BME103:W930 Group2 - Revision history

Matthew J. Mortensen: /* LAB 1 WRITE-UP */

2012-12-11T00:05:39Z

LAB 1 WRITE-UP

←Older revision		Revision as of 00:05, 11 December 2012
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	=LAB 1 WRITE-UP=		=LAB 1 WRITE-UP=

-		+	<br>DISCLAIMER: ALL GROUP MEMBERS PARTICIPATED EQUALLY IN THE WRITING OF REPORTS. SOME OF US HAD ISSUES LOGGING IN SO CONTRIBUTIONS MAY NOT APPEAR TO ADD UP APPROPRIATELY.
	==Initial Machine Testing==		==Initial Machine Testing==

Garrett Salcido: /* Protocols */

2012-11-14T20:52:49Z

Protocols

←Older revision		Revision as of 20:52, 14 November 2012
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	1. A PCR Machine is created to amplify a patient’s DNA sample. In order to use a PCR machine, one must first gather the DNA samples, 50 μL each. <br>		1. A PCR Machine is created to amplify a patient’s DNA sample. In order to use a PCR machine, one must first gather the DNA samples, 50 μL each. <br>
-	2. The frozen DNA samples are ~~separated~~ into tubes and once melted, 8 transfer pipettes ~~were~~ used to add primer. <br>	+	2. The frozen DNA samples are placed into separate tubes and once melted, 8 transfer pipettes are used to add primer. <br>
	3. Once the samples were ready, we processed the DNA in the openPCR system. <br>		3. Once the samples were ready, we processed the DNA in the openPCR system. <br>

Garrett Salcido: /* Protocols */

2012-11-14T20:50:17Z

Protocols

←Older revision		Revision as of 20:50, 14 November 2012
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	Step 1: Denaturation by Heat <br>		Step 1: Denaturation by Heat <br>
-	Initially, heat separates a DNA strand into two separate strands. This is allowed because the hydrogen bonds ~~holding~~ the DNA together are weak and easily separable when heated. <br>	+	Initially, heat separates a DNA strand into two separate strands. This is allowed because the hydrogen bonds that hold the DNA together are weak and easily separable when heated. <br>
	Step 2: Annealing Primer to Target Sequence<br>		Step 2: Annealing Primer to Target Sequence<br>
	We want to target a sequence specifically and in order to accomplish that you must use primers. Primers mark the end of the target sequence. Two primers are included in the PCR; one for each of the strands that were just separated during denaturation. The beginning of the DNA target sequence is also marked by the primers that bind (anneal) to the complementary sequence. <br>		We want to target a sequence specifically and in order to accomplish that you must use primers. Primers mark the end of the target sequence. Two primers are included in the PCR; one for each of the strands that were just separated during denaturation. The beginning of the DNA target sequence is also marked by the primers that bind (anneal) to the complementary sequence. <br>

Garrett Salcido: /* Protocols */

2012-11-14T19:46:31Z

Protocols

←Older revision		Revision as of 19:46, 14 November 2012
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	How to Amplify a Patient’s DNA sample: <br>		How to Amplify a Patient’s DNA sample: <br>

-	1. A PCR Machine is created to amplify a patient’s DNA sample. In order to use a PCR machine, ~~the steps include to~~ first gather the DNA samples, 50 μL each. <br>	+	1. A PCR Machine is created to amplify a patient’s DNA sample. In order to use a PCR machine, one must first gather the DNA samples, 50 μL each. <br>
	2. The frozen DNA samples are separated into tubes and once melted, 8 transfer pipettes were used to add primer. <br>		2. The frozen DNA samples are separated into tubes and once melted, 8 transfer pipettes were used to add primer. <br>
-	3. Once the samples ~~are~~ ready, we processed the DNA in the openPCR system. <br>	+	3. Once the samples were ready, we processed the DNA in the openPCR system. <br>

	<br>		<br>
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	Fluorimeter assembly procedure: <br>		Fluorimeter assembly procedure: <br>

-	Turn on the excitation light on the fluorimeter. Put a smart phone in the cradle and set it up to take pictures of the slide. Place two drops of water in the middle of the first two rows of the slide using a pipette. Align the drop by moving the slide so the drop is in the middle of the black fiber optic fitting. Cover the fluorimeter with the light box while ~~still being able~~ to use the smart phone to take pictures.	+	Turn on the excitation light on the fluorimeter. Put a smart phone in the cradle and set it up to take pictures of the slide. Place two drops of water in the middle of the first two rows of the slide using a pipette. Align the drop by moving the slide so the drop is in the middle of the black fiber optic fitting. Cover the fluorimeter with the light box while maintaining the ability to use the smart phone to take pictures.

