BME103:T130 Group 3 - Revision history

Serena L. Kaplan at 20:26, 15 November 2012

Serena L. Kaplan — Thu, 15 Nov 2012 20:26:12 GMT

←Older revision		Revision as of 20:26, 15 November 2012
Line 158:		Line 158:
	<b>Explanation:</b><br>Baye’s Rule analyzes all available data and allows us to understand the limitations of our diagnostic tests. It shows the relationship between conditional probability and its reverse form. Baye’s reasoning can be applied to find the probability of true positives in relation to false positives and false negatives. This allows us to understand how reliable PCR is in detecting cancer sequences in patients.		<b>Explanation:</b><br>Baye’s Rule analyzes all available data and allows us to understand the limitations of our diagnostic tests. It shows the relationship between conditional probability and its reverse form. Baye’s reasoning can be applied to find the probability of true positives in relation to false positives and false negatives. This allows us to understand how reliable PCR is in detecting cancer sequences in patients.

-	<b>Equation:</b><br>[[Image:Bayes-rule.png\|200px\|]]<br>http://lesswrong.com/lw/774/a_history_of_bayes_theorem/<br>	+	<b>Equation:</b><br>[[Image:Bayes-rule.png\|200px\|]]<br>''source:'' http://lesswrong.com/lw/774/a_history_of_bayes_theorem/<br>
	<b>Known Variables</b><br>		<b>Known Variables</b><br>
	C=cancer present<br> T=positive test<br>		C=cancer present<br> T=positive test<br>

Sierra Morris: /* Research and Development */

Sierra Morris — Thu, 15 Nov 2012 19:41:42 GMT

Research and Development

←Older revision		Revision as of 19:41, 15 November 2012
Line 124:		Line 124:

	'''Components of a PCR reaction:'''<br>		'''Components of a PCR reaction:'''<br>
-	''Template DNA:'' This is the initial strand of DNA amplified in the PCR machine. DNA can contain a certain sequence located on a gene that has been linked ~~with having~~ the disease of cancer. Only one copy of this sequence of nucleotides is located in the cell out ~~off~~ around 6 billion individual nucleotides. The purpose of PCR is to locate this strand using a primer and then amplify the sequence.<br>	+	''Template DNA:'' This is the initial strand of DNA amplified in the PCR machine. DNA can contain a certain sequence located on a gene that has been linked to the disease of cancer. Only one copy of this sequence of nucleotides is located in the cell out of around six billion individual nucleotides. The purpose of PCR is to locate this strand using a primer and then amplify the sequence.<br>

-	''Primer:'' A reagent that is artificially synthesized DNA sequence that binds specifically to the target sequence of the template DNA, in this case the sequence that is linked with cancer. If the target sequence is not present on the template DNA, then the primer will not bind and amplification will not occur.<br>	+	''Primer:'' A reagent that is a artificially synthesized DNA sequence that binds specifically to the target sequence of the template DNA, in this case the sequence that is linked with cancer. If the target sequence is not present on the template DNA, then the primer will not bind and amplification will not occur.<br>

-	''Taq Polymerase:'' This is an enzyme that drives DNA replication. Polymerase builds each single strand of DNA marked by a primer into a new, double-stranded DNA segment. It works by finding the ends of the primers, finding free nucleotides from an added solution, then it scans the template DNA to match the proper nucleotides and attaches these nucleotides with hydrogen bonds. The benefit of using Taq Polymerse is that it can withstand extreme temperatures and does not denature during the process of the PCR reaction.<br>	+	''Taq Polymerase:'' This is an enzyme that drives DNA replication. Polymerase builds each single strand of DNA marked by a primer into a new, double-stranded DNA segment. It works by finding the ends of the primers, finding free nucleotides from an added solution, and then it scans the template DNA to match the proper nucleotides and attaches these nucleotides with hydrogen bonds. The benefit of using Taq Polymerse is that it can withstand extreme temperatures and does not denature during the process of the PCR reaction.<br>

	''Magnesium Chloride:'' This compound is added to the reaction mixture and binds to the Taq Polymerase, it is used to help the reaction function smoothly and can be adjusted to control the speed of the reaction.<br>		''Magnesium Chloride:'' This compound is added to the reaction mixture and binds to the Taq Polymerase, it is used to help the reaction function smoothly and can be adjusted to control the speed of the reaction.<br>

