BME103 s2013:T900 Group8

BME 103 Fall 2012	Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help
OUR TEAM Name: student Role(s) Name: student Role(s) Name: student Role(s) Name: student Role(s) Name: student Role(s) Name: Renee Tran Role: Research and Development Scientist LAB 1 WRITE-UP Initial Machine Testing The Original Design (Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is) Experimenting With the Connections When we unplugged (part 3) from (part 6), the machine ... (did what? fill in your answer) When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer) Test Run (Write the date you first tested Open PCR and your experience(s) with the machine) Protocols Experimental protocol planner summery As experimental protocol planner we have taken on the challenge of making sure that the experiment goes as planned as well as the preparing software that was used to evaluate our samples. We have left the technical portions of experiments to our “Open PCR machine testers” and allowed our R&D scientists to educate us on our experiment so that we (Experimental protocol planners) could create a plan and execute it in order for the experiment as a whole to be successful. Our job as for Experiment Protocol Planner was to : Prepare the software for analysis Prepare DNA samples for tests Analyze the results We have educated our self via “PCR Virtual Lab” that can be found at http://openpcr.ord/use-it/ then downloaded and test software that was responsible for taking the results from PCR machine and displaying those results on PC, as well as to make commends to the PCR machine. This software also gave us real time update of the PCR machine Second and most important part of to prepare our sample. Our sample consisted of two rows of four samples. The table representing the samples is shown below. In this part we have also created a total of 8 different dyes also shown below. The third part was to take the results from the PCR machine and analyze them with the rest of our team, via software. called Thermal Cycler Program DNA Sample Set-up ID : 80175(1), 57483(2) ROW : Tube 1 Tube 2 Tube 3 Tube 4 Row 1 Contains : rep : Label + Control N/A "+" - Control N/A "-" Patient 1 1 "1" Patient 2 1 "2" Row 2 Contains : rep : Label Patient 1 2 "+-" Patient 2 2 "--" Patient 1 3 "1-" Patient 2 3 "2-" "Contains" describes what sample was inserted in the test tube "rep" is the replicate, we have 3 replicates of each patient "label" is simply what symbol we have written on the test tube so that we can identify what sample is where DNA Sample Set-up Procedure 1. Step 1 : Acquire Materials Materials : - A set of four dyes (blue, green, yellow, red) - Sample containing (+,-,P1,P1,P1,P2,P2,P2) - Pipette and tips - two rows of empty test tubes 2. Step 2 : Mix dyes MIX: blue 50μL blue 50μL blue 50μL yellow 50μL blue 50μL green 50μL yellow 50μL yellow 50μL yellow 50μL green 50μL red 50μL red 50μL red 50μL green 50μL green 50μL green 50μL 3. Step 3 : Prepare the samples, and label the samples (tables is shown above) 4. Step 4 : allow other team members to start PCR machine and then load the samples into the machine PCR Reaction Mix What is in the PCR reaction mix? DNA/ primer mix What is in the DNA/ primer mix? Research and Development Specific Cancer Marker Detection - The Underlying Technology The goal of this experiment is to understand the DNA amplification process in order to detect cancerous genes when given Template DNA; otherwise known as DNA taken from the patient. DNA amplification will allow the cancerous genes to replicate. The cancerous gene will produce a positive result, while the non-cancer gene will give a negative result, because the primers are designed to amplify cancerous DNA. Therefore, the cancerous mutation cannot bind to normal DNA, ultimately meaning that amplification cannot occur. The following “3 steps” are repeated for 30 cycles, each step taking about 30 seconds. Step 1:Heat up the Template DNA, Primers, Taq Polymerase, and Magnesium Chloride (MgCl2) to 95 degrees Celsius • What happens? o The bases need to me detected, in order to do so “melting” or unzipping needs to DNA will expose those base pairs. o When the base pairs are exposed the primers will create a forward and reverse strand appropriately. The primers are short pieces (about 20 bases pairs long) of DNA that are synthesized DNA that binds to the Template DNA while directing the new strand to be made. Step 2:The mixture is cooled down to 57 degrees Celsius • What happens? o The primers “anneal,” or in other words the bond. Step 3:Heat the mixture back up to 72 degrees Celsius. • What happens? o The Taq Polymerase and Magnesium Chloride will detect where the template DNA and primer and uses the template DNA strand and primer to build a new copy of DNA Cancer Associated with the gene: Chromosome: Gene being analyzed: SNP #: SNP's Surrounding DNA: Cancer-Sequence Primer: "Partner Primer": Description of Gene: (BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)