Methods in Proteome and Protein Analysis / edited by Raza Maria Kamp ... [et al.]. -- Springer, 2004
索书号: 58.17421/M592
Contents:
1.Helix-Helix Packing Between Transmembrane Fragments 1
2.Mobility Studies in Proteins by 15N Nuclear Magnetic Resonance: Rusticyanin as an Example 15
3.Structure and Dynamics of Proteins in Crowded Media: A Time-Resolved Fluorescence Polaization Study 35
4.Analyses of Wheat Seed Proteome: Exploring Protein-Protein Interactions by Manipulating Genome Composition 49
5.Modification-Specific Proteomic Strategy for Indentification of Glycosyl-Phosphatidylinositol Anchored Membrane Proteins 67
6.Diocleinae Lectins: Clues to Delineate Structure/ Function Correlations 81
7.The Contribution of Optical Biosensors to the Analysis of Structure-Function Ralationships in Proteins 93
8.The Use of Protein-Protein Interaction Networks for Genome-Wide Protein Function Comparisons and Predictions 103
9.Probing Ribosomal Proteins Capable of Interacting with Polyamines 125
10.Applications of Optical Biosensors to Structure-Function Studies on the EGF/EGF Receptor System 133
11.The Functional Interaction Trap: A Novel Strategy to Study Specific Protein-Protein Interactions 165
12.Analysis of Protein-Protein Interactions in Comp;ex Biological Samples by MALDI TOF MS. Feasibility and Use of the Intensity-Fading (IF-) Approach 183
13.Accelerator Mass Spectrometry in Protein Analysis 203
14.The Use of Microcalorimetric Techniques to Study the Structure and Fundation of the Transferrin Receptor from Neisseria Meningitidis 217
15.The Quantitative Advantages of an Internal Standard in Multiplexing 2D Electrophoresis 231
16.Genetic Engineering of Bacterial and Eukaryotic Ribosomal Proteins for Investigation on Elongation Arrest of Nascent Polypeptides and Cell Differentiation 251
17.MALDI-MS Analysis of Peptides Modified with Photolabile Arylazido Groups 261
18.A New Edman-Type Reagent for High Sensitive Protein Sequencing 269
19.Amino Acid Sequencing of Sulfonic Acid-Labeled Trytic Peptides Using Post-Source Decay and Quadratic Field MALDI-ToF Mass Spectrometry 279
20.Separation of Peptides and Amino Acids using High Performance Capillary Electrophoresis 299
21.InterPro and Proteome Analysis - In Silico Analysis of Proteins and Proteomes 307
22.Prediction of Functional Sites in Proteins by Evolutionary Methods 319
23.Extracting and Searching for Structural Information: A Multiresolution Approach 341
24.Peak Erazor: A Windows-Based Programme for Improving Peptide Mass Searches 359
25.Increasing Throughput and Data Quality for Proteomics 371
A Laboratory Guide to the Mammalian Embryo / edited by David K. Gardner ... [et.al.]. -- Oxford, 2004
索书号:59.115/L123a
Contents:
1.Follicle Development in Vitro 3
2.Preparation of Gametes, in Vitro Maturation, in Vitro Fertilization, and Embryo Recovery and Transfer 24
3.Culture of the Mammalian Preimplantation Embryo 41
4.Assessment of Preimplantation Embryo Development and Viability 62
5.Micromanipulation of Gametes 76
6.Micromanipulation: Biopsy 99
7.Analysis of Intracellular Ions in Embryos:pH and Calcium 125
8. Assessment of Nutrient Uptake, Metabolite Production, and Enzyme Activity 139
9.Metabolic Pathway Activity 154
10.Confocal Imaging of Structural Molecules in Mammalian Gametes 165
11.Fluorescent in situ Hybridisation for Detection of Aneuploidy in Single Human Blastomeres for Preimplantation Genetic Diagnosis 184
12.Assessment of Ploidy, Telomere Length, and Telomerase Activity in Oocytes and Embryos 193
13.Microscale RNA Isolation from Mammalian Embryos 217
14.Relative mRNA Transcript Abundance in Early Embryyos by Reverse Transcription-Polymerase Chain Reaction 225
15.Characterization of Novel Genes during Early Development by Application of Differential Display RT-PCR 237
16.Two-Dimensional Protein Gel Database Analysis of Embryos, Oocytes, and Oocyte-Associated Granulosa Cells 247
17. Antisense Distruption of Gene Expression in the Preimplantation Embryo 258
18.Gene Subtration and Analysis 270
