BME103:T930 Group 1 l2 - Revision history

Jessica D. Kemper: /* Research and Development */

Jessica D. Kemper — Thu, 29 Nov 2012 17:42:01 GMT

Research and Development

←Older revision		Revision as of 17:42, 29 November 2012
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	<!--- 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 --->
		+	'''Bayes Theorem''' <br>
		+
		+	P(A/B)= (P(B/A)P(A))/(P(B))<br>
		+
		+	Bayes Theorem is used to determine if the amount of accurate results outweigh the false positives/false negatives that the PCR machine gives. In other words, Bayes Theorem shows either that the PCR machine gives far more accurate results than false positives/negatives (and is therefore worth building and marketing) or that the PCR machine gives fewer accurate results than false positives/negatives (and is therefore not worth building and marketing). <br>

Christian Boden: /* Research and Development */

Christian Boden — Thu, 29 Nov 2012 10:27:17 GMT

Research and Development

←Older revision		Revision as of 10:27, 29 November 2012
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	'''Illustration'''		'''Illustration'''
		+
		+	[[Image:PrimerAmplification.gif]]

	<!--- 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 --->

Christian Boden: /* Research and Development */

Christian Boden — Thu, 29 Nov 2012 10:22:29 GMT

Research and Development

←Older revision		Revision as of 10:22, 29 November 2012
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	'''Background on Disease Markers'''		'''Background on Disease Markers'''

		+	Diabetic insipidus is a kidney disease in which the kidneys are unable to conserve water[http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001415/]. This is controlled by antidiuretic hormone (or vasopressin), and in diabetic insipidus there is a lack of this hormone. It can be caused by damage to the hypothalamus or pituitary gland. This hormone is produced in the hypothalamus and is released from the pituitary gland. The SNP rs121964890[http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=121964890] can cause DI.[http://omim.org/entry/603933] It is located on the 20th chromosome and has the allele change TCC ⇒ TTC which is the residue change S [Ser] ⇒ F [Phe].
	<!--- 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) --->

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	'''Primer Design'''		'''Primer Design'''

		+	3' GAAGACCGGC[C/T]TGACCGTCCC 5'
		+
		+	5' GGGACGGTGA[G/A]GCCGGTCTTC 3'
		+
		+	TCC ⇒ TTC
		+
		+	S [Ser] ⇒ F [Phe]
	<!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. --->		<!--- Include the sequences of your forward and reverse primers. Explain why a disease allele will give a PCR product and the non-disease allele will not. --->

Maile Ravenkamp: /* Protocols */

Maile Ravenkamp — Thu, 29 Nov 2012 07:44:00 GMT

Protocols

←Older revision		Revision as of 07:44, 29 November 2012
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	\| Open PCR Software \|\| 1		\| Open PCR Software \|\| 1
	\|-		\|-
-	\|	+	\| ImageJ Software \|\| 1
		+	\|-
		+	\| Smartphone \|\| 1
		+	\|-
		+	\| Smartphone Cradle \|\| 1
		+	\|-
		+	\| Distilled Water \|\| 50 mL
	\|}		\|}
		+	<br>
	<!--- Place your two tables "Supplied in the kit" and "Supplied by User" here --->		<!--- Place your two tables "Supplied in the kit" and "Supplied by User" here --->