	<br>		<br>

Garrett Salcido: /* Protocols */

2012-11-14T19:42:54Z

Protocols

←Older revision		Revision as of 19:42, 14 November 2012
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	Initially, heat separates a DNA strand into two separate strands. This is allowed because the hydrogen bonds holding the DNA together are weak and easily separable when heated. <br>		Initially, heat separates a DNA strand into two separate strands. This is allowed because the hydrogen bonds holding the DNA together are weak and easily separable when heated. <br>
	Step 2: Annealing Primer to Target Sequence<br>		Step 2: Annealing Primer to Target Sequence<br>
-	We want to target a sequence specifically and in order to accomplish that you must use primers. Primers mark the ~~ends~~ of the target sequence. Two primers are included in the PCR one for each of the strands that were just separated during denaturation. The beginning of the DNA target sequence is also marked by the primers that bind (anneal) to the complementary sequence. <br>	+	We want to target a sequence specifically and in order to accomplish that you must use primers. Primers mark the end of the target sequence. Two primers are included in the PCR; one for each of the strands that were just separated during denaturation. The beginning of the DNA target sequence is also marked by the primers that bind (anneal) to the complementary sequence. <br>
	Step 3: Extension<br>		Step 3: Extension<br>
	After the primers bind to the complementary DNA, the temperature is raised and the enzyme Taq DNA polymerase is used to replicate the strands. The Taq DNA polymerase, active at high temperatures, facilitates the binding and joining of the complementary nucleotides. It synthesizes an identical double-stranded DNA strand. Extension begins at the 3’ end of the primer because Taq DNA polymerase synthesizes exclusively in the 5’ to 3’ direction, so the free nucleotides are only added to the 3’ end of the primer.		After the primers bind to the complementary DNA, the temperature is raised and the enzyme Taq DNA polymerase is used to replicate the strands. The Taq DNA polymerase, active at high temperatures, facilitates the binding and joining of the complementary nucleotides. It synthesizes an identical double-stranded DNA strand. Extension begins at the 3’ end of the primer because Taq DNA polymerase synthesizes exclusively in the 5’ to 3’ direction, so the free nucleotides are only added to the 3’ end of the primer.

Garrett Salcido: /* Protocols */

2012-11-14T19:41:50Z

Protocols

←Older revision		Revision as of 19:41, 14 November 2012
Line 55:		Line 55:
	Initially, heat separates a DNA strand into two separate strands. This is allowed because the hydrogen bonds holding the DNA together are weak and easily separable when heated. <br>		Initially, heat separates a DNA strand into two separate strands. This is allowed because the hydrogen bonds holding the DNA together are weak and easily separable when heated. <br>
	Step 2: Annealing Primer to Target Sequence<br>		Step 2: Annealing Primer to Target Sequence<br>
-	We want to target a sequence specifically and to do that you must use primers. Primers mark the ends of the target sequence. Two primers are included in the PCR one for each of the strands that were just separated during denaturation. The beginning of the DNA target sequence is also marked by the primers that bind (anneal) to the complementary sequence. <br>	+	We want to target a sequence specifically and in order to accomplish that you must use primers. Primers mark the ends of the target sequence. Two primers are included in the PCR one for each of the strands that were just separated during denaturation. The beginning of the DNA target sequence is also marked by the primers that bind (anneal) to the complementary sequence. <br>
	Step 3: Extension<br>		Step 3: Extension<br>
	After the primers bind to the complementary DNA, the temperature is raised and the enzyme Taq DNA polymerase is used to replicate the strands. The Taq DNA polymerase, active at high temperatures, facilitates the binding and joining of the complementary nucleotides. It synthesizes an identical double-stranded DNA strand. Extension begins at the 3’ end of the primer because Taq DNA polymerase synthesizes exclusively in the 5’ to 3’ direction, so the free nucleotides are only added to the 3’ end of the primer.		After the primers bind to the complementary DNA, the temperature is raised and the enzyme Taq DNA polymerase is used to replicate the strands. The Taq DNA polymerase, active at high temperatures, facilitates the binding and joining of the complementary nucleotides. It synthesizes an identical double-stranded DNA strand. Extension begins at the 3’ end of the primer because Taq DNA polymerase synthesizes exclusively in the 5’ to 3’ direction, so the free nucleotides are only added to the 3’ end of the primer.

Garrett Salcido: /* Initial Machine Testing */

2012-11-14T19:41:04Z

Initial Machine Testing

←Older revision		Revision as of 19:41, 14 November 2012
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	When we unplugged part mounting plate from circuit board, Machine #2 had no visible screen and we could not see the the information on the LCD screen.		When we unplugged part mounting plate from circuit board, Machine #2 had no visible screen and we could not see the the information on the LCD screen.

