BME100 s2014:W Group14 L6: Difference between revisions
(7 intermediate revisions by the same user not shown) | |||
Line 12: | Line 12: | ||
=OUR COMPANY= | =OUR COMPANY= | ||
[[Image:PCRandCo_Logo.PNG| | [[Image:PCRandCo_Logo.PNG|500px]]<br> | ||
<br> | <br> | ||
'''Our Team:'''<br><br> | '''Our Team:'''<br><br> | ||
Line 54: | Line 54: | ||
'''Primer design'''<br> | '''Primer design'''<br> | ||
* Disease SNP-specific Forward Primer: 5' | * Disease SNP-specific Forward Primer: 5' - ''G T G A A G C A G A T C A G A T T C C G'' - 3' | ||
* Reverse Primer: 5' | * Reverse Primer: 5' - ''A G T T T T C T A A T T G A G A A T G C'' - 3' | ||
Line 86: | Line 86: | ||
'''The ''Thermal Cycling Spectrum'' System'''<br> | '''The ''Thermal Cycling Spectrum'' System'''<br> | ||
The ''Thermal Cycling Spectrum'' complete system will include one (1) consumables kit, one (1) modified and newly updated OpenPCR machine, and one (1) modified and newly updated fluorimeter. Despite the consumables kit, assembly will be required for the OpenPCR machine and fluorimeter if the consumer does not select the pre-assemble option. If selected, this option will be performed in the ''PCR & Co.'s'' warehouse; however, an additional fee will be applied to the overall purchase. | The ''Thermal Cycling Spectrum'' complete system will include one (1) consumables kit, one (1) modified and newly updated OpenPCR machine, and one (1) modified and newly updated fluorimeter. Despite the consumables kit, assembly will be required for the OpenPCR machine and fluorimeter if the consumer does not select the pre-assemble option. If selected, this option will be performed in the ''PCR & Co.'s'' warehouse; however, an additional fee will be applied to the overall purchase. With all three major components included with packaging, consumers will receive the entire ''Thermal Cycling Spectrum'' system. | ||
<br><br> | <br><br> | ||
'''PCR Machine Modifications'''<br> | '''PCR Machine Modifications'''<br> | ||
This device features a new PCR tube holder that offers different size holes in order to allow different sized PCR tubes to be inserted smoothly. This allows several types of reactions to occur simultaneously during the several-hour thermal cycling period. Next, the new ''Thermal Cycling Spectrum'' features a new integrated internal system that blows the original OpenPCR machine out of the water. This internal system does not require additional computational systems that transfer data to a separate device. The new internal system allows the ''Thermal Cycling Spectrum'' to operate freely; thus, analyzing and computing data that is recorded throughout the cycling period. With the addition of a new internal system, a new port system has been created in order to withdraw and copy data that has been recorded within the internal drive. Two (2) new 3.0 USB ports and a mini-SD memory card slot have been included in order to provide multiple methods of transferring data from one device to another. The extra USB port is available in order to provide an external power source in order to run the ''Thermal Cycling Spectrum''. This eliminates the problem of needing a stationary desktop computer in order to supply enough power to allow the device to function. Finally, the lid fastener has been drastically improved by including an alarm system that alerts the user when the lid has been securely fastened prior to the cycling period. One mini-LED screen will display a red screen until a green screen appears (on the other mini-LED screen), alerting the user that the lid has been properly fastened.<br><br> | This device features a new PCR tube holder that offers different size holes in order to allow different sized PCR tubes to be inserted smoothly. This allows several types of reactions to occur simultaneously during the several-hour thermal cycling period. Next, the new ''Thermal Cycling Spectrum'' features a new integrated internal system that blows the original OpenPCR machine out of the water. This internal system does not require additional computational systems that transfer data to a separate device. The new internal system allows the ''Thermal Cycling Spectrum'' to operate freely; thus, analyzing and computing data that is recorded throughout the cycling period. With the addition of a new internal system, a new port system has been created in order to withdraw and copy data that has been recorded within the internal drive. Two (2) new 3.0 USB ports and a mini-SD memory card slot have been included in order to provide multiple methods of transferring data from one device to another. The extra USB port is available in order to provide an external power source in order to run the ''Thermal Cycling Spectrum''. This eliminates the problem of needing a stationary desktop computer in order to supply enough power to allow the device to function. Finally, the lid fastener has been drastically improved by including an alarm system that alerts the user when the lid has been securely fastened prior to the cycling period. One mini-LED screen will display a red screen until a green screen appears (on the other mini-LED screen), alerting the user that the lid has been properly fastened.<br><br> | ||
'''Fluorimeter Modifications'''<br> | '''Fluorimeter Modifications'''<br><br> | ||
[[Image:BME100_Group14_Lab6_FluorimeterModification.PNG| | [[Image:BME100_Group14_Lab6_FluorimeterModification.PNG|800px]]<br> | ||
<br> | |||
