Microarrays : Current Technology, Innovations and Applications.

Intro -- Contents -- Contributors -- Preface -- 1: Microarrays for Microbial Community Analysis at a Glance -- Introduction -- Microarrays for microbial community analysis at a glance -- Key issues for microarray analysis -- Applications of microarrays for profiling microbial communities -- Advantages and limitations of microarrays for microbial community analysis -- Conclusions and future directions -- 2: Software Tools for the Selection of Oligonucleotide Probes for Microarrays -- Introduction -- General criteria for probe design -- Probe design algorithms for microbial DNA microarrays -- Discussion/challenges and future trends -- Conclusions -- Online resources for oligonucleotide probe design programs and databases -- 3: Development and Evaluation of Functional Gene Arrays with GeoChip as an Example -- Introduction -- FGA development -- FGA construction and experimental evaluation -- Core functional gene families covered by GeoChips -- Challenges and future directions -- 4: Microarray Data Analysis -- Introduction -- Microarray image process -- Microarray data preprocessing -- Statistical analysis -- Conclusions/challenges and future trends -- 5: Microarray of 16S rRNA Gene Probes for Quantifying Population Differences Across Microbiome Samples -- Introduction -- PhyloChip G3 data analysis -- Discussion and future trends -- Conclusions -- 6: GeoChip Applications in Bioremediation Studies -- Introduction -- Functional gene arrays for bioremediation studies -- GeoChip design -- Application of GeoChip to bioremediation studies -- Challenges for microarray analysis -- Future trends -- Conclusions -- 7: GeoChip Applications for Analysing Soil and Water Microbial Communities in Oil-contaminated Sites -- Introduction -- Overall functional gene patterns in response to oil contamination.

Changes of key genes involved in hydrocarbon degradation and biogeochemical cycling processes -- Shifts of functional genes during treatment of oil-contaminated soil/water -- Relationship between microbial functional genes and environmental variables -- Challenges and future trends -- Conclusions -- 8: GeoChip Analysis of Soil Microbial Community Responses to Global Change -- Introduction -- Effects of elevated atmospheric CO2 concentrations on soil microbial communities -- Effects of rising temperature on soil microbial communities -- Effects of rising O3 on soil microbial communities -- Challenges and future trends -- Conclusion -- 9: Soil Functional Gene Microarrays and Applications in Plant-Microbe Interactions -- Introduction -- Development of soil functional gene arrays -- Other methods for metatranscriptomic profiling of soil microbial communities -- Examples of arrays and other methods for transcriptional profiling of plants and soil microbial communities -- Challenges and future directions -- 10: Bioleaching Microarrays for Profiling Microbial Communities in Acid Mine Drainage and Bioleaching Ecosystems -- Introduction -- Bioleaching microarrays -- Applications of microarray technologies in AMD and bioleaching systems -- Challenges and future directions -- Conclusions -- 11: Applications of Phylogenetic Microarrays to Profiling of Human Microbiomes -- Introduction -- Current phylogenetic microarrays -- Phylogenetic microarray optimization -- Phylogenetic microarray applications -- Unique analyses enabled by phylogenetic microarrays -- Future trends and outlook -- 12: Microbial Diagnostic Microarrays for Detection and Typing of Waterborne Pathogens -- Introduction -- Waterborne pathogen detection MDMs -- MDMs with potential for waterborne pathogen detection -- Waterborne pathogen typing MDMs -- Challenges and future trends -- Conclusions.

