The goal of this project is to familiarize you with the field of bioinformatics, which is the use of computers to solve

biological problems, and other genetic technologies. 1. (3 points) The crime is a particularly gruesome one. Professor Hal Wickams was found murdered at home with a tail-less mouse stuffed into his mouth. The victim was a quiet, single man who lived in an apartment in Minneapolis. He was a clean freak and Ms. Doris Dillens was hired to spotlessly clean the apartment every morning. She does not work for anyone else and has no pets. He had no pets, few friends and according to his neighbors he never had visitors. He was afraid of flying and did not travel anywhere. You are part of a forensic team investigating the crime. The crime scene techs have isolated biological samples that they gave to the DNA sequencing labs and the output from the lab results is shown below. Analyze the fragments of DNA sequences below and compile a report of what to look for in a potential suspect a profile of the subject. In your report explain how you made the conclusions. You will get a bonus point for explaining why the mouse had no tail! Sequence 1: Soil bacterium Thermobaculum terrenum from Yellowstone area Sequence 2: Parrot/Exotic Bird Sequence 3: Dog (100% match) or Cat (99% match) Sequence 4: Mouse Qualities the suspect should have: 1. Works/interacts with exotic birds at zoo, home, etc. because the second sequence was a 100% match for an exotic bird. 2. Native to or travelled through Yellowstone National Park because sequence 1 is a match for a localized thermophile from Yellowstone Park. 3. Suspect could potentially own a dog or cat because dog/cat DNA was found at the scene and neither the maid nor victim owned pets. 4. The mouse DNA is from the mouse in the mouth because a mouse was found in the victims mouth. The mouse is tailless because of a mutation that codes for collagen formation, which is the main component of tails. The mouse sequence (which codes for collagen), is not a 100% match for Mus musculus, the common house mouse; therefore, it can be assumed that a mutation caused the tail to not form. All information was found on NCBIs website. 2. (4 points) What is qPCR (also called real-time PCR)? Describe what its used for and how its done (including how it differs from the standard PCR described in the textbook).

qPCR is a lab technique to amplify and quantify cDNA. qPCR is also know as real-time because it can be examined in real time. The quantification property of qPCR allows for efficiency of the reaction to be analyzed. qPCR is not done in a gel like PCR but rather a plate with fluorescent dyes and put into a machine. A difference in a step for qPCR versus PCR is a reverse transcription to go from mRNA to cDNA before the thermocycling step in regular PCR. A camera monitors the fluorescent dye that is the qPCR DNA sample as the number of the genes increases, so does the fluorescent value of the product. It is used to analyze gene expression at transcription level and therefore analyze cell differentiation. PCR/Real-Time PCR Protocols. Protocol Online. Accessed September 4, 2013. http://www.protocol-online.org/prot/Molecular_Biology/PCR/Real-Time_PCR/. qPCR Vs. Digital PCR Vs. Traditional PCR. Life Technologies. Accessed September 4, 2013. http://www.lifetechnologies.com/us/en/home/life-science/pcr/real-time-pcr/qpcreducation/qpcr-vs-digital-pcr-vs-traditional-pcr.html. 3. (3 points) Site-directed mutagenesis is a molecular biology technique used to change specific nucleotides in a gene of interest. Describe a strategy you could use to truncate the protein produced from a gene that has been cloned into a plasmid. (Hint: You need to change a codon that normally specifies an amino acid to a stop codon.) First, we would need to isolate a single strand of DNA. We would then create synthetic, mutagenic, DNA primers. Next, we would add the mutagenic primers to the single stranded DNA, so that they would flank the part of sequence where we want our mutation. Next, we would add taq polymerase to create another strand of DNA. The thermocycler would carry out multiple cycles of this procedure, which is PCR. This would produce many copies of our mutated DNA sequence, which we would then put into our host cell and multiply. We would use gel electrophoresis to test our experiment by running the DNA on a gel. Our truncated protein would run faster, and therefore appear lower on the gel. Win Ping Deng, Jac A. Nickoloff, Site-directed mutagenesis of virtually any plasmid by eliminating a unique site, Analytical Biochemistry, Volume 200, Issue 1, January 1992, Pages 81-88, ISSN 0003-2697, http://dx.doi.org/10.1016/0003-2697(92)90280-K.