Sierra Morris: /* Research and Development */

Sierra Morris — Thu, 15 Nov 2012 19:38:26 GMT

Research and Development

←Older revision		Revision as of 19:38, 15 November 2012
Line 124:		Line 124:

	'''Components of a PCR reaction:'''<br>		'''Components of a PCR reaction:'''<br>
-	''Template DNA:'' This is the initial strand of DNA ~~used to amplify~~ in the PCR machine. DNA can contain a certain sequence located on a gene that has been linked with having the disease of cancer. Only one copy of this sequence of nucleotides is located in the cell out off around 6 billion individual nucleotides. The purpose of PCR is to locate this strand using a primer and then amplify the sequence.<br>	+	''Template DNA:'' This is the initial strand of DNA amplified in the PCR machine. DNA can contain a certain sequence located on a gene that has been linked with having the disease of cancer. Only one copy of this sequence of nucleotides is located in the cell out off around 6 billion individual nucleotides. The purpose of PCR is to locate this strand using a primer and then amplify the sequence.<br>

	''Primer:'' A reagent that is artificially synthesized DNA sequence that binds specifically to the target sequence of the template DNA, in this case the sequence that is linked with cancer. If the target sequence is not present on the template DNA, then the primer will not bind and amplification will not occur.<br>		''Primer:'' A reagent that is artificially synthesized DNA sequence that binds specifically to the target sequence of the template DNA, in this case the sequence that is linked with cancer. If the target sequence is not present on the template DNA, then the primer will not bind and amplification will not occur.<br>

Sierra Morris: /* Protocols */

Sierra Morris — Thu, 15 Nov 2012 19:35:15 GMT

Protocols

←Older revision		Revision as of 19:35, 15 November 2012
Line 103:		Line 103:


-	<b>~~Image J~~ Instructions </b><br>	+	<b>ImageJ Instructions </b><br>
	1.) Open ImageJ<br>		1.) Open ImageJ<br>
	2.) Click <b>ANALYZE</b> tool bar and select <b>SET MEASUREMENTS</b><br>		2.) Click <b>ANALYZE</b> tool bar and select <b>SET MEASUREMENTS</b><br>

Sierra Morris: /* Protocols */

Sierra Morris — Thu, 15 Nov 2012 19:33:58 GMT

Protocols

←Older revision		Revision as of 19:33, 15 November 2012
Line 86:		Line 86:
	<font size=3>'''Fluorimeter Setup'''</font><br><br>		<font size=3>'''Fluorimeter Setup'''</font><br><br>
	1.) The lid was first taken off the the box and one of its sides was unbuttoned in order to create a flap.<br>		1.) The lid was first taken off the the box and one of its sides was unbuttoned in order to create a flap.<br>
-	2.) The box was the flipped upside down in order to create a dark environment for the camera<br>	+	2.) The box was the flipped upside down in order to create a dark environment for the camera.<br>
	3.) A hydrophobic slide was then inserted into the flourimeter.<br>		3.) A hydrophobic slide was then inserted into the flourimeter.<br>
-	4.) Finally the camera phone was placed in the stand.	+	4.) Finally, the camera phone was placed in the stand.

	<font size=3>'''Fluorimeter Measurements'''</font><br><br>		<font size=3>'''Fluorimeter Measurements'''</font><br><br>

Sierra Morris: /* Initial Machine Testing */

Sierra Morris — Thu, 15 Nov 2012 19:30:45 GMT

Initial Machine Testing

←Older revision		Revision as of 19:30, 15 November 2012
Line 29:		Line 29:
	'''The Original Design'''<br>		'''The Original Design'''<br>

-	A Polymerase Chain Reaction (PCR) Machine (shown in the above image) is used to create large quantities of specific Deoxyribose Nucleic Acid (DNA) sequences. This process consists of various heating and cooling cycles to unzip DNA strands and isolate the ~~wanted~~ DNA strands.	+	A Polymerase Chain Reaction (PCR) Machine (shown in the above image) is used to create large quantities of specific Deoxyribose Nucleic Acid (DNA) sequences. This process consists of various heating and cooling cycles to unzip DNA strands and isolate the desired DNA strands.

