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The unscheduled DNA synthesis (UDS) assay measures a cell’s ability to perform global genomic nucleotide excision repair (NER). This chapter provides instructions for the application of this technique in living cells by creating 6−4 photoproducts and pyrimidine dimers using UVC irr ...

Host cell reactivation (HCR) is a transfection-based assay in which intact cells repair damage localized to exogenous DNA. This chapter provides instructions for the application of this technique using UV irradiation as a source of damage to a luciferase reporter plasmid. Through measu ...

A method is described that makes use of a polyclonal antiserum to measure repair of the principal photoproducts induced in DNA by short-wave ultraviolet light (UVC)—pyrimidine-pyrimidone 6-4 photoproducts (PPs) and cyclobutane pyrimidine dimers (CPDs). DNA extracted from irradi ...

Double-strand breaks (DSBs) in genomic DNA are induced by ionizing radiation or radiomimetic drugs, but they also occur spontaneously during the cell cycle at quite significant frequencies. In vertebrate cells, nonhomologous DNA end joining (NHEJ) is considered the major pathway of DSB ...

A method is presented to measure homologous recombination in mouse embryonic stem cells by both gene targeting and short-tract gene conversion of a double-strand break. A fluorescence-based reporter is first gene targeted to the Hprt locus in a quantifiable way. A homing endonuclease exp ...

The analysis of gene expression is an integral part of any research characterizing gene function. A wide variety of techniques have been developed for this purpose, each with their own advantages and limitations. This chapter seeks to provide an overview of some of the most recent as well as conven ...

Pharmacogenomics encompasses several major areas: the study of polymorphic variations in drug response and disease susceptibility, identification of the effects of drugs/xenobiotics at the genomic level, and genotype/phenotype associations. The most common type of human ge ...

Real-time, quantitative reverse transcriptase (RT)-PCR is a very useful and powerful technology for analysis of gene expression. At a first pass, real-time PCR appears to be a simple extension of regular PCR, and it should therefore be easy for an experienced PCR user to convert to quantitative as ...

Membrane phospholipids are gaining increasing attention as important mediators in a variety of signal transduction processes. Oxidation and changes in membrane topography of lipids are probably important elements in the regulation of phospholipid-dependent signaling. P ...

We present here the application of a novel assay that measures the absolute amount of phosphatidylserine (PS) externalized on the surface of cells. Although the assay is based on the same annexin binding principle as the fluorescent flow cytometry assay, we use paramagnetic iron as the ultima ...

Many environmental toxins cause DNA damage. Cells that have sustained significant DNA damage must attempt to repair the damage prior to replication, in which aberrant base incorporation can result in an irreversible mutation. If a cell cannot repair the damage, however, it may commit suici ...

The interaction between genetic variation and environment is widely acknowledged as the underlying explanation for differences in drug response among individuals, as well as the stratifying force behind disease phenotypes. When DNA variation is found to associate with a phenotyp ...

In this chapter we distinguish the use of predictive biomarkers from surrogate endpoint biomarkers. We also distinguish the use of predictive biomarkers for selecting patients for pivotal clinical trials of a new drug from the use of predictive biomarkers for optimizing the utilizati ...

Biomarkers are an integral part of a successful clinical drug development strategy and the associated commercialization of drug development programs. Biomarkers are used as necessary and as they are available to optimize drug development in early and late stage clinical trials. Achi ...

With the relatively short history of pharmacogenomics being applied in the context of the pharmaceutical industry, many questions and concerns (some legitimate, some not so legitimate) arise regarding the appropriate implementation of this technology to deliver the greatest va ...

The molecular diagnostic industry continues to grow at a double-digit pace to meet increasing demand for the integration of diagnostic procedures with the selection of therapy, and the development of personalized drugs whose administration is guided by test results. Newly developed ...

Epilepsy is one of the commonest neurological disorders. Although multiple antiepileptic drugs (AEDs) are available, treatment in individual patients is often problematic due to the unpredictability of efficacy, adverse drug reactions, and optimal dosage. Moreover, up to one thi ...

Serious mental illnesses, including schizophrenia and major depressive disorder, result in considerable chronicity, morbidity, and mortality, and are amongst the leading causes of disability in the developed world. Despite advances in development of pharmacologic agents ov ...

Pharmacogenetics holds promise in HIV treatment because of the complexity and potential toxicity of multidrug therapies that are prescribed for long periods. However, there has been limited success with the current approach, in which one or few candidate genes are examined for a limited n ...

Cardiovascular diseases are a large group of multifactorial pathologies. Thus, it is not surprising that more than 13 classes and many subclasses of drugs have been developed in this field. However, the responses to these drugs differ significantly between patients. Five groups of genes are ...