Interactions between cis-acting elements and proteins play a key role in transcriptional regulation of all known organisms. To better understand these interactions, researchers developed a method that couples chromatin immunoprecipitation with microarrays (also known as ...

The yeast artificial chromosomes (YAC) system makes it possible not only to clone large DNA fragments but also to simplify the physical mapping and functional analysis of chromosomes and genomes through YAC manipulation. To manipulate large DNA fragments cloned into YACs, YAC fragment ...

DNA cloned in yeast artificial chromosomes (YACs) is a valuable resource for functional experiments in cell culture as well as whole animal systems. Where the size or chimerism of a YAC clone are limiting factors it may be desirable to generate recombinant YAC clones. One such approach is based on mi ...

Mouse yeast artificial chromosomes (YACs) are useful platforms for manipulation of targeting vector design and construction, particularly in circumstances where polymerase chain reaction-mediated amplification of targeting arms proves fruitless or the cloned DNA is inh ...

The generation of transgenic animals has become an important tool in helping to understand the roles of genes in maintaining health and the roles of human gene variants in contributing to disease susceptibility. In order to model the subtleties of gene expression, which include tissue-spe ...

Genomic-type transgenes are usually expressed in appropriate spatial- and temporal-specific manners. The largest genomic transgenes can be prepared using yeast artificial chromosomes (YACs). Normally, YAC transgenic mice are produced by standard pronuclear microinjec ...

Transgenic mice produced with human yeast artificial chromosomes (YACs) generally display transgene expression patterns that reflect those of the normal human host. Because mice are expensive and time-consuming to generate and maintain, extensive mutation-phenotype corr ...

In addition to the well-known applications of yeast artificial chromosomes (YACs) in classical molecular genetics, they also are used for molecular cytogenetic studies. YACs, as well as other locus-specific probes like DNA, plasmids, cosmids, P1-clones, or bacterial artificial chr ...

This chapter describes the methodology used both in performing the electrophoretic karyotype of the protozoan parasite Trypanosoma cruzi and mapping the genetic markers of the chromosomal bands, the construction of chromosome-specific YAC contigs, and their use to assign a chrom ...

Whole mount in situ hybridization is a process that allows the visualization of gene expression (mRNA) within the cells of an intact organism. By comparing gene expression domains between organisms that have been subjected to different environmental conditions, an understanding of t ...

Differential display polymerase chain reaction (PCR) can facilitate the identification of novel molecular end points related to contaminant exposure in a wide range of species. To date, various differential display methodologies have been described in detail. Herein, we describe a ...

Nylon membrane-based cDNA macroarrays are a widely available alternative to cDNA microarrays for the collection of large-scale gene expression data. cDNA macroarrays are used in many areas of molecular biology research for applications ranging from gene discovery to gene express ...

Many organisms provide excellent models for studying disease states or for exploring the molecular adaptations that allow cells and organisms to cope with or survive different stresses. The construction of a cDNA library and subsequent screening for genes of interest allows researc ...

The method we describe in this chapter describes the synthesis and use of cDNA macroarrays for determining changes in gene expression due to environmental toxicants as well as the methods and materials that are required to do this work. While the details are for investigators working with nont ...

The use of DNA microarrays has gained wider acceptance as a standard tool for molecular biology studies over the past decade. In particular, biomedical studies embraced this technology as soon as arrays were produced for the common laboratory species. Slower to develop, however, has been the u ...

Environmental pollutants may affect the activities of many cellular enzymes. The effect on the proteome of enzymatic inhibitors can be determined using two-dimensional (2D) gel electrophoresis. In neuroendocrine cells, proprotein convertases 1 and 2 (PC1 and PC2) mediate the prote ...

Pollution in aquatic environment is of increasing concern for its impact on both human and natural populations. Applying proteomics to monitor marine pollution is a new approach to evaluate the effects of environmental pollutants on the biota. Aquatic organisms living in coastal and est ...

DNA methylation patterns are often altered in human cancer and aberrant methylation is considered a hallmark of malignant transformation. Several methods have been developed for the characterization of gene-specific and genome-wide DNA methylation patterns. In this chapter, we ...

A novel procedure for DNA methylation analysis is described that characterizes the extent of DNA methylation in CpG islands. The basic concept relies on direct immunodetection of 5′ methylcytosines (5′ mCs) without the need for bisulfite treatment utilizing a microarray format. This sy ...

noindent Sodium bisulfite modification-based fine mapping of methylated cytosines represents the gold standard technique for DNA methylation studies. A major problem with this approach, however, is that it results in considerable DNA degradation, and large quantities of genom ...