| Some Articles Planned for Future Volumes |
| Nuclear-Receptor-Mediated Transactivation through Interaction with Sp Proteins |
| Lysyl Oxidases: A Novel Multifunctional Amine Oxidase Family, K |
| Site-Specific DNA Damage Recognition by Enzyme-Induced Base Flipping |
| Csiszar |
| Bacteriophage T2Dam DNA-[N6-adenine]-methyltransferases |
| Site-Specific Recombination and Partitioning Systems in the Stable High Copy Propagation of the 2 Micron Yeast Plasmid / T.E. Roche |
| Did an Early Version of the Eukaryal replisome Enable the Emergence of Chromatin? |
| Initiation and Elongation Factors in Mammalian Mitochondrial Protein Biosynthesis / J.C. Baker |
| Cyclin Dependent Kinase 11 in RNA Transcription and Splicing |
| The Eukaryotic Ccr4-Not Complex: A Regulatory Platform Integrating mRNA Metabolism with Cellular Signaling Pathways? / X. Yan |
| Signaling Repression of Transcription by RNA Polymerase III in Yeast |
| Distinct Regulatory Properties of Pyruvate Dehydrogenase Kinase and Phosphatase Isoforms / Y. Hiromasa ; X. Gong ; T. Peng ; J. Dong ; A. Turkan ; S.A. Kasten |
| A Tale of Two HSV-1 Helicases: Roles of Phage and Animal Virus Helicases in DNA Replication and Recombination / B. Marintcheva ; S.K. Weller |
| The RNA World of Plant Mitochondria / M. Hoffmann ; J. Kuhn ; K. Daschner ; S. Binder |
| Multiple Controlling Mechanisms of FGF1 Gene Expression through Multiple Tissue-Specific Promoters / I.M. Chiu ; K. Touhalisky ; C. Baran |
| Structure and Function of Branched Chain Aminotransferases / S. Hutson |
| Functional Significance and Mechanism of elF5-Promoted GTP Hydrolysis in Eukaryotic Translation Initiation / S. Das ; U. Maitra |
| Nonribosomal Biosynthesis of Microbial Chromopeptides / U. Keller ; F. Schauwecker |
| Manipulation of tRNA Properties by Structure-Based and Combinatorial in Vitro Approaches / S. Vortler ; J. Putz ; R. Giege |
| Index |
| Structure and Function of the Human Immunodeficiency Virus Leader RNA / B.K. May ; K.R. Lieberman ; T.W. Traut ; B. Berkhout ; R.M. Blumenthal ; S.C. Dogra ; A.E. Dahlberg ; M.E. Jones |
| Ribosome-Catalyzed Peptide-bond Formation / D.W. Borst ; M. Bustin ; T.J. Sadlon |
| Uracil Metabolism--UMP Synthesis from Orotic Acid or Uridine and Conversion of Uracil to b-Alanine: Enzymes and cDNAs |
| Experimental Analysis of Global Gene Regulation in Escherichia coli / R.G. Matthews ; T. Moss ; P.F. Agris ; R. Reeves ; C.R. Bhasker |
| The Importance of Being Modified: Roles of Modified Nucleosides and Mg 2+ in RNA Structure and Function / V.Y. Stefanovsky |
| High-Mobility-Group Chromosomal Proteins: Architectural Components That Facilitate Chromatin Function |
| Promotion and Regulation of Ribosomal Transcription in Eukaryotes by RNA Polymerase I / J.R. Chamberlain ; T.C. Cox ; N.A. Kolchanov ; D. Carroll |
| Homologous Genetic Recombination in Xenopus: Mechanism and Implications for Gene Manipulation / A.J. Tranguch ; S.S. Bottomley ; M. Hengstschläger ; I.I. Titov |
| Molecular Regulation of Heme Biosynthesis in Higher Vertebrates / N.L. Eberhardt ; E. Pagán-Ramos |
| The Flp Recombinase of the 2-mm Plasmid of Saccharomyces cerevisiae / N. Maizels ; I.E. Vlassova ; P.D. Sadowski ; S.-W. Jiang ; D.R. Engelke ; H. Leung ; V.V. Vlassov |
| Eukaryotic Nuclear RNase P: Structures and Functions / A.R. Shepard |
