BME100 s2014:T Group4 L4

BME 100 Spring 2014	Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help
OUR TEAM Name: Parker Davis Role(s)Research and Development Michael Spina Role(s)Protocols Name: Brian Kalen Role(s)Initial Machine Testing Name: Daniel Munoz Role(s)Research and Development Name: Rakan Aldrssary Role(s)Protocols LAB 1 WRITE-UP Initial Machine Testing The Original Design The OpenPCR machine consists of thin pieces of wood, and a case that contains the hardware of the machine. A second, wood case on top of the main body contains the place where the samples are put into the machine. Small test vials are placed in the holders in the loading area to be heated by the PCR machine. Inside the main body of the machine there is hardware similar to a computer. A processor unit connects to the heating device as well as the power supply and LED screen. Above the power supply there is a heatsink, with a fan attached, facing some vents inside the machine, which allows for efficient temperature control inside the machine to prevent overheating. The machine then has components in order to be hooked up by USB to a computer. With the computer the PCR can be programmed to heat up the samples in the heating lid on certain time intervals, different temperatures, and indicated cycles. Experimenting With the Connections When we unplugged (part 3) from (part 6), the machine br> When part 3 was removed from part 6 the LED display screen shut off. When we unplugged the white wire that connects (part 6) to (part 2), the machine The temperature reading turned negative. Test Run (Write the date you first tested Open PCR and your experience(s) with the machine) The group first tested the machine on March 20, 2014. The first running of the machine went well, but the machine worked very slow. The 35 cycles took well over the two hour mark and the run was not able to be finished on time with class ending. This required us to fail the machines run. Protocols Thermal Cycler Program DNA Sample Set-up row 1 cell 1 row 1 cell 2 row 1 cell 3 row 1 cell 4 row 2 cell 1 row 2 cell 2 row 2 cell 3 row 2 cell 4 C+ p11 p12 p13 C- p21 p22 p23 DNA Sample Set-up Procedure Step 1 Obtain the PCR reaction and DNA primer mix Step 2 Mix the reaction mix and primer mix into one tube Step 3 Put the mixes into the tubes to be inserted into the machine Step 4 Run PCR via computer PCR Reaction Mix What is in the PCR reaction mix? The reaction mix contains Taq DNA polymerase, MgCl2, and dNTP's. DNA/ primer mix What is in the DNA/ primer mix? The primer mix contains a different template DNA. All tubes have the same forward and reverse primer. Research and Development PCR - The Underlying Technology (Add a write-up, essay-style, organized into paragraphs with descriptive headers, based on the Q&A's from Section three of your worksheet) (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 PCR video/ tutorial might be useful. Be sure to credit the sources if you borrow images.) Basic concepts DNA is the blue print of the human being. DNA is made up of nucleotides and peptide bonds. These four types of nucleotides form long strands to make up entire genomes. The human genome is composed of every gene that makes up every trait a human can have. Phenotypes are physically expressed by a human. Phenotypes are things like hair color or skin tone. Each type of phenotype has the possibility of being present in a population. When two or more phenotypes are present in the same population, this is known as polymorphism. Specifics on polymorphism In humans there are many different examples of polymorphism. For example, the single nucleotide polymorphism known as RS237025 is associated with the phenotypes of diabetes. The polymorphism that codes for this can tell if a person will either get type 1 diabetes or not. This polymorphism is associated with the gene SUMO4, or Small Ubiquitin-Modifier 4. This gene is located in the cytoplasm and modifies the protein IKBA. The allele of polymorphism Each polymorphism is due to two or more different alleles which code for the same gene. In this case the allele that is associated with the gene that codes for type 1 diabetes contains the sequence ATG while the non diseased allele contains the sequence GTG. The change of one base determines whether the person in question will have type 1 diabetes or not. Bonus See Images Below How Primers Bind to DNA Template picture found at: http://pulpbits.com/6-dna-semi-conservative-replication-animation/dna-replication-semiconservative-images/ How Taq Polymerases Amplify the DNA picture found at: http://mistralmtn.blogspot.com/2012/12/pcr-technology-that-speeds-dna-tests.html