Publications

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2012
K. J. R. Passos, Togoro, S. Y., Carignon, S., Koundrioukoff, S., Lachages, A. - M., Debatisse, M., and Fernandez, M. A., Molecular combing in the analysis of developmentally regulated amplified segments of Bradysia hygida, vol. 11, pp. 2060-2070, 2012.
Altman AL and Fanning E (2004). Defined sequence modules and an architectural element cooperate to promote initiation at an ectopic mammalian chromosomal replication origin. Mol. Cell Biol. 24: 4138-4150. http://dx.doi.org/10.1128/MCB.24.10.4138-4150.2004 PMid:15121836 PMCid:400449   Anglana M, Apiou F, Bensimon A and Debatisse M (2003). Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114: 385-394. http://dx.doi.org/10.1016/S0092-8674(03)00569-5   Bensimon A, Simon A, Chiffaudel A, Croquette V, et al. (1994). Alignment and sensitive detection of DNA by a moving interface. Science 265: 2096-2098. http://dx.doi.org/10.1126/science.7522347 PMid:7522347   Caburet S, Conti C and Bensimon A (2002). Combing the genome for genomic instability. Trends Biotechnol. 20: 344- 350. http://dx.doi.org/10.1016/S0167-7799(02)01990-X   Claycomb JM and Orr-Weaver TL (2005). Developmental gene amplification: insights into DNA replication and gene expression. Trends Genet. 21: 149-162. http://dx.doi.org/10.1016/j.tig.2005.01.009 PMid:15734574   Coelho PSR (1997). Análise dos Intermediários de Replicação do Pufe de DNA C4 de Bradysia hygida. Doctoral thesis, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto.   Courbet S, Gay S, Arnoult N, Wronka G, et al. (2008). Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 455: 557-560. http://dx.doi.org/10.1038/nature07233 PMid:18716622   Debatisse M, Toledo F, de Saint Vincent RB and Buttin G (1993). Amplification of the Adenylate-Deaminase 2 and Linked Genes in Chinese Hamster Lung Fibroblasts. In: Gene Amplification in Mammalian Cells - A Comprehensive Guide (Kellens RE, ed.). Marcel Dekker Inc., New York, 173-183.   Dijkwel PA, Vaughn JP and Hamlin JL (1991). Mapping of replication initiation sites in mammalian genomes by two-dimensional gel analysis: stabilization and enrichment of replication intermediates by isolation on the nuclear matrix. Mol. Cell Biol. 11: 3850-3859. PMid:2072896 PMCid:361168   Fiorini A, Basso LR Jr, Paco-Larson ML and Fernandez MA (2001). Mapping of intrinsic bent DNA sites in the upstream region of DNA puff BhC4-1 amplified gene. J. Cell Biochem. 83: 1-13. http://dx.doi.org/10.1002/jcb.1188 PMid:11500949   Gad S, Scheuner MT, Pages-Berhouet S, Caux-Moncoutier V, et al. (2001). Identification of a large rearrangement of the BRCA1 gene using colour bar code on combed DNA in an American breast/ovarian cancer family previously studied by direct sequencing. J. Med. Genet. 38: 388-392. http://dx.doi.org/10.1136/jmg.38.6.388 PMid:11424920 PMCid:1734901   Gregory TR (2005). Animal Genome Size Database. Available at [http://www.genomesize.com]. Accessed July 30, 2012.   Herrick J, Michalet X, Conti C, Schurra C, et al. (2000). Quantifying single gene copy number by measuring fluorescent probe lengths on combed genomic DNA. Proc. Natl. Acad. Sci. U. S. A. 97: 222-227. http://dx.doi.org/10.1073/pnas.97.1.222 PMid:10618399 PMCid:26644   Ivankin AV, Koleniskova TD, Demakov SA, Andreenkov OV, et al. (2011). Analysis of DNA replication parameters in isolated organs of Drosophila melanogaster by molecular combing. Cell Tissue Biol. 5: 1-8. http://dx.doi.org/10.1134/S1990519X11010081   Kolesnikova TD, Demakov SA, Ivankin AV, Andreenkova NG, et al. (2009). The mutation of the Suppressor of Underreplication gene does not affect the replication fork rate in the Drosophila melanogaster salivary gland polytene chromosomes. Dokl. Biochem. Biophys. 427: 175-178. http://dx.doi.org/10.1134/S1607672909040024 PMid:19817130   Kolesnikova TD, Demakov SA, Ivankin AV and Zhimulev IF (2010). Molecular combing in studies of the genome organization and DNA replication. Russ. J. Genet. 46: 1243-1246. http://dx.doi.org/10.1134/S102279541010025X   Koszul R, Caburet S, Dujon B and Fischer G (2004). Eucaryotic genome evolution through the spontaneous duplication of large chromosomal segments. EMBO J. 23: 234-243. http://dx.doi.org/10.1038/sj.emboj.7600024 PMid:14685272 PMCid:1271662   Laicine EM, Alves MA, de Almeida JC, Rizzo E, et al. (1984). Development of DNA puffs and patterns of polypeptide synthesis in the salivary glands of Bradysia hygida. Chromosoma 89: 280-284. http://dx.doi.org/10.1007/BF00292475 PMid:6745005   Lebofsky R and Bensimon A (2003). Single DNA molecule analysis: applications of molecular combing. Brief. Funct. Genomic. Proteomic. 