Plasmids: Current Research and Future Trends
Caister Academic Press
University of Bayreuth, Germany
viii + 264
GB £199 or US $319Buy bookEbook:
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Plasmids are fascinating entities which can replicate autonomously in bacterial, archaeal and eukaryotic cells. They profit from the cellular environment of the host but can also carry a rich diversity of genes which can be beneficial for the host. Plasmids confer the ability to degrade organic compounds and to fix nitrogen. In addition plasmids carry antibiotic resistance genes and their spread in pathogenic bacteria is of great medical importance. Plasmids are used in molecular studies of various organisms with ramifications in synthetic biology, medicine, ecology and evolution as well as basic research in molecular and structural biology.
Written by acknowledged experts in the field, this volume provides an up to date treatment of the structure, function and application of plasmids with a particular emphasis on current and future trends. The book is aimed primarily at research scientists, graduate students and professional scientists but will also be of great interest to all molecular biologists and microbiologists involved in research or teaching.
Chapters include a historical perspective on E. coli plasmids and the scientific background of the plasmids used routinely in laboratories to clone genes and to express proteins; an overview on the plasmids of archaea and eukarya; bioinformatic tools; horizontal gene transfer and the process of DNA transfer. Two entire chapters are devoted to the important medical applications of plasmids, including the correction of gene defects and vaccines to treat cancer or infectious diseases.
An essential book for all molecular biology laboratories.
"the fascinating book has a high degree at topicality ... very reader-friendly ... recommended for students" from Biospektrum (September 2008, 14: 557-558)
"the very useful guide to bioinformatics (J.E. Grant and P. Stothard), an in-depth description of the molecular machinery of DNA translocation (S. Russi et al.) and a thoroughly excellent discussion of HGT (M. Sota and E.M. Top)" from Microbiology Today (2008)
"the most useful section of the book covers current advances in the use of plasmids for gene therapy ... There are few books on this important subject." from Doodys (2008)
"... a clear and concise text which will be considered an important reference to plasmid researchers at the graduate level and beyond ... This volume represents an important reference to bridge knowledge gaps and provide useful descriptions rooted in the fundamentals of plasmid biology. Dr. Lipps has done an excellent job in creating a useful, informative, and focused volume that should grace the shelf of many a molecular biologist well into the future." from Expert Review of Vaccines (2009) January Issue
"... a core reference for students and research scientists in molecular biology and microbiology." from Eng. Life Sci. 2008, 8(4): 448
Table of contents
1. Escherichia coli Cloning and Expression Vectors
The introduction of gene technology methods together with the DNA sequencing and PCR methodologies have revoluzionarized basic and applied research in molecular biology involving all kinds of organisms from eubacteria up to humans. Since almost all of the cloning experiments start by insertion of DNA fragments into Escherichia coli plasmid vectors, this chapter describes important cloning vectors from the very beginning up to the present days. Furthermore, it deals in detail with expression vectors and the promoter elements needed for high-level production of recombinant proteins. The last part describes special vectors allowing for the analysis of promoters and terminators, addition of localization and epitope tags.
2. Archaeal Plasmids
Although many archaea harbour plasmids our knowledge on the biology of archaeal plasmids has remained quite limited. In most cases it is not known how the plasmids are replicated and whether the host benefits from the extrachromosomal element. Sequence analysis of the archaeal plasmids has identified many protein genes whose function cannot be predicted by sequence similarity to known protein. These orphan genes provide a rich repertoire for rewarding functional studies on the molecular biology of archaea. Despite this lack of knowledge archaeal plasmids are increasingly important as genetic tools and allow to perform genetic studies in archaea.
3. Plasmid-based Expression Systems for Mammalian Cells
Armin Baiker, Rudolf Haase and Hans Joachim Lipps
In contrast to bacteria and yeast no natural plasmids are found in mammalian cells. Therefore many attempts to construct different expression vector systems for mammalian cells have been made in recent years. These vector systems can be categorized in terms of vector administration, mechanisms of vector replication and mechanisms to achieve nuclear persistence of the vectors. In this chapter we describe various transfection methods, construction principles for an optimal vector and the different strategies to achieve nuclear persistence. We then concentrate on the description of various plasmid-like expression systems for mammalian cells based either on viral or chromosomal functional elements. Finally, their application in biotechnology and gene therapy are discussed.
