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1. Effect of plant growth regulators in the rooting of Pinus cuttings

Author

Andréia Henrique, Eduardo Nogueira Campinhos, Elizabeth Orika Ono, Sheila Zambello de Pinho, Aracruz Celulose S.A. Centro de Pesquisa e Tecnologia, International Paper do Brasil Ltda., and Universidade Estadual Paulista (Unesp)

Subjects
Plant growth, Multidisciplinary, Chemistry, lcsh:Biotechnology, Sowing, Vermiculite, Rice hulls, %22">Pinus , Horticulture, Cutting, Pinus caribaea, lcsh:TP248.13-248.65, Shoot, Botany, Effective treatment, Auxins, paclobutrazol
Abstract

Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2013-08-22T18:40:50Z No. of bitstreams: 1 S1516-89132006000300002.pdf: 70841 bytes, checksum: 62f2a3f4ab69dfee30b7cff44ce2e09f (MD5) Made available in DSpace on 2013-08-22T18:40:50Z (GMT). No. of bitstreams: 1 S1516-89132006000300002.pdf: 70841 bytes, checksum: 62f2a3f4ab69dfee30b7cff44ce2e09f (MD5) Previous issue date: 2006-03-01 Made available in DSpace on 2013-09-30T19:26:59Z (GMT). No. of bitstreams: 2 S1516-89132006000300002.pdf: 70841 bytes, checksum: 62f2a3f4ab69dfee30b7cff44ce2e09f (MD5) S1516-89132006000300002.pdf.txt: 29552 bytes, checksum: be02c05efaa7808d4998bbef255392b5 (MD5) Previous issue date: 2006-03-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T15:07:31Z No. of bitstreams: 2 S1516-89132006000300002.pdf: 70841 bytes, checksum: 62f2a3f4ab69dfee30b7cff44ce2e09f (MD5) S1516-89132006000300002.pdf.txt: 29552 bytes, checksum: be02c05efaa7808d4998bbef255392b5 (MD5) Made available in DSpace on 2014-05-20T15:07:31Z (GMT). No. of bitstreams: 2 S1516-89132006000300002.pdf: 70841 bytes, checksum: 62f2a3f4ab69dfee30b7cff44ce2e09f (MD5) S1516-89132006000300002.pdf.txt: 29552 bytes, checksum: be02c05efaa7808d4998bbef255392b5 (MD5) Previous issue date: 2006-03-01 O trabalho avaliou o enraizamento de estacas de Pinus caribaea var. hondurensis Morelet sob a ação de diferentes níveis de reguladores vegetais. As estacas foram feitas de brotações de 4 a 6cm de comprimento de mudas de P. caribaea var. hondurensis Morelet com corte bisel na base sendo as acículas basais eliminadas. A base das estacas foram submetidas aos tratamentos por 2 segundos com os seguintes tratamentos: 1- NAA 2000mg L-1; 2- NAA 4000mg L-1; 3- NAA 6000mg L-1; 4- NAA 2000mg L-1 + PBZ 100mg L-1; 5- NAA 4000mg L-1 + PBZ; 6- NAA 6000mg L-1 + PBZ; 7- IBA 2000mg L-1; 8- IBA 4000mg L-1; 9- IBA 6000mg L-1; 10-IBA 2000mg L-1 + PBZ; 11- IBA 4000mg L-1 + PBZ; 12- IBA 6000mg L-1 + PBZ e testemunha. Após os tratamentos as estacas foram plantadas em tubetes contendo 50% de palha de arroz carbonizada e 50% de vermiculita. As avaliações realizadas aos 60 dias após o plantio mostraram que estacas de P. caribaea tratadas com IBA levaram a maior porcentagem de estacas enraizadas que aquelas tratadas com NAA, sendo o mais efetivo, IBA a 4000mg L-1 em conjunto com 100mg L-1 de paclobutrazol. This work evaluated the rooting of Pinus caribaea var. hondurensis Morelet cuttings under the action of different levels of plant growth regulators. The cuttings consisted of 4-6 cm long shoots of P. caribaea var. hondurensis Morelet with their basal needles removed. The basal part of the cuttings were treated for 2 seconds with the following treatments: 1- NAA 2000mg L-1; 2- NAA 4000mg L-1; 3- NAA 6000mg L-1; 4- NAA 2000mg L-1 + PBZ 100mg L-1; 5- NAA 4000mg L-1 + PBZ; 6- NAA 6000mg L-1 + PBZ; 7- IBA 2000mg L-1; 8- IBA 4000mg L-1; 9- IBA 6000mg L-1; 10-IBA 2000mg L-1 + PBZ; 11- IBA 4000mg L-1 + PBZ; 12- IBA 6000mg L-1 + PBZ; and a control. After receiving the treatment, the cuttings were planted in tubes containing 50% carbonized rice hulls and 50% vermiculite. The evaluations, performed 60 days after planting, showed that P. caribaea var. hondurensis cuttings treated with IBA produced a higher percentage of rooted cuttings than those treated with NAA; the most effective treatment was IBA 4000mg L-1 plus 100mg L-1 paclobutrazol. Aracruz Celulose S.A. Centro de Pesquisa e Tecnologia International Paper do Brasil Ltda. Universidade Estadual Paulista Instituto de Biociências Departamento de Botânica Universidade Estadual Paulista Instituto de Biociências Departamento de Bioestatística Universidade Estadual Paulista Instituto de Biociências Departamento de Botânica Universidade Estadual Paulista Instituto de Biociências Departamento de Bioestatística

