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Functional Genomics
This collection of robust, readily reproducible methods for microarray-based studies includes expert guidance in the optimal data analysis and informatics. On the methods side are proven techniques for monitoring subcellular RNA localization en masse, for mapping chromosomes at the resolution of a single gene, and for surveying the steady-state genome-wide distribution of DNA binding proteins in vivo. For those workers dealing with massive data sets, the book discusses the methodological aspects of data analysis and informatics in the design of microarray experiments, the choice of test statistic, and the assessment of observational significance, data reduction, and clustering.
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...
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...
Neurogenetics
The rapid identification and characterization of genes of neurological relevance holds great potential for offering insight into the diagnosis, management, and und- standing of the pathophysiologic mechanisms of neurological diseases. This volume in the Methods in Molecular BiologyTM series was conceived to highlight many of the contemporary methodological approaches utilized for the characterization of neu- logically relevant gene mutations and their protein products. Although an emphasis has been placed upon descriptions of methodologies with a defined clinical utility, it is hoped that Neurogenetics: Methods and Protocols will appeal not only to clinical laboratory diagnosticians, but als...
PCR Mutation Detection Protocols
1Bimal D. Theophilus and Ralph Rapley provide biological and clinical investigators with a comprehensive collection of new, recent, and updated PCR-based screening methods suitable for detecting the presence of both known and novel mutations. The methods cover point mutations (e.g., ASO-PCR, SSCP, DGGE, chemical cleavage), deletions (multiplex PCR, FISH, blotting), non-sense mutations (PTT), and more. The new and exciting techniques of DNA array analysis, along with such recently developed experimental methods as conformation-sensitive gel electrophoresis, are also included. Each chapter explains the basic theory behind the technique and provides valuable notes essential for its successful execution.
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..
Molecular Cytogenetics
The new techniques of molecular cytogenetics, mainly fluorescence in situ hybridization (FISH) of DNA probes to metaphase chromosomes or interphase nuclei, have been developed in the past two decades. Many FISH techniques have been implemented for diagnostic services, whereas some others are mainly used for investigational purposes. Several hundreds of FISH probes and hybridization kits are now commercially available, and the list is growing rapidly. FISH has been widely used as a powerful diagnostic tool in many areas of medicine including pediatrics, medical genetics, maternal–fetal medicine, reproductive medicine, pathology, hematology, and oncology. Frequently, a physician may be puzzl...
Cancer Cytogenetics
A collection of key cytogenetic and FISH techniques used by modern clinical laboratories in the genetic analysis of human malignancies. The book's practical advice and methods are suitable for use at every level of expertise, including fully established laboratories, but with a sympathetic bias towards anyone considering setting up a new cytogenetics service. Here the reader will find not only elementary tutorials on the fundamentals of human karyotypes and chromosome analysis, but also detailed discussions on how laboratories may optimally upgrade their repertoire of capabilities to include such newer complementary techniques as CGH, FISH, and M-FISH.
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 ...
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...
