Investigating water transport through the xylem network in vascular plants

A review on experimental methods used to investigate sap flow underlines the necessity to better characterize the relationships between the hydraulic regulation and the structural characteristics of the xylem network.Our understanding of physical and physiological mechanisms depends on the development of advanced technologies and tools to prove or re-evaluate established theories, and test new hypotheses. Water flow in land plants is a fascinating phenomenon, a vital component of the water cycle, and essential for life on Earth. The cohesion-tension theory (CTT), formulated more than a century ago and based on the physical properties of water, laid the foundation for our understanding of water transport in vascular plants. Numerous experimental tools have since been developed to evaluate various aspects of the CTT, such as the existence of negative hydrostatic pressure. This review focuses on the evolution of the experimental methods used to study water transport in plants, and summarizes the different ways to investigate the diversity of the xylem network structure and sap flow dynamics in various species. As water transport is documented at different scales, from the level of single conduits to entire plants, it is critical that new results be subjected to systematic cross-validation and that findings based on different organs be integrated at the whole-plant level. We also discuss the functional trade-offs between optimizing hydraulic efficiency and maintaining the safety of the entire transport system. Furthermore, we evaluate future directions in sap flow research and highlight the importance of integrating the combined effects of various levels of hydraulic regulation.X112418Ysciescopu

Physiological Functions of the COPI Complex in Higher Plants

COPI vesicles are essential to the retrograde transport of proteins in the early secretory pathway. The COPI coatomer complex consists of seven subunits, termed alpha-, beta-, beta'-, gamma-, delta-, epsilon-, and zeta-COP, in yeast and mammals. Plant genomes have homologs of these subunits, but the essentiality of their cellular functions has hampered the functional characterization of the subunit genes in plants. Here we have employed virus-induced gene silencing (VIGS) and dexamethasone (DEX)-inducible RNAI of the COPI subunit genes to study the in vivo functions of the COPI coatomer complex in plants. The beta'-, gamma-, and delta-COP subunits localized to the Golgi as GFP-fusion proteins and interacted with each other in the Golgi. Silencing of beta'-, gamma-, and delta-COP by VIGS resulted in growth arrest and acute plant death in Nicotiana benthamiana, with the affected leaf cells exhibiting morphological markers of programmed cell death. Depletion of the COPI subunits resulted in disruption of the Golgi structure and accumulation of autolysosome-like structures in earlier stages of gene silencing. In tobacco BY-2 cells, DEX-inducible RNAi of beta'-COP caused aberrant cell plate formation during cytokinesis. Collectively, these results suggest that COPI vesicles are essential to plant growth and survival by maintaining the Golgi apparatus and modulating cell plate formation.1196Ysciescopu

The N-terminal methionine of cellular proteins as a degradation signal

The Arg/N-end rule pathway targets for degradation proteins that bear specific unacetylated N-terminal residues while the Ac/N-end rule pathway targets proteins through their N-infinity-terminally acetylated (Nt-acetylated) residues. Here, we show that Ubr1, the ubiquitin ligase of the Arg/N-end rule pathway, recognizes unacetylated N-terminal methionine if it is followed by a hydrophobic residue. This capability of Ubr1 expands the range of substrates that can be targeted for degradation by the Arg/N-end rule pathway because virtually all nascent cellular proteins bear N-terminal methionine. We identified Msn4, Sry1, Arl3, and Pre5 as examples of normal or misfolded proteins that can be destroyed through the recognition of their unacetylated N-terminal methionine. Inasmuch as proteins bearing the Nt-acetylated N-terminal methionine residue are substrates of the Ac/N-end rule pathway, the resulting complementarity of the Arg/N-end rule and Ac/N-end rule pathways enables the elimination of protein substrates regardless of acetylation state of N-terminal methionine in these substrates.X117863Ysciescopu

Functional water flow pathways and hydraulic regulation in the xylem network of arabidopsis

In vascular plants, the xylem network constitutes a complex microfluidic system. The relationship between vascular network architecture and functional hydraulic regulation during actual water flow remains unexplored. Here, we developed a method to visualize individual xylem vessels of the 3D xylem network of Arabidopsis thaliana, and to analyze the functional activities of these vessels using synchrotron X-ray computed tomography with hydrophilic gold nanoparticles as flow tracers. We show how the organization of the xylem network changes dynamically throughout the plant, and reveal how the elementary units of this transport system are organized to ensure both long-distance axial water transport and local lateral water transport. Xylem vessels form distinct clusters that operate as functional units, and the activity of these units, which determines water flow pathways, is modulated not only by varying the number and size of xylem vessels, but also by altering their interconnectivity and spatial arrangement. Based on these findings, we propose a regulatory model of water transport that ensures hydraulic efficiency and safety.X1111Ysciescopu

Mechanism of Cisplatin-Induced Cytotoxicity Is Correlated to Impaired Metabolism Due to Mitochondrial ROS Generation

