Understanding the Sequence-Dependence of DNA Groove Dimensions: Implications for DNA Interactions

BACKGROUND: The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. METHODOLOGY/PRINCIPAL FINDINGS: The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR (31)P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The (31)P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. CONCLUSIONS/SIGNIFICANCE: The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions

Evapotranspiration and surface energy balance of a common reed-dominated riparian system in the Platte River basin, central Nebraska

Quantifying actual evapotranspiration (ETa) of riparian zones is important for more robust water balance analyses that will enable better planning, managing, and allocating of water resources as well as developing strategies to protect delicate riparian ecosystem functions. The ETa, sensible heat flux (H), net radiation (Rn), soil heat flux (G), meteorological variables (air temperature, Ta; incoming shortwave radiation, Rs; wind speed, u3; relative humidity, RH; vapor pressure deficit, VPD; precipitation, etc.), and albedo were measured on an hourly time step, and leaf area index (LAI) and plant height were measured on a weekly basis for a common reed (Phragmites australis) dominated cottonwood (Populus deltoides) and peach-leaf willow (Salix amygdaloides) riparian plant community in 2009 and 2010 through extensive field campaigns conducted in the Platte River basin in central Nebraska. The two growing seasons were contrasted by warmer air temperatures, higher precipitation, and presence of flood water on the surface during the 2010 season. The seasonal variations of daily average ETa were mainly controlled by Rn and air temperature. In 2009, total ETa and precipitation were 679 mm and 280 mm, respectively, and the values were substantially greater in 2010 (982 mm and 508 mm, respectively). The seasonal daily ETa for the mixed plant community ranged from 0.5 to 8.5 mm d-1 with a seasonal average of 3.7 mm d-1 in 2009 and from 0.5 to 11 mm d-1 with a seasonal average of 5.5 mm d-1 in 2010. In 2010, ETa varied widely with meteorological conditions and in response to variations in phenology of the vegetation to flooding. In 2009, on a seasonal average basis, a total of 77% and 14% of the available energy was partitioned into ETa and H, respectively. In 2010, over 90% and -12% (negative due to flooding) of the available energy was partitioned into ETa and H, respectively. The research results presented here provide valuable ETa data and information for enhancing the understanding of the interactions between the surface/vegetation conditions and the surrounding microclimate and surface energy balance for mixed riparian vegetation. The results of this research should aid water managers and decision/policy makers in accounting for water use rates of phragmites-dominated cottonwood and peach-leaf willow riparian plant communities in water balance analyses to make better-informed water resources planning and management decisions

Coupling processes and exchange of energy and reactive and non-reactive trace gases at a forest site – results of the EGER experiment

To investigate the energy, matter and reactive and non-reactive trace gas exchange between the atmosphere and a spruce forest in the German mountain region, two intensive measuring periods were conducted at the FLUXNET site DE-Bay (Waldstein-Weidenbrunnen) in September/October 2007 and June/July 2008. They were part of the project "ExchanGE processes in mountainous Regions" (EGER). Beyond a brief description of the experiment, the main focus of the paper concerns the coupling between the trunk space, the canopy and the above-canopy atmosphere. Therefore, relevant coherent structures were analyzed for different in- and above canopy layers, coupling between layers was classified according to already published procedures, and gradients and fluxes of meteorological quantities as well as concentrations of non-reactive and reactive trace compounds have been sorted along the coupling classes. Only in the case of a fully coupled system, it could be shown, that fluxes measured above the canopy are related to gradients between the canopy and the above-canopy atmosphere. Temporal changes of concentration differences between top of canopy and the forest floor, particularly those of reactive trace gases (NO, NO2, O3, and HONO) could only be interpreted on the basis of the coupling stage. Consequently, only concurrent and vertically resolved measurements of micrometeorological (turbulence) quantities and fluxes (gradients) of trace compounds will lead to a better understanding of the forest-atmosphere interaction