September 15, 2005 (Vol. 25, No. 16)
Range of Offerings Are Available
Nature uses a common framework when building organisms as different as yeast, worms, fruit flies, mice, and humans. This makes it possible for scientists to learn about how our own genes work by studying what similar genes do in tiny, simpler, and rapidly reproducing model organisms. The model organisms can be easily manipulated in the lab and are popular workhorses of genetic research across the world.
The most commonly studied model organisms are yeast, Caenorhabditis elegans, Drosophila, zebrafish, and mouse, and they all share a vast number of genes, proteins, and even genetic pathways with humans.
In spite of the obvious differences in their size and way of life, all these model organisms make proteins that carry out the same core functions as in humans; telling the organism when and how to grow, reproduce, fight off stresses, and eventually die.
Model organisms act as surrogates for organisms with large and complex genomes, says Scott Harrison, marketing manager for custom and model organism microarrays, Agilent Technologies (www.agilent.com). It is possible to conduct experiments on model organisms that would not be allowed on humans for ethical reasons.
Model organism microarrays have been around since microarrays have been available. As genome sequencing projects continue to generate complete genomic sequences of new organisms, the probes on the microarrays have become highly comprehensive and more accurate.
Model organism microarrays provide the researcher with the ability to understand global gene expression changes in response to stresses and stimuli in the model organisms. Instead of trying to look for changes in a small number of known genes, it is possible with whole genome model organism microarrays to shine the light on the entire complement of genes of an organism and get the big picture of gene expression response.
Being able to examine the whole genome enables applications such as comparative genomics, single nucleotide polymorphism (SNP) discovery, and chromosome copy number aberrations, says Lianne McLean, senior director of product marketing, Affymetrix (www.affymetrix.com).
Ocimum Biosolutions (www.ocimumbio.com), which acquired the microarray division of MWG Biotech earlier this year, offers mouse, rat, zebrafish, and Arabidopsis. The mouse 30K OciChip comprises 28,755 mouse genes on three arrays.
The genes represented on the mouse microarrays are selected from NCBI and Ensembl and are non-redundant in their in-house proprietary database. The generated expression data will span a wide range of biological pathways since the microarrays include genes with known functions or clearly defined protein domains.
Ocimum microarrays are useful tools for functional genomics, drug discovery, and toxicogenomics. The Ocimum Rat 10K OciChip, the company asserts, is a good tool not only for identification of disease-relevant genes and fast screening of effects of new drugs, but also for analyzing the correlation of physiology, biochemistry, and biology.
Ocimum microarrays have 50-mer oligo probes which provide the best compromise between sensitivity and specificity, says Christian Betz, global head of production.
Agilent offers microarrays for the model organisms mouse, rat, Arabidopsis and rice as well. Agilents microarray printing process is based on industrial-scale inkjet technologies, and they use 60mer oligos as probes.
Agilent recently released mouse genome CGH microarray kit 44A, which, the company says, is the only commercially available product for genome-wide survey and molecular profiling of genomic aberrations, i.e., copy number changes, in mouse on a single chip. This microarray contains about 43,000 probes sourced from the NCBI genome build 33.
Agilents whole rat genome oligo micorarray has sequences that represent over 41,000 rat genes and transcripts on one slide with the content obtained from public databases, including RefSeq, Ensembl, UCSC Goldenpath, and Unigene. Over 70% of the 60-mer probes on the microarray are empirically validated with sequence orientation, accuracy and clustering assembly classification verified.
Arabidopsis thaliana is the first higher plant to be fully sequenced and annotated, and serves as the primary model organism for gene expression research in higher plants. Agilents Arabidopsis microarrays represent about 40,000 transcriptional units from annotated and unannotated regions of the genome.
This microarray is useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses. Agilents rice microarrays have about 22,000 genes and transcripts.
The Applied Biosystems (www.appliedbiosystems.com) Array system is generated with probes designed against a fully curated set of transcripts identified by the mouse or rat genome sequencing consortium as well as genes from the proprietary Celera Genomics database.
According to John Burrill, senior application scientist, Applied Biosystems has better coverage and the best view of the data and the genes than other microarrays systems because of the combination of the Celera data and the public database of genomic data.
The Applied Biosystems arrays system also includes complete searchable Celera annotations for the transcript sequences interrogated by every probe on the mouse or rat genome survey microarray.
Applied Biosystems offers Mouse Genome Survey and Rat Genome Survey Microarrays. Both the mouse and rat genome survey microarrays contain 32,996 probes that cover 44,498 individual transcripts and target a complete, annotated, and fully curated set of 32,381 mouse or rat genes.
Affymetrix appears to offer the most extensive list of model organism microarrays. The list ranges from Bacillus subtilis to rat and rice. They introduced eight new designs in 2004 and plan on launching seven more during 2005.
The model organism arrays offered this year include sugarcane, canine, medicago, rhesus macaque, citrus, tomato, and poplar. Affymetrix has plans to continue to expand the list, adds McLean.
The Affymetrix GeneChip microarrays combine semiconductor fabrication techniques with biochemistry to create a photolithographic manufacturing process capable of producing microarrays with millions of probes on a single glass chip. GeneChip technology continues to have tremendous room for growth, allowing for higher densities and more content on the same sized arrays, says McLean.
Affymetrix offers C. elegans and Drosophila whole genomic microarrays. The C. elegans array contains 25mer oligonucleotide probes synthesized in situ and designed to measure gene expression in over 22,500 transcripts. The array was designed using the December 2000 genome sequence, predicted transcripts, and EST sequences from the Sanger Center.
The Drosophila genome array was developed from sequences accessible through FlyBase. The 25mer oligo probes represent a total number of 13,500 transcripts.
Both C. elegans and Drosophila microarrays can be used to study genes involved in development, analyze the global effect of mutations, and build quantitative gene expression databases. Since C. elegans and Drosophila are model systems for crop safety and pesticides research, these arrays can be used to study gene expression changes upon exposure to pesticides and crop treatments.
Affymetrixs GeneChip Plasmodium/ Anopheles is the first microarray to provide comprehensive coverage of two organisms on a single array, interrogating over 20,000 transcripts from the malarial parasite Plasmodium falciparum and the mosquito, Anopheles gambiae.
The inclusion of both organisms on a single array allows scientists to better understand the molecular dynamics involved in the host-parasite relationship as well as the mechanism of action and biology behind malaria.
Whole genome microarrays can make excellent starting points for discovering genes that are involved in specific pathways. Scientists can use the whole organism microarrays to perform genome-wide screens for target validation, toxicity screening, or signaling pathway research and then follow up with other assays such as Taqman to validate the microarray results, says Burrill.
Taqman assay is a quantitative PCR assay that can be used for DNA copy number measurements, single nucleotide polymorphism genotyping, or verification of microarrays results.
Once you get a gene list from genomic screens and find their biological functions, it is possible to draw up a list of interesting genes that are related or act in the same or related pathways. This smaller subset of genes can then be studied more intensively using smaller custom microarrays.