Biomedical subjects

Marcelo Menossi

Publications and source records attributed to Marcelo Menossi.

8 recordsLinked to original sources

PubMed2005

Recent advances in gene expression data clustering: a case study with comparative results.

Several advanced techniques have been proposed for data clustering and many of them have been applied to gene expression data, with partial success. The high dimensionality and the multitude of admissible perspectives for data analysis of gene expression require additional computational resources, such as hierarchical structures and dynamic allocation of resources. We present an immune-inspired hierarchical clustering device, called hierarchical artificial immune network (HaiNet), especially devoted to the analysis of gene expression data. This technique was applied to a newly generated data set, involving maize plants exposed to different aluminum concentrations. The performance of the algorithm was compared with that of a self-organizing map, which is commonly adopted to deal with gene expression data sets. More consistent and informative results were obtained with HaiNet.

Algorithms↗

PubMed2005

Transcription profiling of signal transduction-related genes in sugarcane tissues.

A collection of 237,954 sugarcane ESTs was examined in search of signal transduction genes. Over 3500 components involved in several aspects of signal transduction, transcription, development, cell cycle, stress responses and pathogen interaction were compiled into the Sugarcane Signal Transduction (SUCAST) Catalogue. Sequence comparisons and protein domain analysis revealed 477 receptors, 510 protein kinases, 107 protein phosphatases, 75 small GTPases, 17 G-proteins, 114 calcium and inositol metabolism proteins, and over 600 transcription factors. The elements were distributed into 29 main categories subdivided into 409 sub-categories. Genes with no matches in the public databases and of unknown function were also catalogued. A cDNA microarray was constructed to profile individual variation of plants cultivated in the field and transcript abundance in six plant organs (flowers, roots, leaves, lateral buds, and 1st and 4th internodes). From 1280 distinct elements analyzed, 217 (17%) presented differential expression in two biological samples of at least one of the tissues tested. A total of 153 genes (12%) presented highly similar expression levels in all tissues. A virtual profile matrix was constructed and the expression profiles were validated by real-time PCR. The expression data presented can aid in assigning function for the sugarcane genes and be useful for promoter characterization of this and other economically important grasses.

Computational Biology↗

PubMed2005

Effect of anion channel antagonists and La3+ on citrate release, Al content and Al resistance in maize roots.

The correlation between organic acid anion release and Al content was examined in two maize (Zea mays L.) inbred lines, Cat 100-6 (Al-resistant) and S 1587-17 (Al-sensitive) treated with anion channel antagonists and La3+, a cation channel blocker. In the intact roots of Al-resistant maize, the Al-induced excretion of citrate was inhibited by the anion channel antagonists niflumic acid, anthracene-9-carboxylic and ethacrinic acid. Citrate release in excised root apices was reduced by 60% in the presence of 15 microM niflumic acid, while the Al content increased by 42%. Nevertheless, Cat 100-6 accumulated less Al than S 1587-17 when the rate of citrate release was similar in both lines, indicating that other mechanisms of Al-resistance are operating in Cat 100-6. The presence of 60 microM La3+ did not change the rate of citrate release, but the Al content in excised root apices of Al-resistant plants was reduced by 70%. These results suggest that the Al distributed uniformly in the roots does not contribute to citrate release and possibly the activity of anion channels is correlated with the free activities of extracellular Al3+ close to anion channels.

Aluminum↗

PubMed2005

Transcriptionally active transposable elements in recent hybrid sugarcane.

Transposable elements (TEs) are considered to be important components of the maintenance and diversification of genomes. The recent increase in genome sequence data has created an opportunity to evaluate the impact of these active mobile elements on the evolution of plant genomes. Analysis of the sugarcane transcriptome identified 267 clones with significant similarity to previously described plant TEs. After full cDNA sequencing, 68 sugarcane TE clones were assigned to 11 families according to their best sequence alignment against a fully characterized element. Expression was further investigated through a combined study utilizing electronic Northerns, macroarray, transient and stable sugarcane transformation. Newly synthesized cDNA probes from flower, leaf roll, apical meristem and callus tissues confirm previous results. Callus was identified as the tissue with the highest number of TEs being expressed, revealing that tissue culture drastically induced the expression of different elements. No tissue-specific family was identified. Different representatives within a TE family displayed differential expression patterns, showing that each family presented expression in almost every tissue. Transformation experiments demonstrated that most Hopscotch clone-derived U3 regions are, indeed, active promoters, although under a strong transcriptional regulation. This is a large-scale study about the expression pattern of TEs and indicates that mobile genetic elements are transcriptionally active in the highly polyploid and complex sugarcane genome.