| Targeting and Regulation of Immunoglobulin Gene Somatic Hypermutation and Isotype Switch Recombination / R.A. Bambara |
| Chemical and Computer Probing of RNA Structure |
| Capping Enzyme in Eukaryotic mRNA Synthesis / D.P. Mascott ; S. Schuman ; Q.-P. Dou ; A.M. Arnold ; L. Huang ; L.S. Goessling |
| Reconstitution of Mammalian DNA Replication / A.B. Pardee ; M.A. Trujillo |
| Transcriptional Activation of Thymidine Kinase, a Marker for Cell Cycle Control / M. Ares, Jr. ; D. Rup ; E.K. Wagner |
| Hormonal and Cell-specific Regulation of the Human Growth Hormone and Chorionic Somatomammotropin Genes |
| Rearrangement of snRNA Structure During Assembly and Function of the Spliceosome / B. Weiser ; R.O. Laine ; S.R. Kimball ; R.E. Thach ; J.F. Guzowski |
| Effects of the Ferritin Open Reading Frame on Translational Induction by Iron / R.G. Hutson ; H. Mellor |
| Transcription of the Herpes Simplex Virus Genome during Productive and Latent Infection / J. Singh ; B. Levy-Wilson ; C.M.G. Simbulan-Rosenthal ; M.S. Kilberg ; K.M. Flowers |
| Transcriptional Control of the Human Apolipoprotein B Gene in Cell Culture and in Transgenic Animals |
| Eukaryotic Gene Expression: Metabolite Control by Amino Acids / D.S. Rosenthal ; A.E. Pegg ; A. Gashler |
| Role of Translation Initiation Factor eIF-2B in the Regulation of Protein Synthesis in Mammalian Cells / L.S. Jefferson ; W.K. Joklik ; R. Ding ; M.E. Dolan ; V.P. Sukhatme |
| Early Growth Response Protein 1 (Egr-1): Prototype of a Zinc-finger Family of Transcription Factors / M.R. Roner ; W. Pansegrau ; J. Jackman ; R.C. Moschel |
| Molecular Recognition in the Assembly of the Segmented Reovirus Genome / T. Pihlajaniemi |
| Structure, Function, and Inhibition of O 6 -Alkylguanine-DNA Alkyltransferase / E. Lanka ; M.E. Smulson |
| Enzymology of DNA Transfer by Conjugative Mechanisms / C.W. Schmid ; A.B. Chetverin ; M. Rehn |
| Depletion of Nuclear Poly(ADP-ribose) Polymerase by Antisense RNA Expression: Influence on Genomic Stability, Chromatin Organization, DNA Repair, and DNA Replication |
| Alu: Structure, Origin, Evolution, Significance, and Function of One-Tenth of Human DNA |
| Two New Collagen Subgroups: Membrane-associated Collagens and Types XV and XVIII / X. Bi ; J.P.G. Ballesta ; A.S. Spirin |
| Replicable RNA Vectors: Prospects for Cell-free Gene Amplification, Expression, and Cloning / H.M. Darwish ; G.R. Björk ; L.F. Liu ; M. Remacha |
| Genetic Dissection of Synthesis and Function of Modified Nucleosides in Bacterial Transfer RNA / H.F. DeLuca ; H.L. Klein |
| recA-independent DNA Recombination between Repetitive Sequences: Mechanisms and Implications |
| The Large Ribosomal Subunit Stalk as a Regulatory Element of the Eukaryotic Translational Machinery |
| References |
| Recent Advances in the Molecular Biology of Vitamin D Action |
| Examination of Mitotic Recombination by Means of Hyper-recombination Mutants in Saccharomyces cerevisiae / J. Czworkowski ; M.R. Blackburn |
| The Elongation Phase of Protein Synthesis / G.R. Greenberg ; I.S. Owens ; P.B. Moore ; R.E. Kellems ; J.M. Hilfinger ; J.K. Ritter |
| Regulation and Function of Adenosine Deaminase in Mice |
| Regulation of Synthesis of Ribonucleotide Reductase and Relationship to DNA Replication in Various Systems |
