Parasite Genomics Protocols

Parasite Genomics Protocols

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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.
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Product details

  • Hardback | 452 pages
  • 158 x 228 x 30mm | 879.98g
  • Humana Press Inc.
  • Totowa, NJ, United States
  • English
  • 2004 ed.
  • XVI, 452 p.
  • 158829062X
  • 9781588290625

Review quote

"...represents an excellent resource for both students and researchers in the field." - Society for General Microbiolgy
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Back cover copy

Parasitic disease remains an important health issue in most regions of the world and constitutes a major cause of morbidity and mortality in developing countries. In Parasite Genomics Protocols, pioneering bench researchers describe in detail the cutting-edge techniques they have developed for analyzing the genomes and gene products in a diverse range of protozoan and metazoan parasites. These readily reproducible techniques can be used in genomic, functional genomic, and postgenomic studies and include transfection methods and vectors for several protozoan parasites, global analysis using microarrays, gene ablation using RNA interference, gene knockout, mutagenesis, and chromosome manipulation. Some of the protocols require DNA sequence data, whereas others were developed independently of whole-genome sequence data. Additional chapters survey the available genome sequences, helping novice researchers overcome the difficulties of accessing the databases and applying bioinformatics analysis to biological function. The protocols presented follow the successful Methods in Molecular Biology(TM) series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and the avoidance of known pitfalls.
State-of-the-art and highly practical, Parasite Genomics Protocols offers bench investigators in parasitology a wide-ranging collection of diverse methods for elucidating the content of the genomes of parasitic organisms, utilizing the genome sequence for genetic analysis, and ascribing function to the available genome sequences.
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Table of contents

Sequencing Strategies for Parasite Genomes
Daniella Bartholomeu and Najib M. El-Sayed

Annotation of Parasite Genomes
Matthew Berriman and Midori Harris

Parasite Genome Databases and Web-Based Resources
Christiane Hertz-Fowler and Neil Hall

Expressed Sequence Tags: Medium-Throughput Protocols
Claire Whitton, Jennifer Daub, Marian Thompson, and Mark Blaxter

Expressed Sequence Tags: Analysis and Annotation
John Parkinson and Mark Blaxter

Positive Selection Scanning of Parasite DNA Sequences
Winston A. Hide and Raphael D. Isokpehi

RACE and RAGE Cloning in Parasitic Microbial Eukaryotes
Bryony A. P. Williams and Robert P. Hirt

Amplified (Restriction) Fragment Length Polymorphism (AFLP) Analysis
Daniel K. Masiga and C. Michael R. Turner

Minisatellites and MVR-PCR for the Individual Identification of Parasite Isolates
Annette MacLeod

Analysis of Differentially Expressed Parasite Genes and Proteins Using Transcriptomics and Proteomics
Daniel C. Gare

Gene Expression Studies Using Self-Fabricated Parasite cDNA Microarrays
Karl F. Hoffmann and Jennifer M. Fitzpatrick

DNA Content Analysis on Microarrays
Upinder Singh, Preetam H. Shah, and Ryan C. MacFarlane

Typing Single-Nucleotide Polymorphisms in Toxoplasma gondii by Allele-Specific Primer Extension and Microarray Detection
Chunlei Su, Christian Hott, Bernard H. Brownstein, and L. David Sibley

Transfection of the Human Malaria Parasite Plasmodium falciparum
Brendan S. Crabb, Melanie Rug, Tim-Wolf Gilberger, Jennifer K. Thompson, Tony Triglia, Alexander G. Maier, and Alan F. Cowman

A PCR-Based Method for Gene Deletion and Protein Tagging in Trypanosoma brucei
George K. Arhin, Shuiyuan Shen, Elisabetta Ullu, and Christian Tschudi

Analysis of Gene Function in Trypanosoma brucei Using RNA Interference
Appolinaire Djikeng, Shuiyuan Shen, Christian Tschudi, and Elisabetta Ullu

In Vitro Shuttle Mutagenesis Using Engineered Mariner Transposons
Kelly A. Robinson, Sophie Goyard, and Stephen M. Beverley

Random Mutagenesis Strategies for Construction of Large and Diverse Clone Libraries of Mutated DNA Fragments
Sudsanguan Chusacultanachai and Yongyuth Yuthavong

Separation, Digestion, and Cloning of Intact Parasite Chromosomes Embedded in Agarose
Vanessa Leech, Michael A. Quail, and Sara E. Melville

Chromosome Fragmentation in Leishmania
Pascal Dubessay, Christine Blaineau, Patrick Bastien, and Michel Pages

FISH Mapping for Helminth Genomes
Hirohisa Hirai and Yuriko Hirai

Fiber-FISH: Fluorescence In Situ Hybridization on Stretched DNA
Klaus Ersfeld

Yeast Two-Hybrid Assay for Studying Protein-Protein Interactions
Ahmed Osman

From Genomes to Vaccines for Leishmaniasis
Carmel B. Stober

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