BME103:T130 Group 4 l2: Difference between revisions
Brent Russon (talk | contribs) |
|||
(16 intermediate revisions by 3 users not shown) | |||
Line 29: | Line 29: | ||
'''System Design'''<br> | '''System Design'''<br> | ||
[[Image:Larger Weld Plate-1.png|750 px]]<br> | |||
[[Image: | [[Image:Clear Sides.JPG|750 px]]<br> | ||
[[Image:Battery.png|750 px|]]<br> | |||
<br> | |||
'''Key Features'''<br> | '''Key Features'''<br> | ||
*One of the inconveniences of the original design is the limited number of samples it can accommodate. We would expand the plate to 6x6 instead of 4x4, more than doubling the original capacity without significantly affecting the machine's dimensions. | |||
*Another common complaint is the difficulty of seeing how much the lid is screwed down. This is problematic because the lid can't be screwed down too tightly in case it melts the PCR tubes, but it also can't be too loose or else the reaction might not happen properly. We would change the sides of the lid to a clear, heat-resistant plastic so the user can see exactly how much the lid is screwed down. | |||
*The original PCR machine needs to be plugged into an external power source, so we decided it would be helpful to build a backup battery into the system so the PRC machine can continue running even if there's a power outage. Obtaining and preparing the materials for PCR takes time and money, and it would be unfortunate for the user if that all went to waste because of a power loss. Having a backup battery ensures that the reaction will be able to finish, saving the user from having to redo it if there's an unexpected power outage. | |||
<br> | |||
'''Instructions'''<br> | '''Instructions'''<br> | ||
*The modifications to the plate and lid won't change the assembly process, so the original instructions regarding those parts are still valid. | |||
*The backup battery will need to be connected to the terminal inside the machine and to a new piece we will provide called an inverter. The necessary wires will already be attached to the battery. | |||
<ol> | |||
<li>Loosen the necessary terminal screw with a 2 mm screwdriver and connect the blue wire. Hold the wire in place while you tighten the screw and pull gently on it afterwards to make sure it is properly connected. | |||
<li>Repeat the process with the green wire to connect the battery to the inverter. | |||
</ol> | |||
<!--- From Week 4 exercise ---> | <!--- From Week 4 exercise ---> | ||
<br> | |||
==Protocols== | ==Protocols== | ||
Line 157: | Line 159: | ||
==Research and Development== | ==Research and Development== | ||
<br> | |||
<!--- Bonus: explain how Bayesian statistics can be used to assess the reliability of your team's method. Just write the equation using variables that are relevant to your team's new test. You do not need actual numbers ---> | <!--- Bonus: explain how Bayesian statistics can be used to assess the reliability of your team's method. Just write the equation using variables that are relevant to your team's new test. You do not need actual numbers ---> | ||
'''Background on Disease Markers''' | '''Background on Disease Markers''' | ||
Line 165: | Line 166: | ||
<!--- A description of the diseases and their associated SNP's (include the database reference number and web link) ---> | <!--- A description of the diseases and their associated SNP's (include the database reference number and web link) ---> | ||
The marker that is being used is rs137852453. This SNP is associated with hemophilia. Hemophilia is a condition where someone's blood is not clotting properly. Data on this particular SNP variance can be seen here: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=137852453 <br> | The marker that is being used is rs137852453. This SNP is associated with hemophilia. Hemophilia is a condition where someone's blood is not clotting properly. Data on this particular SNP variance can be seen here: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=137852453 <br> | ||
The associated gene change goes from a '''C'''GG (healthy gene sequence) to '''T''' | The associated gene change goes from a '''C'''GG (healthy gene sequence) to '''T'''GG (sequence associated with hemophilia). | ||
The gene alteration leads to a mutated human protein. It goes from R[Arg] to W[Trp] | The gene alteration leads to a mutated human protein. It goes from R[Arg] to W[Trp] | ||
Hemophilia is a blood disorder. There are different types or degrees of hemophilia, but is essentially just different levels of blood not clotting properly. In it's most sever cases the body can have an incredibly hard time stopping a wound from bleeding because it will not clot to form a scab. Hemophilia is more likely to appear in males than in females because it is based in the X chromosome. | |||
Line 183: | Line 186: | ||
<!--- Include an illustration that shows how your system's primers allow specific amplification of the disease-related SNP ---> | <!--- Include an illustration that shows how your system's primers allow specific amplification of the disease-related SNP ---> | ||
[[Image:Figure 1.png|800px|thumb|Figure 1]] | |||
[[Image:Figure 2.png|800px|thumb|Figure 2]] | |||
[[Image:Figure 3.png|800px|thumb|Figure 3: The DNA that is being tested is split and if the primers can attach to a corresponding part then they do. The top primer should always have a match while the bottom primer will only match if the genetic variance is present. The rest of the DNA strands will be filled in with free floating nucleotides. Because the top primer should always have a match, it will always replicate a new set of DNA. If there is no genetic variance present in the DNA being tested then the bottom primer will not match and so, as the process is replicated, only linear growth will be seen. If the genetic variance that is being tested for is present then the bottom will also replicate a new set of DNA and so, as the process is replicated, exponential growth will be seen.]] | |||
[[Image:Figure 4.png|800px|thumb|Figure 4]] | |||
<br> | |||
'''Bayesian Statistics''' | |||
<br> | |||
Because no test is completely accurate there are some useful statistics which can be calculated using Bayes rule after results are gathered. When looking at the probability that a person in a population has hemophilia, [ P(hc) ], the probability that if the test gives a positive result that you do in fact have hemophilia,[ P(T|hc) ], the probability that if the test gives a positive result that you do not have hemophilia, [ P(T|nc) ], and the probability that the test will give a positive result, [ P(T)], only three of them need to be known and then any other could be derived. This is demonstrated by the following equation: | |||
<br><br> | |||
(((100%-P(hc))x P(T|nc)) + ((P(hc) x P(T|hc)) = P(T) | |||
<br><br> | |||
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### --> | <!-- ##### DO NOT edit below this line unless you know what you are doing. ##### --> |
Latest revision as of 14:08, 29 November 2012
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 TEAMLAB 2 WRITE-UPThermal Cycler EngineeringOur re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.
ProtocolsMaterials
Research and Development
Background on Disease Markers The marker that is being used is rs137852453. This SNP is associated with hemophilia. Hemophilia is a condition where someone's blood is not clotting properly. Data on this particular SNP variance can be seen here: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=137852453 Hemophilia is a blood disorder. There are different types or degrees of hemophilia, but is essentially just different levels of blood not clotting properly. In it's most sever cases the body can have an incredibly hard time stopping a wound from bleeding because it will not clot to form a scab. Hemophilia is more likely to appear in males than in females because it is based in the X chromosome.
Bottom Primer (in reverse):
|