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Search Results: 1 - 10 of 31791 matches for " Marcelo Falsarella;Pereira "
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A web-based bioinformatics interface applied to the GENOSOJA project: databases and pipelines
Nascimento, Leandro Costa do;Costa, Gustavo Gilson Lacerda;Binneck, Eliseu;Pereira, Gon?alo Amarante Guimar?es;Carazzolle, Marcelo Falsarella;
Genetics and Molecular Biology , 2012, DOI: 10.1590/S1415-47572012000200002
Abstract: the genosoja consortium is an initiative to integrate different omics research approaches carried out in brazil. basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and asian rust fungal disease. to do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. the initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. in this work, we describe the main features of the genosoja web database, including the pipelines to analyze some kinds of data (ests, supersage, micrornas, subtractive cdna libraries), as well as web interfaces to access information about soybean gene annotation and expression.
Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance
Vidal, Ramon Oliveira;Nascimento, Leandro Costa do;Maurício Costa Mondego, Jorge;Amarante Guimar?es Pereira, Gon?alo;Falsarella Carazzolle, Marcelo;
Genetics and Molecular Biology , 2012, DOI: 10.1590/S1415-47572012000200014
Abstract: the legume glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. the increase in drought events in the last decade has caused production losses in recent harvests. this fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. in order to identify single nucleotide polymorphisms (snps) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (ssh) from two contrasting cultivars upon water deprivation: sensitive (br 16) and tolerant (embrapa 48). a total of 2,222 soybean genes were up-regulated in both cultivars. our method identified more than 6,000 snps in tolerant and sensitive brazilian cultivars in those drought stress related genes. among these snps, 165 (in 127 genes) are positioned at soybean chromosome ends, including transcription factors (myb, wrky) related to tolerance to abiotic stress.
IIS – Integrated Interactome System: A Web-Based Platform for the Annotation, Analysis and Visualization of Protein-Metabolite-Gene-Drug Interactions by Integrating a Variety of Data Sources and Tools
Marcelo Falsarella Carazzolle, Lucas Miguel de Carvalho, Hugo Henrique Slepicka, Ramon Oliveira Vidal, Gon?alo Amarante Guimar?es Pereira, J?rg Kobarg, Gabriela Vaz Meirelles
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0100385
Abstract: Background High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. Results We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. Conclusions We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.
Identification of putative new Escherichia coli flagellar antigens from human origin using serology, PCR-RFlP and DNA sequencing methods
Tiba, Monique Ribeiro;Moura, Claúdia de;Carazzolle, Marcelo Falsarella;Leite, Domingos da Silva;
Brazilian Journal of Infectious Diseases , 2011, DOI: 10.1590/S1413-86702011000200009
Abstract: escherichia coli has been isolated frequently, showing flagellar antigens that are not recognized by any of the 53 antisera, provided by the most important reference center of e. coli, the international escherichia and klebsiella center (who) of the statens serum institute, copenhagen, denmark. the objective of this study was to characterize flagellar antigens of e. coli that express non-typeable h antigens. the methods used were serology, pcr-rflp and dna sequencing. this characterization was performed by gene amplification of the flic (flagellin protein) by polymerase chain reaction in all 53 standards e.coli strains for the h antigens and 20 e. coli strains for which the h antigen was untypeable. the amplicons were digested by restriction enzymes, and different restriction enzyme profiles were observed. anti-sera were produced in rabbits, for the non-typeable strains, and agglutination tests were carried out. in conclusion,the results showed that although non-typeable and typable h antigens strains had similar flagellar antigens, the two types of strains were distinct in terms of nucleotide sequence, and did not phenotypically react with the standard antiserum, as expected. thirteen strains had been characterized as likely putative new h antigen using pcr-rflp techniques, dna sequencing and/or serology.
Visual acuity evaluation in children with hydrocephalus: An electrophysiological study with sweep visual evoked potential  [PDF]
Silvana Alves Pereira, Marcelo Fernandes Costa
World Journal of Neuroscience (WJNS) , 2012, DOI: 10.4236/wjns.2012.21006
Abstract: The objective was to measure the visual acuity (VA) of children with the diagnosis of hydrocephalus with or without peritoneal-ventricular shunt (PVS). A total of 55 children were included in the study (34 Female), with an age range of 0 to 291 weeks. The VA was measured by the sweep visual evoked potential technique. Of those with a PVS, in 31 the ventricular valve was inserted before 15 days after the diagnosis whereas in 14 the ventricular valve was inserted after 15 days. The sweep VEP was performed in all children, 95 exams (94%) were abnormal and only 6 were normal. There was a statistical difference in the VA between children with a PVS inserted before 15 days of the diagnosis and children with a PVS after 15 days (p = 0.038) or those without a shunt (p = 0.031). Children with no complications of the PVS had a better VA as compared to those with shunt complications (p < 0.001). In the group of children with complications, again those who had a shunt inserted be-fore 15 days had better VA results in com- parison to those in whom the shunt was inserted after 15 days (p = 0.029). No statistical difference in the VA was found between children without the PVS and with those in which the shunt was inserted after 15 days of the di-agnosis of hydrocephalus (p = 0.699). We conclude that the delayed insertion of the PVS may compromise the visual development of these children.