| Gene Structure at the Human UGT1 Locus Creates Diversity in Isozyme Structure, Substrate Specificity, and Regulation / A. Stein ; Z.-Y. Wang |
| Chapter References |
| Signals in Eukaryotic DNA Promote and Influence Formation of Nucleosome Arrays / D.R. Morris |
| Growth Control of Translation in Mammalian Cells / T.F. Deuel |
| S1-Nuclease-Sensitive DNA Structures Contribute to Transcriptional Regulation of the Human PDGF A-chain |
| Minute Virus of Mice cis-Acting Sequences Required for Genome Replication and the Role of the trans-Acting Viral Protein, NS-1 / C.R. Astell ; Q. Liu ; C.E. Harris ; J. Brunstein ; H.K. Jindal ; P. Tam |
| Developmental Genome Reorganization in Ciliated Protozoa: The Transposon Link / L.A. Klobutcher ; G. Herrick |
| DNA Excision Repair Assays / D. Mu ; A. Sancar |
| The Mitochondrial Uncoupling Protein: Structural and Genetic Studies / D. Ricquier ; F. Bouillaud |
| Molecular Regulation of Cytokine Gene Expression: Interferong as a Model System / H.A. Young ; P. Ghosh |
| RecA Protein: Structure, Function, and Role in Recombinational DNA Repair / A.I. Roca ; M. Cox |
| Molecular Biology of Axon-Gila Interactions in the Peripheral Nervous System / V. Taylor ; U. Suter |
| Regulation of Eukaryotic Messenger RNA Turnover / L.E. Rajagopalan ; J.S. Malter |
| New and Atypical Families of Type I Interferons in Mammals: Comparative Functions, Structures, and Evolutionary Relationships / R.M. Roberts ; L. Liu ; A. Alexenko |
| General Transcription Factors for RNA Polymerase II / R.C. Conaway ; J.W. Conaway |
| Biochemistry and Molecular Genetics of Cobalamin Biosynthesis / M.R. Rondon ; J.R. Trzebiatowski ; J.C. Escalante-Semerena |
| Preface |
| Keynote Address: Past, Present, and Future Aspects of Base Excision Repair |
| Multiple Pathways for DNA Base Excision Repair: Foreward |
| The Switch Mechanism among Multiple BER Pathways |
| Yeast Base Excision Repair: Interconnections and Networks |
| BER, MGMT, and MMR in Defense Against Alkylation-Induced Genotoxicity and Apoptosis |
| Gene Targeting in the Mouse for Elucidating the Role of BER: Foreward |
| Mammalian DNA b-Polymerase in Base Excision Repair of Alkylation Damage |
| Regulation of Intracellular Localization of Human MTH1, OGG1 and MYH Proteins for Repair of Oxidative DNA Damage |
| Repair of 8-Oxoguanine and OGG1-Incised Apurinic Sites In a CHO Cell Line |
| Mammalian OGG1/MMH Gene Plays a Major Role for Repair of the 8-hydroxyguanine Lesion in DNA |
| Complexities of BER: Foreward |
| Molecular Mechanism of PCNA-Dependent Base Excision Repair |
| Factors Influencing the Removal of Thymine Glycol from DNA in y-Irradiated Human Cells |
| Completion of Base Excision Repair by Mammalian DNA Ligases |
| Uracil-Initiated Base Excision DNA Repair Synthesis Fidelity In Human Colon Adenocarcinoma LoVo and Escherichia coli Cell Extracts |
| DNA Glycosylases: Specificity and Mechanisms: Foreward |
| Multiple DNA Glycosylases for Repair of 8-Oxoguanine and Their Potential In Vivo Functions |
| DNA Substrates Containing Defined Oxidative Base Lesions and Their Application to Study Substrate Specificities of Base Excision Repair Enzymes |
| Mechanism of Action of E |
| coli Formamidopyrimidine N-Glycosylase: Role of K155 in Substrate Binding and Product Release |
| Thymine DNA Glycosylase |
| Mitochondrial BER: Foreward |
