Browsing by Author "Kotchoni, Simeon O."

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    Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases
    (Scientific Research Publishing, 2013-04) Jimenez-Lopez, Jose C.; Gachomo, Emma W.; Sharma, Sweta; Kotchoni, Simeon O.
    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 whole-genome characterization of a wide range of organisms. In the post-genomic era, new technologies have revealed an outbreak of prerequisite genomic sequences and supporting data to understand genome wide functional regulation of gene expression and metabolic pathways reconstruction. However, 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 wide range of species with 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, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis. We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks. We also discuss the importance of establishing a unified nomenclature system through a functional and structural genomics approach.
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    A simple and efficient seed-based approach to induce callus production from B73 maize genotype
    (Scientific Research Publishing, 2012-10) Kotchoni, Simeon O.; Noumavo, Pacôme A.; Adjanohoun, Adolphe; Russo, Daniel P.; Dell’Angelo, John; W. Gachomo, Emma; Baba-Moussa, Lamine
    The wild 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 known callus inducible media have been unsatisfactory. Here we developed and described an efficient protocol for callus induction from B73 maize seedlings. The protocol is based on well known callus inducible media CM4C where we have sequentially subtracted some chemical compounds and added some new compounds mediating cell proliferations. This newly described protocol was able to induce callus production in a wide range of crop species including rice and soybean. We found that cell proliferation factors, NAA (auxin analog) and 2,4 D (auxin influx carrier) were not only very crucial but required for positive B73 maize callus induction. The absence of one or the other will lead to the failure of B73 maize callus production. The well known CM4C callus induction composition lacks NAA. Our findings will advance genetic studies of maize mutants generated from B73 genotype background.