BME103:T930 Group 12 l2 - Revision history

Nathan Moore: /* OUR TEAM */

Nathan Moore — Thu, 29 Nov 2012 17:41:09 GMT

OUR TEAM

←Older revision		Revision as of 17:41, 29 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|-		\|-
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]	+	\| [[Image:Baldy.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]
	\| [[Image:Jackiechan.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]		\| [[Image:Jackiechan.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]
	\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]		\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]

Nathan Moore: /* OUR TEAM */

Nathan Moore — Thu, 29 Nov 2012 17:37:34 GMT

OUR TEAM

←Older revision		Revision as of 17:37, 29 November 2012
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	\|-		\|-
	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]	+	\| [[Image:Jackiechan.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]
	\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]		\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]
	\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]		\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]

Nathan Moore: /* OUR TEAM */

Nathan Moore — Thu, 29 Nov 2012 17:29:54 GMT

OUR TEAM

←Older revision		Revision as of 17:29, 29 November 2012
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	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]
	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]	+	\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]
	\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]		\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>R&D Scientist]]	+	\| [[Image:Arnold.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>R&D Scientist]]
	\|}		\|}

David Tze: /* Thermal Cycler Engineering */

David Tze — Thu, 29 Nov 2012 16:40:06 GMT

Thermal Cycler Engineering

←Older revision		Revision as of 16:40, 29 November 2012
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	[[Image:Heat block group 12 changes.png]]		[[Image:Heat block group 12 changes.png]]

-	The picture above is of the original 4x4 PCR Tube Block which we are redesigning. The purpose of the PCR Tube Block is to hold the samples of DNA. In our redesign of the PCR Block, we are manipulating the sample size to a 3x7 block, making it capable of holding 21 DNA sample spaces instead of the generic 16. One of the 21 sample spaces will ~~be inserted with~~ a platinum temperature sensor.	+	The picture above is of the original 4x4 PCR Tube Block which we are redesigning. The purpose of the PCR Tube Block is to hold the samples of DNA. In our redesign of the PCR Block, we are manipulating the sample size to a 3x7 block, making it capable of holding 21 DNA sample spaces instead of the generic 16. One of the 21 sample spaces will contain a platinum temperature sensor.


	'''Key Features'''<br>		'''Key Features'''<br>
	'''PCR Tube Block.''':<br>		'''PCR Tube Block.''':<br>
-	Our lab group is targeting the process time of the Open PCR; we want to make it quicker and more efficient. In the new design, the PCR Tube Block has been expanded to 21 spaces to encompass more DNA samples~~. The DNA samples will also be shortened to 150 base pairs since it will only take 10 seconds to process the sample. This shortens the initial melting point from three minutes to one minute~~. As samples of DNA are usually done in pairs, the last space will be used to insert a platinum temperature sensor, one of the most accurate sensors. This new placement will develop more accurate readings as the position is identical to what we are measuring: the DNA samples. The accurate temperature readings, along with the increase in sample size, will make the Open PCR more efficient as it minimizes the chance of overheating or over-cooling. This prevention saves wasted time created by inaccurate readings.	+	Our lab group is targeting the process time of the Open PCR; we want to make it quicker and more efficient. In the new design, the PCR Tube Block has been expanded to 21 spaces to encompass more DNA samples. As samples of DNA are usually done in pairs, the last space will be used to insert a platinum temperature sensor, one of the most accurate sensors. This new placement will develop more accurate readings as the position is identical to what we are measuring: the DNA samples. The accurate temperature readings, along with the increase in sample size, will make the Open PCR more efficient as it minimizes the chance of overheating or over-cooling. This prevention saves wasted time created by inaccurate readings. Another change we are making to shorten the process time is shortening the number of base pairs to 150. This difference will cut twenty seconds off the process of each sample and shorten the initial melting point from three minutes to one.

Philip Evan Remick: /* Protocols */

Philip Evan Remick — Thu, 29 Nov 2012 10:32:02 GMT

Protocols

←Older revision		Revision as of 10:32, 29 November 2012
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	'''DNA Measurement Protocol'''		'''DNA Measurement Protocol'''

-	The steps for setting up the samples:<br>	+	<em>The steps for setting up the samples:</em><br>
	1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.		1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.

