The analysis of grapevine (Vitis vinifera) berries at the transcriptomic, proteomic, and metabolomic levels can provide great insight into the molecular events underlying berry development and postharvest drying (withering). However, the large and very different data sets produced by such investigations are difficult to integrate. Here, we report the identification of putative stage-specific biomarkers for berry development and withering and, to our knowledge, the first integrated systems-level study of these processes. Transcriptomic, proteomic, and metabolomic data were integrated using two different strategies, one hypothesis free and the other hypothesis driven. A multistep hypothesis-free approach was applied to data from four developmental stages and three withering intervals, with integration achieved using a hierarchical clustering strategy based on the multivariate bidirectional orthogonal projections to latent structures technique. This identified stage-specific functional networks of linked transcripts, proteins, and metabolites, providing important insights into the key molecular processes that determine the quality characteristics of wine. The hypothesis-driven approach was used to integrate data from three withering intervals, starting with subdata sets of transcripts, proteins, and metabolites. We identified transcripts and proteins that were modulated during withering as well as specific classes of metabolites that accumulated at the same time and used these to select subdata sets of variables. The multivariate bidirectional orthogonal projections to latent structures technique was then used to integrate the subdata sets, identifying variables representing selected molecular processes that take place specifically during berry withering. The impact of this holistic approach on our knowledge of grapevine berry development and withering is discussed.

This paper reports a theory for the dielectric relaxation of dimeric mesogenic molecules in a nematic liquid crystal phase. Liquid crystal dimers consist of two mesogenic groups linked by a flexible chain. Recent experimental studies [D. A. Dunmur, G. R. Luckhurst, M. R. de la Fuente, S. Diez, and M. A. Perez Jubindo, J. Chem. Phys. 115, 8681 (2001)] of the dielectric properties of polar liquid crystal dimers have found unexpected results for both the static (low frequency) and variable frequency dielectric response of these materials. The theory developed in this paper provides a quantitative model with which to understand the observed experimental results. The mean-square dipole moments of alpha,omega-bis[(4-cyanobiphenyl-4'-yl]alkanes in a nematic phase have been calculated using both the rotational isomeric state model and a full torsional potential for the carbon-carbon bonds of the flexible chain. The orienting effect of the nematic phase is taken into account by a parametrized potential of mean torque acting on the mesogenic groups and the segments in the flexible chain. Results of calculations using the full torsional potential are in excellent agreement with experimental results for comparable systems. The probability density p(eq)(beta(A),beta(B)) for the orientation of the mesogenic groups (A,B) along the nematic director is also calculated. The resultant potential of mean torque is a surface characterized by four deep energy wells or sites equivalent to alignment of the terminal groups A and B approximately parallel and antiparallel to the director; of course, the reversal of the director leads to equivalent sites. This potential energy surface provides the basis for a kinetic model of dielectric relaxation in nematic dimers. Solution of the Fokker-Planck equation corresponding to this four-site model gives the time dependence of the site populations, and hence the time-correlation functions for the total dipole moment along the director. In this model the end-over-end rotation of the molecule, corresponding to simultaneous reversal of both mesogenic groups, is excluded because the activation energy is too large. Results are presented for a number of cases, in which a dipole is located on one or both of the mesogenic groups, and additionally where the groups differ in size. For the latter, under particular conditions, the correlation function exhibits a biexponential decay, which corresponds to two low frequency absorptions in the dielectric spectrum. This is exactly what has been observed for nonsymmetric nematic dimers having different groups terminating a flexible chain. Experimental results over a range of temperature for the nonsymmetric dimer alpha-[(4-cyanobiphenyl)-4'-yloxy]-omega-(4-decylanilinebenzylidene-4'-oxy)nonane can be fitted precisely to the theory, which provides new insight into the orientational and conformational dynamics of molecules in ordered liquid crystalline phases.

The metabolomic profiling of EBC could clearly distinguish different biochemical-metabolic profiles in asthmatic children and enabled the severe asthma phenotype to be fully discriminated. The breathomics approach may therefore be suitable for discriminating between different asthma metabolic phenotypes.

BackgroundThe definition of the terroir concept is one of the most debated issues in oenology and viticulture. The dynamic interaction among diverse factors including the environment, the grapevine plant and the imposed viticultural techniques means that the wine produced in a given terroir is unique. However, there is an increasing interest to define and quantify the contribution of individual factors to a specific terroir objectively. Here, we characterized the metabolome and transcriptome of berries from a single clone of the Corvina variety cultivated in seven different vineyards, located in three macrozones, over a 3-year trial period.ResultsTo overcome the anticipated strong vintage effect, we developed statistical tools that allowed us to identify distinct terroir signatures in the metabolic composition of berries from each macrozone, and from different vineyards within each macrozone. We also identified non-volatile and volatile components of the metabolome which are more plastic and therefore respond differently to terroir diversity. We observed some relationships between the plasticity of the metabolome and transcriptome, allowing a multifaceted scientific interpretation of the terroir concept.ConclusionsOur experiments with a single Corvina clone in different vineyards have revealed the existence of a clear terroir-specific effect on the transcriptome and metabolome which persists over several vintages and allows each vineyard to be characterized by the unique profile of specific metabolites.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0584-4) contains supplementary material, which is available to authorized users.

The spontaneous diffusion of solutes through lipid bilayers is still a challenge for theoretical predictions. Since permeation processes remain beyond the capabilities of unbiased molecular dynamics simulations, an alternative strategy is currently adopted to gain insight into their mechanism and time scale. This is based on a monodimensional description of the translocation process only in terms of the position of the solute along the normal to the lipid bilayer, which is formally expressed in the solubility-diffusion model. Actually, a role of orientational and conformational motions has been pointed out, and the use of advanced simulation techniques has been proposed to take into account their effect. Here, we discuss the limitations of the standard solubility-diffusion approach and propose a more general description of membrane translocation as a diffusion process on a free energy surface, which is a function of the translational and rotational degrees of freedom of the molecule. Simple expressions for the permeability coefficient are obtained under suitable conditions. For fast solute reorientation, the classical solubility-diffusion equation is recovered. Under the assumption that well-defined minima can be identified on the free energy landscape, a mechanistic interpretation of the permeability coefficient in terms of all possible permeation paths is given.