This website was constructed as a class project for Genetics 564, an undergraduate Genetics course at UW-Madison.
What is microarray?
Microarrays are a tool used to examine the expression levels of several genes at once [1]. DNA or RNA of interest is loaded on to a "gene chip." This gene chip has up to thousands of spots where cDNA (complimentary DNA) for individual genes has been placed, all of which are known beforehand. If the sample DNA or RNA can bind to the cDNA at a particular spot, it will emit light because of the way it has been fluorescently labeled. This light is read by a computer that measures the brightness of the light. Brighter light means more binding, which indicates higher levels of expression for that gene. Microarray can also be used to compare more than one DNA or RNA sequence at a time. Gene chips like those described above can be compared, or two samples with different fluorescent labels can be loaded on the same gene chip and their light patterns can be analyzed by a computer. Either way, this is useful because it can allow us to draw conclusions about how a given condition (e.g. a genetic mutation, biochemical treatment) may affect gene expression.
A diagram of the comparative microarray process.
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This is a sample microarray table. There are two groups, distinguished by both a title at the bottom and the background color. Each gene is in a gray box about the group title. Four genes are being examined in this set. Gene expression level is indicated by the red bar and measured by the scale on the left.
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Aldolase B Microarrays
A useful resource for looking up already published microarray data is GEO (Gene Expression Omnibus). GEO is a database where researchers submit their microarray and genomic data, and other scientists can look it up by searching for their gene of interest. In searching for aldolase B, I found one study on chickens and fasting. The microarray data (diagram unavailable) indicated that aldolase B in chickens was upregulated when chickens were fasting. This means gene expression of aldolase B was higher when the chickens were not eating.
This result is somewhat unsurprising, since aldolase B also plays a role in gluconeogenesis, the body's process for making glucose to put into the bloodstream. Under fasting conditions, blood glucose drops, so a healthy individual's body compensates by synthesizing glucose to send back into the blood, raising blood glucose back to normal [3]. It would be interesting to see more studies done on different expression levels of aldolase B. On my Specific Aims page, I propose an experiment to contribute to the development of a dietary supplement for individuals with HFI. Microarray could be used in this experiment to determine whether the genes expressed in wild-type (phenotypically normal) Drosophila are also being expressed at the same levels in Drosophila being tested with chemicals that could recover fructose metabolism.
This result is somewhat unsurprising, since aldolase B also plays a role in gluconeogenesis, the body's process for making glucose to put into the bloodstream. Under fasting conditions, blood glucose drops, so a healthy individual's body compensates by synthesizing glucose to send back into the blood, raising blood glucose back to normal [3]. It would be interesting to see more studies done on different expression levels of aldolase B. On my Specific Aims page, I propose an experiment to contribute to the development of a dietary supplement for individuals with HFI. Microarray could be used in this experiment to determine whether the genes expressed in wild-type (phenotypically normal) Drosophila are also being expressed at the same levels in Drosophila being tested with chemicals that could recover fructose metabolism.
References
1. Genetics Home Reference. (2014). Microarray technology. Retrieved May 18, 2014 from http://ghr.nlm.nih.gov/glossary=microarraytechnology.
2. Trakooljul, N., Porter, T.E., Cogburn, L.A. (2007). Hepatic Transcriptional Profiling of Hatchling Chicks and Market-age Broiler Chickens during Fasting and Re-feeding. NCBI GEO April 2008. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9745.
3. Wiley. (2014). Gluconeogenesis. Interactive Concepts in Biochemistry. Retrieved May 18, 2014 from http://www.wiley.com/college/boyer/0470003790/animations/gluconeogenesis/gluconeogenesis.htm.
2. Trakooljul, N., Porter, T.E., Cogburn, L.A. (2007). Hepatic Transcriptional Profiling of Hatchling Chicks and Market-age Broiler Chickens during Fasting and Re-feeding. NCBI GEO April 2008. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9745.
3. Wiley. (2014). Gluconeogenesis. Interactive Concepts in Biochemistry. Retrieved May 18, 2014 from http://www.wiley.com/college/boyer/0470003790/animations/gluconeogenesis/gluconeogenesis.htm.