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

Observations of open-ocean deep convection in the northwestern Mediterranean Sea: Seasonal and interannual variability of mixing and deep water masses for the 2007-2013 Period

We present here a unique oceanographic and meteorological data set focus on the deep convection processes. Our results are essentially based on in situ data (mooring, research vessel, glider, and profiling float) collected from a multiplatform and integrated monitoring system (MOOSE: Mediterranean Ocean Observing System on Environment), which monitored continuously the northwestern Mediterranean Sea since 2007, and in particular high‐frequency potential temperature, salinity, and current measurements from the mooring LION located within the convection region. From 2009 to 2013, the mixed layer depth reaches the seabed, at a depth of 2330m, in February. Then, the violent vertical mixing of the whole water column lasts between 9 and 12 days setting up the characteristics of the newly formed deep water. Each deep convection winter formed a new warmer and saltier “vintage” of deep water. These sudden inputs of salt and heat in the deep ocean are responsible for trends in salinity (3.3 ± 0.2 × 10−3/yr) and potential temperature (3.2 ± 0.5 × 10−3 C/yr) observed from 2009 to 2013 for the 600–2300 m layer. For the first time, the overlapping of the three “phases” of deep convection can be observed, with secondary vertical mixing events (2–4 days) after the beginning of the restratification phase, and the restratification/spreading phase still active at the beginning of the following deep convection event

International conference ICAWA 2016 : extended book of abstract : the AWA project : ecosystem approach to the management of fisheries and the marine environment in West African waters

The Joint International Laboratory ECLAIRS set up an oceanographic and meteorological buoy, dedicated to monitoring and analysis of the short and long-term changes in climate, atmosphere and marine environment within the Senegal coastal upwelling. The buoy "MELAX" was deployed early 2015 in the heart of the Senegalese upwelling by 30 m-depth at (14,20'N, 17,14'W). Data collected are, for the atmosphere, surface wind, solar radiation, humidity and rain, and for the ocean, temperatures, salinity, and currents (from the surface to the bottom) and oxygen. We present the first year and a half of observations, in particular the relationship between wind, sea surface temperatures, and hydrology. Satellite and model data are used to provide a larger-scale context to the local monitoring

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.

The southern Senegal upwelling center : state and functioning during the UPSEN2/ECOAO field experiments (feb.-mar. 2013) [résumé]

International Conference AWA (ICAWA), Dakar, SEN, 09-/12/2014 - 01/01/197

The southern Senegal upwelling center : state and functioning during the UPSEN2/ECOAO field experiments (feb.-mar. 2013) [résumé]

International Conference AWA (ICAWA), Dakar, SEN, 09-/12/2014 - 01/01/197