Base Sequence↗

PubMed2005

Perspectives on bioenergy and biotechnology in Brazil.

Brazil is one of the world's largest producers of alcohol from biomass at low cost and is responsible for more than 1 million direct jobs. In 1973, the Brazilian Program of Alcohol (Proalcool) stimulated the creation of a bioethanol industry that has led to large economic, social, and scientific improvements. In the year 1984, 94.5% of Brazil's cars used bioethanol as fuel. In 2003/2004, 350.3 million of sugarcane produced 24.2 million t of sugar and 14.4 billion L of ethanol for an average 4.3 million cars using ethanol. Since its inception, cumulative investment in Proalcool totals US$11 billion, and Brazil has saved US$27 billion in oil imports. The ethanol production industry from sugarcane gene-rates 152 times more jobs than would have been the case if the same amount of fuel was produced from petroleum, and the use of ethanol as a fuel is advantageous for environmental reasons. In 2003, one of the biggest Brazilian ethanol industries started consuming 50% of the residual sugarcane bagasse to produce electrical energy (60 MW), a new alternative use of bioenergy for the Brazilian market. Other technologies for commercial uses of bagasse are in development, such as in the production of natural fibers, sweeteners (glucose and xylitol), single-cell proteins, lactic acid, microbial enzymes, and many other products based on fermentations (submerged and semisolid). Furthermore, studies aimed at the increase in the biosynthesis of sucrose and, consequently, ethanol productivity are being conducted to understand the genetics of sugarcane. Although, at present, there remain technical obstacles to the economic use of some ethanol industry residues, several research projects have been carried out and useful data generated. Efficient utilization of ethanol industry residues has created new opportunities for new value-added products, especially in Brazil, where they are produced in high quantities.

Biotechnology↗

PubMed2004

A transcript finishing initiative for closing gaps in the human transcriptome.

We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.

Alternative Splicing↗

PubMed2003

Aluminum-induced oxidative stress in maize.

The relation between Al-toxicity and oxidative stress was studied for two inbred lines of maize (Zea mays L.), Cat100-6 (Al-tolerant) and S1587-17 (Al-sensitive). Peroxidase (PX), catalase (CAT) and superoxide dismutase (SOD) activities were determined in root tips of both lines, exposed to different Al(3+) concentrations and times of exposure. No increases were observed in CAT activities in either line, although SOD and PX were found to be 1.7 and 2.0 times greater than initial levels, respectively, in sensitive maize treated with 36 microM of Al(3+) for 48 h. The results indicate that Al(3+) induces the dose- and time dependent formation of reactive oxygen species (ROS) and subsequent protein oxidation in S1587-17, although not in Cat100-6. After exposure to 36 microM of Al(3+) for 48 h, the formation of 20+/-2 nmol of carbonyls per mg of protein was observed in S1587-17. The onset of protein oxidation took place after the drop of the relative root growth observed in the sensitive line, indicating that oxidative stress is not the primary cause of root growth inhibition. The presence of Al(3+) did not induce lipid peroxidation in either lines, contrasting with the observations in other species. These results, in conjunction with the data presented in the literature, indicate that oxidative stress caused by Al may harm several components of the cell, depending on the plant species. Moreover, Al(3+) treatment and oxidative stress in the sensitive maize line induced cell death in root tip cells, an event revealed by the high chromatin fragmentation detected by TUNEL analysis.

Aluminum↗

PubMed2003

RNA expression profiles and data mining of sugarcane response to low temperature.

Tropical and subtropical plants are generally sensitive to cold and can show appreciable variation in their response to cold stress when exposed to low positive temperatures. Using nylon filter arrays, we analyzed the expression profile of 1,536 expressed sequence tags (ESTs) of sugarcane (Saccharum sp. cv SP80-3280) exposed to cold for 3 to 48 h. Thirty-four cold-inducible ESTs were identified, of which 20 were novel cold-responsive genes that had not previously been reported as being cold inducible, including cellulose synthase, ABI3-interacting protein 2, a negative transcription regulator, phosphate transporter, and others, as well as several unknown genes. In addition, 25 ESTs were identified as being down-regulated during cold exposure. Using a database of cold-regulated proteins reported for other plants, we searched for homologs in the sugarcane EST project database (SUCEST), which contains 263,000 ESTs. Thirty-three homologous putative cold-regulated proteins were identified in the SUCEST database. On the basis of the expression profiles of the cold-inducible genes and the data-mining results, we propose a molecular model for the sugarcane response to low temperature.

Cold Temperature↗