Search

Your search keyword '"Pinheiro, D. G."' showing total 19 results
Start Over Author "Pinheiro, D. G."
19 results on '"Pinheiro, D. G."'

3. Caste‐specific gene expression underlying the differential adult brain development in the honeybee Apis mellifera.

Author

Paula Junior, D. E., Oliveira, M. T., Bruscadin, J. J., Pinheiro, D. G., Bomtorin, A. D., Coelho Júnior, V. G., Moda, L. M. R., Simões, Z. L. P., and Barchuk, A. R.

Subjects
NEURAL development, HONEYBEES, GENE expression, ADULT development, QUEEN honeybees, TISSUE remodeling
Abstract

Apis mellifera adult workers feature more developed key brain regions than queens, which allows them to cope with the broad range of duties they need to perform in a colony. However, at the end of larval development, the brain of queens is largely more developed than that of workers. Major morphogenetic changes take place after metamorphosis that shift caste‐specific brain development. Here, we tested the hypothesis that this phenomenon is hormonally governed and involves differential gene expression. Our molecular screening approach revealed a set of differentially expressed genes in Pp (first pharate‐adult phase) brains between castes mainly coding for tissue remodelling and energy‐converting proteins (e.g. hex 70a and ATPsynβ). An in‐depth qPCR analysis of the transcriptional behaviour during pupal and pharate‐adult developmental stage in both castes and in response to artificially augmented hormone titres of 18 genes/variants revealed that: i. subtle differences in hormone titres between castes might be responsible for the differential expression of the EcR and insulin/insulin‐like signalling (IIS) pathway genes; ii. the morphogenetic activity of the IIS in brain development must be mediated by ILP‐2, iii. which together with the tum, mnb and caspase system, can constitute the molecular effectors of the caste‐specific opposing brain developmental trajectories. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

5. MicroRNA signatures characterizing caste-independent ovarian activity in queen and worker honeybees (Apis mellifera L.)

Author

Macedo, Liliane Maria Fróes, Nunes, F.M.F., Freitas, Flávia Cristina de Paula, Pires, Camilla Valente, Tanaka, Erica D., Martins, J. R., Piulachs, Maria-Dolors, Cristino, Alexandre S., Pinheiro, D. G., Simões, Zila Luz Paulino, Fundação de Amparo à Pesquisa do Estado de São Paulo, Ministerio de Ciencia e Innovación (España), Consejo Superior de Investigaciones Científicas (España), and European Commission

Subjects
microRNA, Plasticity, Ovary, Honeybee, Development, Transcriptomes
Abstract

Queen and worker honeybees differ profoundly in reproductive capacity. The queen of this complex society, with 200 highly active ovarioles in each ovary, is the fertile caste, whereas the workers have approximately 20 ovarioles as a result of receiving a different diet during larval development. In a regular queenright colony, the workers have inactive ovaries and do not reproduce. However, if the queen is sensed to be absent, some of the workers activate their ovaries, producing viable haploid eggs that develop into males. Here, a deep-sequenced ovary transcriptome library of reproductive workers was used as supporting data to assess the dynamic expression of the regulatory molecules and microRNAs (miRNAs) of reproductive and nonreproductive honeybee females. In this library, most of the differentially expressed miRNAs are related to ovary physiology or oogenesis. When we quantified the dynamic expression of 19 miRNAs in the active and inactive worker ovaries and compared their expression in the ovaries of virgin and mated queens, we noted that some miRNAs (miR-1, miR-31a, miR-13b, miR-125, let-7 RNA, miR-100, miR-276, miR-12, miR-263a, miR-306, miR-317, miR-92a and miR-9a) could be used to identify reproductive and nonreproductive statuses independent of caste. Furthermore, integrative gene networks suggested that some candidate miRNAs function in the process of ovary activation in worker bees., This project was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) 2011/03171-5, 2010/08150-3 and 2010/06336-2 to Z.L.P.S. and by the Ministry of Science and Innovation, Spain (project BFU2008-00484 to M.D.P.). E.D.T. was the recipient of a postdoctoral research grant JAE-Doc (‘Junta para la Ampliación de Estudios’) financed by ‘Consejo Superior de Investigaciones Cientificas’ and The European Social Fund.

Published
2016

6. MicroRNA signatures characterizing caste-independent ovarian activity in queen and worker honeybees (Apis mellifera L.)

