SIST: stress-induced structural transitions in superhelical DNA.

SUMMARY: Supercoiling imposes stress on a DNA molecule that can drive susceptible sequences into alternative non-B form structures. This phenomenon occurs frequently in vivo and has been implicated in biological processes, such as replication, transcription, recombination and translocation. SIST is a software package that analyzes sequence-dependent structural transitions in kilobase length superhelical DNA molecules. The numerical algorithms in SIST are based on a statistical mechanical model that calculates the equilibrium probability of transition for each base pair in the domain. They are extensions of the original stress-induced duplex destabilization (SIDD) method, which analyzes stress-driven DNA strand separation. SIST also includes algorithms to analyze B-Z transitions and cruciform extrusion. The SIST pipeline has an option to use the DZCBtrans algorithm, which analyzes the competition among these three transitions within a superhelical domain. AVAILABILITY AND IMPLEMENTATION: The package and additional documentation are freely available at https://bitbucket.org/benhamlab/sist_codes. CONTACT: dzhabinskaya@ucdavis.edu.

An alternative treatment approach to mitral regurgitation.

This article aims to increase knowledge and understanding of mitral valve regurgitation to assist nurses in providing effective patient care and support the treatment options available. It focuses on the MitraClip, a procedure to repair the mitral valve using a percutaneous approach.

Treatment of older patients with aortic valve stenosis.

This article aims to increase knowledge and understanding of aortic valve stenosis to support the treatment options available for older patients in the acute setting. The article discusses a relatively new procedure, transcatheter aortic valve implantation, which is appropriate for selected patients with aortic stenosis, and outlines the aftercare involved.

Expanding Flp-RMCE options: the potential of Recombinase Mediated Twin-Site Targeting (RMTT).

Where possible, developments enabling the establishment of cell lines with predictable, long-term stable expression capacity are based on single-copy integrations at safe genomic loci with predictable properties. Robust performance could be assigned to lentiviral transduction systems anchoring single LV-units at sites with adequate transcription potential. In the case of gene therapeutic vectors it is essential that the expression interval can be safely terminated following individual requirements, which has mostly been achieved by lox-mediated excision ("floxing"). To extend the spectrum of possible applications we replaced the common, phage-derived Cre/loxP-setup by modules derived from the yeast "Flp/FRT" site-specific recombination system. This change enables a variety of additional options, for instance by "multiplexing" strategies, which rely on a variety of heterospecific FRT-site variants (F'). If we provide lentiviral LTRs with a "twin-site", here an FF3 fusion, the presence of Flp-recombinase will effectively excise the expression cassette, leaving behind a single neutral, genomically anchored FF3 unit. This tag serves to identify the integration locus and to apply sequence- and structural (SIDD-) analyses to predict its functions. Candidate loci are then used to accommodate, at the given site, other genes of interest by "Recombinase-Mediated Twin Site Targeting" (RMTT), a contemporary extension of existing cassette exchange (RMCE-) routines. Supported by the fact that FF3 twins remain accessible within the host genome, RMTT provides access to certified cell lines as it complies with recently defined stringent genomic safe harbor criteria. Our discussion- and outlook-sections will cover lentiviral targeting strategies and current possibilities to enable their fine-tuning.

Superhelical duplex destabilization and the recombination position effect.

The susceptibility to recombination of a plasmid inserted into a chromosome varies with its genomic position. This recombination position effect is known to correlate with the average G+C content of the flanking sequences. Here we propose that this effect could be mediated by changes in the susceptibility to superhelical duplex destabilization that would occur. We use standard nonparametric statistical tests, regression analysis and principal component analysis to identify statistically significant differences in the destabilization profiles calculated for the plasmid in different contexts, and correlate the results with their measured recombination rates. We show that the flanking sequences significantly affect the free energy of denaturation at specific sites interior to the plasmid. These changes correlate well with experimentally measured variations of the recombination rates within the plasmid. This correlation of recombination rate with superhelical destabilization properties of the inserted plasmid DNA is stronger than that with average G+C content of the flanking sequences. This model suggests a possible mechanism by which flanking sequence base composition, which is not itself a context-dependent attribute, can affect recombination rates at positions within the plasmid.