BME103:W930 Group6 l2 - Revision history

Jason Van Egmond: /* Protocols */

Jason Van Egmond — Thu, 29 Nov 2012 00:02:52 GMT

Protocols

←Older revision		Revision as of 00:02, 29 November 2012
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	'''Polymerase Chain Reaction'''<br>		'''Polymerase Chain Reaction'''<br>
	The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.		The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.
		+

	'''Steps'''<br>		'''Steps'''<br>
-	1. The sample is heated to a temperate of ninety seven degrees Celsius for 20-30 seconds in order to denature the DNA.<br>	+	#The sample is heated to a temperate of ninety seven degrees Celsius for 20-30 seconds in order to denature the DNA.<br>
-	2. The sample is heated to between 50 and 65 degrees Celsius for 20-40 seconds. This allows the primers to anneal to the single strands of DNA.<br>	+	#The sample is heated to between 50 and 65 degrees Celsius for 20-40 seconds. This allows the primers to anneal to the single strands of DNA.<br>
-	3. The samples is heated to 72 degrees Celsius. This step allows Tag to synthesize the double stranded DNA.<br>	+	#The samples is heated to 72 degrees Celsius. This step allows Tag to synthesize the double stranded DNA.<br>
-	4. Step 3 is then repeated 30 times to duplicate the DNA many times. <br>	+	#Step 3 is then repeated 30 times to duplicate the DNA many times. <br>
-	5. Finally the PCR Machine holds a constant 4 degrees Celsius allowing the system to stabilize.<br>	+	#Finally the PCR Machine holds a constant 4 degrees Celsius allowing the system to stabilize.<br>
-		+
-		+
-		+


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-	'''Fluorometer Setup'''<br>1. Remove fluorometer elements from container.<br> 2. Place smartphone into the black stand, creating the camera setup.<br>3. Position camera setup parallel to the LED box so that the camera is shooting along the channel of the LED box.<br>	+	'''Fluorometer Setup'''<br>
-	4. Place Fluorometer Setup Part I onto lid from original container<br>5. While leaving the camera setup side of the container unsnapped, place container around Fluorometer Setup Part I.<br>	+	#Remove fluorometer elements from container.<br>
		+	#Place smartphone into the black stand, creating the camera setup.<br>
		+	#Position camera setup parallel to the LED box so that the camera is shooting along the channel of the LED box.<br>
		+	#Place Fluorometer Setup Part I onto lid from original container.<br>
		+	#While leaving the camera setup side of the container unsnapped, place container around Fluorometer Setup Part I.<br>
		+

		+	'''Fluorometer Use'''<br>
		+	#Remove container covering Fluorometer Final Setup.<br>
		+	#Switch on blue LED.<br>
		+	#Change camera settings by turning flash on, setting ISO to 800+, increasing exposure to maximum and disabling auto-focus.<br>
		+	#Pipette two drops of water (volume of 130-160 microliters per drop) onto the slide in the channel of the LED box.<br>
		+	#Focus LED light on the drops so that the middle of the drop is aligned with the line of light created by the LED.<br>
		+	#Put the container covering back over the Fluorometer Final Setup.<br>
		+	#Take 3 photos, making sure not to disturb the positioning and setup. <br>
		+	#Remove the container covering while again taking care not to change the placement of the setup.<br>
		+	#Remove slide and dispose of the used slide.<br>
		+	#Place new slide into LED box, and do steps 4 through 6 again.<br>
		+	#Note the type of smartphone used throughout the protocol, the distance from smartphone to the base of the LED box (in centimeters), and attach an image of each position of the drops.<br>