| Crystallizing Thoughts about DNA Base Excision Repair |
| DNA Damage Recognition, and Repair Pathway Coordination Revealed by the Structural Biochemistry of DNA Repair Enzymes |
| Potential Double Flipping Mechanism by E |
| coli MutY |
| Properties and Functions of Human Uracil-DNA Glycosylase From the UNG Gene |
| Molecular Regulation, Evolutionary, and Functional Adaptations Associated with C to U Editing of Mammalian ApolipoproteinB mRNA / Shrikant Anant ; Valerie Blanc ; Nicholas O. Davidson |
| RNA Editing: General Overview of Underlying Biochemical Mechanisms and Evolutionary Development / I.： |
| C to U RNA Editing / II.： |
| C to U ApoB RNA Editing: cis-Acting Elements / III.： |
| C to U ApoB RNA Editing: trans-Acting Factors / IV.： |
| Summary / V.： |
| Acknowledgments |
| Polymorphisms in the Genes Encoding Members of the Tristetraprolin Family of Human Tandem CCCH Zinc Finger Proteins / Perry J. Blackshear ; Ruth S. Phillips ; Johana Vazquez-Matias ; Harvey Mohrenweiser |
| Introduction |
| Materials and Methods |
| Results |
| Discussion |
| Molecular and Cell Biology of Phosphatidylserine and Phosphatidylethanolamine Metabolism / Jean E. Vance |
| Membrane Phospholipids |
| Pathways for Biosynthesis of Phosphatidylserine and Phosphatidylethanolamine |
| Enzymes of Phosphatidylserine Biosynthesis |
| Enzymes of Phosphatidylethanolamine Biosynthesis |
| Regulation of PS and PE Biosynthesis |
| Interorganelle Transport of PS and PE / VI.： |
| Intramembrane Transport of PS and PE / VII.： |
| Biological Functions of PS and PE / VIII.： |
| Future Directions / IX.： |
| DNA-Protein Interactions during the Initiation and Termination of Plasmid pT181 Rolling-Circle Replication / Saleem A. Khan |
| Origins of Replication of the Plasmids of the pT181 Family |
| Initiator Proteins of the Plasmid pT181 Family |
| Mechanism of Inactivation of the Plasmid pT181 Family Rep Proteins |
| Role of Host Proteins in pT181 RC Replication |
| Replication of the Lagging Strand of Plasmid pT181 |
| Conclusions and Future Directions |
| Herpes Simplex Virus Type-1: A Model for Genome Transactions / Paul E. Boehmer ; Giuseppe Villani |
| Introduction to Herpesviridae |
| HSV-1 Life Cycle, Genome Structure, and Replication Genes |
| Initiation of Replication |
| Elongation |
| Interaction of the HSV-1 DNA Replication Machinery with DNA Damage |
| Homologous Recombination |
| Concluding Remarks |
| Enzymology and Molecular Biology of Glucocorticoid Metabolism in Humans / Andreas Blum ; Edmund Maser |
| Glucocorticoid Action |
| The Free Hormone Hypothesis |
| Glucocorticoid Receptors |
| Nongenomic Action of Glucocorticoids |
| Glucocorticoid Resistance |
| 11[beta]-Hydroxysteroid Dehydrogenase (11[beta]-HSD) as Prereceptor Control |
| Hydroxysteroid Dehydrogenases: Physiological Role |
| The History of Two Isoforms: 11[beta]-HSD Type 1 and 11[beta]-HSD Type 2 |
| A (Patho)physiological Role for 11[beta]-HSD 1 and 11[beta]-HSD 2 / X.： |
| 11[beta]-HSD 2 and the Syndrome of "Apparent Mineralocorticoid Excess" (AME) / XI.： |
| 11[beta]-Hydroxysteroid Dehydrogenase Type 1 (11[beta]-HSD 1) / XII.： |
| Conclusions / XIII.： |
| Dancing with Complement C4 and the RP-C4-CYP21-TNX (RCCX) Modules of the Major Histocompatibility Complex / C. Yung Yu ; Erwin K. Chung ; Yan Yang ; Carol A. Blanchong ; Natalie Jacobsen ; Kapil Saxena ; Zhenyu Yang ; Webb Miller ; Lilian Varga ; George Fust |