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	3. Measure 400mL of Tris buffer into a 500mL graduated cylinder and pour into each of the Eppendorf tubes.		3. Measure 400mL of Tris buffer into a 500mL graduated cylinder and pour into each of the Eppendorf tubes.

-	4. Extract each sample with one pipette <b>(use a new one for each sample)</b> into an Eppendorf tube that contains 400mL of Tris buffer. Be sure to transfer all of the samples into the tubes.	+	4. Extract each sample with one pipette <b>(use a new one for each sample to prevent contamination)</b> into an Eppendorf tube that contains 400mL of Tris buffer. Be sure to transfer all of the samples into the tubes.

	5. Label the Eppendorf tube with the sample number.		5. Label the Eppendorf tube with the sample number.
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	21. Repeat steps 5-12 as necessary.		21. Repeat steps 5-12 as necessary.

-	The Steps for Image J:<br>	+	<em>The Steps for Image J:</em><br>
	22. Download the Image J software.		22. Download the Image J software.

Philip Evan Remick: /* Protocols */

Philip Evan Remick — Thu, 29 Nov 2012 10:29:58 GMT

Protocols

←Older revision		Revision as of 10:29, 29 November 2012
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	17. Make sure the LED is going through the center of the drops, a cone of light should go around it, however, not at an angle.		17. Make sure the LED is going through the center of the drops, a cone of light should go around it, however, not at an angle.

-	Steps to setting up camera phone:<br>	+	<em>Steps to setting up camera phone:</em><br>
	18. Carefully place the cell phone stand in front of the fluorimeter.		18. Carefully place the cell phone stand in front of the fluorimeter.

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	26. Open them with Image J by going to add image. Find image on the files.		26. Open them with Image J by going to add image. Find image on the files.

-	Edit the picture:<br>	+	<em>Edit the picture:</em><br>
	27. Use the menu selection analyze>set measurements and choose 'area integrated density' and 'mean grey value'.		27. Use the menu selection analyze>set measurements and choose 'area integrated density' and 'mean grey value'.

Philip Evan Remick: /* Protocols */

Philip Evan Remick — Thu, 29 Nov 2012 10:25:49 GMT

Protocols

←Older revision		Revision as of 10:25, 29 November 2012
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	Steps to setting up camera phone:<br>		Steps to setting up camera phone:<br>
-	10. Carefully place the cell phone stand in front of the fluorimeter.	+	18. Carefully place the cell phone stand in front of the fluorimeter.

-	11. Configure the cell phone by going to the camera menu and doing the following:	+	19. Configure the cell phone by going to the camera menu and doing the following:
	*Inactivate the flash		*Inactivate the flash
	*Set ISO to 800 (or higher)		*Set ISO to 800 (or higher)
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	*Set the timer for five seconds		*Set the timer for five seconds

-	12. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.	+	20. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.

-	13. Repeat steps 5-12 as necessary.	+	21. Repeat steps 5-12 as necessary.

-	The Steps for Image J:	+	The Steps for Image J:<br>
-	1. Download the Image J software.	+	22. Download the Image J software.
-	2. Save the pictures to smart phone.	+
-	3. Be sure to name the pictures in the correct order taken in order to separate the images.	+	23. Save the pictures to smart phone.
-	3. Download the pictures onto a computer that has Image J through a USB device or uploading them.	+
-	4. Open them with Image J by going to add image. Find image on the files.	+	24. Be sure to name the pictures in the correct order taken in order to separate the images.
-	5. Edit the picture:	+
-	Use the menu selection analyze>set measurements and choose 'area integrated density' and 'mean grey value'.	+	25. Download the pictures onto a computer that has Image J through a USB device or uploading them.
-	Use the green image.	+
-	Click on the menu bar to activate the oval selection.	+	26. Open them with Image J by going to add image. Find image on the files.
-	Draw the best oval around your green drop image and then select 'analyze>measure'.	+
-	Write down the sample number and numbers measured.	+	Edit the picture:<br>
-	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.	+	27. Use the menu selection analyze>set measurements and choose 'area integrated density' and 'mean grey value'.
		+
		+	28. Use the green image.
		+
		+	29. Click on the menu bar to activate the oval selection.
		+
		+	30. Draw the best oval around your green drop image and then select 'analyze>measure'.
		+
		+	31. Write down the sample number and numbers measured.
		+
		+	32. 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.

