Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences

<p>Abstract</p> <p>Background</p> <p>Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN) is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs) designed to bind specific DNA sequences with high affinity and specificity <it>in vivo</it>. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable.</p> <p>Results</p> <p>Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity⁺of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88%) and specificity⁺(92%), but with reduced ROC AUC (0.77). Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT.</p> <p>Conclusion</p> <p>ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function successfully <it>in vivo</it>, substantially reducing the experimental effort required. ZiFOpT is freely available and incorporated in the Zinc Finger Targeter web server (<url>http://bindr.gdcb.iastate.edu/ZiFiT</url>).</p

Essential Content for Teaching Implementation Practice in Healthcare: A Mixed-Methods Study of Teams Offering Capacity-Building Initiatives

Background Applying the knowledge gained through implementation science can support the uptake of research evidence into practice; however, those doing and supporting implementation (implementation practitioners) may face barriers to applying implementation science in their work. One strategy to enhance individuals’ and teams’ ability to apply implementation science in practice is through training and professional development opportunities (capacity-building initiatives). Although there is an increasing demand for and offerings of implementation practice capacity-building initiatives, there is no universal agreement on what content should be included. In this study we aimed to explore what capacity-building developers and deliverers identify as essential training content for teaching implementation practice. Methods We conducted a convergent mixed-methods study with participants who had developed and/or delivered a capacity-building initiative focused on teaching implementation practice. Participants completed an online questionnaire to provide details on their capacity-building initiatives; took part in an interview or focus group to explore their questionnaire responses in depth; and offered course materials for review. We analyzed a subset of data that focused on the capacity-building initiatives’ content and curriculum. We used descriptive statistics for quantitative data and conventional content analysis for qualitative data, with the data sets merged during the analytic phase. We presented frequency counts for each category to highlight commonalities and differences across capacity-building initiatives. Results Thirty-three individuals representing 20 capacity-building initiatives participated. Study participants identified several core content areas included in their capacity-building initiatives: (1) taking a process approach to implementation; (2) identifying and applying implementation theories, models, frameworks, and approaches; (3) learning implementation steps and skills; (4) developing relational skills. In addition, study participants described offering applied and pragmatic content (e.g., tools and resources), and tailoring and evolving the capacity-building initiative content to address emerging trends in implementation science. Study participants highlighted some challenges learners face when acquiring and applying implementation practice knowledge and skills. Conclusions This study synthesized what experienced capacity-building initiative developers and deliverers identify as essential content for teaching implementation practice. These findings can inform the development, refinement, and delivery of capacity-building initiatives, as well as future research directions, to enhance the translation of implementation science into practice

'Umbrella' review of family-focused care interventions supporting families where a family member has a long-term condition

Aim: To summarise reviews of family-focused care interventions that support families with a family member with a long-term condition across the life course. Design: Umbrella review. Data sources: Medline (1946- 2019), Cochrane Data Base of Systematic Reviews (2019), Database of Abstracts of Reviews of Effect and EMBASE (1947- 2019), CINAHL (1981-2019), Health Technology Assessment Database (2019) and PsycInfo (1806-2019). Review Methods: All authors independently undertook title/abstract screening, data extraction and quality appraisal on a cluster of papers, working in groups of two or three to reach a consensus. The AMSTAR tool was used to appraise the quality of the studies and descriptive syntheses were undertaken. Results: Fifteen reviews met the selection criteria. Overall family-focussed care and associated terms were poorly defined. Typically interventions were educational or psychological therapy/counselling with the goal of empowering individuals to manage their condition. There is some evidence that family-focused care interventions can improve clinical/biological health measures and self-care outcomes such as treatment adherence. Multi-component psychosocial interventions that include cognitive-behavioral therapy, skills training, education and support and are focused on wider family members appear to improve family relationships and martial functioning. Conclusion: Long-term conditions have an impact on individual and family health and well-being, yet the impact of family-focused care interventions on family outcomes was overall inconclusive. A better understanding of how family-focused care interventions improve the health and well-being of individuals and their families is needed to promote the inclusion of family-focused care into practice. Impact: Supporting people with a long-term condition is a key health and social care priority. Family-focused care interventions have potential to improve the health and well-being of individuals and families but there is a need to evaluate their clinical and cost effectiveness. The findings from this review could be used by funding bodies when commissioning research for long-term conditions