Author

Fundação de Amparo à Pesquisa do Estado de São Paulo, Ministerio de Ciencia e Innovación (España), Consejo Superior de Investigaciones Científicas (España), European Commission, Macedo, Liliane Maria Fróes, Nunes, F.M.F., Freitas, Flávia Cristina de Paula, Pires, Camilla Valente, Tanaka, Erica D., Martins, J. R., Piulachs, Maria-Dolors, Cristino, Alexandre S., Pinheiro, D. G., Simões, Zila Luz Paulino, Fundação de Amparo à Pesquisa do Estado de São Paulo, Ministerio de Ciencia e Innovación (España), Consejo Superior de Investigaciones Científicas (España), European Commission, Macedo, Liliane Maria Fróes, Nunes, F.M.F., Freitas, Flávia Cristina de Paula, Pires, Camilla Valente, Tanaka, Erica D., Martins, J. R., Piulachs, Maria-Dolors, Cristino, Alexandre S., Pinheiro, D. G., and Simões, Zila Luz Paulino

Abstract

Queen and worker honeybees differ profoundly in reproductive capacity. The queen of this complex society, with 200 highly active ovarioles in each ovary, is the fertile caste, whereas the workers have approximately 20 ovarioles as a result of receiving a different diet during larval development. In a regular queenright colony, the workers have inactive ovaries and do not reproduce. However, if the queen is sensed to be absent, some of the workers activate their ovaries, producing viable haploid eggs that develop into males. Here, a deep-sequenced ovary transcriptome library of reproductive workers was used as supporting data to assess the dynamic expression of the regulatory molecules and microRNAs (miRNAs) of reproductive and nonreproductive honeybee females. In this library, most of the differentially expressed miRNAs are related to ovary physiology or oogenesis. When we quantified the dynamic expression of 19 miRNAs in the active and inactive worker ovaries and compared their expression in the ovaries of virgin and mated queens, we noted that some miRNAs (miR-1, miR-31a, miR-13b, miR-125, let-7 RNA, miR-100, miR-276, miR-12, miR-263a, miR-306, miR-317, miR-92a and miR-9a) could be used to identify reproductive and nonreproductive statuses independent of caste. Furthermore, integrative gene networks suggested that some candidate miRNAs function in the process of ovary activation in worker bees.

Published
2016

7. Hormonal control and target genes of ftz‐f1 expression in the honeybee Apis mellifera: a positive loop linking juvenile hormone, ftz‐f1, and vitellogenin.

Author

Mello, T. R. P., Aleixo, A. C., Pinheiro, D. G., Nunes, F. M. F., Cristino, A. S., Bitondi, M. M. G., Barchuk, A. R., and Simões, Z. L. P.

Subjects
HONEYBEES, GENE targeting, GENE expression, INSECT genetics, INSECT hormones, VITELLOGENINS
Abstract

Ftz‐f1 is an orphan member of the nuclear hormone receptor superfamily. A 20‐hydroxyecdysone pulse allows ftz‐f1 gene expression, which then regulates the activity of downstream genes involved in major developmental progression events. In honeybees, the expression of genes like vitellogenin (vg), prophenoloxidase and juvenile hormone‐esterase during late pharate‐adult development is known to be hormonally controlled in both queens and workers by increasing juvenile hormone (JH) titres in the presence of declining levels of ecdysteroids. Since Ftz‐f1 is known for mediating intracellular JH signalling, we hypothesized that ftz‐f1 could mediate JH action during the pharate‐adult development of honeybees, thus controlling the expression of these genes. Here, we show that ftz‐f1 has caste‐specific transcription profiles during this developmental period, with a peak coinciding with the increase in JH titre, and that its expression is upregulated by JH and downregulated by ecdysteroids. RNAi‐mediated knock down of ftz‐f1 showed that the expression of genes essential for adult development (e.g. vg and cuticular genes) depends on ftz‐f1 expression. Finally, a double‐repressor hypothesis‐inspired vg gene knock‐down experiment suggests the existence of a positive molecular loop between JH, ftz‐f1 and vg. [ABSTRACT FROM AUTHOR]