Published
2006

2. RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans

Author

Jean-Yves Coppée, Gaëlle Lelandais, Odile Sismeiro, Sophie Lemoine, Frédéric Devaux, Stéphane Le Crom, Rajendra Prasad, Maria Bernard, Sanjiveeni Dhamgaye, Membrane Biology Laboratory, Jawaharlal Nehru University (JNU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris], Génomique des Microorganismes (LGM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), The work presented in this paper has been supported in part by grants to R.P. from Indo-French Center for the Promotion of Advanced Scientific Research (IFC-3403-2/2006) and DST INT/SWISS/P-31/2009., Institut de biologie de l'ENS Paris (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Institut Pasteur [Paris] (IP), BMC, Ed., Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Candida albicans, beta-Glucans, lcsh:QH426-470, lcsh:Biotechnology, Repressor, RNA-Seq, Drug resistance, Multidrug resistance, Fungal Proteins, 03 medical and health sciences, Drug Resistance, Fungal, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Transcriptional regulation, Genetics, CZF1, Gene, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, Sequence Analysis, RNA, Gene Expression Profiling, biology.organism_classification, Yeast, 3. Good health, Multiple drug resistance, Gene expression profiling, lcsh:Genetics, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA-seq, Biotechnology, Transcription Factors, Research Article
Abstract

Background Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart. Results RNA-seq unveiled differential expression of 228 genes including a) genes previously identified as involved in CDR, b) genes not previously associated to the CDR phenotype, and c) novel transcripts whose function as a gene is uncharacterized. In particular, we show for the first time that CDR acquisition is correlated with an overexpression of the transcription factor encoding gene CZF1. CZF1 null mutants were susceptible to many drugs, independently of known multidrug resistance mechanisms. We show that CZF1 acts as a repressor of β-glucan synthesis, thus negatively regulating cell wall integrity. Finally, our RNA-seq data allowed us to identify a new transcribed region, upstream of the TAC1 gene, which encodes the major CDR transcriptional regulator. Conclusion Our results open new perspectives of the role of Czf1 and of our understanding of the transcriptional and post-transcriptional mechanisms that lead to the acquisition of drug resistance in C. albicans, with potential for future improvements of therapeutic strategies.

