Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Sogayar MC

PROVIDER: S-EPMC442158 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

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

Sogayar Mari Cleide MC Camargo Anamaria A AA Bettoni Fabiana F Carraro Dirce Maria DM Pires Lilian C LC Parmigiani Raphael B RB Ferreira Elisa N EN de Sá Moreira Eloísa E do Rosário D de O Latorre Maria M Simpson Andrew J G AJ Cruz Luciana Oliveira LO Degaki Theri Leica TL Festa Fernanda F Massirer Katlin B KB Sogayar Mari C MC Filho Fernando Camargo FC Camargo Luiz Paulo LP Cunha Marco A V MA De Souza Sandro J SJ Faria Milton M Giuliatti Silvana S Kopp Leonardo L de Oliveira Paulo S L PS Paiva Paulo B PB Pereira Anderson A AA Pinheiro Daniel G DG Puga Renato D RD S de Souza Jorge Estefano JE Albuquerque Dulcineia M DM Andrade Luís E C LE Baia Gilson S GS Briones Marcelo R S MR Cavaleiro-Luna Ana M S AM Cerutti Janete M JM Costa Fernando F FF Costanzi-Strauss Eugenia E Espreafico Enilza M EM Ferrasi Adriana C AC Ferro Emer S ES Fortes Maria A H Z MA Furchi Joelma R F JR Giannella-Neto Daniel D Goldman Gustavo H GH Goldman Maria H S MH Gruber Arthur A Guimarães Gustavo S GS Hackel Christine C Henrique-Silva Flavio F Kimura Edna T ET Leoni Suzana G SG Macedo Cláudia C Malnic Bettina B Manzini B Carina V CV Marie Suely K N SK Martinez-Rossi Nilce M NM Menossi Marcelo M Miracca Elisabete C EC Nagai Maria A MA Nobrega Francisco G FG Nobrega Marina P MP Oba-Shinjo Sueli M SM Oliveira Márika K MK Orabona Guilherme M GM Otsuka Audrey Y AY Paço-Larson Maria L ML Paixão Beatriz M C BM Pandolfi Jose R C JR Pardini Maria I M C MI Passos Bueno Maria R MR Passos Geraldo A S GA Pesquero Joao B JB Pessoa Juliana G JG Rahal Paula P Rainho Cláudia A CA Reis Caroline P CP Ricca Tatiana I TI Rodrigues Vanderlei V Rogatto Silvia R SR Romano Camila M CM Romeiro Janaína G JG Rossi Antonio A Sá Renata G RG Sales Magaly M MM Sant'Anna Simone C SC Santarosa Patrícia L PL Segato Fernando F Silva Wilson A WA Silva Ismael D C G ID Silva Neusa P NP Soares-Costa Andrea A Sonati Maria F MF Strauss Bryan E BE Tajara Eloiza H EH Valentini Sandro R SR Villanova Fabiola E FE Ward Laura S LS Zanette Dalila L DL

Genome research 20040614 7

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 ...[more]

PMID: 15197164

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Project description:Global food production needs to be increased by 60-110% between 2005 and 2050 to meet growing food and feed demand. Intensification and/or expansion of agriculture are the two main options available to meet the growing crop demands. Land conversion to expand cultivated land increases GHG emissions and impacts biodiversity and ecosystem services. Closing yield gaps to attain potential yields may be a viable option to increase the global crop production. Traditional methods of agricultural intensification often have negative externalities. Therefore, there is a need to explore location-specific methods of sustainable agricultural intensification. We identified regions where the achievement of potential crop calorie production on currently cultivated land will meet the present and future food demand based on scenario analyses considering population growth and changes in dietary habits. By closing yield gaps in the current irrigated and rain-fed cultivated land, about 24% and 80% more crop calories can respectively be produced compared to 2000. Most countries will reach food self-sufficiency or improve their current food self-sufficiency levels if potential crop production levels are achieved. As a novel approach, we defined specific input and agricultural management strategies required to achieve the potential production by overcoming biophysical and socioeconomic constraints causing yield gaps. The management strategies include: fertilizers, pesticides, advanced soil management, land improvement, management strategies coping with weather induced yield variability, and improving market accessibility. Finally, we estimated the required fertilizers (N, P2O5, and K2O) to attain the potential yields. Globally, N-fertilizer application needs to increase by 45-73%, P2O5-fertilizer by 22-46%, and K2O-fertilizer by 2-3 times compared to the year 2010 to attain potential crop production. The sustainability of such agricultural intensification largely depends on the way management strategies for closing yield gaps are chosen and implemented.

Dataset Information

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

Publications

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

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