Published
2019
Full Text
View/download PDF

9. Global gene expression profiling of oral cavity cancers suggests molecular heterogeneity within anatomic subsites

Author

Severino, Patricia, Alvares, Adriana M., Michaluart, Pedro, Okamoto, Oswaldo K., Nunes, Fabio D., Moreira-Filho, Carlos A., Tajara, Eloiza H., Cury, P. M., Frizzera, A. P.Z., de Carvalho, M. B., Silva, A. M.A., Amar, A., Barbieri, R. B., Bastos, A. U., Carvalho-Neto, P. B., Casemiro, A. F., Chedid, H., Chiappini, P. B.O., Correia, L. A., Costa, A. C.W., Curioni, O. A., Franzi, S. A., Gazito, D., Gutierres, A. P., Lehn, C. N., Martins, A. E., Mercante, A. M.C., Porsani, A. F., Rapoport, A., Rossi, L., Santos, M., Souza, T. B., Takamori, J. T., Dias-Neto, E., Ojopi, E. P.B., Dias, T. H.G., Figueiredo, D. L.A., Mamede, R. C.M., Fukuyama, E. E., Góis-Filho, J. F., Cerione, M., Cicco, R., Settani, F., Valentim, P. J., Yamagushi, F., Cominato, M. L., Mendes, G. S., Paiva, R., Silva, M. J., Leopoldino, A. M., Silva, F. A.M., Moyses, R. A., Arap, S. S., Araújo, N. S.S., Araújo-Filho, V., Brandão, L. G., Cernea, C. R., Durazzo, M., Ferraz, A. R., Gallo, J., Guimarães, P. E.M., Magalhães, R. P., Montenegro, F. L.M., Silva-Filho, G. B., Smith, R. B., Stabenow, E., Tavares, M. R., Turcano, R., Volpi, E. M., Ramos, O., Silva, C., Moreira-Filho, C. A., Nóbrega, F. G. [UNESP], Nóbrega, M. P. [UNESP], Canto, A. L. [UNESP], Macarenco, R. [UNESP], Meneses, C. [UNESP], Correa, P. M.S. [UNESP], Bogossian, A. P. [UNESP], Nunes, F. D., Souza, S. C.O.M., Rodini, C. O., Xavier, F. C.A., Okamoto, O. K., Serafini, L. N., Severino, P., Silva, W. A., Brandão, R. M., Kaneto, C. M., Pinheiro, D. G., Santos, A. R.D., Silva, I. T., Tarlá, M. V.C., Silveira, N. J.F., Tajara, E. H., Rodrigues-Lisoni, F. C., Rodrigues, R. V., Polachini, G. M., Vidotto, A., Cunha, B. R., Carmona-Raphe, J., Wünsch-Filho, V., Costa, A., Figueiredo, R. O., Fortes, C. S., Inamine, R., López, R. V.M., Rodrigues, A. N., Zago, M. A., Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Heliópolis, Universidade de São Paulo (USP), Universidade Federal de São Paulo (UNIFESP), Faculdade de Medicina de São José do Rio Preto, Faculdade de Medicina, Instituto do Câncer Arnaldo Vieira de Carvalho, Universidade Estadual Paulista (UNESP), Instituto de Ensino e Pesquisa Albert Einstein, and UNIVAP

Subjects
Medicine(all), Microarray, Cytoskeleton organization, business.industry, Biochemistry, Genetics and Molecular Biology(all), lcsh:R, Short Report, lcsh:Medicine, General Medicine, Disease, Cell cycle, Bioinformatics, General Biochemistry, Genetics and Molecular Biology, Gene expression profiling, stomatognathic diseases, lcsh:Biology (General), Gene expression, Gene chip analysis, Medicine, lcsh:Science (General), business, lcsh:QH301-705.5, Gene, lcsh:Q1-390
Abstract

Made available in DSpace on 2022-04-29T08:44:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-01-01 Background: Oral squamous cell carcinoma (OSCC) is a frequent neoplasm, which is usually aggressive and has unpredictable biological behavior and unfavorable prognosis. The comprehension of the molecular basis of this variability should lead to the development of targeted therapies as well as to improvements in specificity and sensitivity of diagnosis. Results: Samples of primary OSCCs and their corresponding surgical margins were obtained from male patients during surgery and their gene expression profiles were screened using whole-genome microarray technology. Hierarchical clustering and Principal Components Analysis were used for data visualization and One-way Analysis of Variance was used to identify differentially expressed genes. Samples clustered mostly according to disease subsite, suggesting molecular heterogeneity within tumor stages. In order to corroborate our results, two publicly available datasets of microarray experiments were assessed. We found significant molecular differences between OSCC anatomic subsites concerning groups of genes presently or potentially important for drug development, including mRNA processing, cytoskeleton organization and biogenesis, metabolic process, cell cycle and apoptosis. Conclusion: Our results corroborate literature data on molecular heterogeneity of OSCCs. Differences between disease subsites and among samples belonging to the same TNM class highlight the importance of gene expression-based classification and challenge the development of targeted therapies. Centro de Pesquisa Experimental Instituto Israelita de Ensino e Pesquisa Albert Einstein Laboratório de Biologia Molecular Hospital Heliópolis Departamento de Cirurgia de Cabeça e Pescoço Hospital das Clínicas Faculdade de Medicina Universidade de São Paulo Departamento de Neurologia e Neurocirurgia Universidade Federal de São Paulo Departamento de Estomatologia Faculdade de Odontologia Universidade de São Paulo Departamento de Pediatria Faculdade de Medicina Universidade de São Paulo Departamento de Biologia Molecular Faculdade de Medicina de São José do Rio Preto Departamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo Departamento de Patologia Faculdade de Medicina Hospital Heliópolis Departamento e Instituto de Psiquiatria Faculdade de Medicina USP Serviço de Cirurgia de Cabeça e Pescoço Faculdade de Medicina de Ribeirão Preto USP Serviço de Cirurgia de Cabeça e Pescoço Instituto do Câncer Arnaldo Vieira de Carvalho Departamento de Análises Clínicas Toxicológicas e Bromatológicas Faculdade de Ciências Farmacêuticas de Ribeirão Preto USP Departamento de Cirurgia de Cabeça e Pescoço Faculdade de Medicina USP Departamento de Pediatria Faculdade de Medicina USP Departamento de Biociências e Diagnóstico Bucal Faculdade de Odontologia UNESP Departamento de Estomatologia Faculdade de Odontologia USP Departamento de Neurologia e Neurocirurgia UNIFESP Departamento de Patologia Faculdade de Medicina de Ribeirão Preto USP Instituto de Ensino e Pesquisa Albert Einstein Departamento de Genética Faculdade de Medicina de Ribeirão Preto USP Ciências da Computação UNIVAP Departamento de Biologia Molecular Faculdade de Medicina Departamento de Epidemiologia Faculdade de Saúde Pública USP Departamento de Clínica Médica Faculdade de Medicina de Ribeirão Preto USP Departamento de Biociências e Diagnóstico Bucal Faculdade de Odontologia UNESP

