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

RNA Aptamer Evolution: Two Decades of SELEction

Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First developed in 1990, the SELEX process has become a powerful tool to select structured oligonucleotides for the recognition of targets, starting with small molecules, going through protein complexes until whole cells. SELEX has also evolved along with new technologies positioning itself as an alternative in the design of a new class of therapeutic agents in modern molecular medicine. This review is an historical follow-up of SELEX method over the two decades since its first appearance

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

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

LION observatory data

The Lion mooring is located in the center of the Gulf of Lion where one of the largest open sea convection happens in the winter period. This open sea convection is an active vertical mixing that concerns the whole northern Mediterranean and can reach great deep in the Gulf of Lion (where it may even reach the bottom ~ 2500m) due to the Mistral and Tramontane, cold and dry winds. This is the phenomenon of dense water formation which is the only mechanism for the ventilation of the deep waters of the entire western Mediterranean. It was observed that the deep waters can be formed 1) in a preconditioned open sea area and 2) on the shelf with a subsequent cascading down the slope. There are therefore two modes whose interannual monitoring is necessary to understand the evolution of Mediterranean deep waters and validate ocean numerical models of the region. The LION mooring is deployed and maintained since 2007. It aims to observe the winter dense water formation affecting the north-western Mediterranean Sea water circulation and deep-sea ecosystem (physical data). The mooring is deployed near the ODAS meteorological surface buoy (ODAS Lion, Meteo France) and integrated in the MOOSE network since 2010. It is part of the FIXO3 and OceanSites systems