BME103:T930 Group 7 - Revision history

Wesley M. Karlin at 17:54, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 17:54:32 GMT

←Older revision		Revision as of 17:54, 15 November 2012
Line 138:		Line 138:
	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the following conditions: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>		7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the following conditions: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>
	8. The picture was then sent to the Image J software for processing.<br>		8. The picture was then sent to the Image J software for processing.<br>
-	9. This process was repeated for all 6 patient samples, a positive and negative control, ~~pure SYBR Green~~, and pure water.<br><br>	+	9. This process was repeated for all 6 patient samples, a positive and negative control, Calf Thymus DNA, and pure water.<br><br>
	[[Image:BME103_Group7_PhotoSample.JPG\|200px\|Photo Sample]]		[[Image:BME103_Group7_PhotoSample.JPG\|200px\|Photo Sample]]

Elyse M Candell: /* Initial Machine Testing */

Elyse M Candell — Thu, 15 Nov 2012 16:00:36 GMT

Initial Machine Testing

←Older revision		Revision as of 16:00, 15 November 2012
Line 30:		Line 30:
	[[Image:PCR Machine.png]]		[[Image:PCR Machine.png]]
	'''		'''
-	Description'''	+	Description:'''
	The OpenPCR Machine creates many copies of a small strand of DNA. In order to duplicate these DNA strands the PCR Machine must use many different temperatures during denaturing, annealing and extension. Denaturing is where the two strands of DNA separate. Annealing is where the DNA primer binds to the separate strands. Extension is when Taq Polymerase copies the DNA strands.		The OpenPCR Machine creates many copies of a small strand of DNA. In order to duplicate these DNA strands the PCR Machine must use many different temperatures during denaturing, annealing and extension. Denaturing is where the two strands of DNA separate. Annealing is where the DNA primer binds to the separate strands. Extension is when Taq Polymerase copies the DNA strands.

Line 43:		Line 43:


-	'''Test Run'''	+	'''Test Run:'''

	The date the machine was used was on Thursday October 24th, 2012. We had machine number 13. The team's experience with the device was as follows:		The date the machine was used was on Thursday October 24th, 2012. We had machine number 13. The team's experience with the device was as follows:

Wesley M. Karlin at 07:26, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 07:26:15 GMT

←Older revision		Revision as of 07:26, 15 November 2012
Line 138:		Line 138:
	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the following conditions: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>		7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the following conditions: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>
	8. The picture was then sent to the Image J software for processing.<br>		8. The picture was then sent to the Image J software for processing.<br>
-	9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br>	+	9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br><br>
		+	[[Image:BME103_Group7_PhotoSample.JPG\|200px\|Photo Sample]]

Wesley M. Karlin at 07:14, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 07:14:51 GMT

←Older revision		Revision as of 07:14, 15 November 2012
Line 133:		Line 133:
	2. Take 10 Eppendorf tubes containing 400mL of buffer and label them with the permament marker to their corresponding sample<br>		2. Take 10 Eppendorf tubes containing 400mL of buffer and label them with the permament marker to their corresponding sample<br>
	3. Next, transfer the patient sample into the assigned Eppendorf tube with an appropriate pipette. For example, Patient Sample A will be transferred into Eppendorf Tube A while using Pipette A only. This prevents the samples from contaminating each other.<br>		3. Next, transfer the patient sample into the assigned Eppendorf tube with an appropriate pipette. For example, Patient Sample A will be transferred into Eppendorf Tube A while using Pipette A only. This prevents the samples from contaminating each other.<br>
-	4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, Teflon layer<br>	+	4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, superhydrophobic, Teflon layer<br>
	5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide<br>		5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide<br>
	6. With the SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample<br>		6. With the SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample<br>

Wesley M. Karlin at 07:12, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 07:12:41 GMT

