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

Conformations of closed DNA

We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic expressions leading to the spatial configuration of a family of solutions representing distortions that interpolate between the circular form of DNA and a figure-eight form that represents the onset of interwinding. We are also able to generate knotted loops. We suggest ways to use our approach to produce other configurations relevant to studies of DNA structure. The stability of the distorted configurations is assessed, along with the effects of fluctuations on the free energy of the various configurations.Comment: 39 pages in REVTEX with 14 eps figures. Submitted to Phys. Rev. E. This manuscript updates, expands and revises, to a considerable extent, a previously posted manuscript, entitled "Conformations of Circular DNA," which appeared as cond-mat/970104

A stitch in time: Efficient computation of genomic DNA melting bubbles

Background: It is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic. Results: An efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a maximal bubble length. No approximations, such as windowing, have been introduced to reduce the time complexity. More than just finding the bubbles, the algorithm produces a stitch profile, which is a probabilistic graphical model of bubbles and helical regions. The algorithm applies a probability peak finding method based on a hierarchical analysis of the energy barriers in the Poland-Scheraga model. Conclusions: Exact and fast computation of genomic stitch profiles is thus feasible. Sequences of several megabases have been computed, only limited by computer memory. Possible applications are the genome-wide comparisons of bubbles with promotors, TSS, viral integration sites, and other melting-related regions.Comment: 16 pages, 10 figure

A developmentally regulated chaperone complex for the endoplasmic reticulum of male haploid germ cells

Glycoprotein folding is mediated by lectin-like chaperones and protein disulfide isomerases (PDIs) in the endoplasmic reticulum (ER). Calnexin and the PDI homologue ERp57 work together to help fold nascent polypeptides with glycans located toward the N-terminus of a protein, whereas PDI and BiP may engage proteins that lack glycans or have sugars toward the C-terminus. In this study, we show that the PDI homologue PDILT is expressed exclusively in post-meiotic male germ cells, in contrast to the ubiquitous expression of many other PDI family members in the testis. PDILT is induced during puberty and represents the first example of a PDI family member under developmental control. We find that PDILT is not active as an oxido-reductase, but interacts with the model peptide -somatostatin and nonnative BPTI in vitro, indicative of chaperone activity. In vivo, PDILT forms a tissue-specific chaperone complex with the calnexin homologue calmegin. The identification of a redox-inactive chaperone partnership defines a new system of testis-specific protein folding with implications for male fertility

Ronin Governs Early Heart Development by Controlling Core Gene Expression Programs.

Ronin (THAP11), a DNA-binding protein that evolved from a primordial DNA transposon by molecular domestication, recognizes a hyperconserved promoter sequence to control developmentally and metabolically essential genes in pluripotent stem cells. However, it remains unclear whether Ronin or related THAP proteins perform similar functions in development. Here, we present evidence that Ronin functions within the nascent heart as it arises from the mesoderm and forms a four-chambered organ. We show that Ronin is vital for cardiogenesis during midgestation by controlling a set of critical genes. The activity of Ronin coincided with the recruitment of its cofactor, Hcf-1, and the elevation of H3K4me3 levels at specific target genes, suggesting the involvement of an epigenetic mechanism. On the strength of these findings, we propose that Ronin activity during cardiogenesis offers a template to understand how important gene programs are sustained across different cell types within a developing organ such as the heart

Experimental study exploring the interaction of structural and leakage dynamics

Strategies for managing leakage from water distribution systems require the ability to effectively evaluate such real losses through the understanding of the behavior of individual leaks, including their response to changes in pressure regime due to demand or management strategies. This paper presents the results from an innovative experimental investigation aimed at understanding the response of longitudinal slits in pressurized viscoelastic pipes, specifically considering the interaction between the structural and leakage dynamics. For the first time, leakage flow rate, pressure, leak area, and material strain were recorded simultaneously, providing new knowledge of the complex interaction of these factors. The paper shows that strain and area are directly related, hence it is possible to employ strain as a predictor of leak area, calculated using a calibrated viscoelastic model. Using such an approach, the leakage flow rates under a range of quasi-static pressures were accurately predicted and validated. Overall the paper demonstrates that the orifice equation, with a constant coefficient of discharge, is suitable for accurately estimating dynamic leakage flow rates from longitudinal slits, provided that the leak area is suitably incorporated

Salerno's model of DNA reanalysed: could solitons have biological significance?