4. Bioinformatics Tools and Methods for Plasmid Sequence Analysis and Annotation
Jason R. Grant and Paul Stothard
The past decade has seen tremendous growth in the development and application of bioinformatics databases and software. This chapter provides an overview of some of the current bioinformatics tools and methods available for the analysis of plasmid sequences, including resources for obtaining sequences, performing routine analysis operations, and annotating novel sequences. Specific topics covered include sequence databases, restriction analysis, plasmid construction, gene prediction, similarity searches, sequence alignment, annotation pipelines, and visualization tools. In addition, the most popular sequence formats are described, with an emphasis on open formats. Many of the resources presented are applicable to naturally occurring plasmids and to plasmid vectors, from prokaryotic or eukaryotic systems.
5. Horizontal Gene Transfer Mediated by Plasmids
Masahiro Sota and Eva M. Top
The ever-increasing information from bacterial genome sequences has clearly revealed frequent acquisition of genetic material from phylogenetically distant bacteria and even other organisms such as eukaryotes. The event, generally recognized as horizontal gene transfer (HGT), is now considered as a strong driving force for the evolution of bacterial genome organization and for rapid adaptation to the surrounding environments. Among the mobile elements and mechanisms of HGT, plasmids are undoubtedly critical players because of their ability to transfer by conjugation among both closely and very distantly related bacterial hosts. This feature allows them to broadly distribute genes or gene clusters that code for various host-beneficial phenotypes. This chapter introduces the features of recently characterized plasmids, with an emphasis on horizontal transfer, and the domain Bacteria (mostly Gram-positive and Gram-negative bacteria). We also describe some examples of transposable elements on plasmids, which have greatly contributed to the dissemination of phenotypic traits by HGT. The chapter ends with current research and suggestions for future studies in the areas of molecular biology, ecology and evolution of plasmids.
6. Molecular Machinery for DNA Translocation in Bacterial Conjugation
Silvia Russi, Roeland Boer and Miquel Coll
Whatever the route used, horizontal transfer of DNA requires elaborated multi-protein machinery to enable the long and charged nucleic acid polymer to cross the cell envelope barriers. The best-studied system for cell-to-cell DNA translocation is bacterial conjugation. This system can be divided in two discrete specialized modules: the relaxosome, which triggers and takes part in plasmid DNA processing and replication, and a type IV secretion system (T4SS), which impels protein and single-stranded DNA through the membranes. In addition, a coupling protein (CP), linking both modules, and a number of ancillary proteins are needed. Over the last decades research efforts in the field have resulted in the clarification of many aspects of this system and its machinery assembly. In particular, structural biology has provided details of the molecular architecture of several of the pieces involved in this intricate scenario.
7. Plasmids for Gene Therapy
Karthikeyan Kandavelou and Srinivasan Chandrasegaran
The success of gene therapy depends on the efficient insertion of therapeutic genes at the appropriate chromosomal target sites within the human genome, without causing cell injury, oncogenic mutations or an immune response. Although viral vectors offer excellent vehicles for highly efficient transduction of human cells, the associated safety concerns make non-viral delivery of therapeutic genes by using plasmid DNA into cells more attractive. The construction of plasmid vectors is simple and straightforward. Custom-designed zinc finger nucleases (ZFNs) that combine the non-specific cleavage domain (N) of FokI endonuclease with zinc finger proteins (ZFPs) offer a general way to deliver a site-specific double strand break (DSB) to the genome, and stimulate local homologous recombination (HR) by several orders of magnitude. This makes targeted gene correction or genome editing a viable option in human cells. Since ZFN-encoded plasmids could be used to transiently express ZFNs to target a DSB to a specific gene locus in human cells, they offer an excellent way for targeted delivery of the therapeutic genes to a pre-selected chromosomal site. The ZFN-encoded plasmid-based approach has the potential to circumvent all the problems associated with the viral delivery of therapeutic genes.
8. Plasmid DNA as Prophylactic and Therapeutic vaccines for Cancer and Infectious Diseases
Devin B. Lowe, Michael H. Shearer, Cynthia A. Jumper, En-Min Zhou and Ronald C. Kennedy
Close to two decades of preclinical studies have validated the concept of plasmid DNA as a protective vaccine strategy for cancer and infectious diseases. However, the crossover application into human studies has been met with poor results based on the DNA vectorÕs inability to provide clinically relevant prophylactic and therapeutic benefit. The overall efficacy of plasmid DNA immunization will no doubt rely on a number of strategies that attempt to increase the vectorÕs immunogenicity while also correcting for factors involved in the specific activation of immune effector cells. This chapter will focus on the difficulties surrounding the use of a DNA vaccine in patients suffering from chronic or infectious diseases with particular interest in resolving the roadblocks for future vaccine success in human cancer cases.
How to buy this book
(EAN: 9781904455356 9781913652142 Subjects: [bacteriology] [microbiology] [medical microbiology] [molecular microbiology] )