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

Philip Evan Remick: /* Protocols */

Philip Evan Remick — Thu, 29 Nov 2012 10:16:47 GMT

Protocols

←Older revision		Revision as of 10:16, 29 November 2012
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	'''DNA Measurement Protocol'''		'''DNA Measurement Protocol'''

-	The steps for setting up the samples:	+	The steps for setting up the samples:<br>
	1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.		1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.

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	7. Pipette 100μL of distilled water into the corresponding Eppendorf tube containing 400mL of Tris buffer.		7. Pipette 100μL of distilled water into the corresponding Eppendorf tube containing 400mL of Tris buffer.

-	8.	+	8. Add the SYBR Green to the Eppendorf tubes with separate pipettes.
		+
	9. Open up the fluorimeter box and remove the contents.		9. Open up the fluorimeter box and remove the contents.
-	2. Disassemble the box by unsnapping it.	+
-	3. Put the cover of the box on the bottom facing upside down.	+	10. Disassemble the box by unsnapping it.
-	4. Next, place the fluorimeter on top of the box cover.	+
-	5. Then, carefully add the glass slide in between the fluorimeter.	+	11. Put the cover of the box on the bottom facing upside down.
-	6. Use the pipet and remove about .25ml of the sample or water.	+
-	7. Place a few drops of the ~~substance~~ in the middle of the slots until they conjoin.	+	12. Next, place the fluorimeter on top of the box cover.
-	8. Turn on the LED light.	+
-	9. Make sure the LED is going through the center of the drops, a cone of light should go around it, however, not at an angle.	+	13. Then, carefully add the glass slide in between the fluorimeter.
		+
		+	14. Use the pipet and remove about .25ml of the sample or water.
		+
		+	15. Place a few drops from the samples prepared in steps 1-8 in the middle of the slots until they conjoin.
		+
		+	16. Turn on the LED light.
		+
		+	17. Make sure the LED is going through the center of the drops, a cone of light should go around it, however, not at an angle.
		+
		+	Steps to setting up camera phone:<br>
	10. Carefully place the cell phone stand in front of the fluorimeter.		10. Carefully place the cell phone stand in front of the fluorimeter.
		+
	11. Configure the cell phone by going to the camera menu and doing the following:		11. Configure the cell phone by going to the camera menu and doing the following:
-	Inactivate the flash	+	*Inactivate the flash
-	Set ISO to 800 (or higher)	+	*Set ISO to 800 (or higher)
-	Set white balance to auto	+	*Set white balance to auto
-	Set exposure to highest setting	+	*Set exposure to highest setting
-	Set saturation to the highest setting	+	*Set saturation to the highest setting
-	Set contrast to the lowest setting	+	*Set contrast to the lowest setting
-	Set the timer for five seconds	+	*Set the timer for five seconds
		+
	12. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.		12. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.
		+
	13. Repeat steps 5-12 as necessary.		13. Repeat steps 5-12 as necessary.

Philip Evan Remick: /* Protocols */

Philip Evan Remick — Thu, 29 Nov 2012 10:02:39 GMT

Protocols

←Older revision		Revision as of 10:02, 29 November 2012
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	'''DNA Measurement Protocol'''		'''DNA Measurement Protocol'''

		+	The steps for setting up the samples:
	1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.		1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.

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	3. Measure 400mL of Tris buffer into a 500mL graduated cylinder and pour into each of the Eppendorf tubes.		3. Measure 400mL of Tris buffer into a 500mL graduated cylinder and pour into each of the Eppendorf tubes.

-	4. Extract each sample with one pipette into an Eppendorf tube that contains 400mL of Tris buffer. Be sure to transfer all of the ~~sample~~ into the ~~tube~~.	+	4. Extract each sample with one pipette <b>(use a new one for each sample)</b> into an Eppendorf tube that contains 400mL of Tris buffer. Be sure to transfer all of the samples into the tubes.

	5. Label the Eppendorf tube with the sample number.		5. Label the Eppendorf tube with the sample number.
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	6. Set up the sample DNA calf thymus by pipetting 100μL into an Eppendorf tube containing 400mL of Tris buffer.		6. Set up the sample DNA calf thymus by pipetting 100μL into an Eppendorf tube containing 400mL of Tris buffer.

