BME103:T130 Group 12 l2 - Revision history

Justin Landstrom: /* Protocols */

2012-11-29T07:22:08Z

Protocols

←Older revision		Revision as of 07:22, 29 November 2012
Line 116:		Line 116:
	'''1.''' PCR is a process that uses controlled temperature changes to make copies of DNA. Heat (about 95°C) separates double-stranded DNA into two single strands; this process is called denaturation.		'''1.''' PCR is a process that uses controlled temperature changes to make copies of DNA. Heat (about 95°C) separates double-stranded DNA into two single strands; this process is called denaturation.

-	'''2.''' "Primers", or short DNA strands, binds to the very end of the complimentary sequence that is being replicated. This step is called annealing, which takes place between 40°C and 65°C. The temperature that we ~~used was~~ 57°C.	+	'''2.''' "Primers", or short DNA strands, binds to the very end of the complimentary sequence that is being replicated. This step is called annealing, which takes place between 40°C and 65°C. The temperature that we use for this is 57°C.

	'''3.''' Once the annealing process is done, the temperature is raised to about 72°C and DNA polymerase then extends from the primers copying the DNA.		'''3.''' Once the annealing process is done, the temperature is raised to about 72°C and DNA polymerase then extends from the primers copying the DNA.

Justin Landstrom: /* Research and Development */

2012-11-29T06:59:06Z

Research and Development

←Older revision		Revision as of 06:59, 29 November 2012
Line 202:		Line 202:
	'''Background on Disease Markers'''		'''Background on Disease Markers'''

-	Human Immunodeficiency Virus, or HIV is a horrible disease and is running ~~ramped everywhere,~~ especially in underdeveloped countries. ~~There~~ are also many people with HIV in developed countries such as the United States. This disease affects chromosome 17 and the genome build 36.3. After researching the SNP for HIV, which is rs1024611, the mutation in the sequence was discovered to be '''ATA'''. So then a primer to be used along side a PCR was developed.	+	Human Immunodeficiency Virus, or HIV is a horrible disease and is running rampant worldwide. HIV is especially prevalent in underdeveloped countries. This virus isn't limited to undeveloped countries however, as there are also many people with HIV in developed countries such as the United States. This disease affects chromosome 17 and the genome build 36.3. After researching the SNP for HIV, which is rs1024611, the mutation in the sequence was discovered to be '''ATA'''. So then a primer to be used along side a PCR was developed.

	http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1024611		http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1024611

Chiao May Lee at 05:24, 29 November 2012

2012-11-29T05:24:03Z

←Older revision		Revision as of 05:24, 29 November 2012
Line 182:		Line 182:
	'''12.''' As the last sample was run, the water from the scintillation vial as a blank was run using the same procedure as with the other samples.		'''12.''' As the last sample was run, the water from the scintillation vial as a blank was run using the same procedure as with the other samples.

-	'''13.''' ImageJ ~~will be~~ used to analyze the images taken by the smartphone. To upload the image onto ImageJ, the ANALYZE tab was clicked and SET MEASUREMENTS was chosen. AREA INTEGRATED DENSITY and MEAN GREY VALUE were selected from the menu.	+	'''13.''' ImageJ was used to analyze the images taken by the smartphone. To upload the image onto ImageJ, the ANALYZE tab was clicked and SET MEASUREMENTS was chosen. AREA INTEGRATED DENSITY and MEAN GREY VALUE were selected from the menu.

	'''14.''' The MENU tab was selected and the COLOR tab was chosen, the function SPLIT CHANNELS was used; three separate files were then created. SYBR GREEN fluoresces green, sothe image name with "green" next to it was used.		'''14.''' The MENU tab was selected and the COLOR tab was chosen, the function SPLIT CHANNELS was used; three separate files were then created. SYBR GREEN fluoresces green, sothe image name with "green" next to it was used.

James Kyeh: /* Thermal Cycler Engineering */

2012-11-29T05:20:57Z

Thermal Cycler Engineering

←Older revision		Revision as of 05:20, 29 November 2012
Line 50:		Line 50:
	4. Lower the higher heating plate so the difference in space between the two plates was similar as before<br>		4. Lower the higher heating plate so the difference in space between the two plates was similar as before<br>

-	~~'''~~For the top body part~~'''~~	+	For the top body part<br>
-	~~'''~~1.~~'''~~ Attach the part as you would normally	+	1.Attach the part as you would normally<br>
-	~~'''~~2.~~'''~~ Connect the input buttons to the circuit board.	+	2.Place the buttons in their appropriate spots in the new areas on the top board.<br>
		+	3.Connect the input buttons to the circuit board.<br>

Chiao May Lee at 05:19, 29 November 2012

2012-11-29T05:19:51Z

←Older revision		Revision as of 05:19, 29 November 2012
Line 175:		Line 175:
	'''9.''' Once they have taken enough photos of that sample, the flourimeter was taken back to the sample preparer to prepare the next sample.		'''9.''' Once they have taken enough photos of that sample, the flourimeter was taken back to the sample preparer to prepare the next sample.