Published
2008

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

Author

Sogayar, M. C., Camargo, A. A., Bettoni, F., Carraro, D. M., Pires, L. C., Parmigiani, M. B., Ferreira, E. N., Moreira, E. S., Latorre, MRDO, Simpson, AJG, Cruz, L. O., Degaki, T. L., Festa, F., Massirer, K. B., Camargo, F., Camargo, L. P., Cunha, MAV, De Souza, S. J., Faria, M., Giuliatti, S., Kopp, Oliviera, PSL, Paiva, P. B., Pereira, A. A., Pinheiro, D. G., Puga, R. D., Souza, JES, Albuquerque, D. M., Andrade, LEC, Baia, G. S., Briones, MRS, Cavaleiro-Luna, AMS, Cerutti, J. M., Costa, F. F., Constanzi-Strauss, E., Espreafico, E. M., Ferrasi, A. C., Ferro, E. S., Fortes, MAHZ, Furchi, JRF, Gianella-Neto, D., Goldman, G. H., Goldman, MHS, Gruber, A., Guimaraes, G. S., Hackel, C., Henrique-Silva, F., Kimura, E. T., Leoni, S. G., Macedo, C., Malnic, B., Manzini, C. V., Marie, SKN, Martinez-Rossi, N. M., Menossi, M., Miracca, E. C., Nagai, M. A., Nobrega, F. G., Nobrega, M. P., Oba-Shinjo, S. M., Oliviera, M. K., Orabona, G. M., Otsuke, A. Y., Paco-Larson, M. L., Paixao, BMC, Pandolfi, JRC, Pardini, MIMC, Passos-Bueno, M. R., Passos, GAS, Pesquero, J. B., Pessoa, J. G., Rahal, Paula [UNESP], Rainho, C. A., Reis, C. P., Ricca, T. I., Rodriguez, V, Rogatto, Silvia Regina [UNESP], Romano, C. M., Romeiro, J. G., Rossi, A., Sa, R. G., Sales, M. M., SantAnna, S. C., Santarosa, P. L., Segato, F., Silva, W. A., Silva, IDCG, Silva, N. P., Soares-Costa, A., Sonati, M. F., Strauss, B. E., Tajara, E. H., Valentini, Sandro Roberto [UNESP], Villanova, F. E., Ward, L. S., Zanette, D. L., Universidade de São Paulo (USP), Ludwig Inst Canc Res, Univ Ribeirao Preto, Inst Ludwig, Universidade Federal de São Paulo (UNIFESP), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual Paulista (Unesp), Universidade Federal de São Carlos (UFSCar), and Univ Vale Paraiba

Subjects
Transcription, Genetic, Software Validation, Molecular Sequence Data, Biology, Cell Line, Open Reading Frames, Exon, Software Design, Cell Line, Tumor, Complementary DNA, Consensus Sequence, Databases, Genetic, Methods, Genetics, Consensus sequence, Humans, Gene, Genetics (clinical), Expressed Sequence Tags, Expressed sequence tag, Genome, Human, Alternative splicing, Computational Biology, DNA, Neoplasm, U937 Cells, HISTOLOGIA, Alternative Splicing, Open reading frame, Genes, Human genome, Software, HeLa Cells
Abstract

Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2014-02-26T17:19:33Z No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Made available in DSpace on 2014-02-26T17:19:33Z (GMT). No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Previous issue date: 2004-07-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T13:50:12Z No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Made available in DSpace on 2014-05-20T13:50:12Z (GMT). No. of bitstreams: 1 WOS000222434200023.pdf: 392582 bytes, checksum: eb50adacff00ab5cc37867f0de853492 (MD5) Previous issue date: 2004-07-01 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. Univ São Paulo, Inst Quim, BR-05513970 São Paulo, Brazil Ludwig Inst Canc Res, BR-01509010 São Paulo, Brazil Univ São Paulo, Dept Epidemiol, Sch Publ Hlth, BR-01246904 São Paulo, SP, Brazil Univ Ribeirao Preto, Dept Quim Informat Bioinformat, BR-14096380 Ribeirao Preto, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Centro Terapia Celular, Hemocentro, BR-14051140 Ribeirao Preto, SP, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Clin Med, BR-14051140 Ribeirao Preto, SP, Brazil Inst Ludwig, Lab Biol Computacional, BR-01509010 São Paulo, SP, Brazil Univ São Paulo, Lab Genet Cardiol Mol, Inst Coracao, BR-05403000 São Paulo, SP, Brazil Univ Fed São Paulo, Bioinform Lab, Hlth Informatics Dept, BR-04039032 São Paulo, Brazil Univ Estad Campinas, Dept Clin Med, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ Fed São Paulo, Rheumatol Div, BR-04113001 São Paulo, Brazil Univ São Paulo, Dept Histol Embriol, Inst Ciências Biomed, BR-05508900 São Paulo, Brazil Univ Fed São Paulo, Dept Microbiol Immunol Parasitol, BR-04023062 São Paulo, Brazil Univ São Paulo, Lab Cellular Mol Endocrinol, Sch Med, BR-01246903 São Paulo, Brazil Univ Fed São Paulo, Dept Med, Disciplina Endocrinol, Lab Endocrinol Mol, BR-04039002 São Paulo, Brazil Univ São Paulo, Inst Ciências Biomed, Lab Transferencia Genica, BR-05508900 São Paulo, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Biol Celular Mol Bioagentes Patogenicas, BR-14049900 Ribeirao Preto, SP, Brazil Univ Estadual Paulista, Lab Biol Mol, Hemocentro, Fac Med, BR-18618970 Botucatu, SP, Brazil Univ Fed Sao Carlos, Dept Genet Evol, BR-13565905 Sao Carlos, SP, Brazil Univ São Paulo, Fac Ciências Farmaceuticas Ribeirao Preto, BR-14040903 Ribeirao Preto, SP, Brazil Univ São Paulo, Fac Filosofia Ciências Letras Ribeirao Preto, Ribeirao Preto, SP, Brazil Univ São Paulo, Dept Patol, Fac Med Vet Zootecnia, BR-05508000 São Paulo, Brazil Univ Estadual Campinas, Dept Genet Med, Fac Ciências Med, BR-13081970 Campinas, SP, Brazil Univ São Paulo, Fac Med Ribeirao Preto, Dept Genet, BR-14040900 Ribeirao Preto, SP, Brazil Univ São Paulo, Dept Bioquim, Inst Quim, BR-05599970 São Paulo, Brazil Univ São Paulo, Dept Neurol, Fac Med, BR-01246903 São Paulo, Brazil Univ Estadual Campinas, Lab Genoma Funcional, Centro Biol Mol Engenharia Genet, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Dept Genet Evol, Inst Biol, Campinas, SP, Brazil Univ São Paulo, Dept Radiol, Disciplina Oncol, Fac Med, BR-01246903 São Paulo, Brazil Univ Vale Paraiba, Inst Pesquisa Desenvolvimento, BR-12244000 Sao Jose Dos Campos, SP, Brazil Univ São Paulo, Inst Biociencias, Centro Estudios Genoma Humano, Dept Biol, BR-055508900 São Paulo, Brazil Univ Fed São Paulo, Lab Mol Gynecol, Dept Gynecol, BR-04039001 São Paulo, Brazil São Paulo State Univ, Sch Pharmacol, Dept Biol Sci, BR-14801902 Araraquara, SP, Brazil Univ São Paulo, Discipl Genet, Fac Odontol, BR-14040900 Ribeirao Preto, SP, Brazil Univ Fed São Paulo, Dept Biofisica, BR-04023062 São Paulo, Brazil Univ Estadual Paulista, Dept Biol, Inst Biociencias Letras Ciências Exatas, BR-15054000 Sao Jose do Rio Preto, SP, Brazil Univ Estadual Paulista, Dept Genet, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil Univ São Paulo, Dept Bioquim Imunol, Fac Med Ribeirao Preto, BR-14049900 Ribeirao Preto, SP, Brazil Univ Estadual Campinas, Lab Genet Mol Cancer, Dept Clin Med, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ Estadual Campinas, Dept Patol Clin, Fac Ciências Med, BR-13083970 Campinas, SP, Brazil Univ São Paulo, Setor Vetores Virals, Lab Cardiol Mol, Inst Coracao, BR-15403000 São Paulo, Brazil Univ Estadual Paulista, Lab Biol Mol, Hemocentro, Fac Med, BR-18618970 Botucatu, SP, Brazil São Paulo State Univ, Sch Pharmacol, Dept Biol Sci, BR-14801902 Araraquara, SP, Brazil Univ Estadual Paulista, Dept Biol, Inst Biociencias Letras Ciências Exatas, BR-15054000 Sao Jose do Rio Preto, SP, Brazil Univ Estadual Paulista, Dept Genet, Inst Biociencias, BR-18618000 Botucatu, SP, Brazil

Published
2004

11. MicroRNA signatures characterizing caste-independent ovarian activity in queen and worker honeybees ( A pis mellifera L.).

