarming phenotype in Serratia.
    Keywords Gram-negative bacteria ; Pseudomonas aeruginosa ; Serratia ; antibiotics ; biosynthesis ; cell walls ; enzymes ; genes ; mutation ; phenotype ; pigments ; protein synthesis ; proteins ; quorum sensing ; secondary metabolites ; surfactants
    Language English
    Dates of publication 2008-05
    Size p. 1202-1217.
    Publisher Blackwell Publishing Ltd
    Publishing place Oxford, UK
    Document type Article
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/j.1462-2920.2007.01536.x
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces.

    Williamson, Neil R / Simonsen, Henrik T / Ahmed, Raef A A / Goldet, Gabrielle / Slater, Holly / Woodley, Louise / Leeper, Finian J / Salmond, George P C

    Molecular microbiology

    2005  Volume 56, Issue 4, Page(s) 971–989

    Abstract: The biosynthetic pathway of the red-pigmented antibiotic, prodigiosin, produced by Serratia sp. is known to involve separate pathways for the production of the monopyrrole, 2-methyl-3-n-amyl-pyrrole (MAP) and the bipyrrole, 4-methoxy-2,2'-bipyrrole-5- ... ...

    Abstract The biosynthetic pathway of the red-pigmented antibiotic, prodigiosin, produced by Serratia sp. is known to involve separate pathways for the production of the monopyrrole, 2-methyl-3-n-amyl-pyrrole (MAP) and the bipyrrole, 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC) which are then coupled in the final condensation step. We have previously reported the cloning, sequencing and heterologous expression of the pig cluster responsible for prodigiosin biosynthesis in two Serratia sp. In this article we report the creation of in-frame deletions or insertions in every biosynthetic gene in the cluster from Serratia sp. ATCC 39006. The biosynthetic intermediates accumulating in each mutant have been analysed by LC-MS, cross-feeding and genetic complementation studies. Based on these results we assign specific roles in the biosynthesis of MBC to the following Pig proteins: PigI, PigG, PigA, PigJ, PigH, PigM, PigF and PigN. We report a novel pathway for the biosynthesis of MAP, involving PigD, PigE and PigB. We also report a new chemical synthesis of MAP and one of its precursors, 3-acetyloctanal. Finally, we identify the condensing enzyme as PigC. We reassess the existing literature and discuss the significance of the results for the biosynthesis of undecylprodigiosin by the Red cluster in Streptomyces coelicolor A3(2).
    MeSH term(s) Anti-Bacterial Agents/biosynthesis ; Molecular Structure ; Multigene Family ; Mutation ; Prodigiosin/analogs & derivatives ; Prodigiosin/biosynthesis ; Prodigiosin/chemistry ; Pyrroles/chemistry ; Pyrroles/metabolism ; Serratia/genetics ; Serratia/metabolism ; Streptomyces coelicolor/metabolism
    Chemical Substances Anti-Bacterial Agents ; Pyrroles ; undecylprodigiosin (52340-48-4) ; Prodigiosin (OL369FU7CJ)
    Language English
    Publishing date 2005-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 619315-8
    ISSN 1365-2958 ; 0950-382X
    ISSN (online) 1365-2958
    ISSN 0950-382X
    DOI 10.1111/j.1365-2958.2005.04602.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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