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System biology techniques applied to the agriculture: transcriptomes and interactomes analyses


This project intends to implement high-throughput Computational Biology techniques into the Plant Molecular Biology Laboratory at ESALQ/USP to transcriptome and interactome analysis. The first approach will attempt to deal with all the Bioinformatics involved in the transcriptome analyses, with data derived from microarray or cDNA fragments sequencing. Other will encompass graph analyses to identify protein-protein interactions clusters using AtPIN - Arabidopsis thaliana Protein Interactions Network - and the expression profile from the proposed transcriptomes. The aim of this work is to combine this two research lines to produce a solid dataset of information regarding the metabolic mechanisms of insects with agriculture interest. Especially, identify genes related to the insect capacity to dodge the plant herbivory chemical defense. Besides the academic relevance, the results should subsidize and increase the available data on expression, protein interactions, phylogeny and possible targets of study to explain the intricate mechanisms involved in the relationships between insects and plants as well as strengthen and advance the line of research in Bioinformatics Computational Biology and applied studies in Systems Biology at the host institution. (AU)

Articles published in Pesquisa FAPESP Magazine about the research grant:
La estructura matemática del ADN 
The mathematical structure of DNA 
Articles published in Agência FAPESP Newsletter about the research grant:
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Scientific publications (16)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
MURAD, NATALIA FARAJ; SILVA-BRANDAO, KARINA LUCAS; BRANDAO, MARCELO MENDES. Mechanisms behind polyphagia in a pest insect: Responses of Spodoptera frugiperda (JE Smith) strains to preferential and alternative larval host plants assessed with gene regulatory networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, v. 1864, n. 3, . (12/16266-7, 11/00417-3)
SILVA-BRANDAO, KARINA LUCAS; MURAD, NATALIA FARAJ; PERUCHI, ALINE; MARTINS, CARLOS HENRIQUE ZANINI; OMOTO, CELSO; FIGUEIRA, ANTONIO; BRANDAO, MARCELO MENDES; TRIGO, JOSE ROBERTO. Transcriptome differential co-expression reveals distinct molecular response of fall-armyworm strains toDIMBOA. Pest Management Science, v. 77, n. 1, . (11/00417-3, 12/16266-7)
SILVA-BRANDAO, KARINA LUCAS; PERUCHI, ALINE; SERAPHIM, NOEMY; MURAD, NATALIA FARAJ; CARVALHO, RENATO ASSIS; FARIAS, JULIANO RICARDO; OMOTO, CELSO; CONSOLI, FERNANDO LUIS; FIGUEIRA, ANTONIO; BRANDAO, MARCELO MENDES. Loci under selection and markers associated with host plant and host-related strains shape the genetic structure of Brazilian populations of Spodoptera frugiperda (Lepidoptera, Noctuidae). PLoS One, v. 13, n. 5, . (11/00417-3, 12/16266-7)
SILVA-BRANDAO, KARINA LUCAS; HORIKOSHI, RENATO JUN; BERNARDI, DANIEL; OMOTO, CELSO; FIGUEIRA, ANTONIO; BRANDAO, MARCELO MENDES. Transcript expression plasticity as a response to alternative larval host plants in the speciation process of corn and rice strains of Spodoptera frugiperda. BMC Genomics, v. 18, . (11/00417-3, 12/16266-7)
SOUZA, THAIS P.; DIAS, RENATA O.; CASTELHANO, ELAINE C.; BRANDAO, MARCELO M.; MOURA, DANIEL S.; SILVA-FILHO, MARCIO C.. Comparative analysis of expression profiling of the trypsin and chymotrypsin genes from Lepidoptera species with different levels of sensitivity to soybean peptidase inhibitors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY, v. 196, p. 67-73, . (11/00417-3, 12/03040-0, 08/52067-3, 09/15421-6, 10/17110-5, 08/57908-6)
