Titlebook: Marine Metagenomics; Technological Aspect Takashi Gojobori,Tokio Wada,Katsuhiko Mineta Textbook 2019 Springer Nature Singapore Pte Ltd. 201

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Primer Design, Evaluation of Primer Universality, and Estimation of Identification Power of Amplicondies. Both forward and reverse primers need to match to annealing positions of template sequences of all subtaxa of target taxa in order to amplify target locus sequences. Although there are many existing such “universal” primer sets, the existing primer sets are not able to amplify target locus seq

Enthralling

High Coverage Expression Profiling (HiCEP) of Microbial Community Genomes in the Ocean in the ocean. High coverage expression profiling (HiCEP) is an RNA fingerprinting method able to analyze microbial metabolic responses to various environmental conditions. Although HiCEP has been applied to various types of single organisms and revealed their responses to targeted conditions, there

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The Application of DDCA to Metagenomic Analysisr more. One of the reasons is that for NGS data analysis, it is necessary to key in commands on Linux which is a less common operating system. Therefore, we have developed the digital DNA chip analysis (DDCA) system which processes NGS data to produce results similar to microarray that are familiar

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Comparison of Microscopic and PCR Amplicon and Shotgun Metagenomic Approaches Applied to Marine Diatetermined based on metagenomics has not been fully verified. Among phytoplankton, diatoms can be identified by silica cell wall morphology and enumerated using light microscopy (LM), although identification using either scanning electron microscopy (SEM) or DNA sequencing is required in some species

COM

Seasonal Dynamics of Bacterial Community Composition in Coastal Seawater at Sendai Bay, Japany in coastal areas. We examined bacterial community compositions in coastal seawater from Sendai Bay for 2 years to clarify their temporal variation in relation to physical and biological environmental factors. Sequencing of 16S rRNA gene amplicons revealed obvious annual variation and the significa

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Shotgun Metagenome Analyses: Seasonality Monitoring in Sendai Bay and Search for Red Tide Marker Seq to examine not only taxonomic structure but also functional profile based on the gene repertory. It also allows broad comparative analysis including unknown sequences without annotation. Here we first mention about overview of shotgun metagenomics for microbial community study and then introduce tw

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Distribution and Community Composition of Ammonia-Oxidizing Archaea and Bacteria in Coastal Sediment(AOA) and ammonia-oxidizing bacteria (AOB) were determined along an environmental gradient from the coastal mud to the offshore coarse sand at Sendai Bay, Japan. Sediment samples were collected in December 2011 and July 2012. The abundance of AOA ammonia monooxygenase alpha subunit gene (.) was high

onlooker

Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counomprehensive understanding of key roles played by environmental microorganisms. Generally the microorganisms inhabit a particular niche and correlate well with environmental changes. It is accepted that the read counts obtained through metagenomic analyses correlate semi-quantitatively with the rela