19.Analysis of Apoptosis in the Preimplantation Embryo 279
20.Cytoplasmic Signaling and Cell Cycle Control in the Mouse Egg and Embryo 298
21.Human Embryonic Stem Cells 313
22.Spermatogonial Transplantation 334
23.Somatic Cell Nuclear Transfer 352
24.Cryobiology: Slow Freezing Vitrification of Embryos 375
Signal transduction and human disease / edited by Toren Finkel and J. Silvio Gutkind. -- Wiley, 2003
1. Atherosclerosis: Signal Transduction by Oxygen and Nitrogen Radicals 1
2. NF-kB: A Key Signaling Pathway in Asthma 23
3. Molecular Mechanisms of Cancer 71
4. Apoptotic Pathways in Cancer Progression and Treatment 143
5. Molecular and Cellular Aspects of Insulin Resistance: Implications for Diabetes 171
6. dysfunction of G Protein-Regulated Pathways and Endocrine Diseases 201
7. Bacterial regulation of the Cytoskeleton 233
8. Bacterial toxins and diarrhea 259
9. Molecular Basis of Severe Combined Immunodeficiency: Lessons from Cytokine Signaling Pathways 279
10.Mast Cell-Related Diseases: Genetics, signaling Pathways, and Novel Therapies 307
11. Rheumatology and Signal Transduction 357
12. Molecular Mechanisms of Neurodegenerative Disorders 377
13. Neurotrophic Signaling in Mood Disorders 411
14. Inhibiting signaling Pathways Through Rational Drug Design 447
Microarrays & microplates : applications in biomedical sciences / by S. Ye and I.N.M.Day. -- BIOS, 2003
1. Onstrumentation for Genomics and Proteomics 1
2. Expression Microarrays 23
3. Tissue Microarrays: A High-Throughput Technology for Translational Research 45
4. Protein Chips and Microarrays 61
5. Single Nucleotide Polymorphism genotyping Using Microarrays 89
6. Microplate-Based mRNA Analysis 115
7. A Generalized 96-Well ELISA-Based Assay for Quantitative and Qualitative Monitoring of Cellular Events 131
8. Electrophoresis in Microplate Formats 145
PCR Technology : current innovations / edited by Thomas, Weissensteiner ... [et al.]. --2nd ed. -- CRC, 2004
1. Extraction and Amplification of Ancient DNA 5
2. Long PCR from Damaged DNA 11
3. Quantitative mRNA Analysis in Small Cell Samples by RT-PCR and Flow Cytometry 23
4.Microdissection of Single or Small Numbers of Cells for Analyses of DNA and RNA by PCR 29
5. Pre-PCR Processing Strategies 37
6. Novel PCR-Enhancing Compounds and Their Modes of Action 51
7. Optimizing PCR with the Aid of Experimental Design 65
8. Economic Fluorescent Labeling of PCR Products for Microsatellite and Single-Stranded Conformation Polymorphism (SSCP) Analysis 79
9. Universal Restriction Site-Free Cloning Method Using Chimeric Primers 87
10. High-Throughput Genotyping and the PCR 97
11. High-Throghput Genetic Analysis through Multiplexed PCR and Multicapillary Electrophoresis 111
12. The GOOD Assay: A Purification-Free Assay for Genotyping by MALDI Mass Spectrometry 121
13. Primer Design for Larg-Scale Multiplex PCR and Arrayed Primer Extension (APEX) 131
14. Surface Plasmon Resonance Based Biosensor Technology for Real-Time Detection of PCR Products 141
15. Fluorescent Amplified Fragment Length Polymorphism (FAFLP) Genotyping 155
16. Global Analysis of DNA Allelic Variations (GADAV) by Spectific 163
17. Quantitative DNA-Methylation Analysis by the Bisulfite Conversion Method 175
18. Pyrosequencing Technology 187
19. Octamer-Primed Cycle Sequencing 197
20. In Situ Amplification of cDNA 205
21. Detection of a Single-Copy Sequence on Human Metaphase by Cyclic PRINS 215
22. Meaningful Quantification of mRNA Using Real-Time PCR 225
23. Absolute Quantification of Specific Nucleic Acids by RT-PCR Using a Nonlinear Mathematical Model for Data Analysis 235
24. Single-Molecule PCR- Basic Protocols and Applications 245
25. Gene Expression and Discovery: Application of a Genome-Wide Approach 259
26. The Detection of Differential Gene Expression Changes Using SAGE 267
Current topics in developmental biology. v.54: Cell surface proteases / edited by Stanley Zucker. -- Academic Press, 2003
1. Membrane Type-Matrix Metalloproteinases (MT-MMP) 2
2. Surface Association of Secreted Matrix Metalloproteinases 75
