Avaliação do sistema reprodutivo em acessos de bacabinha (Oenocarpus mapora Karsten.) em Belém-PA.

A bacabinha é uma fruteira nativa da Amazônia com potencial econômico para frutos, sendo utilizados na obtenção de uma bebida conhecida por "bacaba ", mas tem sido pouco estudada. Neste trabalho, avaliou-se o sistema reprodutivo de acessos dessa palmeira existentes na Coleção de Germoplasma da Embrapa Amazônia Oriental, em Belém-PA. Foram escolhidos ao acaso, oito acessos procedentes de Abaetetuba-PA e duas plantas por acesso. Em cada planta foi marcada uma espata próxima a maturação para a aplicação de cinco testes reprodutivos, sendo destinadas três ráquilas para cada teste. As características avaliadas foram: flores fecundadas (FF), flores caídas (FC), flores abortadas (FA) e frutos colhidos (FRC), expressas em percentagens. As análises estatísticas foram feitas com base no modelo matemático inteiramente casualizado, em esquemafatorial8 x 5 com seis repetições. Os acessos, os testes reprodutivos e a interação acessos x testes diferiram entre si para todas as características avaliadas (P ::;0,01). Um acesso exibiu a maior média para flores caídas, enquanto outros três alcançaram as maiores médias para flores fecundadas e abortadas. Para a percentagem de frutos colhidos, quatro acessos se destacaram dos demais. Na agamospermia e na autopolinização natural foram registradas as maiores percentagens de flores caídas. O contrário ocorreu nos teste de polinização cruzada e aberta que tiveram as maiores médias de flores fecundadas e abortadas, e também de frutos colhidos. Com base nesses resultados pode-se concluir que todos os acessos são predominantemente alógamos

A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF

<p>Abstract</p> <p>Background</p> <p>New strategies for high-throughput sequencing are constantly appearing, leading to a great increase in the number of completely sequenced genomes. Unfortunately, computational genome annotation is out of step with this progress. Thus, the accurate annotation of these genomes has become a bottleneck of knowledge acquisition.</p> <p>Results</p> <p>We exploited a proteogenomic approach to improve conventional genome annotation by integrating proteomic data with genomic information. Using <it>Shigella flexneri </it>2a as a model, we identified total 823 proteins, including 187 hypothetical proteins. Among them, three annotated ORFs were extended upstream through comprehensive analysis against an in-house N-terminal extension database. Two genes, which could not be translated to their full length because of stop codon 'mutations' induced by genome sequencing errors, were revised and annotated as fully functional genes. Above all, seven new ORFs were discovered, which were not predicted in <it>S. flexneri </it>2a str.301 by any other annotation approaches. The transcripts of four novel ORFs were confirmed by RT-PCR assay. Additionally, most of these novel ORFs were overlapping genes, some even nested within the coding region of other known genes.</p> <p>Conclusions</p> <p>Our findings demonstrate that current <it>Shigella </it>genome annotation methods are not perfect and need to be improved. Apart from the validation of predicted genes at the protein level, the additional features of proteogenomic tools include revision of annotation errors and discovery of novel ORFs. The complementary dataset could provide more targets for those interested in <it>Shigella </it>to perform functional studies.</p

Accelerating String Set Matching in FPGA Hardware for Bioinformatics Research

<p>Abstract</p> <p>Background</p> <p>This paper describes techniques for accelerating the performance of the string set matching problem with particular emphasis on applications in computational proteomics. The process of matching peptide sequences against a genome translated in six reading frames is part of a proteogenomic mapping pipeline that is used as a case-study. The Aho-Corasick algorithm is adapted for execution in field programmable gate array (FPGA) devices in a manner that optimizes space and performance. In this approach, the traditional Aho-Corasick finite state machine (FSM) is split into smaller FSMs, operating in parallel, each of which matches up to 20 peptides in the input translated genome. Each of the smaller FSMs is further divided into five simpler FSMs such that each simple FSM operates on a single bit position in the input (five bits are sufficient for representing all amino acids and special symbols in protein sequences).</p> <p>Results</p> <p>This bit-split organization of the Aho-Corasick implementation enables efficient utilization of the limited random access memory (RAM) resources available in typical FPGAs. The use of on-chip RAM as opposed to FPGA logic resources for FSM implementation also enables rapid reconfiguration of the FPGA without the place and routing delays associated with complex digital designs.</p> <p>Conclusion</p> <p>Experimental results show storage efficiencies of over 80% for several data sets. Furthermore, the FPGA implementation executing at 100 MHz is nearly 20 times faster than an implementation of the traditional Aho-Corasick algorithm executing on a 2.67 GHz workstation.</p