Parasite Genomics Protocols: (270 Methods in Molecular Biology)

Parasitic diseases remain a major health problem throughout the world, for both humans and animals. For many of us, our technologically advanced lifestyle has decreased the prevalence and transmission of parasitic diseases, but for the majority of the world’s population, they are ever present in homes, domestic animals, food, or the environment. The study of parasites and parasitic disease has a long and distinguished history. In some cases, it has been driven by the great importance of the presence of the parasite to the community, for example, those that affect our livestock. In other cases, it is clear that applied research has suffered for lack of funding because the parasite affects people with few resources, such as the rural poor in resource-poor countries. These instances include the so-called “neglected diseases,” as defined by the World Health Organization (WHO). Parasites have complicated life cycles, and a thorough understanding of the unique characteristics of a particular parasite species is vital in attempts to avoid, prevent, or cure infection or to alleviate symptoms. Of course, the biological characteristics that each parasite has developed to aid survival and transmission, to avoid destruction by the immune system, and to adapt to a changing environment are of lasting fascination to basic biologists as well. The elegance of these biological systems has ensured that the study of protozoan and metazoan parasites also remains an active field of research in countries where the diseases are not a threat to the population.

Table of Contents:
Sequencing Strategies for Parasite Genomes.- Annotation of Parasite Genomes.- Parasite Genome Databases and Web-Based Resources.- Expressed Sequence Tags.- Expressed Sequence Tags.- Positive Selection Scanning of Parasite DNA Sequences.- RACE and RAGE Cloning in Parasitic Microbial Eukaryotes.- Amplified (Restriction) Fragment Length Polymorphism (AFLP) Analysis.- Minisatellites and MVR-PCR for the Individual Identification of Parasite Isolates.- Analysis of Differentially Expressed Parasite Genes and Proteins Using Transcriptomics and Proteomics.- Gene Expression Studies Using Self-Fabricated Parasite cDNA Microarrays.- DNA Content Analysis on Microarrays.- Typing Single-Nucleotide Polymorphisms in Toxoplasma gondii by Allele-Specific Primer Extension and Microarray Detection.- Transfection of the Human Malaria Parasite Plasmodium falciparum.- A PCR-Based Method for Gene Deletion and Protein Tagging in Trypanosoma brucei.- Analysis of Gene Function in Trypanosoma brucei Using RNA Interference.- In Vitro Shuttle Mutagenesis Using Engineered Mariner Transposons.- Random Mutagenesis Strategies for Construction of Large and Diverse Clone Libraries of Mutated DNA Fragments.- Separation, Digestion, and Cloning of Intact Parasite Chromosomes Embedded in Agarose.- Chromosome Fragmentation in Leishmania.- FISH Mapping for Helminth Genome.- Fiber-FISH: Fluorescence In Situ Hybridization on Stretched DNA.- Yeast Two-Hybrid Assay for Studying Protein-Protein Interactions.- From Genomes to Vaccines for Leishmaniasis.