Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.61561

Improved Analysis Of Promoter Activity In Biolistically Transformed Plant Cells.

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Making Colony Pcr Easier By Adding Gel-loading Buffer To The Amplification Reaction.

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Experimental pressure versus temperature isochoric – isoplethic curves for n-pentane – dimethyl ether, n-pentane – dimethyl ether – polybutadiene and n-pentane – dimethyl ether – polybutadiene– hydrogen at high pressures

Loci of isochoric - isoplethic experimental phase equilibrium data, were determined for the binary mixture dimethyl ether (DME) + n-pentane (C5); the ternary mixture: DME + C5 + polybutadiene (PB); and the quaternary mixture DME + C5 + PB + hydrogen (H2). Binary experiments were performed at varying overall density (ρ) and varying quantity of C5. Ternary experiments were performed at varying ρ and varying relative quantities of each light solvent. In the case of quaternary mixtures, the mass fraction of polymer was kept constant, and the amount of H2 and ρ were varied. The experimental data obtained for binary and ternary mixtures were correlated using the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT) equation of state (EoS)

Sugarcane Functional Genomics: Gene Discovery for Agronomic Trait Development

Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land. The genes can also be used as molecular markers of agronomic traits in traditional breeding programs

Prospecting sugarcane genes involved in aluminum tolerance.

Aluminium is one of the major factors that affect plant development in acid soils, causing a substantial reduction in yield in many crops. In South America, about 66% of the land surface is made up of acid soils where high aluminium saturation is one of the main limiting factors for agriculture. The biochemical and molecular basis of aluminium tolerance in plants is far from being completely understood despite a growing number of studies, and in the specific case of sugarcane there are virtually no reports on the effects of gene regulation on aluminium stress. The objective of the work presented in this paper was to prospect the sugarcane expressed sequence tag (SUCEST) data bank for sugarcane genes related to several biochemical pathways known to be involved in the responses to aluminium toxicity in other plant species and yeast. Sugarcane genes similar to most of these genes were found, including those coding for enzymes that alleviate oxidative stress or combat infection by pathogens and those which code for proteins responsible for the release of organic acids and signal transducers. The role of these genes in aluminium tolerance mechanisms is reviewed. Due to the high level of genomic conservation in related grasses such as maize, barley, sorghum and sugarcane, these genes may be valuable tools which will help us to better understand and to manipulate aluminium tolerance in these species

A Novel Stress-induced Sugarcane Gene Confers Tolerance To Drought, Salt And Oxidative Stress In Transgenic Tobacco Plants.

Drought is a major abiotic stress that affects crop productivity worldwide. Sugarcane can withstand periods of water scarcity during the final stage of culm maturation, during which sucrose accumulation occurs. Meanwhile, prolonged periods of drought can cause severe plant losses. In a previous study, we evaluated the transcriptome of drought-stressed plants to better understand sugarcane responses to drought. Among the up-regulated genes was Scdr1 (sugarcane drought-responsive 1). The aim of the research reported here was to characterize this gene. Scdr1 encodes a putative protein containing 248 amino acids with a large number of proline (19%) and cysteine (13%) residues. Phylogenetic analysis showed that ScDR1is in a clade with homologs from other monocotyledonous plants, separate from those of dicotyledonous plants. The expression of Scdr1 in different varieties of sugarcane plants has not shown a clear association with drought tolerance. The overexpression of Scdr1 in transgenic tobacco plants increased their tolerance to drought, salinity and oxidative stress, as demonstrated by increased photosynthesis, water content, biomass, germination rate, chlorophyll content and reduced accumulation of ROS. Physiological parameters, such as transpiration rate (E), net photosynthesis (A), stomatal conductance (gs) and internal leaf CO(2) concentration, were less affected by abiotic stresses in transgenic Scdr1 plants compared with wild-type plants. Overall, our results indicated that Scdr1 conferred tolerance to multiple abiotic stresses, highlighting the potential of this gene for biotechnological applications.7e4469

Characterization Of A Protein-protein Interaction Network Of The Cbl-interacting Protein Kinase 8 From Sugarcane

Plants are sessile organisms and have evolved to tolerate a constantly changing environment. After the onset of different stress conditions, calcineurin B-like (CBL) proteins can sense calcium signals and activate CBL-interacting protein kinase (CIPK) proteins, which can phosphorylate downstream proteins to reestablish plant homeostasis. Previous studies in the bioenergy crop sugarcane showed that the ScCIPK8 gene is induced by drought stress and is also related to sucrose content. Here, we have characterized the protein-protein interactions of ScCIPK8 with six CBL proteins (ScCBL1, ScCBL2, ScCBL3, ScCBL6, ScCBL9, and ScCBL10). Yeast two-hybrid assays showed that ScCIPK8 interacts with ScCBL1, ScCBL3, and ScCBL6. Bimolecular fluorescence complementation assays confirmed in planta the interactions that were observed in yeast cells. 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J, 425, pp. 27-40Felix, J.D.M., Papini-Terzi, F.S., Rocha, F.R., Vêncio, R.Z.N., Expression profile of signal transduction components in a sugarcane population segregating for sugar content (2009) Trop. Plant Biol, 2, pp. 98-109Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Protein Identification and Analysis Tools on the ExPASy Server (2005) The Proteomics Protocols Handbook, pp. 571-607. , Walker JM, ed.). Humana Press, New YorkGong, D., Gong, Z., Guo, Y., Chen, X., Biochemical and functional characterization of PKS11, a novel Arabidopsis protein kinase (2002) J. Biol. 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Biol, 323, pp. 225-229Lee, S.C., Lan, W.Z., Kim, B.G., Li, L., A protein phosphorylation/dephosphorylation network regulates a plant potassium channel (2007) Proc. Natl. Acad. Sci. U. S. A, 104, pp. 15959-15964Luan, S., Kudla, J., Rodriguez-Concepcion, M., Yalovsky, S., Calmodulins and calcineurin B-like proteins: Calcium sensors for specific signal response coupling in plants (2002) Plant Cell, 14, pp. S389-S400Ohta, M., Guo, Y., Halfter, U., Zhu, J.K., A novel domain in the protein kinase SOS2 mediates interaction with the protein phosphatase 2C ABI2 (2003) Proc. Natl. Acad. Sci. U. S. A, 100, pp. 11771-11776Ren, J., Wen, L., Gao, X., Jin, C., CSS-Palm 2.0: An updated software for palmitoylation sites prediction (2008) Protein Eng. Des. 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Academic Press, New YorkXiang, Y., Huang, Y., Xiong, L., Characterization of stress-responsive CIPK genes in rice for stress tolerance improvement (2007) Plant Physiol, 144, pp. 1416-142