Microarray
What are microarrays?
DNA microarrays can be used for a variety of experiments, but the most common use for them is gene expression. To determine what genes are expressed in a cell using a microarray there are a few steps. First, mRNA is collected from a cell. This is the RNA that has been transcribed from DNA that will be translated into protein. Then, cDNA (or 'complementary' DNA) is collected by performing a process called reverse transcription (RT) on the mRNA. This DNA contains only the coding regions of the gene since it was created from RNA that has already undergone post-transcriptional modifications. The DNA nucleotides used during the RT process have been fluorescently labeled, usually with green or red. Then the fluorescent cDNA is placed on the microarray slide which contains fragments of many genes of interest (the researchers know which gene resides in which well from the start of the process) [1].
If a gene is upregulated in a cell then it will produce a lot of mRNA that will result in a lot of cDNA. The large amounts of fluorescent DNA will bind to the appropriate complementary gene fragment and will result in a high intensity of fluorescence in the well. This will indicate to the researchers that the gene is highly expressed. If a gene has a low level of expression or it is inactive in the cell then there will be little to no fluorescence in the well.
To learn more about microarrays, please see the video below.
If a gene is upregulated in a cell then it will produce a lot of mRNA that will result in a lot of cDNA. The large amounts of fluorescent DNA will bind to the appropriate complementary gene fragment and will result in a high intensity of fluorescence in the well. This will indicate to the researchers that the gene is highly expressed. If a gene has a low level of expression or it is inactive in the cell then there will be little to no fluorescence in the well.
To learn more about microarrays, please see the video below.
You can also try this interactive guide to microarrays:
Microarrays and HFE
One database that can be used to look up microarray data from a variety of experiments is called GEO, which stands for Gene Expression Omnibus. When I searched for HFE, I found an enormous amount of experiments (over 10,000) that had HFE on the microarray chip. However, I was able to find one study that was particularly interesting. This study was called "Presymptomatic and symptomatic malaria: peripheral blood mononuclear cells". This study was performed in humans. In looking at the data, I noticed that individuals that had an acute malaria infection showed decreased expression of the HFE gene compared to the individuals who were placed in the uninfected baseline category.
Analysis
This decreased expression of HFE in malaria patients seems logical as the malaria parasite first infects a person by entering the blood stream, after-which it goes to the liver where it grows and multiplies [2]. The liver is where HFE is most highly expressed in uninfected patients. Perhaps the parasites damage the liver so much that the liver cells no longer produce HFE. An interesting future study on this would be to see if malaria patients also have increased iron levels in their blood.
References
1. National Human Genome Research Institute: http://www.genome.gov/10000533
2. CDC - Malaria: http://www.cdc.gov/malaria/about/biology/index.html
3. University of Utah - Health Sciences - Learn Genetics: http://learn.genetics.utah.edu/content/labs/microarray/
4. YouTube - DNA Microarrays: https://www.youtube.com/watch?v=VNsThMNjKhM
5. GEO: http://www.ncbi.nlm.nih.gov/geo/
6. NCBI DataSet Browser - Presymptomatic and symptomatic malaria: peripheral blood mononuclear cells: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2362
2. CDC - Malaria: http://www.cdc.gov/malaria/about/biology/index.html
3. University of Utah - Health Sciences - Learn Genetics: http://learn.genetics.utah.edu/content/labs/microarray/
4. YouTube - DNA Microarrays: https://www.youtube.com/watch?v=VNsThMNjKhM
5. GEO: http://www.ncbi.nlm.nih.gov/geo/
6. NCBI DataSet Browser - Presymptomatic and symptomatic malaria: peripheral blood mononuclear cells: http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2362