BME103:T130 Group 5 - Revision history

Kyle Labban: /* Results */

Kyle Labban — Thu, 15 Nov 2012 21:52:07 GMT

Results

←Older revision		Revision as of 21:52, 15 November 2012
Line 297:		Line 297:
	\| PCR: Patient 2 ID 66913, rep 3 \|\| 2203129 \|\| 7.703 \|\| positive		\| PCR: Patient 2 ID 66913, rep 3 \|\| 2203129 \|\| 7.703 \|\| positive
	\|}		\|}
-	Despite Patient 1's second sample being positive for cancer, patient 1 is more than likely without cancer and this repetition is due to an error like contamination. More testing would be necessary to find out.	+	Despite Patient 1's second sample being positive for cancer, patient 1 is more than likely without cancer and this repetition being positive is due to an error like contamination. More testing would be necessary to find out.

	KEY		KEY

Wade Patrick: /* OUR TEAM */

Wade Patrick — Thu, 15 Nov 2012 21:43:53 GMT

OUR TEAM

←Older revision		Revision as of 21:43, 15 November 2012
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	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Wade Patrick<br>Machine Engineer]]	+	\| [[Image:BME103_Student_Wade.jpg\|100px\|thumb\|Name: Wade Patrick<br>Machine Engineer]]
	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Liann Klein<br>Machine Engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Liann Klein<br>Machine Engineer]]
	\| [[Image:Homecoming_picture_2012.jpg\|100px\|thumb\|Name: Haylee Poncy<br>Protocol Planner]]		\| [[Image:Homecoming_picture_2012.jpg\|100px\|thumb\|Name: Haylee Poncy<br>Protocol Planner]]

Wade Patrick: /* Protocols */

Wade Patrick — Thu, 15 Nov 2012 20:46:44 GMT

Protocols

←Older revision		Revision as of 20:46, 15 November 2012
Line 100:		Line 100:

	'''Flourimeter Measurements'''<br><br>		'''Flourimeter Measurements'''<br><br>
-	After we used a cellphone to take pictures of the samples that had a blue LED light shining through them, we processed these images with ImageJ software to find the amount of green light that was produced (IntDen). The results from this ImageJ analysis of the images can be seen below:	+	[[Image:BME103_Group5_Assembly(1).jpg\|300px\|Flourimeter Assembly]]<br>After we used a cellphone to take pictures of the samples that had a blue LED light shining through them, we processed these images with ImageJ software to find the amount of green light that was produced (IntDen). The results from this ImageJ analysis of the images can be seen below:
	<br>		<br>
	{\|border="1" cellpadding="5"		{\|border="1" cellpadding="5"

Alexandria N. Lam: /* Research and Development */

Alexandria N. Lam — Thu, 15 Nov 2012 05:13:47 GMT

Research and Development

←Older revision		Revision as of 05:13, 15 November 2012
Line 266:		Line 266:
	'''Figure 6 shows the amplification of the sequence to a greater magnitude than Figure 1 after more cycles''' <br> <br>		'''Figure 6 shows the amplification of the sequence to a greater magnitude than Figure 1 after more cycles''' <br> <br>

-	~~''All images courtesy~~ of ~~OpenPCR''~~	+	Source of images: http://learn.genetics.utah.edu/content/labs/pcr/

	<br><br>		<br><br>

Kyle Labban: /* Protocols */

Kyle Labban — Wed, 14 Nov 2012 23:42:44 GMT

Protocols

←Older revision		Revision as of 23:42, 14 November 2012
Line 99:		Line 99:
	\|}<br><br>		\|}<br><br>

-	'''Flourimeter Measurements'''<br>	+	'''Flourimeter Measurements'''<br><br>
-		+	After we used a cellphone to take pictures of the samples that had a blue LED light shining through them, we processed these images with ImageJ software to find the amount of green light that was produced (IntDen). The results from this ImageJ analysis of the images can be seen below:
		+	<br>
	{\|border="1" cellpadding="5"		{\|border="1" cellpadding="5"
	\|-		\|-

Kyle Labban: /* Protocols */

Kyle Labban — Wed, 14 Nov 2012 23:39:46 GMT

Protocols

←Older revision		Revision as of 23:39, 14 November 2012
Line 101:		Line 101:
	'''Flourimeter Measurements'''<br>		'''Flourimeter Measurements'''<br>

