24 research outputs found

    Group II Intron-Based Gene Targeting Reactions in Eukaryotes

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    Mobile group II introns insert site-specifically into DNA target sites by a mechanism termed retrohoming in which the excised intron RNA reverse splices into a DNA strand and is reverse transcribed by the intron-encoded protein. Retrohoming is mediated by a ribonucleoprotein particle that contains the intron-encoded protein and excised intron RNA, with target specificity determined largely by base pairing of the intron RNA to the DNA target sequence. This feature enabled the development of mobile group II introns into bacterial gene targeting vectors ("targetrons") with programmable target specificity. Thus far, however, efficient group II intron-based gene targeting reactions have not been demonstrated in eukaryotes.By using a plasmid-based Xenopus laevis oocyte microinjection assay, we show that group II intron RNPs can integrate efficiently into target DNAs in a eukaryotic nucleus, but the reaction is limited by low Mg(2+) concentrations. By supplying additional Mg(2+), site-specific integration occurs in up to 38% of plasmid target sites. The integration products isolated from X. laevis nuclei are sensitive to restriction enzymes specific for double-stranded DNA, indicating second-strand synthesis via host enzymes. We also show that group II intron RNPs containing either lariat or linear intron RNA can introduce a double-strand break into a plasmid target site, thereby stimulating homologous recombination with a co-transformed DNA fragment at frequencies up to 4.8% of target sites. Chromatinization of the target DNA inhibits both types of targeting reactions, presumably by impeding RNP access. However, by using similar RNP microinjection methods, we show efficient Mg(2+)-dependent group II intron integration into plasmid target sites in zebrafish (Danio rerio) embryos and into plasmid and chromosomal target sites in Drosophila melanogster embryos, indicating that DNA replication can mitigate effects of chromatinization.Our results provide an experimental foundation for the development of group II intron-based gene targeting methods for higher organisms

    Unconscious bias in the suppressive policing of Black and Latino men and boys: neuroscience, Borderlands theory, and the policymaking quest for just policing

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    his article applies neuroscience and Borderlands theory to reveal how unconscious bias currently stabilizes suppressive policing practices in America despite new efforts at reform. Illustrative cases are offered from Oakland and Santa Barbara, California, with a focus on civil gang injunctions (CGIs) and youth gang suppression. Theoretical analysis of these cases reveals how the unconscious biases of validity illusions and framing effects operate despite the best intentions of law enforcement personnel. Such unconscious or implicit biases create contradictions between the stated beliefs and actions of law enforcement. In turn, these unintended self-contradictions then work to the detriment of Latino and Black boys. The analysis here also extends to how unconscious biases and unintended self-contradictions can influence municipal policymaking in favor of suppressive police tactics such as CGIs, thereby displacing evidence-based policies that are proven to be far more effective. The article concludes with brief discussion of some of the means by which the unconscious biases – effects to which everyone is involuntarily prone – can be disrupted

    Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science

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    It is well documented that the majority of adults, children and families in need of evidence-based behavioral health interventionsi do not receive them [1, 2] and that few robust empirically supported methods for implementing evidence-based practices (EBPs) exist. The Society for Implementation Research Collaboration (SIRC) represents a burgeoning effort to advance the innovation and rigor of implementation research and is uniquely focused on bringing together researchers and stakeholders committed to evaluating the implementation of complex evidence-based behavioral health interventions. Through its diverse activities and membership, SIRC aims to foster the promise of implementation research to better serve the behavioral health needs of the population by identifying rigorous, relevant, and efficient strategies that successfully transfer scientific evidence to clinical knowledge for use in real world settings [3]. SIRC began as a National Institute of Mental Health (NIMH)-funded conference series in 2010 (previously titled the “Seattle Implementation Research Conference”; $150,000 USD for 3 conferences in 2011, 2013, and 2015) with the recognition that there were multiple researchers and stakeholdersi working in parallel on innovative implementation science projects in behavioral health, but that formal channels for communicating and collaborating with one another were relatively unavailable. There was a significant need for a forum within which implementation researchers and stakeholders could learn from one another, refine approaches to science and practice, and develop an implementation research agenda using common measures, methods, and research principles to improve both the frequency and quality with which behavioral health treatment implementation is evaluated. SIRC’s membership growth is a testament to this identified need with more than 1000 members from 2011 to the present.ii SIRC’s primary objectives are to: (1) foster communication and collaboration across diverse groups, including implementation researchers, intermediariesi, as well as community stakeholders (SIRC uses the term “EBP champions” for these groups) – and to do so across multiple career levels (e.g., students, early career faculty, established investigators); and (2) enhance and disseminate rigorous measures and methodologies for implementing EBPs and evaluating EBP implementation efforts. These objectives are well aligned with Glasgow and colleagues’ [4] five core tenets deemed critical for advancing implementation science: collaboration, efficiency and speed, rigor and relevance, improved capacity, and cumulative knowledge. SIRC advances these objectives and tenets through in-person conferences, which bring together multidisciplinary implementation researchers and those implementing evidence-based behavioral health interventions in the community to share their work and create professional connections and collaborations

    Topographic controls on shallow groundwater levels in a steep, prealpine catchment: When are the TWI assumptions valid?

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    Topographic indices like the Topographic Wetness Index (TWI) have been used to predict spatial patterns of average groundwater levels and to model the dynamics of the saturated zone during events (e.g., TOPMODEL). However, the assumptions underlying the use of the TWI in hydrological models, of which the most important is that groundwater level variation can be approximated by a series of steady state situations, are rarely tested. It is also not clear how well findings from existing hillslope studies on sites with transmissive soil can be transferred to entire catchments with less permeable soils. This study, therefore, evaluated the suitability of selected topographic indices to describe spatial groundwater level variations based on time series from 51 groundwater wells in a 20 ha catchment with low-permeability soils in Switzerland. Results showed that median groundwater levels were correlated to slope, curvature, and TWI, but the strength of correlation depended on whether the indices characterized the local topography or the topography of the upslope contributing area. The correlation between TWI and groundwater levels was not constant over time but decreased at the beginning of rainfall events, indicating large spatial differences in groundwater responses, and increased after peak flow, when groundwater levels could be considered to be spatially in a steady state. Our findings indicate that topographic indices are useful to predict median groundwater levels in catchments with low-permeability soils and that the TWI assumptions are best met when groundwater levels change slowly. Key Points Median groundwater levels were correlated to topographic indices Correlation between groundwater levels and topographic indices varied over time TWI assumptions were most valid during wet conditions, after peak flows © 2014. American Geophysical Union. All Rights Reserved
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