Fermentation Microbiology and Biotechnology, Fourth Edition

E. M. T. El-Mansi, Jens Nielsen, David Mousdale, Ross P. Carlson, E. M. T. El-Mansi, Jens Nielsen, David Mousdale, Ross P. Carlson

• Publisher: CRC Press
• Year: 2018
• ISBN:
  9780429015953
• Edition: 4
• Topic: Medicine
• Subtopic: Pharmacology

Fermentation Microbiology and Biotechnology, 4th Edition explores and illustrates the broad array of metabolic pathways employed for the production of primary and secondary metabolites, as well as biopharmaceuticals. This updated and expanded edition addresses the whole spectrum of fermentation biotechnology, from fermentation kinetics and dynamics to protein and co-factor engineering. It also sheds light on the new strategies employed by industrialist for increasing tolerance and endurance of microorganisms to the accumulation of toxic wastes in microbial-cell factories. The new edition builds upon the fine pedigree of its earlier predecessors and extends the spectrum of the book to reflect the multidisciplinary and buoyant nature of this subject area.

Key Features

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• Covers the whole spectrum of the field from fermentation kinetics to control of fermentation and protein engineering.

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• Includes case studies specifically designed to illustrate industrial applications and current state-of-the-art technologies.

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• Presents the contributions of eminent international academics and industrial experts.

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• Offers new chapters addressing:

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  • The prospects and the role of bio-fuels refineries,

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  • Control of metabolic efflux to product formation in microbial-cell factories and

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  • Improving tolerance of microorganisms to toxic byproduct accumulation in the fermentation vessel.

Section V

Fermentation Microbiology and Biotechnology

Tools, Monitoring, and Control of Fermentation Processes

14Functional Genomics

Current Trends, Tools, and Future Prospects in the Fermentation and Pharmaceutical Industries

Surendra K. Chikara , Toral Joshi , and Mahmoud M. A. Moustafa

CONTENTS

14.1Introduction

14.2Microarrays: Role in Functional Genomics

14.2.1Applications of Microarray to the Study of Genome Structure

14.2.2Applications of Microarray to the Study of Gene Expression and Profiling

14.3Microarray Quality Control

14.3.1Affymetrix

14.3.2NimbleGen MS 200 Microarray and Scanner

14.3.3Agilent DNA Microarray and Scanner

14.4Microarray Applications

14.4.1Gene Expression Profiling

14.4.2CGH

14.4.3Detection of SNP

14.4.4Chromatin Immunoprecipitation

14.4.5Transcriptome Analysis

14.4.6Application of DNA Microarray in the Pharmaceutical Industries

14.4.7Microarray Future Prospects

14.5Next-Generation DNA Sequencing

14.5.1First-Generation Sequencers

14.5.1.1Sanger’ s Sequencing Method

14.5.2Second-Generation Sequencers

14.5.2.1Roche GS FLX (Pyrosequencing)

14.5.2.2Illumina Genome Analyzer

14.5.2.3Applied Biosystems SOLiD™ 4 System

14.5.2.4Ion Personal Genome Machine Sequencer

14.5.3Third-Generation Sequencers

14.5.3.1Helicos

14.5.3.2Pacific Biosciences

14.5.3.3VisiGen

14.5.3.4BioNanomatrix

14.6Comparison of the Sequencing Techniques

14.7Discovery of SNP

14.8Transcriptome Analysis

14.8.1Gene Expression: Sequencing the Transcriptome

14.8.2Applications of Transcriptomics Analysis

14.8.3Small RNA Analysis

14.8.3.1Techniques for RNA Analysis

14.8.3.2Discovering NC-RNA

14.9Epigenetics

14.10Chromatin Immunoprecipitation, Chip-Seq Technique

14.11Metagenomics

14.12Genome Analysis

14.12.1Whole-Genome Sequencing

14.12.2De Novo Assembly

14.12.3Annotation of Genome Assembly

14.12.4Genome Mapping of Next Generation Sequencing Data

14.12.5Targeting Resequencing

References

“ When you are face to face with a difficulty, you are up against a discovery.”

