BME103:W930 Group1 l2 - Revision history

Karmella Haynes: /* OUR TEAM */

2012-11-30T01:34:07Z

OUR TEAM

←Older revision		Revision as of 01:34, 30 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
-	\|-	+	\|- valign="top"
	\| [[Image:K_Chu.jpg\|100px\|thumb\|Name: Kevin Chu<br>Experimemtal Protocol Planner]]		\| [[Image:K_Chu.jpg\|100px\|thumb\|Name: Kevin Chu<br>Experimemtal Protocol Planner]]
	\| [[Image:Rodin_Thinker.JPG\|100px\|thumb\|Name: Zhiyue Yang<br>Open PCR Machine Engineer]]		\| [[Image:Rodin_Thinker.JPG\|100px\|thumb\|Name: Zhiyue Yang<br>Open PCR Machine Engineer]]

Vanessa Barker: /* Thermal Cycler Engineering */

2012-11-28T18:31:15Z

Thermal Cycler Engineering

←Older revision		Revision as of 18:31, 28 November 2012
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	'''System Design'''<br>		'''System Design'''<br>
	[[Image:PCRLid.png\|800x400px\|]]<br>		[[Image:PCRLid.png\|800x400px\|]]<br>
-	The picture shown above is the top of an Open PCR machine. This part consists of a LCD screen and a heating lid. The top of the machine has several issues. For example, the lid is hard to open before the redesign. To solve these issues, we came up with several possible changes.	+	The picture shown above is the original top of an Open PCR machine. This part consists of a LCD screen and a heating lid. The top of the machine has several issues. For example, the lid is hard to open before the redesign. To solve these issues, we came up with several possible changes.<br>
-		+	[[Image:NewPCR.jpg\|600px]]<br>
		+	This picture show the redesigned Open PCR Machine complete with the modifications detailed below.

	'''Key Features'''<br>		'''Key Features'''<br>

Michael J. Dennison: /* Thermal Cycler Engineering */

2012-11-28T17:30:44Z

Thermal Cycler Engineering

←Older revision		Revision as of 17:30, 28 November 2012
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	'''Key Features'''<br>		'''Key Features'''<br>
-	Our group focuses on the stability of the machine. First of all, many groups have reported that the lid was hard to open. Since the problem is mainly caused by the current latch, the latch will be changed to a magnetic latch, which can be readily opened. Secondly, the machine is extremely fragile and the wooden outside does not provide much durability. In order to solve this problem, we can use transparent plastic instead of wood to make the case. Through this change, we can not only increase durability but also see the inner design of the machine easily. Last but not least, we can remove the knob which adjusts lid height. This knob ultimately makes the machine more confusing, as it is difficult to tell whether the lid is too high - causing the samples to receive less heat - too low - squishing the samples and potentially warping or damaging the test tubes the samples are in - or at the proper height. Instead, the lid will remain at the same height as long as the machine is closed and a specific test tube size will be standardized for the machine.	+	Our group focuses on the stability of the machine. First of all, many groups have reported that the lid was hard to open. Since the problem is mainly caused by the current latch, the latch will be changed to a magnetic latch, which can be readily opened. Secondly, the machine is extremely fragile and the wooden outside does not provide much durability. In order to solve this problem, we can use transparent plastic instead of wood to make the case. Through this change, we can not only increase durability but also see the inner design of the machine easily. Last but not least, we can remove the knob which adjusts the heating lid height. This knob ultimately makes the machine more confusing, as it is difficult to tell whether the lid is too high - causing the samples to receive less heat - too low - squishing the samples and potentially warping or damaging the test tubes the samples are in - or at the proper height. Instead, the lid will remain at the same height as long as the machine is closed and a specific test tube size will be standardized for the machine.

Zhiyue Yang: /* Thermal Cycler Engineering */

2012-11-28T16:34:57Z

Thermal Cycler Engineering

←Older revision		Revision as of 16:34, 28 November 2012
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	'''System Design'''<br>		'''System Design'''<br>
	[[Image:PCRLid.png\|800x400px\|]]<br>		[[Image:PCRLid.png\|800x400px\|]]<br>
-	The picture shown above is the top of an Open PCR machine. This part consists of a LCD screen and a heating lid. The top of the machine has several issues. For example, the lid is hard to open. To solve these issues, we came up with several possible changes.	+	The picture shown above is the top of an Open PCR machine. This part consists of a LCD screen and a heating lid. The top of the machine has several issues. For example, the lid is hard to open before the redesign. To solve these issues, we came up with several possible changes.

