Evaluation of four different strategies to characterize plasma membrane proteins from banana roots

Plasma membrane proteins constitute a very important class of proteins. They are involved in the transmission of external signals to the interior of the cell and selective transport of water, nutrients and ions across the plasma membrane. However, the study of plasma membrane proteins is challenging because of their poor solubility in aqueous media and low relative abundance. In this work, we evaluated four different strategies for the characterization of plasma membrane proteins from banana roots: (i) the aqueous-polymer two-phase system technique (ATPS) coupled to gelelectrophoresis (gel-based), and (ii) ATPS coupled to LC-MS/MS (gel free), (iii) a microsomal fraction and (iv) a full proteome, both coupled to LC-MS/ MS. Our results show that the gel-based strategy is useful for protein visualization but has major limitations in terms of time reproducibility and efficiency. From the gel-free strategies, the microsomal-based strategy allowed the highest number of plasma membrane proteins to be identified, followed by the full proteome strategy and by the ATPS based strategy. The high yield of plasma membrane proteins provided by the microsomal fraction can be explained by the enrichment of membrane proteins in this fraction and the high throughput of the gel-free approach combined with the usage of a fast high-resolution mass spectrometer for the identification of proteins

Characterizing fruit ripening in plantain and Cavendish bananas: A proteomics approach

The fruit physiology of banana cultivars other than Cavendish is poorly understood. To study the ripening process, samples were taken daily from plantain and Cavendish bananas and the ripening stages were determined. We present data from the green to the fully mature stage. By analyzing the protein abundances during ripening we provide some new insights into the ripening process and how plantains fruits are different. Multivariate analysis of the proteins was performed correlated to the starch dynamics. A drop in sucrose synthase and a rise of acid invertase during ripening indicated a change in the balance of the sucrose fate. During ripening, sugars may no longer be available for respiration since they are stored in the vacuoles, making citrate the preferred respiratory substrate. We found significant cultivar specific differences in granule-bound starch synthase, alpha- and beta amylases and cell wall invertase when comparing the protein content at the same ripening stage. This corroborates the difference in starch content/structure between both banana types. Differences in small heat shock proteins and in the cell wall-modifying enzyme xyloglucan endotransglucosylase/hydrolase support respectively the presumed higher carotenoid content and the firmer fruit structure of plantains

A new approach to geobarometry by combining fluid inclusion and clumped isotope thermometry in hydrothermal carbonates

This study presents a new approach to geobarometry by combining fluid inclusion and clumped isotope (\u39447) thermometry on carbonate minerals. The offset between homogenisation temperatures of primary fluid inclusions with known composition and \u39447 temperatures of the host mineral allows a direct estimation of the fluid pressure at the time of carbonate crystallisation. This new approach is illustrated via hydrothermal dolomite samples from the Variscan foreland fold-and-thrust belt in northern Spain. Clumped isotope analyses yield crystallisation temperatures (107\u2013168\ub0C) which are higher than homogenisation temperatures in corresponding samples (95\u2013145\ub0C). The calculated pressure values suggest that dolomitizing fluids were overpressured during formation of zebra dolomite textures, whereas lower pressures are obtained for dolomite cement from breccia textures. This new approach to geobarometry opens up the possibility of estimating the pressure of carbonate crystallisation and has potential applications in diagenesis, basin analysis, ore geology and tectonics

Stochastic series expansion method for quantum Ising models with arbitrary interactions

A quantum Monte Carlo algorithm for the transverse Ising model with arbitrary short- or long-range interactions is presented. The algorithm is based on sampling the diagonal matrix elements of the power series expansion of the density matrix (stochastic series expansion), and avoids the interaction summations necessary in conventional methods. In the case of long-range interactions, the scaling of the computation time with the system size N is therefore reduced from N^2 to Nln(N). The method is tested on a one-dimensional ferromagnet in a transverse field, with interactions decaying as 1/r^2.Comment: 9 pages, 5 figure

Contribution to the understanding of the Ionian Basin sedimentary evolution along the eastern edge of Apulia during the Late Cretaceous in Albania

Integrated in the peri-Adriatic domain, the Ionian Basin extended along a NW-SE direction during the Late Cretaceous, limited on its sides by the Apulian and the Kruja platforms. The basinal/slope succession was studied in seven outcrops exposed in the Albanian fold-and-thrust belt. Sedimentological investigations, supported by bio- and chronostratigraphy were performed on calcareous Upper Cretaceous hemipelagites, gravity-flow deposits and slumps. The western part of the basin was studied, revealing a strong influence of the Apulian margin, alternatively shedding sediment basinward, by means of a tectonically controlled edge. The Late Albian to Cenomanian period is characterized by the settling of muddy debrites along the margin. A deep basinal environment characterizes this period which prolongs until the Santonian, with no significant influx of the platform basinward. This sedimentary setting abruptly changed at the end of the Santonian, with an important influx derived from both platforms. Coarsening and thickening upward sequences show a progressive increase in sediment shedding during the Campanian. The Late Campanian-Early Maastrichtian period points out a major change on the resedimentation processes with the settling of several slumped units reworking thick sediment packages. The latter can be traced along the Apulian margin, testifying of instabilities along the edge of Apulia

How do roots respond to osmotic stress? A transcriptomic approach to address this question in a non-model crop

Drought is a complex phenomenon that is relevant for many crops. Performing high-throughput transcriptomics in non-model crops is challenging. The non-model crop where our workflow has been tested on is banana (Musa spp.), which ranks among the top ten staple foods (total production over 145 million tons in 2013 (FAOstat)[1]). Bananas need vast amounts of water and even mild-drought conditions are responsible for considerable yield losses[2]. To characterize drought in the roots of different banana genotypes, we designed a lab model based on osmotic stress (5% PEG treatment for 3 days) and performed mRNA-seq analysis[3]. Using Illumina technology, 18 cDNA libraries were sequenced producing around 568 million high quality reads, of which 70-84% were mapped to the diploid reference genome[4]. We show that the applied stress leads to a drop in energy levels inducing a metabolic shift towards (i) higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. We also analyzed the expression patterns of paralogous genes belonging to the same gene families and detected possible cases of sub-functionalization