13: Broad-spectrum Viral and Bacterial Pathogen Detection by Microarrays -- Introduction -- Description of methods -- Overview of pathogen detection microarrays -- Discussion -- Conclusions -- Current Books of Interest -- Index -- Contents -- Contributors -- Preface -- 1: Microarrays for Microbial Community Analysis at a Glance -- Introduction -- Microarrays for microbial community analysis at a glance -- Key issues for microarray analysis -- Applications of microarrays for profiling microbial communities -- Advantages and limitations of microarrays for microbial community analysis -- Conclusions and future directions -- 2: Software Tools for the Selection of Oligonucleotide Probes for Microarrays -- Introduction -- General criteria for probe design -- Probe design algorithms for microbial DNA microarrays -- Discussion/challenges and future trends -- Conclusions -- Online resources for oligonucleotide probe design programs and databases -- 3: Development and Evaluation of Functional Gene Arrays with GeoChip as an Example -- Introduction -- FGA development -- FGA construction and experimental evaluation -- Core functional gene families covered by GeoChips -- Challenges and future directions -- 4: Microarray Data Analysis -- Introduction -- Microarray image process -- Microarray data preprocessing -- Statistical analysis -- Conclusions/challenges and future trends -- Microarray of 16S rRNA Gene Probes for Quantifying Population Differences Across Microbiome Samples -- Introduction -- PhyloChip G3 data analysis -- Discussion and future trends -- Conclusions -- 6: GeoChip Applications in Bioremediation Studies -- Introduction -- Functional gene arrays for bioremediation studies -- GeoChip design -- Application of GeoChip to bioremediation studies -- Challenges for microarray analysis -- Future trends -- Conclusions.

7: GeoChip Applications for Analysing Soil and Water Microbial Communities in Oil-contaminated Sites -- Introduction -- Overall functional gene patterns in response to oil contamination -- Changes of key genes involved in hydrocarbon degradation and biogeochemical cycling processes -- Shifts of functional genes during treatment of oil-contaminated soil/water -- Relationship between microbial functional genes and environmental variables -- Challenges and future trends -- Conclusions -- 8: GeoChip Analysis of Soil Microbial Community Responses to Global Change -- Introduction -- Effects of elevated atmospheric CO2 concentrations on soil microbial communities -- Effects of rising temperature on soil microbial communities -- Effects of rising O3 on soil microbial communities -- Challenges and future trends -- Conclusion -- 9: Soil Functional Gene Microarrays and Applications in Plant-Microbe Interactions -- Introduction -- Development of soil functional gene arrays -- Other methods for metatranscriptomic profiling of soil microbial communities -- Examples of arrays and other methods for transcriptional profiling of plants and soil microbial communities -- Challenges and future directions -- Bioleaching Microarrays for Profiling Microbial Communities in Acid Mine Drainage and Bioleaching Ec -- Introduction -- Bioleaching microarrays -- Applications of microarray technologies in AMD and bioleaching systems -- Challenges and future directions -- Conclusions -- 11: Applications of Phylogenetic Microarrays to Profiling of Human Microbiomes -- Introduction -- Current phylogenetic microarrays -- Phylogenetic microarray optimization -- Phylogenetic microarray applications -- Unique analyses enabled by phylogenetic microarrays -- Future trends and outlook -- 12: Microbial Diagnostic Microarrays for Detection and Typing of Waterborne Pathogens -- Introduction.

Waterborne pathogen detection MDMs -- MDMs with potential for waterborne pathogen detection -- Waterborne pathogen typing MDMs -- Challenges and future trends -- Conclusions -- 13: Broad-spectrum Viral and Bacterial Pathogen Detection by Microarrays -- Introduction -- Description of methods -- Overview of pathogen detection microarrays -- Discussion -- Conclusions -- Current Books of Interest -- Index.

Written by expert authors this book is focused on current microarray technologies and their applications in environmental microbiology. In the first chapter microarray technologies and applications are briefly introduced and in following chapters microarray probe design, development and evaluation, and data analysis are described in detail. In later chapters, more attention is paid to phylogenetic arrays (e.g., PhyloChip) and functional gene arrays (e.g., GeoChip). These generic tools for analyzing microbial communities from disparate environments, ecosystems, and habitats including soil, water, sediment, animals and humans, are described in detail with examples of specific applications. Also included are microarrays for analyzing microbial communities from specific environments, such as soil, bioleaching ecosystems, and human microbiomes, and microarrays for detecting specific microorganisms (e.g., pathogens) in the environment. The authors also discuss the advantages and limitations of microarray technologies compared to high throughput sequencing technologies. This book is a valuable and useful source of information about microarrays for microbial community analysis and is recommended for anyone working on microbial communities, biofilms or environmental microbiology.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.