We investigate the sequence-dependent behaviour of localised excitations in a toy, nonlinear model of DNA base-pair opening originally proposed by Salerno. Specifically we ask whether ``breather'' solitons could play a role in the facilitated location of promoters by RNA polymerase. In an effective potential formalism, we find excellent correlation between potential minima and {\em Escherichia coli} promoter recognition sites in the T7 bacteriophage genome. Evidence for a similar relationship between phage promoters and downstream coding regions is found and alternative reasons for links between AT richness and transcriptionally-significant sites are discussed. Consideration of the soliton energy of translocation provides a novel dynamical picture of sliding: steep potential gradients correspond to deterministic motion, while ``flat'' regions, corresponding to homogeneous AT or GC content, are governed by random, thermal motion. Finally we demonstrate an interesting equivalence between planar, breather solitons and the helical motion of a sliding protein ``particle'' about a bent DNA axis.Comment: Latex file 20 pages, 5 figures. Manuscript of paper to appear in J. Biol. Phys., accepted 02/09/0

Conformations of Linear DNA

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link number. We derive a fundamental relation between the Euler angles that describe the curve and the topological linking number. Analytical expressions for the spatial configurations of the molecule in the infinite- length limit were obtained. A unique configuraion minimizes the energy for a given set of physical conditions. An elastic model incorporating thermal fluctuations provides excellent agreement with experimental results on the plectonemic transition.Comment: 5 pages, RevTeX; 6 postscript figure

A Mobile Prenatal Care App to Reduce In-Person Visits: Prospective Controlled Trial.

BACKGROUND: Risk-appropriate prenatal care has been asserted as a way for the cost-effective delivery of prenatal care. A virtual care model for prenatal care has the potential to provide patient-tailored, risk-appropriate prenatal educational content and may facilitate vital sign and weight monitoring between visits. Previous studies have demonstrated a safe reduction in the frequency of in-person prenatal care visits among low-risk patients but have noted a reduction in patient satisfaction. OBJECTIVE: The primary objective of this study was to test the effectiveness of a mobile prenatal care app to facilitate a reduced in-person visit schedule for low-risk pregnancies while maintaining patient and provider satisfaction. METHODS: This controlled trial compared a control group receiving usual care with an experimental group receiving usual prenatal care and using a mobile prenatal care app. The experimental group had a planned reduction in the frequency of in-person office visits, whereas the control group had the usual number of visits. The trial was conducted at 2 diverse outpatient obstetric (OB) practices that are part of a single academic center in Washington, DC, United States. Women were eligible for enrollment if they presented to care in the first trimester, were aged between 18 and 40 years, had a confirmed desired pregnancy, were not considered high-risk, and had an iOS or Android smartphone that they used regularly. We measured the effectiveness of a virtual care platform for prenatal care via the following measured outcomes: the number of in-person OB visits during pregnancy and patient satisfaction with prenatal care. RESULTS: A total of 88 patients were enrolled in the study, 47 in the experimental group and 41 in the control group. For patients in the experimental group, the average number of in-person OB visits during pregnancy was 7.8 and the average number in the control group was 10.2 (P=.01). There was no statistical difference in patient satisfaction (P\u3e.05) or provider satisfaction (P\u3e.05) in either group. CONCLUSIONS: The use of a mobile prenatal care app was associated with reduced in-person visits, and there was no reduction in patient or provider satisfaction. TRIAL REGISTRATION: ClinicalTrials.gov NCT02914301; https://clinicaltrials.gov/ct2/show/NCT02914301 (Archived by WebCite at http://www.webcitation.org/76S55M517)

Dynamics of liquid 4He in Vycor

We have measured the dynamic structure factor of liquid 4He in Vycor using neutron inelastic scattering. Well-defined phonon-roton (p-r) excitations are observed in the superfluid phase for all wave vectors 0.3 < Q < 2.15. The p-r energies and lifetimes at low temperature (T = 0.5 K) and their temperature dependence are the same as in bulk liquid 4He. However, the weight of the single p-r component does not scale with the superfluid fraction (SF) as it does in the bulk. In particular, we observe a p-r excitation between T_c = 1.952 K, where SF = 0, and T_(lambda)=2.172 K of the bulk. This suggests, if the p-r excitation intensity scales with the Bose condensate, that there is a separation of the Bose-Einstein condensation temperature and the superfluid transition temperature T_c of 4He in Vycor. We also observe a two-dimensional layer mode near the roton wave vector. Its dispersion is consistent with specific heat and SF measurements and with layer modes observed on graphite surfaces.Comment: 3 pages, 4 figure