Maile Ravenkamp: /* Protocols */

Maile Ravenkamp — Thu, 29 Nov 2012 07:28:13 GMT

Protocols

←Older revision		Revision as of 07:28, 29 November 2012
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	\|-		\|-
	\| PCR Machine \|\| 1		\| PCR Machine \|\| 1
		+	\|-
		+	\| Fluorimeter \|\| 1
		+	\|-
		+	\| Black Box \|\| 1
	\|-		\|-
	\| Positive Control DNA Sample\|\| 100 μL		\| Positive Control DNA Sample\|\| 100 μL
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	\| Negative Control DNA Sample \|\| 100 μL		\| Negative Control DNA Sample \|\| 100 μL
	\|-		\|-
-	\| ~~Patient 1 DNA Sample~~ \|\| ~~100~~ μL	+	\| 10 μM Forward Primer \|\| 10 μL
		+	\|-
		+	\| 10 μM Reverse Primer \|\| 10 μL
		+	\|-
		+	\| GoTaq Colorless Master Mix \|\| 400 μL
		+	\|-
		+	\| Eppendorf Tubes \|\| 8
		+	\|-
		+	\| Test Tubes \|\| 8
		+	\|-
		+	\| Pipettes \|\| 10
		+	\|-
		+	\| Hydrophobic Glass Slides \|\| 5
	\|-		\|-
-	\| ~~Patient 2 DNA Sample~~ \|\| 100 μL	+	\| Tris Buffer (0.025% SYBR Green) \|\| 100 μL
		+	\|}
		+	<br>
		+	{\| {{table}}
		+	\|- style="background:#f0f0f0;"
		+	\| '''Supplied by User''' \|\| '''Amount'''
	\|-		\|-
-	\| ~~GoTaq Colorless Master Mix~~ \|\| ~~100~~ μL	+	\| DNA Samples \|\| 200 μL
	\|-		\|-
-	\| PCR~~: Patient 2 ID 11260, rep 2~~ \|\| ~~5214727~~	+	\| Open PCR Software \|\| 1
	\|-		\|-
-	\| ~~PCR: Patient 2 ID 11260, rep 3 \|\| 5099077~~	+	\|
	\|}		\|}
	<!--- Place your two tables "Supplied in the kit" and "Supplied by User" here --->		<!--- Place your two tables "Supplied in the kit" and "Supplied by User" here --->

Maile Ravenkamp: /* Protocols */

Maile Ravenkamp — Thu, 29 Nov 2012 06:58:16 GMT

Protocols

←Older revision		Revision as of 06:58, 29 November 2012
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	\| PCR Machine \|\| 1		\| PCR Machine \|\| 1
	\|-		\|-
-	\| Positive Control DNA Sample\|\| ~~27282151~~	+	\| Positive Control DNA Sample\|\| 100 μL
	\|-		\|-
-	\| Negative Control DNA Sample \|\| ~~35526894~~	+	\| Negative Control DNA Sample \|\| 100 μL
	\|-		\|-
-	\| Patient 1 DNA Sample \|\| ~~19073943~~	+	\| Patient 1 DNA Sample \|\| 100 μL
	\|-		\|-
-	\| Patient 2 DNA Sample \|\| ~~29391013~~	+	\| Patient 2 DNA Sample \|\| 100 μL
	\|-		\|-
-	\| ~~PCR: Patient 2 ID 11260 , rep 1~~ \|\| ~~1903450~~	+	\| GoTaq Colorless Master Mix \|\| 100 μL
	\|-		\|-
	\| PCR: Patient 2 ID 11260, rep 2 \|\| 5214727		\| PCR: Patient 2 ID 11260, rep 2 \|\| 5214727

Jessica D. Kemper: /* Protocols */

Jessica D. Kemper — Thu, 29 Nov 2012 06:08:33 GMT

Protocols

←Older revision		Revision as of 06:08, 29 November 2012
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	'''DNA Measurement Protocol''' <br>		'''DNA Measurement Protocol''' <br>
		+	'''Flourimeter Procedure'''<br>
		+
		+	1. Turn on the excitation light using the switch for the Blue LED. <br>
		+	2. Place your smart phone on the cradle at a right angle from the slide. <br>
		+	3. Turn on the camera setting on the smartphone. Turn off the flash and set the ISO to 800 or higher and increase the exposure to maximum. You should also turn off the autofocus, if possible, and make sure that you can take an image where the drop on the slide will be in focus. <br>
		+	4. Adjust the distance between the smartphone on its cradle and the first two rows of the slide so that it is as close as you can get without having a blurry image. <br>
		+	5. The pipette should be filled with liquid only to the bottom of the black line. Then, carefully place two drops of water in the middle of the first two rows of the slide using the plastic pipette. Then add two more drops. The drop should then be pinned and look like a beach ball. It should be between 130-160 μL. <br>
		+	6. Align the drop by moving the slide so that the blue LED light is focused by the drop to the middle of the black fiber optic fitting on the other side of the drop (you will see that it has a small opening that is used for spectral measurement). <br>
		+	7. Cover the fluorimeter with the light box, but make sure you can access your smartphone to take the image. The light box should be used to remove as much stray light as possible, but do not worry if you have some light. <br>
		+	8. Take three images of the drop of water. Do not move your smartphone. <br>
		+	9. Remove the box and be careful not to move your smartphone. If you want to adjust for any movement, use the ruler provided to measure the distance so that you can return to that location. You can also use ImageJ to compensate for moving the camera, but it makes the analysis more complicated. <br>
		+	10. Use a clean plastic pipette to remove the water drop from the surface. <br>
		+	11. Push the slide in so that you are now in the next set of two holes. <br>
		+	12. Repeat steps 5-10 four more times so that you have now imaged all 5 positions on the slide. <br>
		+	13. Record the type of smartphone you used, the distance from the base of smartphone cradle to measurement device, and attach one image for each position of the drop. <br>
		+
	'''Image J Procedure'''<br>		'''Image J Procedure'''<br>
	1. Search Image J in Google and then download Image J <br>		1. Search Image J in Google and then download Image J <br>

