Progress in Nucleic Acid Research and Molecular Biology

by Elsevier Science

Overview

Provides a forum for discussion of new discoveries, approaches, and ideas in molecular biology. Contains contributions from leaders in their fields and abundant references.

Product Details

ISBN-13:	9780080863481
Publisher:	Elsevier Science
Publication date:	06/02/1998
Series:	ISSN , #60
Sold by:	Barnes & Noble
Format:	eBook
Pages:	353
File size:	8 MB

About the Author

Moldave, Kivie (UC Irvine)

Read an Excerpt

Compilation of reviews on topics in molecular biology.

Table of Contents

	Some Articles Planned for Future Volumes	xi
	DNA Modifications by Antitumor Platinum and Ruthenium Compounds: Their Recognition and Repair	1
I.	Introduction	2
II.	Current State of Knowledge on DNA Interactions of "Classical" Antitumor Cisplatin and Its Clinically Ineffective trans Isomer	3
III.	DNA Interactions of Cisplatin Analogs	25
IV.	Activation of trans Geometry	38
V.	Polynuclear Platinum Antitumor Drugs	42
VI.	Antitumor Ruthenium Compounds	49
VII.	Concluding Remarks	54
	References	54
	AMP- and Stress-Activated Protein Kinases: Key Regulators of Glucose-Dependent Gene Transcription in Mammalian Cells?	69
I.	AMP-Activated Protein Kinase	70
II.	SNF1 and Glucose Repression in Yeast	71
III.	AMPK and Regulation of Gene Transcription in Mammals	71
IV.	Downstream Targets of AMPK and Gene Transcription	77
V.	Mitogen- and Stress-Activated Protein Kinases	78
VI.	Conclusions	82
	References	82
	Molecular Basis of Fidelity of DNA Synthesis and Nucleotide Specificity of Retroviral Reverse Transcriptases	91
I.	Introduction	92
II.	The Role of Reverse Transcriptase in Retroviral Mutagenesis	93
III.	Retroviral Reverse Transcriptases	94
IV.	Fidelity of Retroviral Reverse Transcriptases	97
V.	Control of Fidelity at Initiation of Reverse Transcription	108
VI.	Fidelity of Strand Transfer: Implications for Retroviral Recombination	109
VII.	Contribution of Accessory Proteins to Fidelity of Reverse Transcription	110
VIII.	Mutational Analysis of HIV-1 Reverse Transcriptase: The Effects of Mutations on Fidelity of DNA Synthesis	112
IX.	Biological Consequences of Increasing or Decreasing Fidelity	129
X.	Conclusions and Future Perspectives	131
	References	132
	Muc4/Sialomucin Complex, the Intramembrane ErbB2 Ligand, in Cancer and Epithelia: To Protect and To Survive	149
I.	Membrane Mucins	150
II.	Muc4/SMC Structure and Functions	153
III.	Muc4/SMC Contributions to Tumor Progression	160
IV.	Muc4/SMC in Simple Epithelia	163
V.	Muc4/SMC in Glandular Secretory Epithelia	170
VI.	Muc4/SMC in Stratified Epithelia	177
VII.	Conclusions and Future Directions	179
	References	180
	Functions of Alphavirus Nonstructural Proteins in RNA Replication	187
I.	Introduction	187
II.	Replication Cycle of Alphaviruses	188
III.	Alphavirus-Like Superfamily	190
IV.	Replication of Alphavirus RNAs	192
V.	Processing of Alphavirus Nonstructural Polyprotein P1234	197
VI.	nsP1: A Unique RNA-Capping Enzyme and Membrane Anchor	198
VII.	nsP2: A Multifunctional Enzyme and Regulatory Protein	204
