Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin

Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the [small alpha]-hemolysin ([small alpha]HL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180[degree]. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside [small alpha]-HL are used to derive thermodynamic ([capital Delta]H, [capital Delta]S) and kinetic (Ea) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of [small alpha]HL out of the helix (18 +/- 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the [small alpha]HL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level

Peer-reviewed publishing of results from Citizen Science projects

Citizen science (CS) terms the active participation of the general public in scientific research activities. With increasing amounts of information generated by citizen scientists, best practices to go beyond science communication and publish these findings to the scientific community are needed. This letter is a synopsis of authors' personal experiences when publishing results from citizen science projects in peer-reviewed journals, as presented at the Austrian Citizen Science Conference 2018. Here, we address authors' selection criteria for publishing CS data in open-access, peer-reviewed scientific journals as well as barriers encountered during the publishing process. We also outline factors that influence the probability of publication using CS data, including 1) funding to cover publication costs; 2) quality, quantity and scientific novelty of CS data; 3) recommendations to acknowledge contributions of citizen scientists in scientific, peer-reviewed publications; 4) citizen scientists' preference of the hands-on experience over the product (publication) and 5) bias among scientists for certain data sources and the scientific jargon. These experiences show that addressing these barriers could greatly increase the rate of CS data included in scientific publications. © 2018, Scuola Internazionale Superiore di Studi Avanzati

Simplified and still meaningful: assessing butterfly habitat quality in grasslands with data collected by pupils

Public participation in scientific research, now commonly referred to as citizen science, is increasingly promoted as a possibility to overcome the large-scale data limitations related to biodiversity and conservation research. Furthermore, public data-collection projects can stimulate public engagement and provide transformative learning situations. However, biodiversity monitoring depends on sound data collection and warranted data quality. Therefore, we investigated if and how trained and supervised pupils are able to systematically collect data about the occurrence of diurnal butterflies, and how this data could contribute to a permanent butterfly monitoring system. We developed a specific assessment scheme suitable for laypeople and applied it at 35 sampling sites in Tyrol, Austria. Data quality and its explanatory power to predict butterfly habitat quality was investigated comparing data collected by pupils with independent assessments of professional butterfly experts. Despite substantial identification uncertainties for some species or species groups, the data collected by pupils was successfully used to predict the general habitat quality for butterflies using a linear regression model (r=0.73, p<0.001). Applying the proposed method in a citizen science context with laypeople could support both the long term monitoring of butterfly habitat quality, as well as the efficient selection of sites for professional in-depth assessments.(VLID)459075

Modular Oxime Formation by a trans-AT Polyketide Synthase

Modular trans-acyltransferase polyketide synthases (trans-AT PKSs) are enzymatic assembly lines that biosynthesize complex polyketide natural products. Relative to their better studied cis-AT counterparts, the trans-AT PKSs introduce remarkable chemical diversity into their polyketide products. A notable example is the lobatamide A PKS, which incorporates a methylated oxime. Here we demonstrate biochemically that this functionality is installed on-line by an unusual oxygenase-containing bimodule. Furthermore, analysis of the oxygenase crystal structure coupled with site-directed mutagenesis allows us to propose a model for catalysis, as well as identifying key protein-protein interactions that support this chemistry. Overall, our work adds oxime-forming machinery to the biomolecular toolbox available for trans-AT PKS engineering, opening the way to introducing such masked aldehyde functionalities into diverse polyketides.ISSN:1433-7851ISSN:1521-3773ISSN:0570-083