BRANDAO, MARCELO M.; SPOLADORE, LARISSA; FARIA, LUZINETE C. B.; ROCHA, ANDREA S. L.; SILVA-FILHO, MARCIO C.; PALAZZO, JR., REGINALDO. Ancient DNA sequence revealed by error-correcting codes. SCIENTIFIC REPORTS, v. 5, . (11/00417-3, 08/52067-3)
DIAS, RENATA O.; VIA, ALLEGRA; BRANDAO, MARCELO M.; TRAMONTANO, ANNA; SILVA-FILHO, MARCIO C.. Digestive peptidase evolution in holometabolous insects led to a divergent group of enzymes in Lepidoptera. Insect Biochemistry and Molecular Biology, v. 58, p. 1-11, . (12/03040-0, 11/00417-3, 10/17110-5, 08/52067-3)
BROWER, ANDREW V. Z.; WILLMOTT, KEITH R.; SILVA-BRANDAO, KARINA L.; GARZON-ORDUNA, IVONNE J.; FREITAS, ANDRE V. L.. Phylogenetic relationships of ithomiine butterflies (Lepidoptera: Nymphalidae: Danainae) as implied by combined morphological and molecular data. SYSTEMATICS AND BIODIVERSITY, v. 12, n. 2, p. 133-147, . (11/00417-3, 12/50260-6)
BUSSO-LOPES, ARIANE F.; NEVES, LEANDRO X.; CAMARA, GUILHERME A.; GRANATO, DANIELA C.; PRETTI, MARCO ANTONIO M.; HEBERLE, HENRY; PATRONI, FABIO M. S.; SA, JAMILE; YOKOO, SAMI; RIVERA, CESAR; et al. Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer. NATURE COMMUNICATIONS, v. 13, n. 1, p. 24-pg., . (19/21815-9, 15/19191-6, 15/50612-8, 09/53998-3, 18/18496-6, 11/00417-3, 09/54067-3, 10/19278-0, 16/07846-0)
CRIVELENTE HORTA, MARIA AUGUSTA; FERREIRA FILHO, JAIRE ALVES; MURAD, NATALIA FARAJ; SANTOS, EIDY DE OLIVEIRA; DOS SANTOS, CLELTON APARECIDO; MENDES, JULIANO SALES; BRANDAO, MARCELO MENDES; AZZONI, SINDELIA FREITAS; DE SOUZA, ANETE PEREIRA. Network of proteins, enzymes and genes linked to biomass degradation shared by Trichoderma species. SCIENTIFIC REPORTS, v. 8, . (11/00417-3, 14/18856-1, 15/09202-0, 15/50612-8, 16/19775-0)
MASSARDO, DARLI; VANKUREN, NICHOLAS W.; NALLU, SUMITHA; RAMOS, RENATO R.; RIBEIRO, PEDRO G.; SILVA-BRANDAO, KARINA L.; BRANDAO, MARCELO M.; LION, MARILIA B.; FREITAS, ANDRE V. L.; CARDOSO, MARCIO Z.; et al. The roles of hybridization and habitat fragmentation in the evolution of Brazil's enigmatic longwing butterflies, Heliconius nattereri and H. hermathena. BMC Biology, v. 18, n. 1, . (12/50260-6, 12/16266-7, 11/00417-3, 11/50225-3)
PABLOS, JULIA LEME; SILVA, ANA KRISTINA; SERAPHIM, NOEMY; MAGALDI, LUIZA DE MORAES; DE SOUZA, ANETE PEREIRA; LUCCI FREITAS, ANDRE VICTOR; SILVA-BRANDAO, KARINA LUCAS. North-south and climate-landscape-associated pattern of population structure for the Atlantic Forest White Morpho butterflies{*}. Molecular Phylogenetics and Evolution, v. 161, . (11/00417-3)
BAJAY, STEPHANIE K.; CRUZ, MARIANA V.; DA SILVA, CARLA C.; MURAD, NATALIA F.; BRANDAO, MARCELO M.; DE SOUZA, ANETE P.. Extremophiles as a Model of a Natural Ecosystem: Transcriptional Coordination of Genes Reveals Distinct Selective Responses of Plants Under Climate Change Scenarios. FRONTIERS IN PLANT SCIENCE, v. 9, . (14/11426-1, 13/26793-7, 11/00417-3)
SPERLING, JANET L.; SILVA-BRANDAO, K. L.; BRANDAO, M. M.; LLOYD, V. K.; DANG, S.; DAVIS, C. S.; SPERLING, F. A. H.; MAGOR, K. E.. Comparison of bacterial 16S rRNA variable regions for microbiome surveys of ticks. TICKS AND TICK-BORNE DISEASES, v. 8, n. 4, p. 453-461, . (11/00417-3)
SILVA-BRANDAO, KARINA LUCAS; BATISTA NETO E SILVA, OSCAR ARNALDO; BRANDAO, MARCELO MENDES; OMOTO, CELSO; SPERLING, FELIX A. H.. Genotyping-by-sequencing approach indicates geographic distance as the main factor affecting genetic structure and gene flow in Brazilian populations of Grapholita molesta (Lepidoptera, Tortricidae). EVOLUTIONARY APPLICATIONS, v. 8, n. 5, p. 476-485, . (11/00417-3)

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