Michael J. Dennison: /* Research and Development */

2012-11-28T16:29:30Z

Research and Development

←Older revision		Revision as of 16:29, 28 November 2012
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	<!--- 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 --->

-	[[Image:BME103_Group1_Heterotaxy_primer.jpg‎\|~~200px~~\|Heterotaxy PCR primer design]]	+	[[Image:BME103_Group1_Heterotaxy_primer.jpg‎\|800px\|Heterotaxy PCR primer design]]


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Benjamin S. Duguay: /* Research and Development */

2012-11-28T16:27:51Z

Research and Development

←Older revision		Revision as of 16:27, 28 November 2012
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	<!--- 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 --->

		+	[[Image:BME103_Group1_Heterotaxy_primer.jpg‎\|200px\|Heterotaxy PCR primer design]]


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Benjamin S. Duguay: /* Research and Development */

2012-11-28T16:23:23Z

Research and Development

←Older revision		Revision as of 16:23, 28 November 2012
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	<!--- 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 --->

-	~~5’G C G C A A A A C A C A3’~~
-	~~G C G T T T T G T G~~
-
-	~~C G C A A A A C A C~~
-	~~3’C G C G T T T T G T G T5’~~


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Michael J. Dennison: /* Protocols */

2012-11-28T16:22:56Z

Protocols

←Older revision		Revision as of 16:22, 28 November 2012
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	#In Image J, select Analyze > Set Measurements and choose area, integrated density, and mean grey value.		#In Image J, select Analyze > Set Measurements and choose area, integrated density, and mean grey value.
	#Select Image > Color > Split Channels. Three images will appear; choose the one named green.		#Select Image > Color > Split Channels. Three images will appear; choose the one named green.
-	#~~Draw~~ an oval around the drop. Then, go to analyze and measure, and record the measurements.	+	#Select the oval tool and draw an oval around the drop. Then, go to analyze and measure, and record the measurements.
	#Obtain the background reading by moving the oval over the dark area around the drop, and record the INTDEN and RAWINTDEN.		#Obtain the background reading by moving the oval over the dark area around the drop, and record the INTDEN and RAWINTDEN.
	#Repeat steps 16-20 for all of the pictures. Make sure each sample lines up with the correct INTDEN measurements.		#Repeat steps 16-20 for all of the pictures. Make sure each sample lines up with the correct INTDEN measurements.

Michael J. Dennison: /* Protocols */

2012-11-28T16:20:53Z

Protocols

←Older revision		Revision as of 16:20, 28 November 2012
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	#Turn on the fluorimeter so that a blue light shines.		#Turn on the fluorimeter so that a blue light shines.
	#From one of the labeled Eppendorf tubes containing SYBR green dye, use the corresponding pipette to place two drops adjacent to one another on<br> a glass slide. The two drops should combine to form a single larger drop.		#From one of the labeled Eppendorf tubes containing SYBR green dye, use the corresponding pipette to place two drops adjacent to one another on<br> a glass slide. The two drops should combine to form a single larger drop.
		+	#Adjust the slide so that the blue light shines through the drops.
	#Dull the lights in the room, letting in as little light as possible into the box containing the fluorimeter.		#Dull the lights in the room, letting in as little light as possible into the box containing the fluorimeter.
	#On the Smartphone, adjust the following settings		#On the Smartphone, adjust the following settings

Benjamin S. Duguay: /* Research and Development */

2012-11-28T16:14:54Z

Research and Development

←Older revision		Revision as of 16:14, 28 November 2012
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	<!--- 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 --->

-	~~Forward primer (in '''bold''')~~	+	5’G C G C A A A A C A C A3’
		+	G C G T T T T G T G
		+
		+	C G C A A A A C A C
		+	3’C G C G T T T T G T G T5’

-	~~GCGC'''A'''AAACACA~~
-	~~'''GTTTTGTGT'''~~

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