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Cis/Transgene Optimization

Systematic Discovery of Novel Gene Expression Elements Using Bioinformatics and Computational Biology Approaches

  • Book
  • © 2018

Overview

Authors:
  1. Saeid Kadkhodaei

    1. Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, Iran

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  2. Farahnaz Sadat Golestan Hashemi

    1. Plant Genetics, AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium

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  3. Morvarid Akhavan Rezaei

    1. Tropical Infectious Diseases Research and Education Centre (TIDREC), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia

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  4. Sahar Abbasiliasi

    1. Halal Products Research Institute, Universiti Putra Malaysia, Seri Kembangan, Malaysia

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  5. Joo Shun Tan

    1. Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, George Town, Penang, Malaysia

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  6. Hamid Rajabi Memari

    1. SynHiTech, Thornhill, Canada

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  7. Faruku Bande

    1. Department of Veterinary Services, Ministry of Animal Health and Fisheries Development, Usman Faruk Secretariat, Sokoto, Sokoto, Nigeria

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  8. Ali Baradaran

    1. Mater Research, Translational Research Institute, Woolloongabba, Australia

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  9. Mahdi Moradpour

    1. Institute of Plantation Studies, Universiti Putra Malaysia, Seri Kembangan, Malaysia

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  10. Arbakariya B, Ariff

    1. Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Seri Kembangan, Malaysia

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  • Explains how in silico tools could be efficiently used in gene expression studies
  • Broadens the understanding of bioinformatics and computational biology applications
  • Offers step-by-step procedures for systematic discovery of key gene expression elements

Part of the book series: SpringerBriefs in Systems Biology (BRIEFSBIOSYS)

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Table of contents (5 chapters)

  1. Front Matter

    Pages i-xix
    Download chapter PDF

  2. Introduction

    • Saeid Kadkhodaei, Farahnaz Sadat Golestan Hashemi, Morvarid Akhavan Rezaei, Sahar Abbasiliasi, Joo Shun Tan, Hamid Rajabi Memari et al.
    Pages 1-7

  3. Systematic Strategies

    • Saeid Kadkhodaei, Farahnaz Sadat Golestan Hashemi, Morvarid Akhavan Rezaei, Sahar Abbasiliasi, Joo Shun Tan, Hamid Rajabi Memari et al.
    Pages 9-18

  4. Outcomes Assessment

    • Saeid Kadkhodaei, Farahnaz Sadat Golestan Hashemi, Morvarid Akhavan Rezaei, Sahar Abbasiliasi, Joo Shun Tan, Hamid Rajabi Memari et al.
    Pages 19-32

  5. Conceptual Models

    • Saeid Kadkhodaei, Farahnaz Sadat Golestan Hashemi, Morvarid Akhavan Rezaei, Sahar Abbasiliasi, Joo Shun Tan, Hamid Rajabi Memari et al.
    Pages 33-45

  6. Erratum to: Cis/Transgene Optimization

    • Saeid Kadkhodaei, Farahnaz Sadat Golestan Hashemi, Morvarid Akhavan Rezaei, Sahar Abbasiliasi, Joo Shun Tan, Hamid Rajabi Memari et al.
    Pages E1-E1

  7. Back Matter

    Pages 47-120
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Keywords

About this book

This book is a practical review which focuses on computational analysis and on in silico approaches towards the systematic discovery of various key functional gene expression elements in microalgae as a model. So far, in this regard very little information is available. Efficient stepwise procedures for analysing the matrix attachment regions (MARs) are outlined, as well as for translation initiation sites (TIS), signal peptide (SP) sequences, gene optimization and transformation systems. These outlines can be efficiently deployed as practical models for the systematic discovery of key expression elements and for the optimization of cis/transgenes in other micro/organisms. 

The first chapter is an introduction on the key gene expression elements analysed in this book, including scaffold/matrix attachment regions, translation initiation sites, signal peptides as well as gene optimization. Chapter 2 focuses on systematic strategies and computational approaches toward in silico analysis of each factor. The analyses outcomes is assessed individually in chapter 3 followed by developing the specific conceptual models for each element in Chapter 4. The concluding remarks are discussed in Chapter 5. 

This work is of interest to computational and experimental biologists interested in transcriptional regulation analysis as well as to researchers and scientists who wish to consider the use of bioinformatics and computational biology in design, analysis, or regulatory reviews of key gene expression elements for the production of recombinant proteins experiments.

Authors and Affiliations

  • Research Institute for Biotechnology and Bioengineering, Isfahan University of Technology, Isfahan, Iran

    Saeid Kadkhodaei

  • Plant Genetics, AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium

    Farahnaz Sadat Golestan Hashemi

  • Tropical Infectious Diseases Research and Education Centre (TIDREC), Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia

    Morvarid Akhavan Rezaei

  • Halal Products Research Institute, Universiti Putra Malaysia, Seri Kembangan, Malaysia

    Sahar Abbasiliasi

  • Bioprocess Technology, School of Industrial Technology, Universiti Sains Malaysia, George Town, Penang, Malaysia

    Joo Shun Tan

  • SynHiTech, Thornhill, Canada

    Hamid Rajabi Memari

  • Department of Veterinary Services, Ministry of Animal Health and Fisheries Development, Usman Faruk Secretariat, Sokoto, Sokoto, Nigeria

    Faruku Bande

  • Mater Research, Translational Research Institute, Woolloongabba, Australia

    Ali Baradaran

  • Institute of Plantation Studies, Universiti Putra Malaysia, Seri Kembangan, Malaysia

    Mahdi Moradpour

  • Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Seri Kembangan, Malaysia

    Arbakariya B, Ariff

Bibliographic Information

  • Book Title: Cis/Transgene Optimization

  • Book Subtitle: Systematic Discovery of Novel Gene Expression Elements Using Bioinformatics and Computational Biology Approaches

  • Authors: Saeid Kadkhodaei, Farahnaz Sadat Golestan Hashemi, Morvarid Akhavan Rezaei, Sahar Abbasiliasi, Joo Shun Tan, Hamid Rajabi Memari, Faruku Bande, Ali Baradaran, Mahdi Moradpour, … Arbakariya B, Ariff

  • Series Title: SpringerBriefs in Systems Biology

  • DOI: https://doi.org/10.1007/978-3-319-90391-0

  • Publisher: Springer Cham

  • eBook Packages: Biomedical and Life Sciences, Biomedical and Life Sciences (R0)

  • Copyright Information: The Author(s) 2018

  • Softcover ISBN: 978-3-319-90390-3Published: 25 May 2018

  • eBook ISBN: 978-3-319-90391-0Published: 16 May 2018

  • Series ISSN: 2193-4746

  • Series E-ISSN: 2193-4754

  • Edition Number: 1

  • Number of Pages: XIX, 120

  • Number of Illustrations: 24 b/w illustrations

  • Topics: Computer Appl. in Life Sciences, Systems Biology, Computational Biology/Bioinformatics, Proteomics

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