Improved deoxyribozymes for synthesis of covalently branched DNA and RNA

A covalently branched nucleic acid can be synthesized by joining the 2′-hydroxyl of the branch-site ribonucleotide of a DNA or RNA strand to the activated 5′-phosphorus of a separate DNA or RNA strand. We have previously used deoxyribozymes to synthesize several types of branched nucleic acids for experiments in biotechnology and biochemistry. Here, we report in vitro selection experiments to identify improved deoxyribozymes for synthesis of branched DNA and RNA. Each of the new deoxyribozymes requires Mn2+ as a cofactor, rather than Mg2+ as used by our previous branch-forming deoxyribozymes, and each has an initially random region of 40 rather than 22 or fewer combined nucleotides. The deoxyribozymes all function by forming a three-helix-junction (3HJ) complex with their two oligonucleotide substrates. For synthesis of branched DNA, the best new deoxyribozyme, 8LV13, has kobs on the order of 0.1 min−1, which is about two orders of magnitude faster than our previously identified 15HA9 deoxyribozyme. 8LV13 also functions at closer-to-neutral pH than does 15HA9 (pH 7.5 versus 9.0) and has useful tolerance for many DNA substrate sequences. For synthesis of branched RNA, two new deoxyribozymes, 8LX1 and 8LX6, were identified with broad sequence tolerances and substantial activity at pH 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA. These experiments provide new, and in key aspects improved, practical catalysts for preparation of synthetic branched DNA and RNA

Sampling in health geography: reconciling geographical objectives and probabilistic methods. An example of a health survey in Vientiane (Lao PDR)

<p>Abstract</p> <p>Background</p> <p>Geographical objectives and probabilistic methods are difficult to reconcile in a unique health survey. Probabilistic methods focus on individuals to provide estimates of a variable's prevalence with a certain precision, while geographical approaches emphasise the selection of specific areas to study interactions between spatial characteristics and health outcomes. A sample selected from a small number of specific areas creates statistical challenges: the observations are not independent at the local level, and this results in poor statistical validity at the global level. Therefore, it is difficult to construct a sample that is appropriate for both geographical and probability methods.</p> <p>Methods</p> <p>We used a two-stage selection procedure with a first non-random stage of selection of clusters. Instead of randomly selecting clusters, we deliberately chose a group of clusters, which as a whole would contain all the variation in health measures in the population. As there was no health information available before the survey, we selected <it>a priori </it>determinants that can influence the spatial homogeneity of the health characteristics. This method yields a distribution of variables in the sample that closely resembles that in the overall population, something that cannot be guaranteed with randomly-selected clusters, especially if the number of selected clusters is small. In this way, we were able to survey specific areas while minimising design effects and maximising statistical precision.</p> <p>Application</p> <p>We applied this strategy in a health survey carried out in Vientiane, Lao People's Democratic Republic. We selected well-known health determinants with unequal spatial distribution within the city: nationality and literacy. We deliberately selected a combination of clusters whose distribution of nationality and literacy is similar to the distribution in the general population.</p> <p>Conclusion</p> <p>This paper describes the conceptual reasoning behind the construction of the survey sample and shows that it can be advantageous to choose clusters using reasoned hypotheses, based on both probability and geographical approaches, in contrast to a conventional, random cluster selection strategy.</p

“OMG, Yes!”: Feasibility, Acceptability, and Preliminary Efficacy of an Online Intervention for Female Sexual Pleasure

The purpose of this study was to evaluate the acceptability, feasibility, and preliminary efficacy of using an online educational resource that presents research-informed strategies for women’s pleasure, OMGyes.com, as a resource to empower women to broaden the ways in which they understand, advocate for, and enjoy sexual pleasure. A cohort of 870 adult women was given access to OMGyes.com and asked to explore the resource over a four-week period and complete online pre/post questionnaires. Participants reported a high level of satisfaction with the relatability, usefulness, and functionality of OMGyes.com. We observed statistically significant, large effect size increases in participants’ knowledge about their own pleasure preferences, their confidence and positivity about that knowledge, as well as how pleasurable their sexual experiences were during both masturbation and partner sex. Many participants reported that after using OMGyes.com they felt more motivated to explore their preferences and more confident to explain their preferences to their partners. Our data suggest that OMGyes.com may be useful for positively impacting how women think about sexual pleasure, how they understand their own specific preferences, how they advocate for what they enjoy with partners, and how they actually experience pleasure

A Dopaminergic Gene Cluster in the Prefrontal Cortex Predicts Performance Indicative of General Intelligence in Genetically Heterogeneous Mice

Background: Genetically heterogeneous mice express a trait that is qualitatively and psychometrically analogous to general intelligence in humans, and as in humans, this trait co-varies with the processing efficacy of working memory (including its dependence on selective attention). Dopamine signaling in the prefrontal cortex (PFC) has been established to play a critical role in animals ’ performance in both working memory and selective attention tasks. Owing to this role of the PFC in the regulation of working memory, here we compared PFC gene expression profiles of 60 genetically diverse CD-1 mice that exhibited a wide range of general learning abilities (i.e., aggregate performance across five diverse learning tasks). Methodology/Principal Findings: Animals ’ general cognitive abilities were first determined based on their aggregate performance across a battery of five diverse learning tasks. With a procedure designed to minimize false positive identifications, analysis of gene expression microarrays (comprised of &lt;25,000 genes) identified a small number (,20) of genes that were differentially expressed across animals that exhibited fast and slow aggregate learning abilities. Of these genes, one functional cluster was identified, and this cluster (Darpp-32, Drd1a, and Rgs9) is an established modulator of dopamine signaling. Subsequent quantitative PCR found that expression of these dopaminegic genes plus one vascular gene (Nudt6) were significantly correlated with individual animal’s general cognitive performance. Conclusions/Significance: These results indicate that D1-mediated dopamine signaling in the PFC, possibly through it

Historical Sources of Institutional Trajectories in Economic Development: China, Japan, and Korea Compared

This essay provides a game-theoretic, endogenous view of institutions, and then applies the idea to identify the sources of institutional trajectories of economic development in China, Japan, and Korea. It stylizes the Malthusian-phase of East Asian economies as peasant-based economies in which small families allocated their working time between farming on small plots - leased or owned - and handcrafting for personal consumption and markets. It then compares institutional arrangements across these economies that sustained otherwise similar economies. It characterizes the varied nature of the political states of Qing China, Tokugawa Japan, and Yi Korea by focusing on the way in which agricultural taxes were enforced. It also identifies different patterns of social norms of trust that were institutional complements to, or substitutes for, political states. Finally, it traces the path-dependent transformations of these state-norm combinations along subsequent transitions to post-Malthusian phases of economic growth in the respective economies