-	'''10.''' Now ~~either rerun~~ the sample again or that sample and its pipette was discarded. The SYBR Green I labeled pipette was kept.	+	'''10.''' Now the sample was either rerun again or that sample and its pipette was discarded. The SYBR Green I labeled pipette was kept.

	'''11.''' This procedure was then repeated for all the samples. 5 samples can be run per glass slide.		'''11.''' This procedure was then repeated for all the samples. 5 samples can be run per glass slide.

James Kyeh: /* Thermal Cycler Engineering */

2012-11-29T05:19:46Z

Thermal Cycler Engineering

←Older revision		Revision as of 05:19, 29 November 2012
Line 44:		Line 44:
	'''Instructions'''		'''Instructions'''

-	For the lid design	+	For the lid design<br>
-	1. Remove the knob on the lid	+	1. Remove the knob on the lid<br>
-	2. Once the knob is removed, the bolt will be able to be removed.	+	2. Once the knob is removed, the bolt will be able to be removed.<br>
-	3. Lower the bottom heating plate to the desired height	+	3. Lower the bottom heating plate to the desired height<br>
-	4. Lower the higher heating plate so the difference in space between the two plates was similar as before	+	4. Lower the higher heating plate so the difference in space between the two plates was similar as before<br>

	'''For the top body part'''		'''For the top body part'''

James Kyeh: /* Thermal Cycler Engineering */

2012-11-29T05:19:26Z

Thermal Cycler Engineering

←Older revision		Revision as of 05:19, 29 November 2012
Line 45:		Line 45:

	For the lid design		For the lid design
-	1. Remove the knob on the lid	+	1. Remove the knob on the lid
-	2. Once the knob is removed, the bolt will be able to be removed.	+	2. Once the knob is removed, the bolt will be able to be removed.
-	3. Lower the bottom heating plate to the desired height	+	3. Lower the bottom heating plate to the desired height
-	4. Lower the higher heating plate so the difference in space between the two plates was similar as before	+	4. Lower the higher heating plate so the difference in space between the two plates was similar as before

	'''For the top body part'''		'''For the top body part'''

James Kyeh: /* Thermal Cycler Engineering */

2012-11-29T05:19:05Z

Thermal Cycler Engineering

←Older revision		Revision as of 05:19, 29 November 2012
Line 44:		Line 44:
	'''Instructions'''		'''Instructions'''

-	~~'''~~For the lid design~~'''~~	+	For the lid design
-	~~'''~~1.~~'''~~ Remove the knob on the lid	+	1. Remove the knob on the lid
-	~~'''~~2.~~'''~~ Once the knob is removed, the bolt will be able to be removed.	+	2. Once the knob is removed, the bolt will be able to be removed.
-	~~'''~~3.~~'''~~ Lower the bottom heating plate to the desired height	+	3. Lower the bottom heating plate to the desired height
-	~~'''~~4.~~'''~~ Lower the higher heating plate so the difference in space between the two plates was similar as before	+	4. Lower the higher heating plate so the difference in space between the two plates was similar as before

	'''For the top body part'''		'''For the top body part'''

James Kyeh: /* Research and Development */

2012-11-29T05:17:21Z

Research and Development

←Older revision		Revision as of 05:17, 29 November 2012
Line 216:		Line 216:

	'''Illustration'''		'''Illustration'''
		+
	[[Image:N.JPG\|border\|widthp800heightp800x]]		[[Image:N.JPG\|border\|widthp800heightp800x]]

Chiao May Lee at 05:16, 29 November 2012

2012-11-29T05:16:22Z

←Older revision		Revision as of 05:16, 29 November 2012
Line 187:		Line 187:
	'''15.''' The oval selection was used to draw an oval around the green drop. Then, the MEASURE tab was selected from the ANALYZE tab, and the sample number and the numbers measured from the image were recorded.		'''15.''' The oval selection was used to draw an oval around the green drop. Then, the MEASURE tab was selected from the ANALYZE tab, and the sample number and the numbers measured from the image were recorded.

-	'''16.''' To get the readings from the background of the image, another oval of approximately the same size was drawn in the background green image and MEASURE was selected from ANALYZE tab. The sample number and the numbers measured from the image were recorded , this data was labeled as "background".	+	'''16.''' To get the readings from the background of the image, another oval of approximately the same size was drawn in the background green image and the MEASURE tab was selected from ANALYZE tab. The sample number and the numbers measured from the image were recorded , this data was labeled as "background".

	'''17.''' The measurements were saved in an excel file by clicking SAVED AS from the FILE tab.		'''17.''' The measurements were saved in an excel file by clicking SAVED AS from the FILE tab.