Published
2012

3. BMC Genomics

Author

Grace C. Davey, Penelope K. Lindeque, Richard Reinhardt, Christophe Klopp, Pascal Favrel, Dario Moraga, Pierre Boudry, Sylvie Lapegue, Patrick Prunet, Arnaud Huvet, Julien de Lorgeril, Jeanne Moal, Viviane Boulo, Elodie Fleury, Christophe Lelong, Christopher Sauvage, Patrick Wincker, François Moreews, Michel Mathieu, Frédérick Gavory, Arnaud Tanguy, Caroline Fabioux, Charlotte Corporeau, Evelyne Bachère, Jenny P. Shaw, Yannick Gueguen, Laboratoire Environnement Ressources Morbihan Pays de Loire (LERMPL), LITTORAL (LITTORAL), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiologie et Ecophysiologie des Mollusques Marins (PE2M), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ecosystèmes lagunaires : organisation biologique et fonctionnement (ECOLAG), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Brest (UBO), Plymouth Marine Laboratory (PML), Max-Planck-Institut für Molekulare Genetik (MPIMG), Max-Planck-Gesellschaft, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA), Génétique fonctionnelle, agronomie et santé [IFR 140] (GFAS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Diagnostics Centre (NDC), National University of Ireland [Galway] (NUI Galway), Laboratoire de Génétique et Pathologie (LGP), Amélioration génétique, du contrôle des performances et de la santé des mollusques marins (AGSAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biological systems and models, bioinformatics and sequences (SYMBIOSE), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Laboratoire de Physiologie des Invertébrés (LPI), Physiologie Fonctionnelle des Organismes Marins (PFOM), The research presented in this paper was performed within the framework of several research projects funded by: Genoscope (11/AP2006-2007), Marine Genomics Network of Excellence (GOCE-CT-2004-505403), the European project 'Aquafirst' (513692) in the Sixth Framework Program, ANR 'CgPhysiogène' (ANR-06-GANI-0009) and 'Gametogenes' (ANR-08-GENM-041), ANR-06-GANI-0009,CgPhysiogene,Bases moléculaires des fonctions physiologiques de l'huître Crassostrea gigas : interactions hôte/pathogène/milieu(2006), ANR-08-GENM-0041,Gametogenes,Génomiques de la gamétogénèse chez l'huître creuse Crassostrea gigas(2008), Laboratoire Laboratoire Environnement Ressources Morbihan Pays de Loire (LER/MPL), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS), Adaptation et Biologie des Invertébrés en Conditions Extrêmes (ABICE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory, Institut National de la Recherche Agronomique (INRA)-IFR140, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Ecole Nationale Supérieure Agronomique de Rennes-Institut National de la Recherche Agronomique (INRA), Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Laboratoire de Physiologie des Invertébrés [Plouzané] (LPI), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Oyster, genome annotation, génomique fonctionnelle, computer.software_genre, Genome, User-Computer Interface, single nucleotide polymorphisms, Databases, Genetic, crassostrea gigas, structure du génome, Expressed Sequence Tags, base de données, 0303 health sciences, Expressed sequence tag, biology, Database, 04 agricultural and veterinary sciences, Genomics, crustacea, Pacific oyster, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], energy-balance, factor-beta superfamily, DNA microarray, expression des gènes, Biotechnology, lcsh:QH426-470, Sequence analysis, lcsh:Biotechnology, kappa-b, Polymorphism, Single Nucleotide, génomique, 03 medical and health sciences, biology.animal, lcsh:TP248.13-248.65, Genetics, summer mortality, Animals, Crassostrea, 030304 developmental biology, Gene Library, Whole genome sequencing, [SDV.GEN]Life Sciences [q-bio]/Genetics, huître, cell-development, génome, Gene Expression Profiling, linkage maps, Sequence Analysis, DNA, biology.organism_classification, lcsh:Genetics, coquillage, 040102 fisheries, 0401 agriculture, forestry, and fisheries, identification, marine genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Microsatellite Repeats
Abstract

Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

Published
2009