BME103:T930 Group 12 - Revision history

Divya Amrelia: /* Initial Machine Testing */

2012-11-15T07:57:47Z

Initial Machine Testing

←Older revision		Revision as of 07:57, 15 November 2012
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	[[Image:Group 12 PCR Image.png]]		[[Image:Group 12 PCR Image.png]]

-	Description: The Open PCR(polymerase chain reaction) machine cycles samples of DNA through different temperatures with the purpose of replicating the DNA. The machine cycles through different temperatures to denature, anneal, and extend the DNA. At a high temperature, DNA denatures, meaning the DNA separates into two single strands. Then primers bind to the two separate strands to prevent them from joining back together and the sample is cooled. Finally, the DNA sample is heated once more and enzymes (Taq Polymerase) attach to the separated strands and begin replication.	+	'''Description'''<br>
		+	The Open PCR(polymerase chain reaction) machine cycles samples of DNA through different temperatures with the purpose of replicating the DNA. The machine cycles through different temperatures to denature, anneal, and extend the DNA. At a high temperature, DNA denatures, meaning the DNA separates into two single strands. Then primers bind to the two separate strands to prevent them from joining back together and the sample is cooled. Finally, the DNA sample is heated once more and enzymes (Taq Polymerase) attach to the separated strands and begin replication.
		+
	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>

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	On October 25, 2012, we experimented with the Open PCR. The experience was not pleasant as the machine took an hour and forty minutes to finish the experiment. The time estimate was also incorrect as it fluctuated. Fortunately, the experiment was a success as the machine finished the testing, revealing whether the DNA contained mutations.		On October 25, 2012, we experimented with the Open PCR. The experience was not pleasant as the machine took an hour and forty minutes to finish the experiment. The time estimate was also incorrect as it fluctuated. Fortunately, the experiment was a success as the machine finished the testing, revealing whether the DNA contained mutations.
-	~~(Write the date you first tested Open PCR and your experience(s) with the machine)<br>~~

Divya Amrelia: /* Initial Machine Testing */

2012-11-15T07:54:21Z

Initial Machine Testing

←Older revision		Revision as of 07:54, 15 November 2012
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	[[Image:Group 12 PCR Image.png]]		[[Image:Group 12 PCR Image.png]]

-	The Open PCR(polymerase chain reaction) machine cycles samples of DNA through different temperatures. DNA ~~samples are placed in~~ the ~~16 tube PCR block~~ and the ~~PCR~~ is ~~set~~ to ~~a certain number of temperatures~~ and ~~cycles~~.	+	Description: The Open PCR(polymerase chain reaction) machine cycles samples of DNA through different temperatures with the purpose of replicating the DNA. The machine cycles through different temperatures to denature, anneal, and extend the DNA. At a high temperature, DNA denatures, meaning the DNA separates into two single strands. Then primers bind to the two separate strands to prevent them from joining back together and the sample is cooled. Finally, the DNA sample is heated once more and enzymes (Taq Polymerase) attach to the separated strands and begin replication.
-		+
	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>

Divya Amrelia: /* Initial Machine Testing */

2012-11-15T07:37:51Z

Initial Machine Testing

←Older revision		Revision as of 07:37, 15 November 2012
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	'''The Original Design'''<br>		'''The Original Design'''<br>
-	[[Image:Th Group 12 ~~pcr image~~.png]]	+	[[Image:Group 12 PCR Image.png]]

	The Open PCR(polymerase chain reaction) machine cycles samples of DNA through different temperatures. DNA samples are placed in the 16 tube PCR block and the PCR is set to a certain number of temperatures and cycles.		The Open PCR(polymerase chain reaction) machine cycles samples of DNA through different temperatures. DNA samples are placed in the 16 tube PCR block and the PCR is set to a certain number of temperatures and cycles.

Philip Evan Remick: /* Research and Development */

2012-11-15T06:59:33Z

Research and Development

←Older revision		Revision as of 06:59, 15 November 2012
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	Here are step-by-step illustrations of how the primer binds to the wanted DNA template, and how the Taq polymerase amplifies the DNA: <br>		Here are step-by-step illustrations of how the primer binds to the wanted DNA template, and how the Taq polymerase amplifies the DNA: <br>

-	[[Image:BME103-12-1.png‎\|thumb\|frame\|left\|~~A description of the image goes here~~]]	+	[[Image:BME103-12-1.png‎\|thumb\|frame\|left\|]]
-	[[Image:BME103-12-2.png‎‎\|thumb\|frame\|left\|~~A description of the image goes here~~]]	+	[[Image:BME103-12-2.png‎‎\|thumb\|frame\|left\|]]
-	[[Image:BME-12-3.png‎\|thumb\|frame\|left\|~~A description of the image goes here~~]]	+	[[Image:BME-12-3.png‎\|thumb\|frame\|left\|]]
-	[[Image:BME-12-4.png‎\|thumb\|frame\|left\|~~A description of the image goes here~~]]	+	[[Image:BME-12-4.png‎\|thumb\|frame\|left\|]]
	Images from (http://openpcr.org/use-it/) <br><br>		Images from (http://openpcr.org/use-it/) <br><br>
	The r17879961 sample is a cancer causing polymorphism prevalent in homo sapiens. It is located in chromosome 22 and is identified by an allele change of ATT → ACT. This missense causes a residue change of I [Ile] ⇒ T [Thr]. Here is the sequence surrounding the mutation: <br>		The r17879961 sample is a cancer causing polymorphism prevalent in homo sapiens. It is located in chromosome 22 and is identified by an allele change of ATT → ACT. This missense causes a residue change of I [Ile] ⇒ T [Thr]. Here is the sequence surrounding the mutation: <br>

