BME103:W930 Group3: Difference between revisions
Jake Swartz (talk | contribs) |
|||
Line 125: | Line 125: | ||
== Fluorimeter Assembly Procedure == | == Fluorimeter Assembly Procedure == | ||
*Step 1) Switch on excitation light for blue LED | *Step 1) Switch on excitation light for blue LED | ||
*Step 2) Place smartphone on the provided cradle at an angle perpendicular to the slide. | *Step 2) Place smartphone on the provided cradle at an angle perpendicular to the slide (make sure to keep cradle in place throughout pictures to ensure consistency). | ||
*Step 3) Adjust camera settings if possible: Turn on flash, set ISO to 800+, increase exposure to maximum and disable auto-focus. | *Step 3) Adjust camera settings if possible: Turn on flash, set ISO to 800+, increase exposure to maximum and disable auto-focus. | ||
*Step 4) Position cradle as near as possible to the slide so that an clear image will be taken. | *Step 4) Position cradle as near as possible to the slide so that an clear image will be taken. | ||
Line 131: | Line 131: | ||
*Step 6) Adjust the slide so that the blue LED light is focused on the drops so that the middle of the black fiber optic is on the other side of the drop. | *Step 6) Adjust the slide so that the blue LED light is focused on the drops so that the middle of the black fiber optic is on the other side of the drop. | ||
*Step 7) Create a dark environment by covering the fluorimeter setup with the box (either width can be unbuttoned so that an access slot for the phone to take a photo is available) so as to reduce as much stray light as possible. | *Step 7) Create a dark environment by covering the fluorimeter setup with the box (either width can be unbuttoned so that an access slot for the phone to take a photo is available) so as to reduce as much stray light as possible. | ||
*Step 8) Take three separate photos of the water droplet while taking care to move the phone as little as possible. | *Step 8) Take three separate photos of the water droplet while taking care to move the phone as little as possible to ensure consistency. | ||
*Step 9) Remove the box while again taking care not to change the phone's position, as it is crucial to maintaining a constant. | *Step 9) Remove the box while again taking care not to change the phone's position, as it is crucial to maintaining a constant. | ||
*Step 10) Dispose of the drops by extracting them with another clean pipette from the slide and disposing of them in the proper hazardous waste receptacle. | *Step 10) Dispose of the drops by extracting them with another clean pipette from the slide and disposing of them in the proper hazardous waste receptacle. | ||
Line 143: | Line 143: | ||
*Step 2) Either press the '''Windows Key''' or '''Start''' and then browse to '''My Computer'''/'''Computer'''. | *Step 2) Either press the '''Windows Key''' or '''Start''' and then browse to '''My Computer'''/'''Computer'''. | ||
*Step 3) Under the category '''Portable Devices''', the smartphone should be listed (if not check the USB cable connection and try unplugging and replugging it), double-click the icon. | *Step 3) Under the category '''Portable Devices''', the smartphone should be listed (if not check the USB cable connection and try unplugging and replugging it), double-click the icon. | ||
*Step 4) Find the folder labeled '''DCIM''' and open it, then the following | *Step 4) Find the folder labeled '''DCIM''' and open it, then the following sub-folder '''Camera'''. | ||
*Step 5) If the pictures that you wish to transfer are the only images in the library then drag and select all of the images and right-click and select '''Copy''' then '''Paste''' them into your preferred destination (Suggested folder: '''Pictures''', under '''Libraries''', alternatively '''Control + C''' then '''Control + V'''), otherwise hold down '''Control''' and left-click each picture that needs to be transferred and repeat the above instructions. | *Step 5) If the pictures that you wish to transfer are the only images in the library then drag and select all of the images and right-click and select '''Copy''' then '''Paste''' them into your preferred destination (Suggested folder: '''Pictures''', under '''Libraries''', alternatively '''Control + C''' then '''Control + V'''), otherwise hold down '''Control''' and left-click each picture that needs to be transferred and repeat the above instructions. | ||
*Step 6) Open the ImageJ software by either double-clicking the icon on the '''Desktop''' or by browsing the '''Start Menu'''. | *Step 6) Open the ImageJ software by either double-clicking the icon on the '''Desktop''' or by browsing the '''Start Menu'''. |
Revision as of 16:36, 8 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 1 WRITE-UP(Please finish by 11/7/2012) Initial Machine TestingThe Original Design If the Arduino UNO board is disconnected fron the LCD screen, then then LCD screen will not be able to display information; this includes information such as the current cycle of the PCR and the current tempereture. If the Arduino UNO board is disconnected from the 16-tube PCR block, then the LCD wouldn't be able to display any temperatures, this is because temperatures in the 16-tube block are not being monitored.
The experiences of first testing the Open PCR machine, on October 24th, 1012, were of mixed results. As for the set up of the Open PCR, things went fairly well. Connecting the Open PCR to a computer was not a problem and neither was finding a suitable location to let the machine run. However, the first computer we connected the Open PCR to had problems running the Open PCR software. The experiment design part of the software would not allow for editing of the number of cycle, resting temperature, time length of the cycles and all other variables of the experiment. The software might have been corrupted or the computer may not have been running correctly; whatever the case, the Open PCR had to be moved to another computer in order to solve this problem. The use of the second computer allowed for editing of the experimental variables and the initiation of the experiment. However, further problems arose once the experiment was in progress. From the beginning of the experiment the Open PCR machine being used took a considerable amount of time on the cooling part of the cycle, much longer than the other groups running the experiment. If the machine does not cool down correctly and to the right temperature, then the PCR cannot move onto the next cycle. And eventually, due to this problem, the Open PCR machine became stuck on the cooling part of cycle 5 of 30 and would not move forward in the experiment. After trouble shooting from TA's and the professor the problem could not be reverse and additional amplified DNA samples will have to be created for group 3.
ProtocolsPolymerase Chain Reaction Polymerase Chain Reaction is a biochemical technology that is used in molecular biology to amplify single/multiple copies of a piece of DNA, generating thousands to millions of copies of a targeted DNA sequence. To do so, PCR relies on thermal cycling, which consists of repeated cycles of heating and cooling the samples in order to melt the DNA and have the enzymes replicate the targeted strand if found. Primers, which are short DNA fragments, have complementary sequences to the target strand of DNA, in addition to a DNA polymerase, which allows selective and repeated amplification of the target strand. As the cycles progress, the DNA is used as a template for exponential amplification (or creation of copies). How to Amplify a DNA Sample with PCR
Components of GoTaq® Colorless Master Mix
8 Samples, 3 each patient, positive and negative control
Fluorimeter Assembly Procedure
Transferal of Images to ImageJ
Research and DevelopmentSpecific Cancer Marker Detection - The Underlying Technology
Bayes Rule: Predicting the possibility of cancer.
Bayes Theorem: (.008)/(.008+0.095)=7.8%
Results(Your group will add the results of your Fluorimeter measurements from Week 4 here)
|