-	'''Fluorometer Use'''<br>1. Remove container covering Fluorometer Final Setup.<br>2. Switch on blue LED.<br>3. Change camera settings by turning flash on, setting ISO to 800+, increasing exposure to maximum and disabling auto-focus.<br>4. Pipette two drops of water (volume of 130-160 microliters per drop) onto the slide in the channel of the LED box.<br>5. Focus LED light on the drops so that the middle of the drop is aligned with the line of light created by the LED.<br>6. Put the container covering back over the Fluorometer Final Setup.<br>6. Take 3 photos, making sure not to disturb the positioning and setup. <br> 7. Remove the container covering while again taking care not to change the placement of the setup.<br>8. Remove slide and dispose of the used slide.<br>9. Place new slide into LED box, and do steps 4 through 6 again.<br>10. Note the type of smartphone used throughout the protocol, the distance from smartphone to the base of the LED box (in centimeters), and attach an image of each position of the drops.<br>	+	'''Transferal of Fluorometer Data to ImageJ'''<br>
-	~~<br>~~'''Transferal of Fluorometer Data to ImageJ'''<br>1. Use a USB cable to connect the smartphone that was used to a computer with the ImageJ software.<br>2. Open the '''Start Menu''' and double click on '''My Computer''' or '''Computer'''.<br>3. Select '''Portable Devices''' where the smartphone should be listed and double-click the icon.<br>4. Locate the '''DCIM''' folder and open it, and continue to the sub-folder '''Camera'''.<br>5. Select each picture that needs to be transferred, then '''Copy''' and '''Paste''' them into the folder you choose to store them in.<br> 6. Open ImageJ software from '''Start Menu''' or by double-clicking the ImageJ icon on the '''Desktop'''.<br>7. Once ImageJ software is open, click on '''File''' and select '''Open''' in the toolbar located in the top left of the computer screen.<br>8. Select '''Browse''' then select the image you want out of the folder where you stored your photos (in step 5)<br>9. Repeat steps 7 and 8 to continue process with different pictures.<br>	+	#Use a USB cable to connect the smartphone that was used to a computer with the ImageJ software.<br>
		+	#Open the '''Start Menu''' and double click on '''My Computer''' or '''Computer'''.<br>
		+	#Select '''Portable Devices''' where the smartphone should be listed and double-click the icon.<br>
		+	#Locate the '''DCIM''' folder and open it, and continue to the sub-folder '''Camera'''.<br>
		+	#Select each picture that needs to be transferred, then '''Copy''' and '''Paste''' them into the folder you choose to store them in.<br>
		+	#Open ImageJ software from '''Start Menu''' or by double-clicking the ImageJ icon on the '''Desktop'''.<br>
		+	#Once ImageJ software is open, click on '''File''' and select '''Open''' in the toolbar located in the top left of the computer screen.<br>
		+	#Select '''Browse''' then select the image you want out of the folder where you stored your photos (in step 5)<br>
		+	#Repeat steps 7 and 8 to continue process with different pictures.<br>

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

Jason Van Egmond: /* Thermal Cycler Engineering */

Jason Van Egmond — Wed, 28 Nov 2012 23:53:54 GMT

Thermal Cycler Engineering

←Older revision		Revision as of 23:53, 28 November 2012
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	'''Key Features'''<br>		'''Key Features'''<br>
-	Our group decided to increase the sample size~~. We increased it~~ to 48 samples. We designed our Open PCR machine to include this increased sample size. We increased the size of the machine itself to be able to hold 2 more heating plates and lids. We ~~changed~~ the overall shape of the machine ~~to make it wider~~ to include the new heating plates on one of the sides. ~~The~~ controls and the machine itself ~~run~~ in the same way. ~~This would benefit~~ in diagnosing diseases more quickly across multiple patients.	+	Our group decided to increase the sample size to 48 samples. Then, we designed our Open PCR machine to include this increased sample size. We increased the size of the machine itself to be able to hold 2 more heating plates and lids. Also, We widened the overall shape of the machine so as to include the new heating plates on one of the sides. However, no changes were made to the controls and the machine itself still runs in the same way. The increased sample size will be beneficial in diagnosing diseases more quickly across multiple patients, as it is more efficient than the original Open PCR machine.

	(Content by Sairah F)		(Content by Sairah F)

Jason Van Egmond: /* OUR TEAM */

Jason Van Egmond — Wed, 28 Nov 2012 23:48:32 GMT

OUR TEAM

←Older revision		Revision as of 23:48, 28 November 2012
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	\| [[Image:GayaPieBeach.jpg\|100px\|thumb\|Name: Kim<br>Reasearch and Development(s)]]		\| [[Image:GayaPieBeach.jpg\|100px\|thumb\|Name: Kim<br>Reasearch and Development(s)]]
	\| [[Image:CreepyMalcom.jpg\|100px\|thumb\|Name: Malcolm<br>Experimental Protocol Planner]]		\| [[Image:CreepyMalcom.jpg\|100px\|thumb\|Name: Malcolm<br>Experimental Protocol Planner]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: ~~Student~~<br>~~Role(s)~~]]	+	\| [[Image:Jason_profile.jpg\|100px\|thumb\|Name: Jason<br>Experimental Protocol Planner]]
	\|}		\|}

Antonio T. Garcia: /* Protocols */

Antonio T. Garcia — Wed, 28 Nov 2012 23:13:23 GMT

Protocols

←Older revision		Revision as of 23:13, 28 November 2012
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	#Open the lid of the PCR machine and remove the 2 controls and the 6 samples (or more if the user added more of their own samples) from the PCR tray after the PCR protocol has finished.<br>		#Open the lid of the PCR machine and remove the 2 controls and the 6 samples (or more if the user added more of their own samples) from the PCR tray after the PCR protocol has finished.<br>
	#Using a fine point sharpie, label each transfer pipette and micro test tube to avoid contamination. <br>		#Using a fine point sharpie, label each transfer pipette and micro test tube to avoid contamination. <br>
-	#Using one of the pipettes, place two drops of ~~Sybr~~ green solution in the middle of the first two rows of the slide.<br>	+	#Using one of the pipettes, place two drops of SYBR green solution in the middle of the first two rows of the slide.<br>
	#Fill a different pipette with one of the samples from the micro test tube and carefully place two additional drops on the glass slide so that the drops combine to form one drop that should then be pinned and look like a beach ball.<br>		#Fill a different pipette with one of the samples from the micro test tube and carefully place two additional drops on the glass slide so that the drops combine to form one drop that should then be pinned and look like a beach ball.<br>