| The Sophisticated Genetic Diversities of Human C4 and RCCX Modules |
| Structural Diversities of the Human and Mouse C4 Proteins |
| Nucleotide Polymorphisms in Human C4A and C4B Genes |
| Expression of C4A and C4B Transcripts and Proteins |
| The Endogenous Retrovirus that Mediates the Dichotomous Size Variation of C4 Genes |
| Evolution of Complement C3/C4/C5 and the RCCX Modules in the MHC |
| Afterthoughts: Eleven Outstanding Issues to be Addressed |
| The Roles and Regulation of Potassium in Bacteria / Wolfgang Epstein |
| Paths of K[superscript +] Movement |
| Regulation of K[superscript +] Transport Systems |
| K As An Intracellular Activator |
| Regulation of Internal pH by K[superscript +] |
| Conformational Polymorphism of d(A-G)[subscript n] and Related Oligonucleotide Sequences / Nina G. Dolinnaya ; Jacques R. Fresco |
| [alpha]-DNA Helix[left and right double arrow]Acid-Dependent Duplex Equilibrium |
| Acid-Dependent Parallel Duplex[left and right double arrow]pH-Independent Parallel Duplex Equilibrium |
| pH-Independent Parallel Duplex[left and right double arrow]Single-Hairpin Duplex[left and right double arrow]Two-Hairpin Tetraplex Equilibria |
| Some Articles Planner for Future Volumes |
| Genetic Switches During Bacteriophage [lambda] Development / Grzegorz Wegrzyn ; Alicja Wegrzyn |
| Bacteriophage [lambda] as a Model in Molecular Studies / I： |
| Developmental Pathways of Bacteriophage [lambda] / II： |
| Genetic Switches: A Way to Regulate Bacteriophage [lambda] Development / III： |
| Molecular Aspects of Meiotic Chromosome Synapsis and Recombination / S. Anuradha ; K. MuniyappaIV： |
| General Introduction |
| Meiosis |
| G-quartets |
| Non-HKD Phospholipase D Enzymes: New Players in Phosphatidic Acid Signaling? / Carlo Zambonelli ; Mary F. Roberts |
| Phosphatidic Acid (PA) |
| Phospholipase D (PLD) Enzymes |
| Dimetal Enzymes "Similar" to scPLD; Can They Do PLD Chemistry? |
| Prospectus / V： |
| Nucleotide Excision Repair / Joyce T. Reardon ; Aziz Sancar |
| Damage Recognition |
| Excision Repair in Escherichia coli |
| Excision Repair in Humans |
| Modulation of DNA Repair by Transcription |
| Repair of Chromatin / VI： |
| Repair of DNA Interstrand and DNA-Protein Cross-Links / VII： |
| Concluding Comments / VIII： |
| Signal Transduction Pathways in Cancer Development and as Targets for Cancer Prevention / Ann M. Bode ; Zigang Dong |
| Signals Involved in Neoplastic Cell Transformation and Carcinogenesis |
| Carcinogen-Induced Signal Transduction |
| Chemoprevention and Signal Transduction Targets |
| Conclusions/Summaries |
| ADAR Gene Family and A-to-l RNA Edition: Diverse Roles in Posttranscriptional Gene Regulation / Louis Valente ; Kazuko Nishikura |
| Historical Overview |
| A Family of Editors |
| Requirement of Double-Stranded RNA in the A-to-I RNA Editing Mechanism |
| Cellular Consequences |
| Future Prospects |
| The Second Paradigm for Activation of Transcription / S. R. Wigneshweraraj ; P. C. Burrows ; P. Bordes ; J. Schumacher ; M. Rappas ; R. D. Finn ; W. V. Cannon ; X. Zhang ; M. Buck |
| Two Major Steps in Transcription Initiation |
| The Bacterial Transcription Machinery |
| The [sigma superscript 54] Factor |
| The AAA Activator |
| Determinants in Core RNAP |
