Unfolding and unzipping of single-stranded DNA by stretching

We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of chain elasticity. In a generic case, we show that the stretching curve of ssDNA exhibits two distinct features: the second-order "unfolding" phase transition, and a sharp crossover, reminiscent of the first-order "unzipping" transition in dsDNA. We apply the theory to the particular cases of Worm-like Chain (WLC) and Freely-Joint Chain (FJC) models, and discuss the universal and model--dependent features of the mechanical response of ssDNA. In particular, we show that variation of the width of the unzipping crossover with interaction strength is very sensitive to the energetics of hairpin loops. This opens a new way of testing the elastic properties of ssDNA.Comment: 7 pages, 4 figures, substantially revised versio

Constraints on filament models deduced from dynamical analysis

The conclusions deduced from simultaneous observations with the Ultra-Violet Spectrometer and Polarimeter (UVSP) on the Solar Maximum Mission satellite, and the Multichannel Subtractive Double Pass (MSPD) spectrographs at Meudon and Pic du Midi observatories are presented. The observations were obtained in 1980 and 1984. All instruments have almost the same field of view and provide intensity and velocity maps at two temperatures. The resolution is approx. 0.5 to 1.5" for H alpha line and 3" for C IV. The high resolution and simultaneity of the two types of observations allows a more accurate description of the flows in prominences as functions of temperature and position. The results put some contraints on the models and show that dynamical aspects must be taken into account

Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Phase transition in a non-conserving driven diffusive system

An asymmetric exclusion process comprising positive particles, negative particles and vacancies is introduced. The model is defined on a ring and the dynamics does not conserve the number of particles. We solve the steady state exactly and show that it can exhibit a continuous phase transition in which the density of vacancies decreases to zero. The model has no absorbing state and furnishes an example of a one-dimensional phase transition in a homogeneous non-conserving system which does not belong to the absorbing state universality classes

The GSFC scientific data storage problem

Scientific data storage problems of telemetry tape

The ethanolamide metabolite of DHA, docosahexaenoylethanolamine, shows immunomodulating effects in mouse peritoneal and RAW264.7 macrophages: evidence for a new link between fish oil and inflammation

Several mechanisms have been proposed for the positive health effects associated with dietary consumption of long-chain n-3 PUFA (n-3 LC-PUFA) including DHA (22 : 6n-3) and EPA (20 : 5n-3). After dietary intake, LC-PUFA are incorporated into membranes and can be converted to their corresponding N-acylethanolamines (NAE). However, little is known on the biological role of these metabolites. In the present study, we tested a series of unsaturated NAE on the lipopolysaccharide (LPS)-induced NO production in RAW264.7 macrophages. Among the compounds tested, docosahexaenoylethanolamine (DHEA), the ethanolamide of DHA, was found to be the most potent inhibitor, inducing a dose-dependent inhibition of NO release. Immune-modulating properties of DHEA were further studied in the same cell line, demonstrating that DHEA significantly suppressed the production of monocyte chemotactic protein-1 (MCP-1), a cytokine playing a pivotal role in chronic inflammation. In LPS-stimulated mouse peritoneal macrophages, DHEA also reduced MCP-1 and NO production. Furthermore, inhibition was also found to take place at a transcriptional level, as gene expression of MCP-1 and inducible NO synthase was inhibited by DHEA. To summarise, in the present study, we showed that DHEA, a DHA-derived NAE metabolite, modulates inflammation by reducing MCP-1 and NO production and expression. These results provide new leads in molecular mechanisms by which DHA can modulate inflammatory processes

Comment on "Why is the DNA denaturation transition first order?"

In this comment we argue that while the conclusions in the original paper (Y. Kafri, D. Mukamel and L. Peliti, Phys. Rev. Lett. 85, 4988 (2000)) are correct for asymptotically long DNA chains, they do not apply to the chains used in typical experiments. In the added last paragraph, we point out that for real DNA the average distance between denatured loops is not of the order of the persistence length of a single-stranded chain but much larger. This corroborates our reasoning that the double helix between loops is quite rigid, and thereby our conclusion.Comment: 1 page, REVTeX. Last paragraph adde