Antonio T. Garcia: /* Protocols */

Antonio T. Garcia — Wed, 28 Nov 2012 23:11:44 GMT

Protocols

←Older revision		Revision as of 23:11, 28 November 2012
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	'''DNA Measurement Protocol'''<br>		'''DNA Measurement Protocol'''<br>
		+	#Open the lid of the PCR machine and remove the 2 controls and the 6 samples (or more if the user added more of their own samples) from the PCR tray after the PCR protocol has finished.<br>
		+	#Using a fine point sharpie, label each transfer pipette and micro test tube to avoid contamination. <br>
		+	#Using one of the pipettes, place two drops of Sybr green solution in the middle of the first two rows of the slide.<br>
		+	#Fill a different pipette with one of the samples from the micro test tube and carefully place two additional drops on the glass slide so that the drops combine to form one drop that should then be pinned and look like a beach ball.<br>

Malcolm Cavin: /* Protocols */

Malcolm Cavin — Wed, 28 Nov 2012 22:02:01 GMT

Protocols

←Older revision		Revision as of 22:02, 28 November 2012
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	'''Total Volume'''--------------750μL<br>		'''Total Volume'''--------------750μL<br>

-	'''Supplied by User'''-----Amount<br>	+	'''Supplied by User'''-----'''Amount'''<br>
	Sample of DNA----------.5μL<br>		Sample of DNA----------.5μL<br>
	Safety Gloves<br>		Safety Gloves<br>

Malcolm Cavin: /* Protocols */

Malcolm Cavin — Wed, 28 Nov 2012 18:23:02 GMT

Protocols

←Older revision		Revision as of 18:23, 28 November 2012
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	'''Steps'''<br>		'''Steps'''<br>
-	1. The sample is heated to a temperate of ninety seven degrees Celsius for 20-30 seconds in order to denature the DNA.	+	1. The sample is heated to a temperate of ninety seven degrees Celsius for 20-30 seconds in order to denature the DNA.<br>
-	2. The sample is heated to between 50 and 65 degrees Celsius for 20-40 seconds. This allows the primers to anneal to the single strands of DNA.	+	2. The sample is heated to between 50 and 65 degrees Celsius for 20-40 seconds. This allows the primers to anneal to the single strands of DNA.<br>
-	3. The samples is heated to 72 degrees Celsius. This step allows Tag to synthesize the double stranded DNA.	+	3. The samples is heated to 72 degrees Celsius. This step allows Tag to synthesize the double stranded DNA.<br>
-	4. Step 3 is then repeated 30 times to duplicate the DNA many times.	+	4. Step 3 is then repeated 30 times to duplicate the DNA many times. <br>
-	5. Finally the PCR Machine holds a constant 4 degrees Celsius allowing the system to stabilize.	+	5. Finally the PCR Machine holds a constant 4 degrees Celsius allowing the system to stabilize.<br>

Malcolm Cavin: /* Protocols */

Malcolm Cavin — Wed, 28 Nov 2012 18:22:23 GMT

Protocols

←Older revision		Revision as of 18:22, 28 November 2012
Line 101:		Line 101:
	The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.		The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.

-	Steps	+	'''Steps'''<br>
-	1. The sample is heated to a temperate of ninety seven degrees ~~Celcius~~	+	1. The sample is heated to a temperate of ninety seven degrees Celsius for 20-30 seconds in order to denature the DNA.
		+	2. The sample is heated to between 50 and 65 degrees Celsius for 20-40 seconds. This allows the primers to anneal to the single strands of DNA.
		+	3. The samples is heated to 72 degrees Celsius. This step allows Tag to synthesize the double stranded DNA.
		+	4. Step 3 is then repeated 30 times to duplicate the DNA many times.
		+	5. Finally the PCR Machine holds a constant 4 degrees Celsius allowing the system to stabilize.

Malcolm Cavin: /* Protocols */

Malcolm Cavin — Wed, 28 Nov 2012 18:13:59 GMT

Protocols

←Older revision		Revision as of 18:13, 28 November 2012
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	'''PCR Protocol'''		'''PCR Protocol'''
-	Polymerase Chain Reaction	+	'''Polymerase Chain Reaction'''<br>
	The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.		The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.

Malcolm Cavin: /* Protocols */

Malcolm Cavin — Wed, 28 Nov 2012 18:12:46 GMT

Protocols

←Older revision		Revision as of 18:12, 28 November 2012
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	'''PCR Protocol'''		'''PCR Protocol'''
		+	Polymerase Chain Reaction
		+	The patients DNA will be amplified through a process called Polymerase Chain Reaction or PCR. Steps for this process include; denaturation, annealing, and extension. These steps require the PCR machine to run through a multitude of temperatures.
		+
		+	Steps
		+	1. The sample is heated to a temperate of ninety seven degrees Celcius
		+