-	When we unplugged the white wire that connects the circuit board to the sample holder, the machine's temperature was unable to be monitored and could not be regulated	+	When we unplugged the white wire that connects the circuit board to the sample holder, the machine's temperature was unable to be monitored and could not be regulated.


	'''Test Run'''		'''Test Run'''

-	Our group did our test run on October 24, 2012. During the test run, we ran into no problems with Machine #2. We were done and found our results in a matter of 1 to 2 hours. The Open PCR machine was connected to one ~~computers~~ to control ~~each~~ temperature of each cycle of PCR during the experimental.	+	Our group did our test run on October 24, 2012. During the test run, we ran into no problems with Machine #2. We were done and found our results in a matter of 1 to 2 hours. The Open PCR machine was connected to one computer to control the temperature of each cycle of PCR during the experimental.

Garrett Salcido: /* Initial Machine Testing */

2012-11-14T18:58:24Z

Initial Machine Testing

←Older revision		Revision as of 18:58, 14 November 2012
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	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>

-	When we unplugged part mounting plate from circuit board, ~~the machine~~ had no visible screen and we could not see the the information on the LCD screen.	+	When we unplugged part mounting plate from circuit board, Machine #2 had no visible screen and we could not see the the information on the LCD screen.

	When we unplugged the white wire that connects the circuit board to the sample holder, the machine's temperature was unable to be monitored and could not be regulated		When we unplugged the white wire that connects the circuit board to the sample holder, the machine's temperature was unable to be monitored and could not be regulated
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	'''Test Run'''		'''Test Run'''

-	Our group did our test run on October 24, 2012. During the test run, we ran into no problems with ~~the machine~~. We were done and found our results in a matter of 1 to 2 hours. The Open PCR machine was connected to one computers to control each temperature of each cycle of PCR during the experimental.	+	Our group did our test run on October 24, 2012. During the test run, we ran into no problems with Machine #2. We were done and found our results in a matter of 1 to 2 hours. The Open PCR machine was connected to one computers to control each temperature of each cycle of PCR during the experimental.

Ramesh Tadayon: /* Results */

2012-11-14T18:28:46Z

Results

←Older revision		Revision as of 18:28, 14 November 2012
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	\| PCR: Positive Control \|\| 6369082 \|\| 2 \|\| Calf Thymus		\| PCR: Positive Control \|\| 6369082 \|\| 2 \|\| Calf Thymus
	\|-		\|-
-	\| PCR: Patient 1 ID 43825, rep 1 \|\| 1193961 \|\| 0 \|\| negative	+	\| PCR: Patient 1 ID 43825 Female Age:53, rep 1 \|\| 1193961 \|\| 0 \|\| negative
	\|-		\|-
-	\| PCR: Patient 1 ID 43825, rep 2 \|\| 5237029 \|\| 1.1 \|\| negative	+	\| PCR: Patient 1 ID 43825 Female Age:53, rep 2 \|\| 5237029 \|\| 1.1 \|\| negative
	\|-		\|-
-	\| PCR: Patient 1 ID 43825, rep 3 \|\| 5437872 \|\| 1.2 \|\| negative	+	\| PCR: Patient 1 ID 43825 Female Age:53, rep 3 \|\| 5437872 \|\| 1.2 \|\| negative
	\|-		\|-
-	\| PCR: Patient 2 ID 12079, rep 1 \|\| 10726518 \|\| 4 \|\| positive	+	\| PCR: Patient 2 ID 12079 Female Age:56, rep 1 \|\| 10726518 \|\| 4 \|\| positive
	\|-		\|-
-	\| PCR: Patient 2 ID 12079, rep 2 \|\| 2711977 \|\| 0.7 \|\| negative	+	\| PCR: Patient 2 ID 12079 Female Age:56, rep 2 \|\| 2711977 \|\| 0.7 \|\| negative
	\|-		\|-
-	\| PCR: Patient 2 ID 12079, rep 3 \|\| 7637000 \|\| 2.2 \|\| positive	+	\| PCR: Patient 2 ID 12079 Female Age:56, rep 3 \|\| 7637000 \|\| 2.2 \|\| positive
	\|}		\|}

Alanie Harmon: /* Results */

2012-11-14T18:12:14Z

Results

←Older revision		Revision as of 18:12, 14 November 2012
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	==Results==		==Results==
		+
		+	Water<br>
	[[Image:waterdrop-BME103-Group2.png\|200px\|Water]]<br>		[[Image:waterdrop-BME103-Group2.png\|200px\|Water]]<br>

		+	Calf Thymus<br>
	[[Image:ImageJ-BME103-Group2.png‎\|200px\|DNA]]<br>		[[Image:ImageJ-BME103-Group2.png‎\|200px\|DNA]]<br>