-	7. Pipette 100μL of distilled water into the corresponding Eppendorf tube containing 400mL of Tris buffer	+	7. Pipette 100μL of distilled water into the corresponding Eppendorf tube containing 400mL of Tris buffer.
		+
		+	8.
		+	9. Open up the fluorimeter box and remove the contents.
		+	2. Disassemble the box by unsnapping it.
		+	3. Put the cover of the box on the bottom facing upside down.
		+	4. Next, place the fluorimeter on top of the box cover.
		+	5. Then, carefully add the glass slide in between the fluorimeter.
		+	6. Use the pipet and remove about .25ml of the sample or water.
		+	7. Place a few drops of the substance in the middle of the slots until they conjoin.
		+	8. Turn on the LED light.
		+	9. Make sure the LED is going through the center of the drops, a cone of light should go around it, however, not at an angle.
		+	10. Carefully place the cell phone stand in front of the fluorimeter.
		+	11. Configure the cell phone by going to the camera menu and doing the following:
		+	Inactivate the flash
		+	Set ISO to 800 (or higher)
		+	Set white balance to auto
		+	Set exposure to highest setting
		+	Set saturation to the highest setting
		+	Set contrast to the lowest setting
		+	Set the timer for five seconds
		+	12. Place the cell phone on the stand and take the picture while placing the cover over the fluorimeter.
		+	13. Repeat steps 5-12 as necessary.
		+
		+	The Steps for Image J:
		+	1. Download the Image J software.
		+	2. Save the pictures to smart phone.
		+	3. Be sure to name the pictures in the correct order taken in order to separate the images.
		+	3. Download the pictures onto a computer that has Image J through a USB device or uploading them.
		+	4. Open them with Image J by going to add image. Find image on the files.
		+	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'.
		+	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.

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

Philip Evan Remick: /* Protocols */

Philip Evan Remick — Thu, 29 Nov 2012 07:10:47 GMT

Protocols

←Older revision		Revision as of 07:10, 29 November 2012
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	*Final Hold: 4 Degrees Celsius		*Final Hold: 4 Degrees Celsius
	'''DNA Measurement Protocol'''		'''DNA Measurement Protocol'''
		+
		+	1. Open the lid of the PCR machine, and remove the 21 samples from the PCR tray.
		+
		+	2. With the fine point Sharpie, label the transfer pipettes and Eppendorf tubes accordingly to prevent contamination.
		+
		+	3. Measure 400mL of Tris buffer into a 500mL graduated cylinder and pour into each of the Eppendorf tubes.
		+
		+	4. Extract each sample with one pipette into an Eppendorf tube that contains 400mL of Tris buffer. Be sure to transfer all of the sample into the tube.
		+
		+	5. Label the Eppendorf tube with the sample number.
		+
		+	6. Set up the sample DNA calf thymus by pipetting 100μL into an Eppendorf tube containing 400mL of Tris buffer.
		+
		+	7. Pipette 100μL of distilled water into the corresponding Eppendorf tube containing 400mL of Tris buffer

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

←Older revision		Revision as of 17:41, 29 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|-		\|-
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]	+	\| [[Image:Baldy.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]
	\| [[Image:Jackiechan.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]		\| [[Image:Jackiechan.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]
	\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]		\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]

←Older revision		Revision as of 17:37, 29 November 2012
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	\|-		\|-
	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]	+	\| [[Image:Jackiechan.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]
	\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]		\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]
	\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]		\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]

←Older revision		Revision as of 17:29, 29 November 2012
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	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Divya Amrelia<br> PCR engineer]]
	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: David Tze<br>PCR engineer]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]	+	\| [[Image:Chuck-norris.jpg\|100px\|thumb\|Name: Nathan Moore<br>Protocol Planner]]
	\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]		\| [[Image:Lamborghini.jpg\|100px\|thumb\|Name: Philip Remick<br>Protocol Planner]]
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>R&D Scientist]]	+	\| [[Image:Arnold.jpg\|100px\|thumb\|Name: Ryan Magnuson<br>R&D Scientist]]
	\|}		\|}