VIII.	nsP3: An Ancient Conserved Protein and Phosphoprotein	208
IX.	nsP4: A Catalytic RNA Polymerase Subunit	210
X.	The Replication Complex	211
	References	214
	The Unique Biochemistry of Methanogenesis	223
I.	Introduction	224
II.	Methanogens: A Unique Group of Microorganisms	225
III.	Biochemistry of Methanogenesis	228
IV.	Mechanism of ATP Synthesis in Methanogenic Archaea	240
V.	Energy-Conserving Systems in Methanosarcina Strains	242
VI.	Energy Conservation in Obligate Hydrogenotrophic Methanogens	270
	References	274
	A History of Poly A Sequences: From Formation to Factors to Function	285
I.	Introduction	287
II.	From Polymerases to Poly A(+) mRNA	290
III.	Sequences Required for Polyadenylation	291
IV.	The Biochemistry of Polyadenylation	296
V.	Cleavage/Polyadenylation Proteins	306
VI.	The Core Components of Cleavage/Polyadenylation	313
VII.	Cloning, Sequencing, and Expressing the Core Proteins	320
VIII.	Regulation of Polyadenylation	335
IX.	Polyadenylation in Yeast	351
X.	Polyadenylation in E. coli	364
XI.	Polyadenylation in Vaccina Virus	375
	References	381
	A Growing Family of Guanine Nucleotide Exchange Factors Is Responsible for Activation of Ras-Family GTPases	391
I.	Introduction	392
II.	Regulation of in Vivo Ras-GTP Levels by Inhibition of GTPase-Activating Proteins	394
III.	Early Identification of Ras-Family GEFs	395
IV.	GEF Structure and the Nucleotide Exchange Reaction	398
V.	Dominant Inhibitory Ras Proteins Target GEFs	404
VI.	Biological Assays for GEF Activity	406
VII.	Ras-Family GEFs	407
VIII.	GEFs and Disease	427
IX.	Are There More GEFs in Our Future?	428
	References	428
	Practical Approaches to Long Oligonucleotide-Based DNA Microarray: Lessons from Herpesviruses	445
I.	A Rationale for Developing DNA Microarrays for Herpesviruses	446
II.	Herpes Simplex and Cytomegaloviruses--Two Herpesviruses That Share Features of Productive Infection but Differ Markedly in Patterns of Latency and Reactivation	447
III.	Design Criteria for Herpesvirus DNA Microarrays	451
IV.	The Construction and Validation of an Oligonucleotide-Based Hsv-1 DNA Microarray on Glass Slides	455
V.	Exemplary Applications	472
VI.	Conclusions	486
	References	487
	Sphingosine Kinases: A Novel Family of Lipid Kinases	493
I.	Pleiotropic Functions of Sphingosine-1-Phosphate	494
II.	Sphingosine Kinase and Sphingosine-1-Phosphate in Yeast and Plants	495
III.	Cellular Functions of Sphingosine Kinase in Mammalian Cells	497
IV.	How Is Sphingosine Kinase Activated?	498
V.	Cloning of Mammalian Sphingosine Kinases	500
VI.	Sphingosine Kinase Family	504
VII.	Five Conserved Domains of the SPHK Superfamily	505
VIII.	Phylogenetic Analysis of Sphingosine Kinases	508
IX.	Concluding Remarks	508
	References	509
	Mechanisms of EF-Tu, a Pioneer GTPase	513
I.	Introduction	514
II.	Structure-Function Relationships	524
III.	EF-Ts as a Steric Chaperone for EF-Tu Folding	529
IV.	EF-Tu as Target of Antibiotics	531
V.	Specific Aspects of EF-Tu GTPase Activity	538
VI.	Conclusions and Perspectives	542
	References	543
	Index	553

