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

Identification of aptamers against the DNA template for in vitro transcription of the HIV-1 TAR element

We have extracted from a random population of about 10⁹ oligodeoxynucleotides a series of 21-mers that are able to bind to a folded DNA 76-mer used as a template for in vitro transcription of the TAR element of the retrovirus HIV-1, by the T7 RNA polymerase. Five aptastrucs, that is, aptamers able to bind to the structure, out of 15 analyzed sequences, share the consensus motif 5'-PyGGG(TG)PyC, complementary in part to a weak double-stranded region of the target. (The parentheses indicate that either T or G is missing in one of these aptastrucs.) A dissociation constant of about 3 microM was evaluated by electrophoretic mobility shift assay for the winner sequence. Interactions between the aptastruc and the target sequences involve more than Watson-Crick base pairing of the consensus octamer. The binding is chemistry dependent. Phosphorothioate oligodeoxyribonucleotides and 2'-O-methyl oligoribonucleotides derived from the selected aptastrucs exhibit a weak if any affinity for the target

Tidal marshes and biogenic silica recycling at the land-sea interface

We studied the seasonal exchange of biogenic silica (BSi) and dissolved silica (DSi) between a freshwater and a saltwater tidal marsh and the adjacent coastal waters. Export of DSi was observed from both tidal marshes, whereas BSi was imported in association with suspended solids. The export of DSi was highest (23.4% and 123.8% in the freshwater and saltwater marsh, respectively) in summer when DSi concentrations were low in the nearby coastal waters. Combined data from both marshes suggested a logarithmic decrease in DSi export with increasing DSi concentrations in the inundating waters. BSi import was observed year round in the freshwater marsh, but only in summer in the saltwater marsh. The results show that DSi export from tidal marshes, both freshwater and salt water, contributes significantly to estuarine Si availability in summer and provide new insights regarding potential linkages between tidal marshes and secondary production in nearby coastal waters.

Biogeochemical functioning of grazed estuarine tidal marshes along a salinity gradient

Depending on their location along an estuarine salinity gradient, tidal marshes are thought to have different impacts on the chemical composition of the water during flooding. However, there is a lack of direct measurements of fluxes occurring between the marsh surface and the water column to corroborate this hypothesis. This study compared fluxes of nutrient and dissolved organic carbon (DOC) between the water column and the marsh surface and the emission of greenhouse gases, at four sites located along the salinity gradient of an estuary of north-western Wales (UK). The exchanges of dissolved organic carbon and nitrogen (DON), dissolved inorganic nitrogen (DIN), soluble reactive phosphorus and silicic acid, carbon dioxide, methane and nitrous oxide were measured during tidal inundation in May and September 2008 using in situ incubation chambers. There was no linear pattern along the salinity gradient and the concentration of nutrients and DOC in the flood water did not appear to control the biogeochemical processes driving the marsh surface/water column exchanges in the studied marshes. Multivariate analysis showed a clear discrimination in functioning between sites with the fresh and brackish marshes having a more similar functioning compared to low and middle marshes. The main differences between these two groupings were in the fluxes of DOC and nitrate. The phenology of plant species, soil organic matter content and soil oxygenation appear be the dominant factors explaining the observed fluxes

Exclusion of genes coding for proteins of the cytoskeleton and the extracellular matrix in familial hypertrophic cardiomyopathy using a candidate gene approach

Familial hypertrophic cardiomyopathy (FHC), a primary cardiac pathology, is a genetically heterogeneous disease, with autosomal dominant inheritance. The first gene identified as responsible for FHC codes for beta-myosin heavy chain (beta-MHC). To find a second locus, a candidate gene approach was applied on two families for which the beta-MHC locus was excluded. Selection of candidate genes is based on the observation of tissular and cellular disorganisation in FHC, and included genes coding for proteins involved in human myocardium architecture: the extracellular matrix components and cytoskeleton proteins. Chromosomal areas containing the candidate genes were examined by linkage analysis with microsatellite markers. The genes coding for different types of collagens, laminins, fibronectin, fibrillins, desmin, titin, alpha-actinin, vinculin, cardiac and skeletal alpha-actins, ankyrin and spectrin were excluded as responsible for FHC

Diagnostic performance of QT interval variables from 24-h electrocardiography in the long QT syndrome

International audienceThe long QT syndrome is mainly defined by QT interval prolongation (QTc > 0.44s). However, data obtained in genotyped patients showed that resting QTc measurement alone may be inaccurate for ascertaining the phenotype. The aim of this study was to evaluate the diagnostic performance of QT interval rate-dependence in untreated chromosome 11-linked patients