	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>

-	When the Liquid Crystal Display (LCD) screen is disconnected from the open PCR circuit board, the LCD screen is shut off. The circuit board provides the power and input signals for the LCD screen~~, therefore~~, when the two parts are not connected the LCD screen will not function. When the 16-tube PCR block is disconnected from the PCR circuit board the block will not heat or cool. The fan and lid heater are both connected to the PCR circuit board with wires, so if this connection is disrupted, those parts will not function.	+	When the Liquid Crystal Display (LCD) screen is disconnected from the open PCR circuit board, the LCD screen is shut off. The circuit board provides the power and the input signals for the LCD screen. Therefore, when the two parts are not connected, the LCD screen will not function. When the 16-tube PCR block is disconnected from the PCR circuit board the block will not heat or cool. The fan and lid heater are both connected to the PCR circuit board with wires, so if this connection is disrupted, those parts will not function.

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

-	The initial test was ran on October 25, 2012 on machine number 9. The DNA sample was placed into the PCR machine, closed and activated. The machine worked well, going through all the test run cycles with relative ease. There were no problems during ~~this~~ test.	+	The initial test was ran on October 25, 2012 on machine number 9. The DNA sample was placed into the PCR machine, closed, and activated. The machine worked well, going through all the test run cycles with relative ease. There were no problems during the test.
	<br><br>		<br><br>

Gabriel R. McInnis: /* Initial Machine Testing */

Gabriel R. McInnis — Thu, 15 Nov 2012 06:31:46 GMT

Initial Machine Testing

←Older revision		Revision as of 06:31, 15 November 2012
Line 29:		Line 29:
	'''The Original Design'''<br>		'''The Original Design'''<br>

-	A Polymerase Chain Reaction (PCR) Machine (shown in the above image) is used to create large quantities of specific DNA sequences. This process consists of various heating and cooling cycles to unzip DNA strands and isolate the wanted DNA strands.	+	A Polymerase Chain Reaction (PCR) Machine (shown in the above image) is used to create large quantities of specific Deoxyribose Nucleic Acid (DNA) sequences. This process consists of various heating and cooling cycles to unzip DNA strands and isolate the wanted DNA strands.

	'''Experimenting With the Connections'''<br>		'''Experimenting With the Connections'''<br>

Gabriel R. McInnis: /* Results */

Gabriel R. McInnis — Thu, 15 Nov 2012 06:30:17 GMT

Results

←Older revision		Revision as of 06:30, 15 November 2012
Line 208:		Line 208:

	KEY		KEY
-	* '''Sample''' = Sample DNA from the patient.	+	* '''Sample''' = Sample Deoxyribose Nucleic Acid (DNA) from the patient.
	* '''Integrated Density''' = The integrated density (INTDEN) was calculated by subtracting the INTDEN of the drop from the INTDEN of the backround.		* '''Integrated Density''' = The integrated density (INTDEN) was calculated by subtracting the INTDEN of the drop from the INTDEN of the backround.
	* '''DNA μg/mL''' = The DNA concentration was calculated by diving the INTDEN of the selected sample by INTDEN of the positive control and the multiplying by the DNA concentration of the positive control		* '''DNA μg/mL''' = The DNA concentration was calculated by diving the INTDEN of the selected sample by INTDEN of the positive control and the multiplying by the DNA concentration of the positive control

Serena L. Kaplan at 06:10, 15 November 2012

Serena L. Kaplan — Thu, 15 Nov 2012 06:10:38 GMT

←Older revision		Revision as of 06:10, 15 November 2012
Line 82:		Line 82:
	Female, 55 years old<br>		Female, 55 years old<br>

-	[[Image:Flourimeter Group 3.jpg~~\|thumb\|left~~\|600x300px]]<br><br>	+	[[Image:Flourimeter Group 3.jpg\|600x300px]]<br><br>

	<font size=3>'''Fluorimeter Setup'''</font><br><br>		<font size=3>'''Fluorimeter Setup'''</font><br><br>

Blake E. Eichler: Undo revision 655809 by Blake E. Eichler (Talk)

Blake E. Eichler — Thu, 15 Nov 2012 06:08:58 GMT

Undo revision 655809 by Blake E. Eichler (Talk)

←Older revision		Revision as of 06:08, 15 November 2012
Line 103:		Line 103:


-	~~font size=3~~>~~'''~~Image J Instructions~~'''~~</~~font><br~~><br>	+	<b>Image J Instructions </b><br>
	1.) Open ImageJ<br>		1.) Open ImageJ<br>
	2.) Click <b>ANALYZE</b> tool bar and select <b>SET MEASUREMENTS</b><br>		2.) Click <b>ANALYZE</b> tool bar and select <b>SET MEASUREMENTS</b><br>