The chemotherapeutic use of cisplatin is limited by its severe side effects. In this study, by conducting different omics data analyses, we demonstrated that cisplatin induces cell death in a proximal tubular cell line by suppressing glycolysis-and tricarboxylic acid (TCA)/mitochondria-related genes. Furthermore, analysis of the urine from cisplatin-treated rats revealed the lower expression levels of enzymes involved in glycolysis, TCA cycle, and genes related to mitochondrial stability and confirmed the cisplatin-related metabolic abnormalities. Additionally, an increase in the level of p53, which directly inhibits glycolysis, has been observed. Inhibition of p53 restored glycolysis and significantly reduced the rate of cell death at 24 h and 48 h due to p53 inhibition. The foremost reason of cisplatin-related cytotoxicity has been correlated to the generation of mitochondrial reactive oxygen species (ROS) that influence multiple pathways. Abnormalities in these pathways resulted in the collapse of mitochondrial energy production, which in turn sensitized the cells to death. The quenching of ROS led to the amelioration of the affected pathways. Considering these observations, it can be concluded that there is a significant correlation between cisplatin and metabolic dysfunctions involving mROS as the major player.116224Ysciescopu

Structural design of a double layered porous hydrogel for effective mass transport.

Mass transport in porous materials is universal in nature, and its worth attracts great attention in many engineering applications. Plant leaves, which work as natural hydraulic pumps for water uptake, have evolved to have the morphological structure for fast water transport to compensate large water loss by leaf transpiration. In this study, we tried to deduce the advantageous structural features of plant leaves for practical applications. Inspired by the tissue organization of the hydraulic pathways in plant leaves, analogous double-layered porous models were fabricated using agarose hydrogel. Solute transport through the hydrogel models with different thickness ratios of the two layers was experimentally observed. In addition, numerical simulation and theoretical analysis were carried out with varying porosity and thickness ratio to investigate the effect of structural factors on mass transport ability. A simple parametric study was also conducted to examine unveiled relations between structural factors. As a result, the porosity and thickness ratio of the two layers are found to govern the mass transport ability in double-layered porous materials. The hydrogel models with widely dispersed pores at a fixed porosity, i.e., close to a homogeneously porous structure, are mostly turned out to exhibit fast mass transport. The present results would provide a new framework for fundamental design of various porous structures for effective mass transport. (C) 2015 AIP Publishing LLC.open1

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.1178Ysciescopu

Structural design of a double layered porous hydrogel for effective mass transport.

Mass transport in porous materials is universal in nature, and its worth attracts great attention in many engineering applications. Plant leaves, which work as natural hydraulic pumps for water uptake, have evolved to have the morphological structure for fast water transport to compensate large water loss by leaf transpiration. In this study, we tried to deduce the advantageous structural features of plant leaves for practical applications. Inspired by the tissue organization of the hydraulic pathways in plant leaves, analogous double-layered porous models were fabricated using agarose hydrogel. Solute transport through the hydrogel models with different thickness ratios of the two layers was experimentally observed. In addition, numerical simulation and theoretical analysis were carried out with varying porosity and thickness ratio to investigate the effect of structural factors on mass transport ability. A simple parametric study was also conducted to examine unveiled relations between structural factors. As a result, the porosity and thickness ratio of the two layers are found to govern the mass transport ability in double-layered porous materials. The hydrogel models with widely dispersed pores at a fixed porosity, i.e., close to a homogeneously porous structure, are mostly turned out to exhibit fast mass transport. The present results would provide a new framework for fundamental design of various porous structures for effective mass transport. (C) 2015 AIP Publishing LLC.open112sciescopu

Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks

Multi-dimensional proteomic analyses provide different layers of protein information, including protein abundance and post-translational modifications. Here, we report an integrated analysis of protein expression, phosphorylation, and N-glycosylation by serial enrichments of phosphorylation and N-glycosylation (SEPG) from the same tissue samples. On average, the SEPG identified 142,106 unmodified peptides of 8,625 protein groups, 18,846 phosphopeptides (15,647 phosphosites), and 4,019 N-glycopeptides (2,634 N-glycosites) in tumor and adjacent normal tissues from three gastric cancer patients. The combined analysis of these data showed that the integrated analysis additively improved the coverages of gastric cancer-related protein networks; phosphoproteome and N-glycoproteome captured predominantly low abundant signal proteins, and membranous or secreted proteins, respectively, while global proteome provided abundances for general population of the proteome. Therefore, our results demonstrate that the SEPG can serve as an effective approach for multi-dimensional proteome analyses, and the holistic profiles of protein expression and PTMs enabled improved interpretation of disease-related networks by providing complementary information.11103Ysciescopu

From Practice to Theory: The "Bright Illumination" Attack on Quantum Key Distribution Systems

The "Bright Illumination" attack [Lydersen et al., Nat. Photon. 4, 686-689 (2010)] is a practical attack, fully implementable against quantum key distribution systems. In contrast to almost all developments in quantum information processing (for example, Shor's factorization algorithm, quantum teleportation, Bennett-Brassard (BB84) quantum key distribution, the "Photon-Number Splitting" attack, and many other examples), for which theory has been proposed decades before a proper implementation, the "Bright Illumination" attack preceded any sign or hint of a theoretical prediction. Here we explain how the "Reversed-Space" methodology of attacks, complementary to the notion of "quantum side-channel attacks" (which is analogous to a similar term in "classical" - namely, non-quantum - computer security), has missed the opportunity of predicting the "Bright Illumination" attack.Comment: 17 page