Bioinformatics Lab Report

Introduction We set out to help treat prostate cancer. The prostate is a gland that is part of the male reproductive system (Early Prostate Cancer, 2009). Prostate cancer forms within the tissue of the prostate and is the second most common cancer among men (Early Prostate Cancer, 2009). Symptoms of prostate cancer include urinary problems, difficulty having an erection, blood in the urine or semen and pain in the lower back, hips or upper thigh regions (Early Prostate Cancer, 2009). The importance of this lab was to find a way to help locate prostate cancer and allow for more localized radiation therapy. Marking of the cancer was done by using genetic engineering. Genetic engineering is the process of manipulating an organisms DNA material to change it to a state that does not naturally occur (Genetic Engineering, 2010). Genetic engineering used in this experiment was able to create a DNA sequence that would cause the prostate cancer cells to be marked by a certain protein. To create the DNA that would cause the marking of prostate cancer cells we had to create a promoter sequence that contained the transcription factors SRY, NF-YA and TBP (Bioinformatics Handout, 2007). With the correct promoter sequence it allows for the gene to be expressed. By creating a DNA containing these necessary components it allows the Green Florescent Protein to target and mark prostate cancer cells. The Green Florescent Protein was derived from a jellyfish, the Aequorea victoria, and glows when a light is shone on it (Zimmer, 2009). Because the protein glows it allows for easy tracking in organisms when it is genetically engineered into certain cell type DNA. The gene construct we made will allow for prostate cancer cells to be marked with the Green Fluorescent Protein. By marking the cancer cells it would allow for the cancer to be tracked throughout the entire body because the cells will now glow a neon green color when placed under a light. Once located the cancer could be fought more effectively

and less harm could be done to healthy cells because radiation therapy could be targeted to specific areas hosting cancer. By creating this gene construct we hope to help be able to better fight prostate cancer.

Methods As a group we were assigned a cancer, which was prostate cancer, by the TA. The marker decided upon to mark this cancer was Green Florescent Protein (GFP). Next we went online to the Pub Med Online Database and searched for GFP isolated from the jellyfish, the Aequorea victoria. The next step was finding the correct mRNA sequence, including a 5 UTR and 3 UTR, that was not synthetic. This sequence was then copy and pasted into a program named APE. Once the sequence was pasted into APE the correct open reading frame was found using the APE software. We then labeled components of the sequence such as the 5 UTR, 3 UTR and the coding sequence. Next we read through the lab manual and found a transcription factor and two basal promoters that were needed for a prostate tumor to express the coding sequence. We decided that the SRY and two basal promoters were needed to be located in the promoter attaching to GFP. Then we went onto the UMass Amherst biology website to download possible promoters. Next we went onto the JASPER database to find which promoter sequences contained the transcription factors as well as the correct basal promoters. To do this different promoter sequences and basal promoters were compared until the correct one was found. After the correct promoter sequence was found we copy and pasted it into APE in front of the 5 UTR. Then the promoter sequence and basal promoters were labeled. Finally the complete annotated sequence was printed out. Results

The results and full promoter sequence are attached and located at Figure 1. The genetic construct contains several key components to it. The promoter sequence contains three transcription factors that are labeled with different colors in Figure 1. The SRY transcription factor is labeled orange, the NF-YA is labeled in light green and the TBP is labeled in pink. The SRY transcription factor allows GFP to be expressed in a prostate cancer cell. NF-YA and TBP are required to have a proper functioning promoter. The final parts labeled in the genetic construct are the 5 UTR that is labeled in green, the actual coding sequence for the GFP that is labeled in blue and the 3 UTR that is labeled in light pink. Without all of these necessary components the genetic sequence would not work correctly. Discussion The gene construct is expected to target prostate cancer cells and attach GFP to the cancerous cells. The gene construct should work this way because the proper components, promoter sequence basal promoters TBP etc., have been put into the gene construct. Having these components should allow the gene construct to act properly and cause the prostate cancer cells to glow when a light is shone over them. Sadly it is not this easy to cure cancer. There are many variables that must be taken into account and could cause this to be ineffective. The GFP could be expressed in other cells due to the possibility that other cells contain the same transcription factors that GFP does. Therefore GFP could appear in locations that are not affected by cancer. Also this may not work because not all cancerous tumors have the same genetic makeup and the GFP would therefore not be found in these tumors (Winslow, 2010). By using this gene construct it does not cure cancer but allows it to be located much easier. Once the cancerous cells are located they can be killed using radiation therapies. These therapies often kill healthy cells in the process though and that is why having GFP

locate the cancer would make it less harmful. The GFP does have great potential to be helpful in the future though. This is because if in the future we are able to find very specific transcription factors that only appear in certain types of cancerous cells then we could locate those cells using GFP. Once GFP is able to locate cancerous cells and only cancerous cells then we will be able to fight cancer more effectively. Overall GFP shows get potential to be beneficial in the near future. Citations Bioinformatics Handout. University of Massachusetts, Amherst, MA. June 26, 2007. Retrieved November 15, 2010, From http://intro.bio.umass.edu/manual/index.php/BioinformaticsHandout Bioinformatics-Intro Lab Manual. University of Massachusetts, Amherst, MA. June 26 2007. Retrieved November 15, 2010, From, http://intro.bio.umass.edu/manual/index.php/Bioinformatics Genetic Engineering. Retrieved November 15, 2010, from Wikipedia: http://en.wikipedia.org/wiki/Genetic_engineering National Cancer Institute. (2009). Early Prostate Cancer. Retrieved November 15, 2010 from, http://www.cancer.gov/cancertopics/factsheet/Detection/earlyprostate PubMed Nucleotide Database. (October 28, 2009). Aequorea victoria green-fluorescent protein (GFP) mRNA, complete cds. Retrieved November 3, 2010 from http://www.ncbi.nlm.nih.gov/nuccore/L29345.1 Winslow, Ron. (February 19, 2010). New Tests Genetically Fingerprints Tumors. Wall Street Journal. Retrieved November 15, 2010 from, http://online.wsj.com/article/SB1000142405274870426900457507 3640581947242.html Zimmer, Marc. (2009). History: Marty Chalfie. Retrieved November 15, 2010 from,

http://www.conncoll.edu/ccacad/zimmer/GFP-ww/chalfie.html Zimmer, Marc. (2009). Cool Uses. Retrieved November 15, 2010 from, http://www.conncoll.edu/ccacad/zimmer/GFP-ww/cooluses1.html (January 16, 2000). The JASPAR Database. Retrieved November 3, 2010. From http://jaspar.genereg.net/cgibin/jaspar_db.pl? rm=browse&db=core&tax_group=vertebrates