Combined analysis of genome-wide expression profiling of maize (Zea mays L.) leaves infected with Ustilago maydis.

Although many gene expression profiling studies of maize leaves infected with Ustilago maydis have been published, heterogeneity of the results, caused by various data processing methods and pathogenic strains in different data sets, remains strong. Hence, we conducted a combined analysis of six genome-wide expression data sets of maize leaves infected with five different U. maydis strains by using the same pre-processing and quality control procedures. Six data sets were regrouped into five groups according to pathogenic strain used. Subsequently, each group of data set was processed by Multi-array Average for pre-processing and by pair-wise Pearson correlation for quality control. The differentially expressed genes were calculated by a standard linear mixed-effect model and then validated by various sensitivity analysis and multiple evidences. Finally, 44 unique differentially expressed genes were identified. Pathway enrichment analysis indicated that these genes related to response to fungus, oxidation-reduction, transferase activity, and several carbohydrate metabolic and catabolic processes. In addition, the hub genes within protein-protein interaction networks showed high relevance with the basic pathogenesis. We report a highly credible differentially expressed list, and the genes with multiple validations may denote a common signature of U. maydis in maize, which provides a new window for disease-resistant protection of maize plants.

High-throughput micro-phenotyping measurements applied to assess stalk lodging in maize (Zea mays L.).

BACKGROUND: The biomechanical properties of maize stalks largely determine their lodging resistance, which affects crop yield per unit area. However, the quantitative and qualitative relationship between micro-phenotypes and the biomechanics of maize stalks is still under examined. In particular, the roles of the number, geometry, and distribution of vascular bundles of stalks in maize lodging resistance remain unclear. Research on these biomechanical properties will benefit from high-resolution micro-phenotypic image acquisition capabilities, which have been improved by modern X-ray imaging devices such as micro-CT and the development of micro-phenotyping analysis software. Hence, high-throughput image analysis and accurate quantification of anatomical phenotypes of stalks are necessary. RESULTS: We have updated VesselParser version 1.0 to version 2.0 and have improved its performance, accuracy, and computation strategies. Anatomical characteristics of the second and third stalk internodes of the cultivars 'Jingke968' and 'Jingdan38' were analyzed using VesselParser 2.0. The relationships between lodging resistance and anatomical phenotypes of stalks between the two different maize varieties were investigated. The total area of vascular bundles in the peripheral layer, auxiliary axis diameter, and total area of vascular bundles were revealed to have the highest correlation with mechanical properties, and anatomical phenotypes of maize stalk were better predictors of mechanical properties than macro features observed optically from direct measurement, such as diameter and perimeter. CONCLUSIONS: This study demonstrates the utility of VesselParser 2.0 in assessing stalk mechanical properties. The combination of anatomical phenotypes and mechanical behavior research provides unique insights into the problem of stalk lodging, showing that micro phenotypes of vascular bundles are good predictors of maize stalk mechanical properties that may be important indices for the evaluation and identification of the biomechanical properties to improve lodging resistance of future maize varieties.

Arabidopsis kinesin KP1 specifically interacts with VDAC3, a mitochondrial protein, and regulates respiration during seed germination at low temperature.

The involvement of cytoskeleton-related proteins in regulating mitochondrial respiration has been revealed in mammalian cells. However, it is unclear if there is a relationship between the microtubule-based motor protein kinesin and mitochondrial respiration. In this research, we demonstrate that a plant-specific kinesin, Kinesin-like protein 1 (KP1; At KIN14 h), is involved in respiratory regulation during seed germination at a low temperature. Using in vitro biochemical methods and in vivo transgenic cell observations, we demonstrate that KP1 is able to localize to mitochondria via its tail domain (C terminus) and specifically interacts with a mitochondrial outer membrane protein, voltage-dependent anion channel 3 (VDAC3). Targeting of the KP1-tail to mitochondria is dependent on the presence of VDAC3. When grown at 4° C, KP1 dominant-negative mutants (TAILOEs) and vdac3 mutants exhibited a higher seed germination frequency. All germinating seeds of the kp1 and vdac3 mutants had increased oxygen consumption; the respiration balance between the cytochrome pathway and the alternative oxidase pathway was disrupted, and the ATP level was reduced. We conclude that the plant-specific kinesin, KP1, specifically interacts with VDAC3 on the mitochondrial outer membrane and that both KP1 and VDAC3 regulate aerobic respiration during seed germination at low temperature.

Micron-scale Phenotyping Techniques of Maize Vascular Bundles Based on X-ray Microcomputed Tomography.

It is necessary to accurately quantify the anatomical structures of maize materials based on high-throughput image analysis techniques. Here, we provide a 'sample preparation protocol' for maize materials (i.e., stem, leaf, and root) suitable for ordinary microcomputed tomography (micro-CT) scanning. Based on high-resolution CT images of maize stem, leaf, and root, we describe two protocols for the phenotypic analysis of vascular bundles: (1) based on the CT image of maize stem and leaf, we developed a specific image analysis pipeline to automatically extract 31 and 33 phenotypic traits of vascular bundles; (2) based on the CT image series of maize root, we set up an image processing scheme for the three-dimensional (3-D) segmentation of metaxylem vessels, and extracted two-dimensional (2-D) and 3-D phenotypic traits, such as volume, surface area of metaxylem vessels, etc. Compared with traditional manual measurement of vascular bundles of maize materials, the proposed protocols significantly improve the efficiency and accuracy of micron-scale phenotypic quantification.

Micron-scale phenotyping quantification and three-dimensional microstructure reconstruction of vascular bundles within maize stalks based on micro-CT scanning.

