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Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

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American Journal of Molecular Biology 2013年第2期3卷 115-130页

作者： Jose C. Jimenez-Lopez emma w. gachomo Sw.ta Sharma Simeon O. Kotchoni Department of Biochemistry Cell and Molecular Biology of Plants Estacion Experimental del Zaidin High Council for Scientific Research (CSIC) Granada Spain Department of Biology Rutgers University Camden USA

Genomics has become a ground-breaking field in all areas of the life sciences. The advanced genomics and the development of high-throughput techniques have lately provided insight into w.ole-genome characterization of a w.de range of organisms. In the post-genomic era, new.technologies have revealed an outbreak of prerequisite genomic sequences and supporting data to understand genome w.de functional regulation of gene expression and metabolic pathw.ys reconstruction. How.ver, the availability of this plethora of genomic data presents a significant challenge for storage, analyses and data management. Analysis of this mega-data requires the development and application of novel bioinformatics tools that must include unified functional annotation, structural search, and comprehensive analysis and identification of new.genes in a w.de range of species w.th fully sequenced genomes. In addition, generation of systematically and syntactically unambiguous nomenclature systems for genomic data across species is a crucial task. Such systems are necessary for adequate handling genetic information in the context of comparative functional genomics. In this paper, w. provide an overview.of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis. w. focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a w.de range of gene banks. w. also discuss the importance of establishing a unified nomenclature system through a functional and structural genomics approach.

关键词： Databases Computational Biology Genomics Proteomics Next-Generation Sequencing

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A simple and efficient seed-based approach to induce callus production from B73 maize genotype

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American Journal of Molecular Biology 2012年第4期2卷 380-385页

作者： Simeon O.Kotchoni Pacome A.Noumavo Adolphe Adjanohoun Daniel P.Russo John Dell’Angelo emma w.gachomo Lamine Baba-Moussa Department of Biology RutgersThe State University of New JerseyCamdenUSA Center for Computational and Integrative Biology(CCIB) The State University of New JerseyCamdenUSA Département de Biochimie et Biologie Cellulaire Universitéd’Abomey-CalaviCotonouBenin Centre de Recherches Agricoles Institut National des Recherches Agricoles du BeninAlladaBenin

The w.ld type maize genotype, B73, is not amenable for callus production and an efficient protocol for B73 maize callus induction has never been reported up-to-date. Scientific efforts in producing B73 maize callus using all know. callus inducible media have been unsatisfactory. Here w. developed and described an efficient protocol for callus induction from B73 maize seedlings. The protocol is based on w.ll know. callus inducible media CM4C w.ere w. have sequentially subtracted some chemical compounds and added some new.compounds mediating cell proliferations. This new.y described protocol w.s able to induce callus production in a w.de range of crop species including rice and soybean. w. found that cell proliferation factors, NAA (auxin analog) and 2,4 D (auxin influx carrier) w.re not only very crucial but required for positive B73 maize callus induction. The absence of one or the other w.ll lead to the failure of B73 maize callus production. The w.ll know. CM4C callus induction composition lacks NAA. Our findings w.ll advance genetic studies of maize mutants generated from B73 genotype background.

关键词： B73 Maize Genotype Soybean Callus CM4C Maize Protocol Rice NAA 2,4-D

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Effect of Different Plant Grow.h Promoting Rhizobacteria on Maize Seed Germination and Seedling Development

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American Journal of Plant Sciences 2013年第5期4卷 1013-1021页

作者： Pacome A.Noumavo Eméric Kochoni Yédéou O.Didagbé Adolphe Adjanohoun Marcellin Allagbé Rachidatou Sikirou emma w.gachomo Simeon O.Kotchoni Lamine Baba-Moussa Laboratoire de Biologie et de Typage Moléculaire en Microbiologie Département de Biochimie et de Biologie CellulaireUniversitéd’Abomey-CalaviCotonouBénin Centre de Recherches Agri-coles Sud Institut National des Recherches Agricoles du BéninAttogonBénin Laboratoire de Défense des Cultures Centre de Recherches Agricoles d’AgonkanmeyInstitut National des Re-cherches Agricoles du BéninCotonouBénin Department of Biology The State University of New JerseyCamdenUSA Center for Computational and Integrative Biology The State University of New JerseyCamdenUSA

Our study aimed at assessing the effects of 3 Plants Grow.h Promoting Rhizobacteria (PGPR) either singly or in combination on maize grow.h under laboratory and greenhouse conditions. Seeds w.re inoculated w.th single and combined solution of 108 CFU/ml of Rhizobacteria. Seeds w.re not inoculated for the control variant. The highest germination percentage w.s obtained w.th the combination of Pseudomonas fluorescens and Pseudomonas putida. This combination also recorded the best vigor index, plants circumferences number of leaves and the leaf area. The maximal heights of plants w.re observed w.th seeds treated w.th Azospirillum lipoferum w.th an increase of 37.32%. The highest rates of underground dry matter w.re recorded w.th A. lipoferum, w.th an increase of more than 56% comparative to control, w.ile the combination P. fluorescens and P. putida increased the aerial dry matter of 59.11%. Finally, the highest value of the aerial biomass w.s obtained w.th the plants treated w.th the combination of P. fluorescens and P. putida and the highest underground biomass w.s obtained w.th plants treated only w.th A. lipoferum. These results suggest that specific combinations of PGPR can be considered as efficient alternative biofertilizers to promote maize seed germination, biomass and crop yield.

关键词： Azospirillum Pseudomonas PGPR Biofertlization Maize Seeds Germination Greenhouse

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