3. Biochemical Properties and Functions of Membrane-Anchored Metalloprotease-Disintegrin Proteins (ADAMs) 101
4. Shedding of Plasma Membrane Proteins 125
5. Expression of Meprins in Health and Disease 150
6. Type II Transmembrane Serine Proteases 168
7. DPPIV, Seprase, and Related Serine Peptidases in Multiple Cellular Functions 207
8. The Secretases of Alzheimer‘s Disease 233
9. Plasminogen Activation ar the Cell Surface 263
10. Cell-Surface Cathepsin B: Understanding Its Functional Significance 313
11. Protease-Activated Receptors 343
12. Emmprin (CD147), a Cell Surface Regulator of Matrix Metalloproteinase Production and Function 372
13. The Evolving Roles of Cell Surface Proteases in Health and Disease: Implications for Developmental, Adaptive, Inflammatory, and Neoplastic Processes 391
14. Shed Membrane Vesicles and Clustering of Membrane-Bound Proteolytic Enzymes 411
Gene Biotechnology / by William Wu ... [et. al.]. -- 2nd ed. -- CRC, 2004
1. Strategies for Novel Research Projects 1
2. Rapid Isolation of Specific cDNAs or Genes by PCR 15
3. Construction and Screening of Subtracted and Complete Expression cDNA Libraries 31
4. Subcloning of Genes or DNA Fragments 73
5. Nonisotopic and Isotopic DNA or RNA Sequencing 99
6. Information Superhighway and Computer Databases of Nucleic Acids and Proteins 139
7. Characterization of DNA or Genes by Southern Blot Hybridization 165
8. Gene Overexpression by Sense RNA in Mammalian Systems 193
9. Gene Underexpression in Cultured Cells and Animals by Antisecse DNA and RNA Strategies 223
10. Analysis of Gene Expression at the Functional Genomic Level 247
11. Analysis of Gene Expression at the Proteomic Level 265
12. Analysis of Cellular DNA or Abundance of mRNA by Radioactivity in Situ Hybridization (RISH) 287
13. Localization of DNA or Abundance of mRNA by Fluorescence in Situ Hybridization (FISH) 311
14. In Situ PCR Hybridization of Low Copy Genes and in Situ RT-PCR Detection of Low Abumdance mRNAs 323
15. Isolation and Characterization of Genes from Genomic DNA Libraries 341
16. Culture of Mouse Embryonic Stem Cells as a Model Mammalian Cell Line for Gene Expression 365
17. New Strategies for Gene Knockout 375
18. Large-Scale Expression and Purification of Recombinant Proteins in Cultured Cells 409
19. Quantitative Analysis of Functional Genome by Current Real-Time RT-PCR 445
20. High-Throughput Analysis of Gene Expression by Cutting-Edge Technology- DNA Microarrays (Gene Chips) 461
21. Construction and Screening of Human Antibody Libraries: Using State-of-the-Art Technology - Phage Display 471
22. Dowm-Regulation of Gene Expression in Mammalian Systems via Current siRNA Technology 493
Biotechnology Annual Review. v.9 / edited by M. Raafat El-Gewely. -- Elsevier, 2003
1. Biochips beyond DNA: technologies and applications 1
2. Non-ribosomal peptide synthetases as technological platforms for the synthesis of highly modified peptide bioeffectors - Cyclosporin synthetase as a complex example 151
3. Horseradish peroxidase: a valuable tool in biotechnology 199
4. Considerations for the planning and conduct of reproducibility studies of in vitro diagnostic tests for infectious agents 249
5. Clinical trial methods to discover and validate predictive markers for treatment response in cancer 259
6. Production of high-quality marketing applications: strategies for biotechnology companies working with contract research organizations 269
7. Use of benchmarking in the development of biopharmaceutical products 279
8. The State of biopharmaceutical manufacturing 285
9. review of current authorship guideline and the controversy regarding publication of clinical trial data 303
10. Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules - Applications in biotechnology 315
11. The development of supportive-care agents for patients with cancer 315
Life sciences for the 21st century / edited by E. Keinan ... -- Wiley, 2004
1. Ribosomes, The Machines of Life 1
2. RNase P: Variations and Uses 49
3. The Antiquity of RNA-Based Evolution 61
