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

Variability of nutrient and particulate matter fluxes between the sea and a polder after partial tidal

This paper aims to investigate the patterns of exchanges of nutrients and suspended sediments between the sea and a polder, after partial tidal restoration, and to assess if these are comparable to those observed in natural salt marshes. The study site, situated in the Bay of Veys, in Northwestern France, was embanked in the 1870s and accidentally reconnected to the sea in 1990. Water now flows in and out of the polder by a single communication point with the sea, which facilitated water sampling and flux calculation for dissolved and particulate elements. The study was carried out for two years, from May 2002 to April 2004. Results showed that for all the months studied the water flowing out of the polder had lower concentrations of nitrates and suspended sediments, which lead to a retention of these elements throughout the year. Nitrates uptakes in the polder were much higher in winter (up to 473.9 g N ha(-1) tide(-1)) than in summer where they were close to zero. The retention of suspended sediment could be over 80% of the import and was mainly composed of organic matter. Finally, the concentrations of dissolved organic carbon were higher in outflow than inflow water, but due to unbalanced water budgets this lead to low quantities imported in summer and higher amounts exported for all other seasons. No interpretable pattern was observed for ammonium. The nature of these fluxes, according to literature, is close to those observed in immature salt marshes, so as far as restoration is concerned, it has been shown that partial tidal restoration can allow the restitution of the salt marsh exchange functions that were studied. (c) 2005 Elsevier Ltd. All rights reserved

DECAPITATION OF MAN HEADS IN ACARI VALLEY, PERU

Las excavaciones arqueológicas efectuadas en Amato, un sitio establecido a inicios del periodo Intermedio Temprano (circa 50 a.C – 300 d.C) en el valle de Acarí de la costa sur del Perú, permitió recuperar dos cabezas humanas en dos contextos diferentes. El primero proviene de las inmediaciones de decenas de esqueletos humanos decapitados, mientras que el segundo fue expuesto asociado al muro perimétrico que fortifica al sitio. Ambas cabezas recibieron un tratamiento similar a las cabezas trofeo; sin embargo, éstas no tienen el orificio en el hueso frontal, como tampoco presentan el foramen magnum alterado, características propias de las cabezas trofeo. Estos dos hallazgos demuestran que por lo menos en el valle de Acarí, la decapitación humana no fue efectuada exclusivamente para obtener cabezas trofeo. Esto implica además, que la decapitación y la toma de las cabezas fueron efectuadas por diversas razones y para cumplir funciones distintas.Archaeological excavations at Amato, a site established at the beginning of the Early Intermediate period (circa 50 BC – 300 AD) in the Acari Valley of the Peruvian south coast, uncovered two isolated human heads from different contexts. One head was found near an area where dozens intentionally decapitated skeletons were recovered. The second head was located in association with the main wall that encloses the site. Both heads were buried in similar fashion to Early Intermediate period south coast trophy heads; however, these heads from Amato were not culturally modified (e.g. perforated frontal bone and/or artificially enlarged foramen magnum). These two isolated heads demonstrate that not all human decapitation in the Acari Valley was for the purposes of securing trophy heads. Based on these findings, we suggest that the purpose and motivation for human decapitation and head-taking in the past was complex

Decapitación y cabezas humanas del valle de Acarí, Perú

International audienceArchaeological excavations at Amato, a site established at the beginning of the Early Intermediate period (circa 50 BC – 300 AD) in the Acari Valley of the Peruvian south coast, uncovered two isolated human heads from different contexts. One head was found near an area where dozens intentionally decapitated skeletons were recovered. The second head was located in association with the main wall that encloses the site. Both heads were buried in similar fashion to Early Intermediate period south coast trophy heads; however, these heads from Amato were not culturally modified (e.g. perforated frontal bone and/or artificially enlarged foramen magnum). These two isolated heads demonstrate that not all human decapitation in the Acari Valley was for the purposes of securing trophy heads. Based on these findings, we suggest that the purpose and motivation for human decapitation and head-taking in the past was complex. (source éditeur)Las excavaciones arqueológicas efectuadas en Amato, un sitio establecido a inicios del periodo Intermedio Temprano (circa 50 a.C – 300 d.C) en el valle de Acarí de la costa sur del Perú, permitió recuperar dos cabezas humanas en dos contextos diferentes. El primero proviene de las inmediaciones de decenas de esqueletos humanos decapitados, mientras que el segundo fue expuesto asociado al muro perimétrico que fortifica al sitio. Ambas cabezas recibieron un tratamiento similar a las cabezas trofeo; sin embargo, éstas no tienen el orificio en el hueso frontal, como tampoco presentan el foramen magnum alterado, características propias de las cabezas trofeo. Estos dos hallazgos demuestran que por lo menos en el valle de Acarí, la decapitación humana no fue efectuada exclusivamente para obtener cabezas trofeo. Esto implica además, que la decapitación y la toma de las cabezas fueron efectuadas por diversas razones y para cumplir funciones distintas. (source éditeur

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

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

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.