-	~~(Add your work from Week~~ 3, ~~Part~~ 2 ~~here)<br>~~	+	{\|border="1" cellpadding="5"
-		+	\|-
		+	! scope="col" \| Sample
		+	! scope="col" \| Area
		+	! scope="col" \| Mean
		+	! scope="col" \| IntDen
		+	! scope="col" \| RawIntDen
		+	\|-
		+	\|Negative control
		+	\|16268
		+	\|21.125
		+	\|343656
		+	\|343656
		+	\|-
		+	\|N.c. background
		+	\|16268
		+	\|.326
		+	\|5297
		+	\|5297
		+	\|-
		+	\|Positive control
		+	\|16800
		+	\|76.351
		+	\|1282697
		+	\|1282697
		+	\|-
		+	\|P.c. background
		+	\|16800
		+	\|.282
		+	\|4732
		+	\|4732
		+	\|-
		+	\|Patient 1, sample 1
		+	\|25464
		+	\|14.135
		+	\|359937
		+	\|359937
		+	\|-
		+	\|Patient 1, sample 1, background
		+	\|25464
		+	\|0.063
		+	\|1603
		+	\|1603
		+	\|-
		+	\|Patient 1, sample 2
		+	\|26924
		+	\|44.721
		+	\|1204073
		+	\|1204073
		+	\|-
		+	\|Patient 1, sample 2, background
		+	\|26924
		+	\|0.009
		+	\|232
		+	\|232
		+	\|-
		+	\|Patient 1, sample 3
		+	\|16958
		+	\|20.176
		+	\|342142
		+	\|342142
		+	\|-
		+	\|Patient 1, sample 3, background
		+	\|16958
		+	\|0.088
		+	\|1486
		+	\|1486
		+	\|-
		+	\|Patient 2, sample 1
		+	\|15276
		+	\|79.489
		+	\|1214276
		+	\|1214276
		+	\|-
		+	\|Patient 2, sample 1, background
		+	\|15276
		+	\|0.264
		+	\|4040
		+	\|4040
		+	\|-
		+	\|Patient 2, sample 2
		+	\|22628
		+	\|72.753
		+	\|1646248
		+	\|1646248
		+	\|-
		+	\|Patient 2, sample 2, background
		+	\|22628
		+	\|0.066
		+	\|1493
		+	\|1493
		+	\|-
		+	\|Patient 2, sample 3
		+	\|22804
		+	\|96.671
		+	\|2204484
		+	\|2204484
		+	\|-
		+	\|Patient 2, sample 3, background
		+	\|22804
		+	\|0.059
		+	\|1355
		+	\|1355
		+	\|-
		+	\|Water
		+	\|31856
		+	\|11.147
		+	\|355104
		+	\|355104
		+	\|-
		+	\|Water Background
		+	\|31856
		+	\|0.021
		+	\|672
		+	\|672
		+	\|-
		+	\|Calf Thymus
		+	\|13580
		+	\|61.625
		+	\|836872
		+	\|836872
		+	\|-
		+	\|Calf Thymus Background
		+	\|12212
		+	\|0.05
		+	\|611
		+	\|611
		+	\|-
		+	\|}

	<br><br>		<br><br>

Alexandria N. Lam: /* Research and Development */

Alexandria N. Lam — Wed, 14 Nov 2012 21:40:39 GMT

Research and Development

←Older revision		Revision as of 21:40, 14 November 2012
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	'''Figure 6 shows the amplification of the sequence to a greater magnitude than Figure 1 after more cycles''' <br> <br>		'''Figure 6 shows the amplification of the sequence to a greater magnitude than Figure 1 after more cycles''' <br> <br>

-		+	''All images courtesy of OpenPCR''

	<br><br>		<br><br>

Alexandria N. Lam: /* Research and Development */

Alexandria N. Lam — Wed, 14 Nov 2012 21:40:06 GMT

Research and Development

←Older revision		Revision as of 21:40, 14 November 2012
Line 123:		Line 123:
	'''Figure 1 shows the sequence of DNA containing the sequence containing the missense that leads to colon cancer.''' <br> <br>		'''Figure 1 shows the sequence of DNA containing the sequence containing the missense that leads to colon cancer.''' <br> <br>

-	[[Image:Primersattaching112493.png]]	+	[[Image:Primersattaching112493.png]] <br> <br>
		+	'''Figure 2 shows the DNA primers specific to the sequence attaching.''' <br> <br>

-	[[Image:Polymeraseattaching112493.png]]	+	[[Image:Polymeraseattaching112493.png]] <br> <br>
		+	'''Figure 3 shows Taq polymerase recognizing where to attach due to the primers.''' <br> <br>