4. Aminoacyl tRNA Synthetases as potential markers for the development of the genetic code 81
5. The Ubiquitin-Mediated Proteolytic System 93
6. How Proteins Speak With One Another in Cell Signaling 151
7. From Tyrphostins to Gleevec: Signal Transduction Therapy - From Concept to the Clinic 175
8. Protein Phosphorlation: What Does the Future Hold? 191
9. The Concept of Specificity in Peptide Vaccines for Infectious, Autoimmune and Neoplastic Diseases 225
10. The Prospect of Cell Replacement Therapy by Nuclear Transplantation 259
11. The Control of Hematopoiesis and Leukemia: From Basic Biology to the Clinica 269
12. No Future for Agriculture without Plant Biotechnology 287
13. The Phantom Vector of an Emerging Viroid 297
14. From Rapeseed ti Canola 305
15. Future of Maize Improvement 311
16. Population Dynamics in Evolutionary Ecology 327
Bioinformatics and functional genomics / by Jonathan Pevsner. -- Wiley, 2003
1. Introduction 3
2. Access to Sequence Data and Literature Information 15
3. Pairwise Sequence Alignment 41
4. Basic Local Alignment Search Tool (BLAST) 87
5. Advanced BLAST Searching 127
6. Bioinformatic Approaches to Gene Expression 157
7. Gene Expression: Microarray Data Analysis 189
8. Protein Analysis and Proteomics 223
9. Protein Structure 273
10. Multiple Sequence Alignment 319
11. Molecular Phylogeny and Evolution 357
12. Completed Genomes and the Tree of Life 397
13. Completed Genomes: Viruses 437
14. Completed Genomes: Bacteria and Archaea 465
15. Eukaryotic Genomes: Fungi 503
16. Eukaryotic Genomes: From Parasites to Primates 539
17. Human Genome 607
18. Human Disease 647
A Practical Guide to Developmental Biology / by Melissa Gibbs. -- Oxford, 2003
Part.1
1. Introduction to developmental biology 3
2. Axial Patterning 28
3. Plant cell totipotency 32
4. Fertilization 35
5. Early plant development 39
6. Morphogenesis 44
7. Cell adhesion 48
8. Embryogenesis 51
9. Neural induction 64
10. Gametogenesis 69
11. Regeneration 76
12. Metamorphosis 80
13. External influences on development 85
Pt.2 Information for the Instructor 89
Pt.3 Glossaries 109
Patterning in vertebrate development / edited by Cheryll Tickle. -- Oxford, 2003
1. Patterning and positional information 1
2. Laying down the vertebrate body plan 10
3. Patterning the Xenopus embryo 24
4. Somite and axial development in vertebrates 48
5. Vertebrate neurogenesis 90
6. Anteroposterior regionalization of the vertebrate nervous system 114
7. Axon guidance in the developing vertebrate nervous system 138
8. Patterning of the neural crest 166
9. Insights into the nolecular basis of vertebrate forelimb and hindlimb identity 198
10. Evolutionary aspects of vertebrate patterning 214
Cancer Cytogenetics: methods and protocols / edited by John SwansburyHumana Press c2003
Content
1.Cytogenetic Studies in Hematologic Malignancies: An Overiew 9
2.The Myeloid Disorders:Background 23
3.Cytogenetic Techniques for Myeloid Disorders 43
4.Acute Lymphoblastic Leukemia: Background 59
5.Conventional Cytogenetic Techniques in the Diagnosis of Childhood Acute Lymphoblastic Leukemia 73
6.Chromosome Preparations from Bone Marrow in Acute Lymphoblastic Leukemia: Cytogenetic Techniques 83
7.Lymphoid Disorders Other than Common Acute Lymphoblastic Leukemia:Background 93
8.Other Lymphoid Maligancies: Cytogenetic Techniques 111
9.Cytogenetic and Genetic Studies in Solid Tumors:Background 125
10.Human Solid Tumors:Cytogenetic Techniques 135
11.Analysis and Interpretation of Cytogenetic Findings in Malignancies 151
12.Cytogenetic Studies Using FISH: Background 173
13.FISH Techniques 193
14.FISH, CGH, amd SKY in the Diagnosis of Childhood Acuten Lymphoblastic Leukemia 213
15.Solving Problems in Multiplex FISH 235
16.Some Difficult Choices in Cytogenetics 245
17.Introduction to the Analysis of the Human G-Banded Karyotype 259
新书介绍
Design and Analysis of DNA Microarray Investigations
by Richard M. Simon, Edward L. Korn, Lisa M. McShane, Michael D. Radmacher, George W. Wright, and Yingdong Zhao
New York:Springer-Verlag, 2004. 199 pp.
