Web-based platform for analysis of RNA folding from high throughput chemical probing data

RNA structures play critical roles in regulating gene expression across all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and ease of the experimental procedure, DMS-MaPseq has been adopted by labs worldwide. However, bioinformatic analysis remains a substantial hurdle for labs that often lack the necessary infrastructure and computational expertise. Here we present a modern web-based interface that automates the analysis of chemical probing profiles from raw sequencing files (http://rnadreem.org). The availability of a simple web-based platform for DMSMaPseq analysis will dramatically expand studies of RNA structure and aid in the design of structurebased therapeutics

Absorption and Scattering in Nonlinear Optical Polymeric Systems

Nonlinear organic systems often consist of a polymer matrix with a optical chromophore as a guest or an attached side chain. For enhanced optical nonlinearity, the chromophore absorption band should be located near the desired operating wavelength, but with no absorption. Good optical transmission is critical, and both the absorption and the scattering need to be minimized. Since the films are usually thin and weakly absorbing, it is difficult to determine either of these two material properties. By using the highly sensitive absorption technique of photothermal deflection spectroscopy (PDS), it is possible to obtain the fundamental optical spectrum of the nonlinear optical (NLO) systems over a wide energy range, and separate the absorption from the scattering. With this information, one can then select optimal polymer-chromophore systems. The absorption data indicates what the intrinsic waveguide loss should be for any given wavelength. For materials with low absorption, if there is high waveguide loss, either improved processing is necessary to lower the scattering, or insertion losses need to be reduced.</jats:p

Risk Factors Associated with Women\u27s Marital Infidelity

This study used a qualitative approach to explore the complexity of marital infidelity and understand issues within the marriage that could increase the risk of having a marital affair. Semi-structured interviews were used to explore women\u27s participation in an extramarital affair(s). The information gathered was audio taped, transcribed, and analyzed using the transcendental phenomenological model (Moustakas in Phenomenological research methods, Sage, Thousand Oaks, CA, 1994). All four of the women described a lack of quality time, inability to resolve conflict, and a lack of attention within the marriage as predisposing factors to the affair(s). Clinical and research implications are discussed. © 2014 Springer Science+Business Media New York