-	[[Image:ReplicatedDNA112493.png]]	+	[[Image:ReplicatedDNA112493.png]] <br> <br>
		+	'''Figure 4 shows a successful double-stranded replication of the original DNA.''' <br> <br>

-	[[Image:ReplicatedDesiredSequence112493.png]]	+	[[Image:ReplicatedDesiredSequence112493.png]] <br> <br>
		+	'''Figure 5 shows the desired sequence replicated after several cycles''' <br> <br>

-	[[Image:AmplifiedDNA112493.png]]	+	[[Image:AmplifiedDNA112493.png]] <br> <br>
		+	'''Figure 6 shows the amplification of the sequence to a greater magnitude than Figure 1 after more cycles''' <br> <br>

-	~~<br>~~
-	(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)

Alexandria N. Lam: /* Research and Development */

Alexandria N. Lam — Wed, 14 Nov 2012 21:35:24 GMT

Research and Development

←Older revision		Revision as of 21:35, 14 November 2012
Line 118:		Line 118:

	If the r1789961 SNP is not present, the primer will not bind to the DNA template. Because the primers tell Taq polymerase where to replicate, Taq polymerase will not have anywhere to bind. Replication will not occur with the product of a double-stranded DNA, but linearly. The SYBR Green I dye only binds to double-stranded DNA, so it will not show because it is single-stranded. There would not be enough double-stranded DNA to fluoresce if the cancer gene is not present. Therefore, the test will display a negative result.		If the r1789961 SNP is not present, the primer will not bind to the DNA template. Because the primers tell Taq polymerase where to replicate, Taq polymerase will not have anywhere to bind. Replication will not occur with the product of a double-stranded DNA, but linearly. The SYBR Green I dye only binds to double-stranded DNA, so it will not show because it is single-stranded. There would not be enough double-stranded DNA to fluoresce if the cancer gene is not present. Therefore, the test will display a negative result.
		+	<br> <br>

-	<center> [[Image:Targetsequence112493.png‎]]	+	<center> [[Image:Targetsequence112493.png‎]] <br> <br>
		+	'''Figure 1 shows the sequence of DNA containing the sequence containing the missense that leads to colon cancer.''' <br> <br>

	[[Image:Primersattaching112493.png]]		[[Image:Primersattaching112493.png]]

Alexandria N. Lam: /* Research and Development */

Alexandria N. Lam — Wed, 14 Nov 2012 21:32:36 GMT

Research and Development

←Older revision		Revision as of 21:32, 14 November 2012
Line 119:		Line 119:
	If the r1789961 SNP is not present, the primer will not bind to the DNA template. Because the primers tell Taq polymerase where to replicate, Taq polymerase will not have anywhere to bind. Replication will not occur with the product of a double-stranded DNA, but linearly. The SYBR Green I dye only binds to double-stranded DNA, so it will not show because it is single-stranded. There would not be enough double-stranded DNA to fluoresce if the cancer gene is not present. Therefore, the test will display a negative result.		If the r1789961 SNP is not present, the primer will not bind to the DNA template. Because the primers tell Taq polymerase where to replicate, Taq polymerase will not have anywhere to bind. Replication will not occur with the product of a double-stranded DNA, but linearly. The SYBR Green I dye only binds to double-stranded DNA, so it will not show because it is single-stranded. There would not be enough double-stranded DNA to fluoresce if the cancer gene is not present. Therefore, the test will display a negative result.

-	[[Image:Targetsequence112493.png‎]]	+	<center> [[Image:Targetsequence112493.png‎]]

	[[Image:Primersattaching112493.png]]		[[Image:Primersattaching112493.png]]

←Older revision		Revision as of 21:43, 15 November 2012
Line 13:		Line 13:
	{\| style="wikitable" width="700px"		{\| style="wikitable" width="700px"
	\|- valign="top"		\|- valign="top"
-	\| [[Image:~~BME103student~~.jpg\|100px\|thumb\|Name: Wade Patrick<br>Machine Engineer]]	+	\| [[Image:BME103_Student_Wade.jpg\|100px\|thumb\|Name: Wade Patrick<br>Machine Engineer]]
	\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Liann Klein<br>Machine Engineer]]		\| [[Image:BME103student.jpg\|100px\|thumb\|Name: Liann Klein<br>Machine Engineer]]
	\| [[Image:Homecoming_picture_2012.jpg\|100px\|thumb\|Name: Haylee Poncy<br>Protocol Planner]]		\| [[Image:Homecoming_picture_2012.jpg\|100px\|thumb\|Name: Haylee Poncy<br>Protocol Planner]]