Author

Macedo, L. M. F., Nunes, F. M. F., Freitas, F. C. P., Pires, C. V., Tanaka, E. D., Martins, J. R., Piulachs, M.‐D., Cristino, A. S., Pinheiro, D. G., and Simões, Z. L. P.

Subjects
QUEENS (Insects), WORKER honeybees, MICRORNA, INSECT larvae, INSECT reproduction, INSECT genetics, GENE expression
Abstract

Queen and worker honeybees differ profoundly in reproductive capacity. The queen of this complex society, with 200 highly active ovarioles in each ovary, is the fertile caste, whereas the workers have approximately 20 ovarioles as a result of receiving a different diet during larval development. In a regular queenright colony, the workers have inactive ovaries and do not reproduce. However, if the queen is sensed to be absent, some of the workers activate their ovaries, producing viable haploid eggs that develop into males. Here, a deep-sequenced ovary transcriptome library of reproductive workers was used as supporting data to assess the dynamic expression of the regulatory molecules and microRNAs (miRNAs) of reproductive and nonreproductive honeybee females. In this library, most of the differentially expressed miRNAs are related to ovary physiology or oogenesis. When we quantified the dynamic expression of 19 miRNAs in the active and inactive worker ovaries and compared their expression in the ovaries of virgin and mated queens, we noted that some miRNAs ( miR-1, miR-31a, miR-13b, miR-125, let-7 RNA, miR-100, miR-276, miR-12, miR-263a, miR-306, miR-317, miR-92a and miR-9a) could be used to identify reproductive and nonreproductive statuses independent of caste. Furthermore, integrative gene networks suggested that some candidate miRNAs function in the process of ovary activation in worker bees. [ABSTRACT FROM AUTHOR]

Published
2016
Full Text
View/download PDF

12. SAGE analysis highlights the putative role of underexpression of ribosomal proteins in GH-secreting pituitary adenomas

Author

de Lima, D. S., primary, Martins, C. S., additional, Paixao, B. M. d. C., additional, Amaral, F. C., additional, Colli, L. M., additional, Saggioro, F. P., additional, Neder, L., additional, Machado, H. R., additional, dos Santos, A. R. D., additional, Pinheiro, D. G., additional, Moreira, A. C., additional, Silva, W. A., additional, and Castro, M., additional

Published
2012
Full Text
View/download PDF

13. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

Author

Ferreira, E. N., Pires, L. C., Parmigiani, R. B., Bettoni, F., Puga, R. D., Pinheiro, D. G., Andrade, L. E. C., Cruz, L. O., Degaki, T. L., Faria Jr, M., Festa, F., Giannella-Neto, D., Giorgi, R. R., Goldman, G. H., Granja, F., Gruber, A., Hackel, C., Henrique-Silva, F., Malnic, B., Manzini, C. V. B., Marie, S. K. N., Martinez-Rossi, N. M., Oba-Shinjo, S. M., Pardini, M. I. M. C., Rahal, P., Rainho, C. A., Rogatto, S. R., Romano, C. M., Rodrigues, V., Sales, M. M., Savoldi, M., Da Silva, I. D. C. G., Da Silva, N. P., Souza, S. J., Tajara, E. H., Wilson Araujo Silva Jr, Simpson, A. J. G., Sogayar, M. C., Camargo, A. A., and Carraro, D. M.

Subjects
Male, Mice, DNA, Complementary, Transcription, Genetic, Genome, Human, Molecular Sequence Data, Testis, Animals, Chromosome Mapping, Humans, Amino Acid Sequence, Sequence Analysis, DNA, Gene Library
Abstract

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

15. miRNApath: a database of miRNAs, target genes and metabolic pathways

Author

Chiromatzo, A. O., Oliveira, T. Y. K., Pereira, G., Costa, A. Y., Montesco, C. A. E., Gras, D. E., Yosetake, F., Vilar, J. B., Cervato, M., Prado, P. R. R., Cardenas, R. G. C. C. L., Cerri, R., Borges, R. L., Lemos, R. N., Alvarenga, S. M., Perallis, V. R. C., Pinheiro, D. G., Silva, I. T., Brandão, R. M., Cunha, M. A. V., Giuliatti, S., and Wilson Araujo Silva Jr

Subjects
MicroRNAs, Animals, Computational Biology, Humans, Databases, Nucleic Acid, Metabolic Networks and Pathways, Software
Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression and hence play important roles in metabolic pathways. Recent studies have evidenced the interrelation of miRNAs with cell proliferation, differentiation, development, and diseases. Since they are involved in gene regulation, they are intrinsically related to metabolic pathways. This leads to questions that are particularly interesting for investigating medical and laboratorial applications. We developed an miRNApath online database that uses miRNA target genes to link miRNAs to metabolic pathways. Currently, databases about miRNA target genes (DIANA miRGen), genomic maps (miRNAMap) and sequences (miRBase) do not provide such correlations. Additionally, miRNApath offers five search services and a download area. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic pathways, which results in different views, depending upon the input data, concerning relationships between the target genes, miRNAs and metabolic pathways. There are also internal links that lead to a deeper analysis and cross-links to other databases with more detailed information. miRNApath is being continually updated and is available at http://lgmb.fmrp.usp.br/mirnapath.