ISBN: 0-387-00135-2. $59.95 cloth
Out damned spot! Out, I say!
--William Shakespeare, Macbeth
Or put another way, so many spots, yet so little space. Like the computer chip, the microarray chip represents a relentless striving toward cramming ever-increasing information (be it integrated circuits, DNA sequences, or proteins) onto an ever-shrinking area. The goals are greater complexity and miniaturization. Although the microarray industry will probably never approach the impact that computers have had, the innovative uses of microarrays in nearly all aspects of biologic, pharmaceutical, and medical research make it a force to be reckoned with both scientifically and economically. The microarray chip, like the computer chip, invokes a daunting, sometimes overwhelming amount of data. Thus, microarray experiments must be properly designed and carried out to reduce costs and limit misleading and statistically insignificant data.
This book by Richard Simon and his colleagues at the National Cancer Institute will help keep costs and lousy data minimal. It covers essentially three major topics: how to design microarray experiments, how to carry out microarray experiments, and how to analyze microarray data. The book is intended for scientists who wish to learn more about the design and analysis of microarray experiments and for computational scientists who want to learn what functional genomics is all about. It is also appropriate for graduate students interested in newer technologies. Its most positive aspect is the emphasis on experimental design, essential to a genomics experiment--a facet that is barely touched on and more often ignored by other books. Careful design helps minimize false positives, and when scanning the results of 30,000 genes per time point and/or dosage, extraneous data can become an issue.
For nonmolecular biologists, the authors admirably describe how benchtop techniques are carried out for different microarray platforms. One appendix explains some relevant basic cellular biology and another describes some noted examples of how microarray data sets have been applied to medical and biologic research. Mostly the book addresses data analysis (including a third appendix identifying some useful data analysis software tools). These chapters ably cover one of the most rapidly progressing fields in biology, high-throughput computational analysis. Most recently developed microarray analysis methods are described in sufficient detail that the nonmathematician can understand the underlying premise.
The book contains a few weaknesses, omissions, and errors. Unfortunately, one of the potentially most important and useful sections of the book--on experimental designs--is somewhat dogmatic without sufficiently covering other design options or referencing some relevant work in the area. The designs are rigidly divided into reference design (RD), balanced block design (BBD), and loop design (LD), without considering the possibility of mixing different types. For example, BBD is the most efficient for comparing only two classes of samples, whereas RD is most appropriate for comparing a very large number of samples. However, most microarray experiments actually fall between these two extremes, and the most appropriate design often warrants a combination of the three. The authors are particularly and unfairly critical of the LD, describing only one possible instance, in which each sample is tested twice and no "spokes" connecting nonadjacent experimental conditions are used. A simple modification, in which differentially labeled biologic replicates instead of same sample replicates are used, would significantly improve the efficiency of the design. Further, adding more spokes would greatly reduce the effect that a few bad arrays will have on the outcome while maintaining statistical superiority over the reference design in the number of effective measurements. Readers are urged to seek additional references when choosing their design. Lastly, there are a few minor printing mistakes; for example, the legends for Figures 3.3 and 3.4 are switched. Nonetheless, the book is a well-written, fairly comprehensive introduction on how to carry out functional genomics studies and can be recommended to students and researchers in mathematics, computer science, or bioinformatics as well as biology or medicine.