Undergraduate Biology Education Research Gordon Research Conference: A Meeting Report

The 2019 Undergraduate Biology Education Research Gordon Research Conference (UBER GRC), titled “Achieving Widespread Improvement in Undergraduate Education,” brought together a diverse group of researchers and practitioners working to identify, promote, and understand widespread adoption of evidence-based teaching, learning, and success strategies in undergraduate biology. Graduate students and postdocs had the additional opportunity to present and discuss research during a Gordon Research Seminar (GRS) that preceded the GRC. This report provides a broad overview of the UBER GRC and GRS and highlights major themes that cut across invited talks, poster presentations, and informal discussions. Such themes include the importance of working in teams at multiple levels to achieve instructional improvement, the potential to use big data and analytics to inform instructional change, the need to customize change initiatives, and the importance of psychosocial supports in improving undergraduate student well-being and academic success. The report also discusses the future of the UBER GRC as an established meeting and describes aspects of the conference that make it unique, both in terms of facilitating dissemination of research and providing a welcoming environment for conferees

Determination of the gravitational constant at an effective mass separation of 22 m

Copyright @ 1988 The American Physical SocietyA vacuum balance that compares the weights of 10-kg stainless-steel masses suspended in evacuated tubes at different levels in a hydroelectric reservoir is being used to measure the gravitational attractions of layers of lake water up to 10 m in depth. The mean effective distance between interacting masses in this experiment is 22 m, making it the largest-scale measurement of G using precisely controlled moving masses. The experiment extends laboratory-type measurements into the range previously explored only by geophysical methods. Assuming purely Newtonian physics the value of the gravitational constant determined from data obtained so far is G=6.689(57)×10-11 m3 kg-1s-2, which agrees with laboratory estimates. The data admit at a 0.6 standard deviation level the parameters of non-Newtonian gravity inferred from geophysical measurements in mines and a tower. These measurements push the estimated ranges of non-Newtonian forces down to a scale accessible to our reservoir experiment, so that experimental improvements now at hand may provide a critical test of non-Newtonian effects

Selection-Free Zinc-Finger Nuclease Engineering by Context-Dependent Assembly (CoDA)

Engineered zinc-finger nucleases (ZFNs) enable targeted genome modification. Here we describe Context-Dependent Assembly (CoDA), a platform for engineering ZFNs using only standard cloning techniques or custom DNA synthesis. Using CoDA ZFNs, we rapidly altered 20 genes in zebrafish, Arabidopsis, and soybean. The simplicity and efficacy of CoDA will enable broad adoption of ZFN technology and make possible large-scale projects focused on multi-gene pathways or genome-wide alterations

Why Are Some Plant Genera More Invasive Than Others?

Determining how biological traits are related to the ability of groups of organisms to become economically damaging when established outside of their native ranges is a major goal of population biology, and important in the management of invasive species. Little is known about why some taxonomic groups are more likely to become pests than others among plants. We investigated traits that discriminate vascular plant genera, a level of taxonomic generality at which risk assessment and screening could be more effectively performed, according to the proportion of naturalized species which are pests. We focused on the United States and Canada, and, because our purpose is ultimately regulatory, considered species classified as weeds or noxious. Using contingency tables, we identified 11 genera of vascular plants that are disproportionately represented by invasive species. Results from boosted regression tree analyses show that these categories reflect biological differences. In summary, approximately 25% of variation in genus proportions of weeds or noxious species was explained by biological covariates. Key explanatory traits included genus means for wetland habitat affinity, chromosome number, and seed mass