←Older revision		Revision as of 07:12, 15 November 2012
Line 135:		Line 135:
	4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, Teflon layer<br>		4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, Teflon layer<br>
	5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide<br>		5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide<br>
-	6. With th SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample<br>	+	6. With the SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample<br>
-	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the conditions of: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>	+	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the following conditions: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>
	8. The picture was then sent to the Image J software for processing.<br>		8. The picture was then sent to the Image J software for processing.<br>
	9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br>		9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br>


-	<br>	+	'''Image J Software Procedure'''<br>

	The process at which an image is turned into an Image J involves several steps. The first step is to set the settings of a camera's phone and then take a picture. The picture should then be emailed or downloaded onto a computer, and it then should be saved to the computer and opened in the Image J software. There are several parameters needed to be adjusted to produce the wanted picture so the measurement needs to be set to integrate the density and the linear gray value. The bubble's green spot is subsequently isolated, integrated density is measured and the background is then deleted to have the isolated desired picture.		The process at which an image is turned into an Image J involves several steps. The first step is to set the settings of a camera's phone and then take a picture. The picture should then be emailed or downloaded onto a computer, and it then should be saved to the computer and opened in the Image J software. There are several parameters needed to be adjusted to produce the wanted picture so the measurement needs to be set to integrate the density and the linear gray value. The bubble's green spot is subsequently isolated, integrated density is measured and the background is then deleted to have the isolated desired picture.

Wesley M. Karlin at 07:08, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 07:08:11 GMT

Wesley M. Karlin at 07:03, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 07:03:00 GMT

←Older revision		Revision as of 07:03, 15 November 2012
Line 128:		Line 128:
	'''Flourimeter Procedures'''<br>		'''Flourimeter Procedures'''<br>

-	The Flourimeter is a device that detects flourescence, when a molecue produces a light after being excited ~~byanother~~ light with a ~~shorther~~ wavelength. The process ~~begins~~<br>	+	The Flourimeter is a device that detects flourescence, when a molecue produces a light after being excited by another light with a shorter wavelength. The process is completed through the following steps:
		+
		+	1. To keep the patient samples and solutions separate, 10 pipettes were labeled at the top with a permament marker with their corresponding sample
		+	2. Take 10 Eppendorf tubes containing 400mL of buffer and label them with the permament marker to their corresponding sample
		+	3. Next, transfer the patient sample into the assigned Eppendorf tube with an appropriate pipette. For example, Patient Sample A will be transferred into Eppendorf Tube A while using Pipette A only. This prevents the samples from contaminating each other.
		+	4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, Teflon layer
		+	5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide
		+	6. With th SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample
		+	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the conditions of: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.
		+	8. The picture was then sent to the Image J software for processing.
		+	9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br>

Lauren Edwards: /* Protocols */

Lauren Edwards — Thu, 15 Nov 2012 06:55:40 GMT

Protocols

←Older revision		Revision as of 06:55, 15 November 2012
Line 132:		Line 132:

	<br><br>		<br><br>
		+
		+	The process at which an image is turned into an Image J involves several steps. The first step is to set the settings of a camera's phone and then take a picture. The picture should then be emailed or downloaded onto a computer, and it then should be saved to the computer and opened in the Image J software. There are several parameters needed to be adjusted to produce the wanted picture so the measurement needs to be set to integrate the density and the linear gray value. The bubble's green spot is subsequently isolated, integrated density is measured and the background is then deleted to have the isolated desired picture.

	==Research and Development==		==Research and Development==

Lauren Edwards: /* Protocols */

Lauren Edwards — Thu, 15 Nov 2012 06:44:44 GMT

Protocols

←Older revision		Revision as of 06:44, 15 November 2012
Line 122:		Line 122:

	The Samples		The Samples
-	There were eight samples that were ran PCR on during this experiment. This included a positive control cancer DNA template and a negative control without a DNA template.	+
		+	There were eight samples that were ran PCR on during this experiment. This included a positive control cancer DNA template and a negative control without a DNA template. Patient 1, a 57 year old male with an ID of 58515, had three samples tested on and patient 2, a 59 year old female with an ID of 19033, also had three samples tested on.