1: 385-396. http://dx.doi.org/10.1093/bfgp/1.4.385   Lebofsky R and Bensimon A (2005). DNA replication origin plasticity and perturbed fork progression in human inverted repeats. Mol. Cell Biol. 25: 6789-6797. http://dx.doi.org/10.1128/MCB.25.15.6789-6797.2005 PMid:16024811 PMCid:1190330   Lengronne A, Pasero P, Bensimon A and Schwob E (2001). Monitoring S phase progression globally and locally using BrdU incorporation in TK(+) yeast strains. Nucleic Acids Res. 29: 1433-1442. http://dx.doi.org/10.1093/nar/29.7.1433 PMid:11266543 PMCid:31278   Liang C, Spitzer JD, Smith HS and Gerbi SA (1993). Replication initiates at a confined region during DNA amplification in Sciara DNA puff II/9A. Genes Dev. 7: 1072-1084. http://dx.doi.org/10.1101/gad.7.6.1072 PMid:8504930   Mesner LD and Hamlin JL (2009). Isolation of Restriction Fragments Containing Origins of Replication from Comples Genomes. In: DNA Replication: Methods and Protocols (Vengrova S and Dalgaard JZ, eds.). Humana Press, New York, 315-328. PMid:19563114 PMCid:2898177   Michalet X, Ekong R, Fougerousse F, Rousseaux S, et al. (1997). Dynamic molecular combing: stretching the whole human genome for high-resolution studies. Science 277: 1518-1523. http://dx.doi.org/10.1126/science.277.5331.1518 PMid:9278517   Mikami LR (2000). Associação à Matriz Nuclear de Segmento à Montante do Gene BhC4-1 em Núcleo Politenico de Bradysia hygida. Master's thesis, Universidade Estadual de Maringá, Maringá.   Monesi N, Fernandez MA, Fontes AM, Basso LR Jr, et al. (1995). Molecular characterization of an 18 kb segment of DNA puff C4 of Bradysia hygida (Diptera, sciaridae). Chromosoma 103: 715-724. http://dx.doi.org/10.1007/BF00344233 PMid:7664619   Myllykangas S and Knuutila S (2006). Manifestation, mechanisms and mysteries of gene amplifications. Cancer Lett. 232: 79-89. http://dx.doi.org/10.1016/j.canlet.2005.07.045 PMid:16288831   Norio P and Schildkraut CL (2001). Visualization of DNA replication on individual Epstein-Barr virus episomes. Science 294: 2361-2364. http://dx.doi.org/10.1126/science.1064603 PMid:11743204   Omasa T (2002). Gene amplification and its application in cell and tissue engineering. J. Biosci. Bioeng. 94: 600-605. PMid:16233356   Paçó-Larson ML (1976). Análise Quantitativa do Conteúdo de DNA da Glândula Salivar de Bradysia hygida. Master's thesis, Faculdade de Medicina de Ribeirão Preto, USP, Ribeirão Preto.   Paçó-Larson ML, Coelho PSC, Yokosawa J and Lara FJS (2002). Uso de Métodos de Eletroforese Bi-dimensional Neutro-alcalina e Neutro-neutra para o Mapeamento Físico de Origens de Replição em Pufes de DNA. In: Hibridação de Ácidos Nucléicos (Lara FJS, ed.). 2ª ed. Holos, Ribeirão Preto, 122-133.   Polinarski CA, Silva JL da C, Mikami LR and Fernandez MA (2005). Nuclear halo from Bradysia hygida (Diptera:Sciaridae) salivary gland polytene cells. Braz. Arch. Biol. Technol. 48: 351-357. http://dx.doi.org/10.1590/S1516-89132005000300004   Rizzo E (1980). Descrição dos Pufes Cromossômicos da Glândula Salivar de Bradysia hygida (Díptera, Sciaridade). Master's thesis, Faculdade de Medicina de Ribeirão Preto, USP, Ribeirão Preto.   Sauaia H (1971). Cromossomas Politênicos de Bradysia hygida. Inibição do Desenvolvimento dos Puffs de DNA pela Hidroxiluréia. Doctoral thesis, Faculdade de Medicina de Ribeirão Preto, USP, Ribeirão Preto.   Sauaia H and Alves MAR (1968). A description of a new species of Bradysia (Diptera, Sciaridae). Pap. Avulsos Zool. 22: 85-88.   Schurra C and Bensimon A (2009). Combing Genomic DNA for Structural and Functional Studies. In: The Nucleus (Ronald Hancock, ed.). Vol. 2. Humana Press, New York, 71-90.   Silva JLC and Fernandez MA (2000). Feulgen stain in heterogeneous egg samples from non-synchronized Bradysia hygida (Diptera:Sciaridae) laboratory culture. Cytologia 65: 167-171. http://dx.doi.org/10.1508/cytologia.65.167   Souza JF (1999). Um Homólogo do Gene Dhr 38 é Expresso em Bradysia hygida (Díptera, Sciaridae) Durante o Final do Quarto Estádio Larval. Master's thesis, Faculdade de Medicina de Ribeirão Preto, USP, Ribeirão Preto.   Toledo F, Baron B, Fernandez MA, Lachages AM, et al. (1998). oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques. Nucleic Acids Res. 26: 2313-2321. http://dx.doi.org/10.1093/nar/26.10.2313 PMid:9580680 PMCid:147574   Yokosawa J, Soares MA, Dijkwel PA, Stocker AJ, et al. (1999). DNA replication during amplification of the C3 puff of Rhynchosciara americana initiates at multiple sites in a 6 kb region. Chromosoma 108: 291-301. http://dx.doi.org/10.1007/s004120050380 PMid:10525965