Editorial Reviews

3 Stars from Doody

This volume is a compilation of disparate, apparently unrelated chapters that cover a wide range of topics, including nucleic acid structure, gene expression of the malic enzyme, antisense technology, and control of translational stop signals in prokaryotes and eukaryotes. "The book does not contain a preface and it is unclear what the purpose of the book is. "With no preface, the book also lacks a discussion of the target audience for which the book is intended. However, the target audience for this book is very limited, because the book lacks a coherent theme. "The various chapters are well written and for the most part very informative. For example, there is a very interesting theoretical discussion on the intricacies of the mechanics of translational stop codons. "I would recommend purchase of this book only by libraries, because the book contains chapters that cover so many different topics.

Philip M. Sass

This is an up-to-date review of the state-of-the-art in research of the structure and function of large molecules such as proteins, RNA, DNA, viruses, ferritin, and various subjects related to replication and control of living organisms. "The purpose is to review a number of research areas dealing with molecular biology of nucleoproteins, nucleic acids, and interaction both in vivo and in vitro. "The volume is directed at those individuals working in the area of macromolecules, their structure and functions. The articles are aimed at biochemists, molecular biologists working in these fields, and graduate students learning the subject in class or laboratory. "Included are discussions of global gene regulation in E.coli; the structure and function of eukaryotic nuclear RNase and its ability to self-splice and cleave various t-RNAs; feritin, a multimeric iron-storage protein and its regulation of synthesis coupled with iron concentration that affects m-RNA; and the effect of parvoviruses and other linear DNA genome viruses causing changes in DNA structure in insects and vertebrates. "I enjoyed this book. It is an excellent review of a number of interesting topics. However, I would criticize the lack of sufficient diagrams to describe the three-dimensional structures in relation to function. There is, unfortunately, no glossary to interpret the many acronyms used in the various articles. In spite of this, I highly recommend this book for libraries and scientific personnel working in the field.

Howard H. Sky-Peck

This latest volume in a long-running series includes ten authoritative reviews on diverse subjects concerned with aspects of nucleic acid metabolism. "It is intended as a review for active investigators. "Researchers in this area are the audience. "Several of the articles are interrelated: the role of PriA in replication and recombination, genetic diseases of DNA repair, recombinational repair and RecA, and genetic disorders which lead to genomic instability and cancer. Aspects of development are discussed in chapters on retinoic acid and pituitary development. Additionally, syndecan expression and cyclic nucleotide phosphodiesterases are discussed. Each article is accompanied by a useful, detailed bibliography and can serve as a reference source and up-to-date compilation of work in the noted areas. "Investigators working in these areas will want access to this material. The volume would be improved if the editor had provided some prefatory remarks linking related materials and providing an overall theme.

Eugene A. Davidson

Full of interest not only for the molecular biologist—for whom the numerous references will be invaluable—but will also appeal to a much wider circle of biologists, and in fact to all those who are concerned with the living cell.

British Medical Journal

Volume 44 of the series comprises seven articles on structure and action of mammalian ribonuclease (angiogenin) inhibitor; bacterial adenylyl cyclases; initiation of transcription by RNA polymerase II--a multi-step process; regulation of repair of alkylation damage in mammalian genomes; cell delivery and mechanisms of action of antisense oligonucleotides; enzyme organization in DNA precursor biosynthesis; and identification and characterization of novel substrates for protein tyrosine kinases. Annotation c. Book News, Inc., Portland, OR (booknews.com)

Booknews

Praise for the Serial "In perusing these chapters, I found much of interest. It is worth investigating." —P. BRICKELL in BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

"Full of interest not only for the molecular biologist—for whom the numerous references will be invaluable—but will also appeal to a much wider circle of biologists, and in fact to all those who are concerned with the living cell." —BRITISH MEDICAL JOURNAL

From the Publisher

Reviewer: Eugene A Davidson, PhD (Georgetown University School of Medicine)
Description: The nine chapters in this latest review volume cover a broad variety of topics ranging from a discussion of ATP-dependent restriction enzymes to a class of mammalian transposons.
Purpose: The purpose is to provide reviews of selected topics in nucleic acid research.
Audience: Investigators wishing to stay current in these areas will wish to use this volume, which should be in the medical or science library.
Features: Each of the presentations is authoritatively written, contains a brief summary, and is accompanied by an extensive and current bibliography. The only chapter not concerned with DNA-RNA and related material is one on myelin basic protein 22, a transmembrane protein within which mutations are associated with peripheral neuropathies.
Assessment: This volume maintains the high standards of its predecessors but, as with many of its type, suffers from the lack of a coordinating prefatory chapter and a failure to present related topics in an integrated fashion.

Doody's Review Service