Wesley M. Karlin at 06:29, 15 November 2012

Wesley M. Karlin — Thu, 15 Nov 2012 06:29:15 GMT

←Older revision		Revision as of 06:29, 15 November 2012
Line 127:		Line 127:
	'''Flourimeter Procedures'''<br>		'''Flourimeter Procedures'''<br>

-	~~(Add your work from Week 3~~, ~~Part 2 here)~~<br>	+	The Flourimeter is a device that detects flourescence, when a molecue produces a light after being excited byanother light with a shorther wavelength. The process begins<br>

←Older revision		Revision as of 07:08, 15 November 2012
Line 128:		Line 128:
	'''Flourimeter Procedures'''<br>		'''Flourimeter Procedures'''<br>

-	The Flourimeter is a device that detects flourescence, when a molecue produces a light after being excited by another light with a shorter wavelength. The process is completed through the following steps:	+	The Flourimeter is a device that detects flourescence, when a molecue produces a light after being excited by another light with a shorter wavelength. The process is completed through the following steps:<br>

-	1. To keep the patient samples and solutions separate, 10 pipettes were labeled at the top with a permament marker with their corresponding sample	+	1. To keep the patient samples and solutions separate, 10 pipettes were labeled at the top with a permament marker with their corresponding sample<br>
-	2. Take 10 Eppendorf tubes containing 400mL of buffer and label them with the permament marker to their corresponding sample	+	2. Take 10 Eppendorf tubes containing 400mL of buffer and label them with the permament marker to their corresponding sample<br>
-	3. Next, transfer the patient sample into the assigned Eppendorf tube with an appropriate pipette. For example, Patient Sample A will be transferred into Eppendorf Tube A while using Pipette A only. This prevents the samples from contaminating each other.	+	3. Next, transfer the patient sample into the assigned Eppendorf tube with an appropriate pipette. For example, Patient Sample A will be transferred into Eppendorf Tube A while using Pipette A only. This prevents the samples from contaminating each other.<br>
-	4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, Teflon layer	+	4. Using the SYBR Green and its assigned pipette, two drops are placed in the first two center circles on the glass slide with the rough, Teflon layer<br>
-	5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide	+	5. Then two drops of a patient sample were placed on top of the SYBR Green drops on the slide<br>
-	6. With th SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample	+	6. With th SYBR Green mixed with the patient sample on the slide, the slide was positioned so that the blue ray of light would pass through the SYBR Green and patient sample<br>
-	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the conditions of: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.	+	7. Afterwards, the smarphone operator took a picture of the slide (as seen below) under the conditions of: an inactive flash, iso changed to 800, white balance set to auto, exposure set to maximum, and the contrast is set to minimum.<br>
-	8. The picture was then sent to the Image J software for processing.	+	8. The picture was then sent to the Image J software for processing.<br>
	9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br>		9. This process was repeated for all 6 patient samples, a positive and negative control, pure SYBR Green, and pure water.<br>


-	~~<br>~~<br>	+	<br>

	The process at which an image is turned into an Image J involves several steps. The first step is to set the settings of a camera's phone and then take a picture. The picture should then be emailed or downloaded onto a computer, and it then should be saved to the computer and opened in the Image J software. There are several parameters needed to be adjusted to produce the wanted picture so the measurement needs to be set to integrate the density and the linear gray value. The bubble's green spot is subsequently isolated, integrated density is measured and the background is then deleted to have the isolated desired picture.		The process at which an image is turned into an Image J involves several steps. The first step is to set the settings of a camera's phone and then take a picture. The picture should then be emailed or downloaded onto a computer, and it then should be saved to the computer and opened in the Image J software. There are several parameters needed to be adjusted to produce the wanted picture so the measurement needs to be set to integrate the density and the linear gray value. The bubble's green spot is subsequently isolated, integrated density is measured and the background is then deleted to have the isolated desired picture.