Philip Evan Remick: /* OUR TEAM */

2012-11-15T06:57:40Z

OUR TEAM

←Older revision		Revision as of 06:57, 15 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Philip Remick <br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Philip Remick <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ David Tze<br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| David Tze<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Ryan Magnuson<br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Ryan Magnuson<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Nathan Moore <br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Nathan Moore <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Divya Amrelia <br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Divya Amrelia <br>]]
	\|}		\|}

Philip Evan Remick: /* OUR TEAM */

2012-11-15T06:57:06Z

OUR TEAM

←Older revision		Revision as of 06:57, 15 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Philip Remick <br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Philip Remick <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Nathan Moore <br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Nathan Moore <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia <br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia <br>]]
	\|}		\|}

Philip Evan Remick: /* Protocols */

2012-11-15T06:56:23Z

Protocols

←Older revision		Revision as of 06:56, 15 November 2012
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	*Draw another oval for the of the same size in the green file for the background about the drop to get the "noise". Select 'analyze>measure'. Write drown the sample number and the numbers measure and label this as background. Save your measurements.		*Draw another oval for the of the same size in the green file for the background about the drop to get the "noise". Select 'analyze>measure'. Write drown the sample number and the numbers measure and label this as background. Save your measurements.
	[[Image:Green Drop.png]]		[[Image:Green Drop.png]]
		+	<br>
	Sample of the image from a smart phone showing the DNA amplified sample (green) in the fluorimeter.<br>		Sample of the image from a smart phone showing the DNA amplified sample (green) in the fluorimeter.<br>
	<br><br>		<br><br>

Philip Evan Remick: /* Protocols */

2012-11-15T06:55:24Z

Protocols

←Older revision		Revision as of 06:55, 15 November 2012
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	*Draw another oval for the of the same size in the green file for the background about the drop to get the "noise". Select 'analyze>measure'. Write drown the sample number and the numbers measure and label this as background. Save your measurements.		*Draw another oval for the of the same size in the green file for the background about the drop to get the "noise". Select 'analyze>measure'. Write drown the sample number and the numbers measure and label this as background. Save your measurements.
	[[Image:Green Drop.png]]		[[Image:Green Drop.png]]
-		+	Sample of the image from a smart phone showing the DNA amplified sample (green) in the fluorimeter.<br>
	<br><br>		<br><br>

Philip Evan Remick: /* Protocols */

2012-11-15T06:53:06Z

Protocols

←Older revision		Revision as of 06:53, 15 November 2012
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	*Use the green image.		*Use the green image.
	*Click on the menu bar to activate the oval selection.		*Click on the menu bar to activate the oval selection.
-	*Draw the best oval around your green drop image and then select 'analyze>measure.'	+	*Draw the best oval around your green drop image and then select 'analyze>measure'.
		+	*Write down the sample number and numbers measured.
		+	*Draw another oval for the of the same size in the green file for the background about the drop to get the "noise". Select 'analyze>measure'. Write drown the sample number and the numbers measure and label this as background. Save your measurements.
	[[Image:Green Drop.png]]		[[Image:Green Drop.png]]

Philip Evan Remick: /* Protocols */

2012-11-15T06:50:04Z

Protocols

←Older revision		Revision as of 06:50, 15 November 2012
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	12. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.<br>		12. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.<br>
	13. Repeat steps 5-12 as necessary.<br>		13. Repeat steps 5-12 as necessary.<br>
-		+	<br>
-		+	''The Steps for Image J:''<br>
-	1. Download the ~~ImageJ~~ software ~~from the internet~~	+	1. Download the Image J software.<br>
-	2. Save the pictures to smart phone.	+	2. Save the pictures to smart phone.<br>
-	3. Download the pictures onto a computer that has Image J.	+	3. Be sure to name the pictures in the correct order taken in order to separate the images.<br>
-	4. Open them with Image J by going to add image. Find image.	+	3. Download the pictures onto a computer that has Image J through a USB device or uploading them.<br>
-	5. ~~Change~~ the picture:	+	4. Open them with Image J by going to add image. Find image on the files.<br>
		+	5. Edit the picture:
		+	*Use the menu selection analyze>set measurements and choose 'area integrated density' and 'mean grey value'.
		+	*Use the green image.
		+	*Click on the menu bar to activate the oval selection.
		+	*Draw the best oval around your green drop image and then select 'analyze>measure.'
	[[Image:Green Drop.png]]		[[Image:Green Drop.png]]

←Older revision		Revision as of 06:57, 15 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Philip Remick <br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Philip Remick <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ David Tze<br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| David Tze<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Ryan Magnuson<br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Ryan Magnuson<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Nathan Moore <br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Nathan Moore <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|~~Name:~~ Divya Amrelia <br>]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\| Divya Amrelia <br>]]
	\|}		\|}

←Older revision		Revision as of 06:57, 15 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Philip Remick <br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Philip Remick <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Nathan Moore <br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Nathan Moore <br>]]
-	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia <br>~~Role(s)~~]]	+	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia <br>]]
	\|}		\|}