Vascular bundles within maize (Zea mays L.) stalks play a key role in the mechanical support of plant architecture as well as in water and nutrient transportation. Convenient and accurate phenotyping of vascular bundles may help phenotypic identification of germplasm resources for breeding. Based on practical sample preparation procedures for maize stalks, we acquired serials of cross-sectional images using a micro-computed tomography (CT) imaging device. An image processing pipeline dedicated to the phenotyping of vascular bundles was also developed to automatically segment and validate vascular bundles from the cross-sectional images of maize stalks, from which phenotypic traits of vascular bundles, i.e. number, area, and spatial distribution, were calculated. More profound quantification of spatial distribution was given as area ratio of vascular bundles, which described the distribution of vascular bundles associated with the centroid of maize stalks. In addition, three-dimensional visualisation was performed to reveal the spatial configuration and distribution of vascular bundles. The proposed method significantly improves computation accuracy for the phenotypic traits of vascular bundles compared with previous methods, and is expected to be useful for illustrating relationships between phenotypic traits of vascular bundles and their function.

Arabidopsis voltage-dependent anion channel 1 (AtVDAC1) is required for female development and maintenance of mitochondrial functions related to energy-transaction.

The voltage-dependent anion channels (VDACs), prominently localized in the outer mitochondrial membrane, play important roles in the metabolite exchange, energy metabolism and mitochondria-mediated apoptosis process in mammalian cells. However, relatively little is known about the functions of VDACs in plants. To further investigate the function of AtVDAC1 in Arabidopsis, we analyzed a T-DNA insertion line for the AtVDAC1 gene. The knock-out mutant atvdac1 showed reduced seed set due to a large number of undeveloped ovules in siliques. Genetic analyses indicated that the mutation of AtVDAC1 affected female fertility and belonged to a sporophytic mutation. Abnormal ovules in the process of female gametogenesis were observed using a confocal laser scanning microscope. Interestingly, both mitochondrial transmembrane potential (ΔΨ) and ATP synthesis rate were obviously reduced in the mitochondria isolated from atvdac1 plants.

High-throughput micro-phenotyping measurements applied to assess stalk lodging in maize ( Zea mays L. )

BACKGROUND: The biomechanical properties of maize stalks largely determine their lodging resistance, which affects crop yield per unit area. However, the quantitative and qualitative relationship between micro-phenotypes and the biomechanics of maize stalks is still under examined. In particular, the roles of the number, geometry, and distribution of vascular bundles of stalks in maize lodging resistance remain unclear. Research on these biomechanical properties will benefit from high-resolution micro-phenotypic image acquisition capabilities, which have been improved by modern X-ray imaging devices such as micro-CT and the development of micro-phenotyping analysis software. Hence, high-throughput image analysis and accurate quantification of anatomical phenotypes of stalks are necessary. RESULTS: We have updated VesselParser version 1.0 to version 2.0 and have improved its performance, accuracy, and computation strategies. Anatomical characteristics of the second and third stalk internodes of the cultivars 'Jingke968' and 'Jingdan38' were analyzed using VesselParser 2.0. The relationships between lodging resistance and anatomical phenotypes of stalks between the two different maize varieties were investigated. The total area of vascular bundles in the peripheral layer, auxiliary axis diameter, and total area of vascular bundles were revealed to have the highest correlation with mechanical properties, and anatomical phenotypes of maize stalk were better predictors of mechanical properties than macro features observed optically from direct measurement, such as diameter and perimeter. CONCLUSIONS: This study demonstrates the utility of VesselParser 2.0 in assessing stalk mechanical properties. The combination of anatomical phenotypes and mechanical behavior research provides unique insights into the problem of stalk lodging, showing that micro phenotypes of vascular bundles are good predictors of maize stalk mechanical properties that may be important indices for the evaluation and identification of the biomechanical properties to improve lodging resistance of future maize varieties.

Synthesis of cationic poly(4-vinylpyridine)-functionalized colloidal particles by emulsion polymerization with reactive block copolymer for protein adsorption.

We report here a novel protein sequestration method using polymeric colloidal particles prepared by emulsion polymerization with reactive block copolymers. Specifically, poly(4-vinyl-N-ethylpyridine bromide)-block-polymethylacrylate block copolymers were synthesized from reversible addition-fragmentation chain transfer polymerization and used as emulsifiers for emulsion polymerization of poly(4-vinyl-N-ethylpyridine bromide)-functionalized polymeric colloidal particles. The particles have high and stable zeta potentials when dispersed in solution, regardless of pH variations. As a result, the polymeric colloids demonstrate a high affinity for oppositely charged proteins, even though the isoelectric points of proteins may vary greatly. We show here that BSA can be sequestered highly efficiently with a maximum binding capacity (~900 mg/g). The adsorbed protein is easily released, and the polymeric colloids are regenerated after washing with a buffer solution of high ionic strength. These properties may prompt this type of novel macromolecule-functionalized colloids to be utilized for effective protein adsorption and separation.

Synthesis and property of chitosan graft copolymer by RAFT polymerization with tosylic acid-chitosan complex.

pH- and thermo-sensitive (1→4)-2-amino-2-deoxy-ß-d-glucan (i.e. chitosan) graft copolymer was prepared by reversible addition fragmentation chain transfer polymerizations of N-isopropylacrylamide with 4-methylbenzenesulfonic acid (i.e. tosylic acid)-chitosan complex. The polymerization was controlled well, and the amino group of chitosan could be deprotected easily and mildly with 15% Tris solution. The model aldehyde vanillin was conjugated with amino group of chitosan-g-PNIPAM via Schiff base bond (Loading efficiency, LE=77.6 mg/g), and the drug release could be controlled with temperature and pH. This property may promote the chitosan graft copolymer to be used in the field of "smart" drug delivery.