DNA methylation is an epigenetic mechanism of gene regulation, and aberrant methylation has been associated with various types of diseases, especially cancers. Detection of DNA methylation has thus become an important approach for studying gene regulation and has potential diagn ...

The design of adequate primers for polymerase chain reaction (PCR) is sometimes a difficult task. This is the case when either the target sequence harbors unusual nucleotide motifs or the template is complex. Unusual nucleotide motifs can be repeat elements, whereas complex templates are t ...

PerlPrimer is a cross-platform application for the design of standard PCR, bisulfite PCR, real-time PCR, and sequencing primers. The program combines accurate primer-design algorithms with powerful interfaces to commonly used Internet databases, such as sequence retrieval from ...

Many serial analysis of gene expression (SAGE) tags can be matched to multiple genes, leading to difficulty in SAGE data interpretation and analysis. As only a subset of genes in the human genome are transcribed in a certain type of tissue/cell, we used microarray expression data from different ti ...

To gain insights into the biological function and relevance of genes using serial analysis of gene expression (SAGE) transcription profiles, one essential method is to perform clustering analysis on genes. A successful clustering analysis depends on the use of effective distance or si ...

Serial analysis of gene expression (SAGE) and microarrays have found a widespread application, but much ambiguity exists regarding the amalgamation of the data resulting from these technologies. Cross-platform utilization of gene expression data from the SAGE and microarray tec ...

Serial analysis of gene expression (SAGE) is a powerful technique for measuring global gene expression through sampling of transcript tags. SAGE tag collections or libraries serve as a rich data source for differential gene expression analysis, transcriptome mapping, and gene disco ...

Random fingerprinting strategies have been applied to a number of genome projects using unordered collections of phage or cosmid clones, e.g., Escherichia coli (1), Saccharomyces cerevisiae (2), and Caenorhabditis elegans (3). Overlaps were identified between either phage or cosmid ...

Chimerism, the presence of noncontiguous DNA fragments in the same clone, is one of the most common problems encountered when working with yeast artificial chromosomes (YACs). Its frequency can vary among the different libraries, but on average, 40–60% of YAC clones among the most used librari ...

Several methods have been published that rely on the use of short oligonucleotide primers with arbitrary sequences to amplify discrete DNA fragments by the polymerase chain reaction (PCR) (1,2). Typically, a single arbitrary primer is used in each reaction and amplification is achieved w ...

The vectorette unit (1) consists of a pair of annealed oligonucleotides that contain two regions of complementary nucleotide sequence flanking a 29-bp noncomplementary segment (Fig. 1). The 5′ terminus of one of these complementary regions is phosphorylated and displays a restriction ...

The termini of yeast artificial chromosome (YAC) inserts can serve as probes or sequence tagged sites (STSs) that are useful in genomic analysis. For example, these elements can be used to:

In the construction and characterization of yeast artificial chromosome (YAC) contigs, it is necessary to be able to isolate and map the ends of the genomic inserts. This is important with respect to both extending contigs, and identifying chimerism. A number of techniques have now been descri ...

The detailed analysis of the DNA cloned in yeast artificial chromosomes (YACs) is performed by subcloning into vectors such as phages or cosmids, which allow a simpler purification of insert DNA in addition to allowing high resolution mapping. Cosmids or phages are still a preferred DNA source ...

The very large cloning capacity of yeast artificial chromosomes (YACs) has facilitated the analysis of complex genomes by bridging physical and genetic maps. The large size of YAC inserts also creates some unique problems, including identification of novel genes on large stretches of un ...

Gene-based in vivo electroporation has the potential to be used as a “protein-free” method to elicit immune responses and to generate monoclonal antibodies (mAb) against proteins/peptides in hosts. However, the method is very useful to raise mAbs against proteins and peptides and not for ca ...

Effective multi-agent/multivalent vaccines that confer protection against more than one disease are highly desirable to the patient and to health-care professionals. Electroporation of DNA vaccines, whereby tissues injected with DNA are subjected to localized electrical c ...

Vaccination is historically one of the most important methods for preventing infectious diseases in humans and animals. New insights in the biology of the immune system allow a more rational design of vaccines, and new vaccination strategies are emerging. DNA vaccines have been proposed as a ...

Strategies to improve vaccine efficacy are still required. The immunogenicity of DNA vaccines is strongly improved by electroporation (EP). The skin is populated with a wide variety of immune cells, making it an attractive tissue for vaccine delivery. Here we describe a method for the EP-medi ...

Vaccines to prevent HIV remain desperately needed, but a number of challenges, including retroviral integration, establishment of anatomic reservoir sites, high sequence diversity, and heavy envelope glycosylation. have precluded development of a highly effective vaccine. ...