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Biostatistical Methods
Leading biostatisticians and biomedical researchers describe many of the key techniques used to solve commonly occurring data analytic problems in molecular biology, and demonstrate how these methods can be used in the development of new markers for exposure to a risk factor or for disease outcomes. Major areas of application include microarray analysis, proteomic studies, image quantitation, genetic susceptibility and association, evaluation of new biomarkers, and power analysis and sample size.
Oxidants and Antioxidants
In our first protocols book, Free Radical and Antioxidant Protocols (1), r- erence to in vivo, ex vivo, or in situ techniques were few compared to classical biochemical assays and only 6 of the 40 chapters were concerned with these applications. In our second book, Oxidative Stress Biomarkers and Antioxidant Protocols (2), which is being published concurrently with this third volume, Oxidants and Antioxidants: Ultrastructure and Molecular Biology Protocols, the number of such chapters has increased. The literature dealing with histoche- cal/cytochemical and immunohistochemical techniques and staining to identify cellular/subcellular sites of oxidative stress has expanded rapidly, as has the ...
Superantigen Protocols
Leading researchers in the biological, chemical, and physical investigation of superantigens describe in step-by-step detail their best experimental techniques to assess the physical characteristics and biological effects of superantigens. Their protocols range from those for investigating the interactions of superantigens with cellular receptors to those for the analysis of their immunological and biological effects, including methods for using BIOcore to determine binding kinetics and establishing various lymphocyte cell culture systems. There are also accounts of such methods as the RNase protection assay, cytokine ELISA, FACS analysis, and cytokine production at the single cell level..
DNA Methylation Protocols
DNA Methylation Protocols offer a set of readily reproducible protocols of the analysis of DNA methylation and methylases. These powerful methods provide the tools necessary for studying methylation at both the global level and the level of sequence, and include many techniques for identifying genes that might be aberrantly methylated in cancer and aging. Additional methods cover genome-wide analysis of abnormal DNA methylation and the isolation and measurement of demethylases and related proteins.
Protein Sequencing Protocols
Determination of the protein sequence is as important today as it was a half century ago, even though the techniques and purposes have changed over time. Mass spectrometry has continued its recent rapid development to find notable application in the characterization of small amounts of protein, for example, in the field of proteomics. The “traditional” chemical N-terminal sequencing is still of great value in quality assurance of the increasing number of biopharmaceuticals that are to be found in the clinic, checking processing events of recombinant proteins, and so on. It is joined in the armory of me- ods of protein analysis by such techniques as C-terminal sequencing and amino acid an...
High Throughput Screening
In High Throughput Screening, leading scientists and researchers expert in molecular discovery explain the diverse technologies and key techniques used in HTS and demonstrate how they can be applied generically. Writing to create precisely the introductory guidebook they wish had been available when they started in HTS, these expert seasoned authors illuminate the HTS process with richly detailed tutorials on the biological techniques involved, the management of compound libraries, and the automation and engineering approaches needed. Extensive discussions provide readers with all those key elements of pharmacology, molecular biology, enzymology, and biochemistry that will ensure the identification of suitable targets and screens, and detail the technology necessary to mine millions of data points for meaningful knowledge.
In Situ Detection of DNA Damage
Detection and analysis of DNA damage is of critical importance in a variety of biological disciplines studying apoptosis, cell cycle and cell di- sion, carcinogenesis, tumor growth, embryogenesis and aging, neu- degenerative and heart diseases, anticancer drug development, environmental and radiobiological research, and others. Individual cells within the same tissue or in cell culture may vary in the extent of their DNA damage and, consequently, can display different re- tions to it. These differences between individual cells in the same cell popu- tion are detected using in situ approaches. In situ is a Latin term meaning “on site” or “in place.” It is used to denote the processes ...
MHC Protocols
The aim of MHC Protocols is to document protocols that can be used for the analysis of genetic variation within the human major histocompatibility complex (MHC; HLA region). The human MHC encompasses approximately 4 million base pairs on the short arm of chromosome 6 at cytogenetic location 6p21. 3. The region is divided into three subregions. The telomeric class I region contains the genes that encode the HLA class I molecules HLA-A, -B, and -C. The centromeric class II region contains the genes encoding the HLA class II molecules HLA-DR, -DQ, and -DP. In between is the class III region, originally identified because it contains genes encoding components of the complement pathway. The entir...
Single Nucleotide Polymorphisms
A comprehensive collection of readily reproducible techniques for the difficult process of single nucleotide polymorphisms (SNP) discovery and genotyping. These cutting-edge protocols for mutation/SNP detection utilize denaturing high-performance liquid chromatography (dHPLC), single-strand conformation polymorphism (SSCP), conformation-sensitive gel electrophoresis (CSGE), chemical cleavage, and direct sequencing. Equally powerful and up-to-date methods are given for genotyping SNPs, including molecular beacons, the Taqman assay, single-base extension approaches, pyrosequencing, ligation, the Invader assay, and primer extension with mass spectrometry detection.
Liposome Methods and Protocols
In vitro utilization of liposomes is now recognized as a powerful tool in many bioscience investigations and their associated clinical studies, e.g., liposomes in drug targeting; liposomes in gene transport across plasma and nuclear membranes; liposomes in enzyme therapy in patients with genetic disorders. However, before these areas can be effectively explored, many basic areas in liposome research require elucidation, including: (a) attachment of liposomes to cell surfaces; (b) permeation of liposomes through the plasma membranes; and (c) stability of liposomes in cell or nuclear matrices. None of these areas have been exhaustively explored and liposome researchers have ample opportunities...