16. Predicting maximal lactate steady state from lactate thresholds determined using methods based on an incremental exercise test in beagle dogs: A study using univariate and multivariate approaches.

Author

Ferraz GC, Sgarbiero T, Carvalho JRG, Almeida MLM, Pereira GT, Funnicelli MIG, Pinheiro DG, and Restan AZ

Subjects
Dogs, Male, Animals, Reproducibility of Results, Linear Models, Exercise Test veterinary, Lactic Acid
Abstract

The reliability of four lactate threshold (LT) methods to estimate the maximal lactate steady state (MLSS), defined as the highest intensity that can be maintained without plasma lactate ([La - ]) accumulation over time, was determined in Beagle dogs. Six male Beagle dogs performed a standardized incremental exercise test on a treadmill when plasma lactate ([La - ]) measurements were performed. The LTs for predicting MLSS, were determined by visual inspection (LT V ), using a bi-segmented linear regression model (LT BI ), or using a polynomial function on the [La - ]/velocity ratio (LT P ) by considering the vertices of the curve and calculating the point that yields the maximal distance from a curve representing [La - ] as a function of velocity to the line formed by the two endpoints of the curve (LT DMAX method). The agreement was assessed using Bland-Altman plots and ordinary least products (OLP) regression among the velocities corresponding to the LTs identified using different methods (VLT v , VLT BI , VLT P , and VLT DMAX ) and the velocity corresponding to the MLSS (VMLSS). A principal component (PC) analysis approach was performed to detect the degree of co-relatedness among the variables. The mean ± SD [La - ] at MLSS was 1.03 ± 0.24 mM. VMLSS had a lower mean bias with VLT v , followed by VLT BI . The VLT DMAX underestimated MLSS. VLT v and VLT BI had the lowest limits of agreement with the VMLSS. The VLT P and VLT DMAX showed relatively high limits of agreement with MLSS. VLT v , VLTBI, and VMLSS had more collinearity and were dominantly aligned with the second component (PC2). VLT v and VLT BI can be used as simple methods to objectively determine aerobic fitness in Beagle dogs., Competing Interests: Declaration of Competing Interest None of the authors has financial or personal relationships that could inappropriately influence or bias the content of the paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Published
2022
Full Text
View/download PDF

17. De novo transcriptome assembly of sugarcane leaves submitted to prolonged water-deficit stress.

Author

Belesini AA, Carvalho FMS, Telles BR, de Castro GM, Giachetto PF, Vantini JS, Carlin SD, Cazetta JO, Pinheiro DG, and Ferro MIT

Subjects
Droughts, Gene Expression Regulation, Plant, Plant Leaves genetics, Saccharum embryology, Osmotic Pressure, Plant Leaves metabolism, Saccharum genetics, Transcriptome
Abstract

Sugarcane production is strongly influenced by drought, which is a limiting factor for agricultural productivity in the world. In this study, the gene expression profiles obtained by de novo assembly of the leaf transcriptome of two sugarcane cultivars that differ in their physiological response to water deficit were evaluated by the RNA-Seq method: drought-tolerant cultivar (SP81-3250) and drought-sensitive cultivar (RB855453). For this purpose, plants were grown in a greenhouse for 60 days and were then submitted to three treatments: control (-0.01 to -0.015 MPa), moderate water deficit (-0.05 to -0.055 MPa), and severe water deficit (-0.075 to -0.08 MPa). The plants were evaluated 30, 60, and 90 days after the beginning of treatment. Sequencing on an Illumina platform (RNA-Seq) generated more than one billion sequences, resulting in 177,509 and 185,153 transcripts for the tolerant and sensitive cultivar, respectively. These transcripts were aligned with sequences from Saccharum spp, Sorghum bicolor, Miscanthus giganteus, and Arabidopsis thaliana available in public databases. The differentially expressed genes detected during the prolonged period of water deficit permit to increase our understanding of the molecular patterns involved in the physiological response of the two cultivars. The tolerant cultivar differentially expressed a larger number of genes at 90 days, while in the sensitive cultivar the number of differentially expressed genes was higher in 30 days. Both cultivars perceived the lack of water, but the tolerant cultivar responded more slowly than the sensitive cultivar. The latter requires rapid activation of different water-deficit stress response mechanisms for its survival. This rapid activation of metabolic pathways in response to water stress does not appear to be the key mechanism of drought tolerance in sugarcane. There is still much to clarify on the molecular and physiological pattern of plants in response to drought.