Lord Kelvin

14.1Introduction

Functional genomics is a discipline and enterprise that exploits the vast wealth of data produced by genome sequencing projects. A key feature of functional genomics is their genome-wide approach, which invariably utilizes high-throughput technologies and relies on sophisticated analytical tools.

Understanding the genome sequence and its relevance for various applications is therefore central to the development and production of new biopharmaceuticals. Current advances in bioinformatics and high-throughput technologies such as microarray analysis have revolutionized our perception and understanding of the molecular mechanisms underlying normal and abnormal (dysfunctional) biological functions. Microarray studies and other genomic techniques are also inspiring the discovery of new targets for disease treatment and control, thus aiding drug development immunotherapeutics, and gene therapy (Zhao et al., 2011; Beitelshees et al., 2017). Current trends and challenges in the field include

• Exploitation of new innovations in nanotechnology and microfluidics for the development of low-cost technologies for sequencing and genotyping as well as for the identification and confirmation of functional elements that do not encode protein (e.g., introns, promoters, telomeres , and regulatory and structural features);

• Telomere : A telomere is a region of repetitive DNA located at the end of chromosomes to protect them from degradation.

• In vivo , real-time monitoring of gene expression and functional modification of gene products in all relevant cell types using large-scale mutagenesis, small-molecule inhibitors, and knockdown approaches;

• Identifying genes and pathways that have thus far proved difficult to study biochemically and deciphering cellular phenomena related to the networking of metabolic pathways;

• Monitoring of membrane proteins, modified proteins, and regulatory proteins of low concentrations; and

• Correlation of genetic variation to human health and disease using haplotype and comprehensive variation information to provide large databases that are amenable to statistical methods.

The challenges faced in the human genome project and the need for high-throughput capacity have led to the development of next-generation sequencing technology (NGST), which has dramatically accelerated biological and biomedical research because it renders the comprehensive analysis of genomes, transcriptomes, and interactomes inexpensive, which should be helpful toward achieving the goal of personalized medicine and designer crops (Horner et al., 2010). Of pharmaceutical relevance is sequencing of multiple strains of pathogens to monitor drug resistance and pathogenicity. Resequencing of selected regions to search for human variation in population and for tumor profiling to guide cancer therapies is also of great interest. In this chapter, we review current trends and methodologies in functional genomics and assess their relevance, strengths, and weaknesses.

Completion of the human genome project signaled a new beginning for modern biology, one in which most biological and biomedical research will be conducted in a sequence-based fashion. It is now possible to deconstruct the genomic sequences of multiple organisms with the view to unravel the interrelationship between the physiology or the pathogenicity of a given organism and its genome constituent parts (genes) (Cook Degan, 1991; 56Johnson, 1992; Greenhalgh, 2005; Evans, 2010). The deconstruction of the genome to assign biological functions to genes, groups of genes, and particular gene-gene or gene-protein interactions is well underway and documented in MEDLINE (Patterson and Gabriel, 2009). These functions may be directly or indirectly the result of a gene’ s transcription (Mamanova et al., 2010). A computationally intensive branch of functional genomics has emerged as a result of the practical implementation of technologies to assess gene expression of thousands of genes at a time. The ability to comprehensively measure gene expression affords an excellent opportunity to further expand a target-oriented approach as opposed to the conventional hypothetical-based approach.

The need to generate, analyze, and integrate large and complex sets of molecular data has led to the development of whole-genome approaches, such as microarray technology, to expedite the process of translating molecular data into biologically meaningful information (Miyake and Matsumoto, 2005). The comparison of the strengths and weakness of next-generation sequencing and microarray techniques is illustrated in Table 14.1 (Asmann et al., 2008).

TABLE 14.1 The Strength and Weaknesses of NGS and Microarray Techniques

Source: I...