An Informal Science Educator/Elementary School Teacher Collaboration: Changing Fifth Grade Girls’ Perceptions of Scientists and Engineers  [PDF]
Florence F. McCann, Edmund A. Marek, Carell Falsarella
Creative Education (CE) , 2016, DOI: 10.4236/ce.2016.716234
Abstract: This study examined how an informal science educator-elementary school teacher partnership based on a coordination relationship (Weiland & Akerson, 2013) operated in the development and implementation of a STEM (Science, Technology, Engineering and Mathematics) Club for girls. A case study methodology was used to understand how the informal science educator-elementary school teacher partnership functioned in the context of the STEM Club. Images of scientists and engineers drawn by the girls before and after participation in the STEM Club were written artifacts used to assess the girls’ perceptions of scientists and engineers. The girls maintained the traditional images of scientists that they brought to the Club, modified, however, to include more female images after participation in STEM Club. The girls’ perceptions of engineers changed dramatically from non-existent or mechanics/ repairmen to realistic images of engineers, including female images, involved in design, laboratory investigation and testing activities. The percentage of female images drawn by the girls increased by 30% and 42% for scientist images and engineer images, respectively.
Performance e educa??o: rela??es, significados e contextos de investiga??o
Pereira, Marcelo de Andrade;
Educa??o em Revista , 2012, DOI: 10.1590/S0102-46982012000100013
Abstract: the following article presents and discusses the concept of performance. it intends to relate the meanings of performance to educational practice. as a meta-philosophical investigation this paper tries to analyze performance (making performance itself the object of investigation) considering the contributions of anthropology, theory of literature, linguistics, arts and pedagogy. to this extent this text makes an attempt to retain the meaning of pedagogical practice as based in aesthetical principles. as one might expect, the investigation takes place in the context of performance - art, communication and culture - the purpose being, to prove (justify) a theory of performance in education, because by taking the proposition of a practical performance pedagogy further, it points the way for educational action of an expressive character/nature. as well as qualitatively evaluating the aesthetic experience, and an aesthetic education, the investigation also intends to measure the teacher's communication, empirically (another words, quantitatively).
Exhaustive exploration of Prisoner's Dilemma Parameter space in one-dimensional cellular automata
Pereira, Marcelo Alves;
Brazilian Journal of Physics , 2008, DOI: 10.1590/S0103-97332008000100013
Abstract: the prisoner's dilemma (pd) is one of the most popular games of the game theory due to the emergence of cooperation among competitive rational players. in this paper, we present the pd played in cells of one-dimension cellular automata, where the number of possible neighbors that each cell interacts, z, can vary. this makes possible to retrieve results obtained previously in regular lattices. exhaustive exploration of the parameters space is presented. we show that the final state of the system is governed mainly by the number of neighbors z and there is a drastic difference if it is even or odd.
El espacio por aprender, el mismo que ense?ar: las urgencias de la educación geográfica
Pereira, Marcelo Garrido;
Cadernos CEDES , 2005, DOI: 10.1590/S0101-32622005000200002
Abstract: the present reflection questions the possibilities of the pedagogical speech when the informal space knowledge is considered as an antecedent of transformations practices. the informal space knowledge has been widely banned from the national curricula and is disdained in the didactic proposals developed by geography professors. it is thus urgent to identify the relations between a knowledge that is experience and a project of actor and subject in crisis. this leads us to propose pedagogical intervention spaces, synthesis categories of the space experience and problematizing ways to develop a significant geographic education.
A dimens?o performativa do gesto na prática docente
Pereira, Marcelo de Andrade;
Revista Brasileira de Educa??o , 2010, DOI: 10.1590/S1413-24782010000300012
Abstract: the present study, in the form of an essay, argues, from a philosophical point of view, about the meaning of gestures in general and in teaching practice. the analysis proceeds from the differentiation of the meaning of the gesture from a mere motor gesture to symbolic or expressive gestures from which one perceives the proper meaning of gesture for this investigation. it is inferred that the performative, and therefore expressive, dimension of the gesture allows for the creation of a space for experimentation and construction of knowledge that is qualitatively distinct from the ordinary and not regulated by merely biological, cognitive or instrumental purposes. this perspective comprehends gesture from its performative dimension as an aesthetic act. the study describes and analyzes the contents, the objects, the conditions and the effects of the aesthetic element with regard to a performative teaching practice. the investigation is supported by the intuitions of osman lins, walter benjamin, hans ulrich gumbrecht, jean galard, baldine saint girons, among others.
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