Published
2017
Full Text
View/download PDF

18. Genomics and proteomics approaches to the study of cancer-stroma interactions.

Author

Rodrigues-Lisoni FC, Peitl P Jr, Vidotto A, Polachini GM, Maniglia JV, Carmona-Raphe J, Cunha BR, Henrique T, Souza CF, Teixeira RA, Fukuyama EE, Michaluart P Jr, de Carvalho MB, Oliani SM, Tajara EH, Cury PM, de Carvalho MB, Dias-Neto E, Figueiredo DL, Fukuyama EE, Góis-Filho JF, Leopoldino AM, Mamede RC, Michaluart-Junior P, Moyses RA, Nóbrega FG, Nóbrega MP, Nunes FD, Ojopi EF, Serafini LN, Severino P, Silva AM, Silva WA Jr, Silveira NJ, Souza SC, Tajara EH, Wünsch-Filho V, Amar A, Bandeira CM, Braconi MA, Brandão LG, Brandão RM, Canto AL, Cerione M, Cicco R, Chagas MJ, Chedid H, Costa A, Cunha BR, Curioni OA, Fortes CS, Franzi SA, Frizzera AP, Gazito D, Guimarães PE, Kaneto CM, López RV, Macarenco R, Magalhães MR, Meneses C, Mercante AM, Pinheiro DG, Polachini GM, Rapoport A, Rodini CO, Rodrigues-Lisoni FC, Rodrigues RV, Rossi L, Santos AR, Santos M, Settani F, Silva FA, Silva IT, Souza TB, Stabenow E, Takamori JT, Valentim PJ, Vidotto A, Xavier FC, Yamagushi F, Cominato ML, Correa PM, Mendes GS, Paiva R, Ramos O, Silva C, Silva MJ, and Tarlá MV

Subjects
Annexin A5 metabolism, Apoptosis, Cell Proliferation, Down-Regulation, Electrophoresis, Gel, Two-Dimensional, Fibroblasts metabolism, Genomics, Hep G2 Cells, Humans, Keratins metabolism, Mouth Neoplasms genetics, Nucleic Acid Hybridization, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Stromal Cells metabolism, Vimentin metabolism, Gene Expression Regulation, Neoplastic, Mouth Neoplasms metabolism, Proteome metabolism
Abstract

Background: The development and progression of cancer depend on its genetic characteristics as well as on the interactions with its microenvironment. Understanding these interactions may contribute to diagnostic and prognostic evaluations and to the development of new cancer therapies. Aiming to investigate potential mechanisms by which the tumor microenvironment might contribute to a cancer phenotype, we evaluated soluble paracrine factors produced by stromal and neoplastic cells which may influence proliferation and gene and protein expression., Methods: The study was carried out on the epithelial cancer cell line (Hep-2) and fibroblasts isolated from a primary oral cancer. We combined a conditioned-medium technique with subtraction hybridization approach, quantitative PCR and proteomics, in order to evaluate gene and protein expression influenced by soluble paracrine factors produced by stromal and neoplastic cells., Results: We observed that conditioned medium from fibroblast cultures (FCM) inhibited proliferation and induced apoptosis in Hep-2 cells. In neoplastic cells, 41 genes and 5 proteins exhibited changes in expression levels in response to FCM and, in fibroblasts, 17 genes and 2 proteins showed down-regulation in response to conditioned medium from Hep-2 cells (HCM). Nine genes were selected and the expression results of 6 down-regulated genes (ARID4A, CALR, GNB2L1, RNF10, SQSTM1, USP9X) were validated by real time PCR., Conclusions: A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein.

Published
2010
Full Text
View/download PDF

19. miRNApath: a database of miRNAs, target genes and metabolic pathways.

Author

Chiromatzo AO, Oliveira TY, Pereira G, Costa AY, Montesco CA, Gras DE, Yosetake F, Vilar JB, Cervato M, Prado PR, Cardenas RG, Cerri R, Borges RL, Lemos RN, Alvarenga SM, Perallis VR, Pinheiro DG, Silva IT, Brandão RM, Cunha MA, Giuliatti S, and Silva WA Jr

Subjects
Animals, Humans, Computational Biology methods, Databases, Nucleic Acid, Metabolic Networks and Pathways, MicroRNAs genetics, Software
Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression and hence play important roles in metabolic pathways. Recent studies have evidenced the interrelation of miRNAs with cell proliferation, differentiation, development, and diseases. Since they are involved in gene regulation, they are intrinsically related to metabolic pathways. This leads to questions that are particularly interesting for investigating medical and laboratorial applications. We developed an miRNApath online database that uses miRNA target genes to link miRNAs to metabolic pathways. Currently, databases about miRNA target genes (DIANA miRGen), genomic maps (miRNAMap) and sequences (miRBase) do not provide such correlations. Additionally, miRNApath offers five search services and a download area. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic pathways, which results in different views, depending upon the input data, concerning relationships between the target genes, miRNAs and metabolic pathways. There are also internal links that lead to a deeper analysis and cross-links to other databases with more detailed information. miRNApath is being continually updated and is available at http://lgmb.fmrp.usp.br/mirnapath.

Published
2007

Catalog

Books, media, physical & digital resources
See catalog results