Jessica D. Kemper: /* Protocols */

Jessica D. Kemper — Thu, 29 Nov 2012 06:06:26 GMT

Protocols

←Older revision		Revision as of 06:06, 29 November 2012
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-	'''DNA Measurement Protocol'''	+	'''DNA Measurement Protocol''' <br>
-	'''Image J Procedure'''	+	'''Image J Procedure'''<br>
	1. Search Image J in Google and then download Image J <br>		1. Search Image J in Google and then download Image J <br>
	2. Open Image J then click "file" and click "open" and open the image you want to analyze <br>		2. Open Image J then click "file" and click "open" and open the image you want to analyze <br>

Jessica D. Kemper: /* Protocols */

Jessica D. Kemper — Thu, 29 Nov 2012 06:06:09 GMT

Protocols

←Older revision		Revision as of 06:06, 29 November 2012
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	'''DNA Measurement Protocol'''		'''DNA Measurement Protocol'''
		+	'''Image J Procedure'''
		+	1. Search Image J in Google and then download Image J <br>
		+	2. Open Image J then click "file" and click "open" and open the image you want to analyze <br>
		+	3. Once your image is open click "analyze" and then click "set measurements" and check the boxes "area" "integrated density" and "mean gray value" leave the rest of the boxes empty <br>
		+	4. now click "image" then click "color" and then click "split channels" <br>
		+	5. This will split your image into three, you will use the one that is marked as the "green" picture, cancel the others <br>
		+	6. Activate the oval tool <br>
		+	7. draw the best oval you can around the drop and then press the control button+ the "m" key <br>
		+	8. Move the oval over to the background (the black around the picture) and press the control button and the m key again <br>
		+	9. repeat steps for all pictures <br>
		+	10. Save your data in an excel format by clicking "file" and then clicking "save as" then save the file with the name you want <br>

	==Research and Development==		==Research and Development==

Sir Nicholas Hool: /* Thermal Cycler Engineering */

Sir Nicholas Hool — Thu, 29 Nov 2012 05:37:52 GMT

Thermal Cycler Engineering

←Older revision		Revision as of 05:37, 29 November 2012
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-	The first piece of this PCR machine that we changed was the power supply source. We decided to make it smaller and more compact. A smaller power source 1), makes the entire machine lighter and adds mobility and 2), greatly reduces the chance of the power source overheating and causing the machine to melt or catch fire. As a result of making the power source smaller, we had to change the design of one of the side panels.	+	The first piece of this PCR machine that we changed was the power supply source. We decided to make it smaller and more compact. A smaller power source 1), makes the entire machine lighter and adds mobility and 2), greatly reduces the chance of the power source overheating and causing the machine to melt or catch fire. As a result of making the power source smaller, we had to change the design of one of the side panels. The original side panels were crafted to fit the large power source. With the smaller power source, we had to re-align the holes so that they fit perfectly with our smaller power source. The biggest change we made to the PCR machine is changing the material from wood to ABS material. This material is similar to PVC material, but it is a cheaper substance to come by. A big advantage of a machine made of ABS material is that ABS is compatible with a 3D printer. That means that we can actually make PCR machines right in the lab because we have 3D printers.