| Toward a Detailed Mechanism for Activation |
| Families of Protein Phosphatase 1 Modulators Activated by Protein Kinases A and C: Focus on Brain / Qing-Rong Liu ; Jian-Ping Gong ; George R. Uhl |
| A Family of Protein Kinase A (PKA)-Activated PP1 Inhibitors |
| A Family of Protein Kinase C (PKC)-Activated PP1 Inhibitors |
| Function of PKA- and PKC-Dependent PP1 Inhibitors |
| Comparisons of the Families of PKA- and PKC-Dependent PP1 Inhibitors |
| Drosophila Orthologues to Human Disease Genes: An Update on Progress / Sergey Doronkin ; Lawrence T. Reiter |
| Neurological Disease |
| Drosophila in Cancer Research |
| Tumorigenesis, Neuroprotection, and Fortitude: The Hypoxic Response in Drosophila |
| Blood, Immune Response, and Infectious Disease |
| Future Candidates |
| Applications of Fluorescence Correlation Spectroscopy to the Study of Nucleic Acid Conformational Dynamics / Kaushik Gurunathan ; Marcia Levitus |
| Introduction: Fluorescence and Energy Transfer |
| Fluorescence Correlation Spectroscopy |
| Conformational Dynamics of Nucleic Acids |
| Experimental Techniques |
| RNA Structure and Modeling: Progress and Techniques / Dinggeng Chai |
| Chemical and Enzymatic Methods |
| Physical Approaches to Study RNA Folding and Structure |
| A Molecular Dynamic View of RNA Molecules |
| Computer-Assisted Modeling |
| Conclusion |
| DNA Polymerase [epsilon]: A Polymerase of Unusual Size (and Complexity) / Zachary F. Pursell ; Thomas A. Kunkel |
| Pol [epsilon] Structure |
| Physical and Functional Interactions of Pol [epsilon] |
| Biochemical Properties of Pol [epsilon] |
| Pol [epsilon] in DNA Replication |
| The Role of Pol [epsilon] in Checkpoint Control |
| Pol [epsilon] Involvement in Regulating Chromatin States |
| Pol [epsilon] Relationship with Chromatin Remodeling Complexes |
| The Roles of Pol [epsilon] in Excision Repair of DNA Damage / IX： |
| Pol [epsilon] in Recombination / X： |
| Schizosaccharomyces pombe Pol [epsilon] / XI： |
| Xenopus Pol [epsilon] / XII： |
| Site-directed Spin Labeling Studies on Nucleic Acid Structure and Dynamics / Glenna Z. Sowa ; Peter Z. QinXIII： |
| Overview |
| Basic Physics Underlying SDSL |
| Site-Specific Attachment of Nitroxides to Nucleic Acids |
| Distance Measurements Using SDSL |
| Site-Specific Structural and Dynamic Information from a Single-Labeled Nitroxide |
| Beyond Distance Measurements and Nitroxide Dynamics Analysis |
| Molecular Computing with Deoxyribozymes / Milan N. Stojanovic |
| Introduction to Molecular Computing by Deoxyribozymes |
| Deoxyribozyme-Based Logic Gates |
| Deoxyribozyme-Based Circuits for Arithmetical Operations |
| Deoxyribozyme-Based Automata: Circuits that Play Tic-Tac-Toe |
| Deoxyribozyme-Based Control of Downstream Elements |
| Expanding Molecular Logic to Nanoparticles |
| Other Approaches to Autonomous Computing with DNA |
| Conclusions and Future Visions |
| Molecular Colony Technique: A New Tool for Biomedical Research and Clinical Practice / Alexander B. Chetverin ; Helena V. Chetverina |
| Detection of Airborne RNAs |
| Monitoring Reactions Between Single Molecules |
| Cell-Free Gene Cloning |
| Molecular Colonies as a Precellular Form of Life |
| Molecular Colony Diagnostics |
| Gene and Gene Expression Analysis |
| Opportunities Provided by the Molecular Colony Technology |