The fluorimeter will be made up of a cellphone docking station, a device that produces a blue LED light for each drop sampling, a rolling tray (with wheels) and a black box that protects any fraction of light from entering the premise of the fluorimeter setup. The cellphone docking station will feature a new way to dock your cellular device. By plugging in your cellular device, your cellphone will stay charged while performing during the length of the lab experiment. This will also securely fasten the device; thus, the distance between the drop sampling and the camera of the cellphone will not change. The docking station will have an external USB-cable that can plug into any computer to provide charging power. Next, the device that produces the blue LED light and holds the drop sampling will feature a rotational knob that raises or lowers the height of the drop sampling device. This will promote an equal level for the camera's perspective on the drop sampling; thus, an accurate side-view of the "beach ball" shaped drop sampling will be produced. The black box will not feature any modifications; however, the device that produces the blue LED light and the cellphone docking station will be placed on a moving tray. Before and after each trial of each drop sampling, the door for the black box will open upwards, like usual, and the tray will roll inwards/outwards of the black box. This will provide an easier and effective way of changing out each drop sampling without affecting the distance between the drop sampling and the camera of the cellphone; meanwhile, the black box will not have to be interfered with. | The fluorimeter will be made up of a cellphone docking station, a device that produces a blue LED light for each drop sampling, a rolling tray (with wheels) and a black box that protects any fraction of light from entering the premise of the fluorimeter setup. The cellphone docking station will feature a new way to dock your cellular device. By plugging in your cellular device, your cellphone will stay charged while performing during the length of the lab experiment. This will also securely fasten the device; thus, the distance between the drop sampling and the camera of the cellphone will not change. The docking station will have an external USB-cable that can plug into any computer to provide charging power. Next, the device that produces the blue LED light and holds the drop sampling will feature a rotational knob that raises or lowers the height of the drop sampling device. This will promote an equal level for the camera's perspective on the drop sampling; thus, an accurate side-view of the "beach ball" shaped drop sampling will be produced. The black box will not feature any modifications; however, the device that produces the blue LED light and the cellphone docking station will be placed on a moving tray. Before and after each trial of each drop sampling, the door for the black box will open upwards, like usual, and the tray will roll inwards/outwards of the black box. This will provide an easier and effective way of changing out each drop sampling without affecting the distance between the drop sampling and the camera of the cellphone; meanwhile, the black box will not have to be interfered with. | ||
Latest revision as of 23:31, 22 April 2014
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 COMPANYOur Product: The Thermal Cycling Spectrum
LAB 6 WRITE-UPComputer-Aided DesignTinkerCAD TinkerCAD is a tool that is used to create 3-D digital designs of objects and other 3-D printing compatible items. In class, each member was required to register (for free) on TinkerCAD. Two members of Wednesday's Group 14 were required to take at least 7 lessons online in order to learn how to maneuver throughout the program and the various tools. For the class period, our lab group was designated to select a specific portion of the OpenPCR machine and improve it in a way that resulted in a positive manner. Our Design: OpenPCR Machine Modifications
Feature 1: Disease SNP-Specific PrimersBackground on the cancer-associated mutation Nucleotides are organic molecules that serve as the monomers of nucleic acid, and are also commonly known as the building blocks of nucleic acids. Polymorphisms are coined terms for when two or more clearly different phenotypes exist in the same population of a species. For example, a DNA sequence - A, T, C, or G - in the same genome differs between members of a biological species or paired chromosomes. Short genetic variations are made up of single nucleotide polymorphisms (SNP's). After researching the SNP rs237025, it has been found in single nucleotide variations of the Homo sapiens (human) species. It is located on chromosome 6, and has no clinical significance; however, it has been linked to the health-related illness diabetes. The gene SUM04 stands for small ubiquitin-like modifier 4, which are attached to proteins and control the target proteins' sub-cellular localization, stability, and activity. Alleles are one of a number of forms of the same gene; they produce different effects. The disease associated allele for rs237025 is A-T-G, different from the non-disease allele containing G-T-G. Primer design
Feature 2: Consumables Kit
Feature 3: Hardware - PCR Machine & FluorimeterThe Thermal Cycling Spectrum System
Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach[Instructions: This section is OPTIONAL, and will get bonus points if answered thoroughly and correctly. Here is a chance to flex some intellectual muscle. In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of PCR for predicting the disease. Please do NOT type the actual numerical values here. Just refer to them as being "less than one" or "very small." The instructors will ask you to submit your actual calculations via a Blackboard quiz. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]
|