Difference between revisions of "Team:Cadets2Vets/Collaborations"

Cadets2Vets Adviser Judy Nguyen and Cadets2Vets Collaborator from Center for Urban Waters Joel Baker had a conference call with two team members from iTesla-SoundBio: Anna Vasyura and Advisor Zach Mueller. They shared information about each others’ projects and the status of their experiments.

Anna and Zach are looking for help regarding the analysis of the degradation of polychlorinated biphenyls (PCBs). Joel had previously collaborated with a lab that performed this type of research and had a lot of valuable information to share. One of the significant bits of advice was to pivot the analysis from PCBs to PCEs (tetrachloroethene).

PCBs take a really long time to degrade and the analysis is not fast or easy to do. PCEs degrade a little quicker and make more sense to measure for the iGEM timeline. Joel will meet face to face with iTesla-SoundBio to work out more details of what the analytical experiments would involve. Judy has also joined the team’s Slack workspace and is available to help with any other technical questions or assistance with laboratory space.

The Cadets2Vets team had a Skype call with Dallas McDonald from the Lab Pats (AFRL) team. Our teams had Skype’d previously during the summer and we wanted to talk a little more about the Interlab Measurement Study.

We are sharing the results from our Interlab Study and wanted to see if Lab Pats had measured data that was similar to ours. Cadets2Vets had graphed the fluorescence values from the 6 Devices and positive and negative controls, and found that the Devices all had variable performance, although there were a few Devices that had very low GFP fluorescence. We also found that some Devices performed at or below the LB+Chloramphenicol blank, which means that the previously known autofluorescence of LB was being picked up by the plate reader. The Devices that performed worse than LB+Chloramphenicol are promoter/RBS sites that we would want to avoid in the future when trying to express GFP, because the amount of GFP expressed was unable to rise higher than the background autofluorescence under the given experimental conditions.

Cadets2Vets will work with Dallas to establish a collaboration where Cadets2Vets will send Dallas the plasmids we have created so that he can help us characterize the GFP fluorescence. We will base the assay off the InterLab study and we will consider these questions:

Do our plasmids produce GFP as they are expected to?
How does our plasmid compare to the Interlab positive and negative controls?
What is the appropriate density of cells and duration of growth to get significant GFP fluorescence?
Can other labs reproduce our data?

Members of the Cadets2Vets team had a teleconference with Yoshi Goto from the UW-Seattle iGEM team. The Washington team has a really interesting and complex project that involves the creation of a bioreactor and manipulation and development of a violacein reporter system to monitor metabolite production from chemical reactions made by bacteria or yeast.

The violacein pigment is produced through a series of 5 different genes and altering the synthetic pathway can produce different colors. This project is also developing an analytical system that monitors the turbidity and color of the culture in the bioreactor. There are many possible applications of this technology for monitoring metabolic reactions while maintaining affordability.

We discussed the possibility of sharing some reagents to help each other characterize some Parts. Cadets2Vets is looking for collaborators to measure the GFP fluorescence from the plasmids we made and Washington is looking for ways to characterize some of its plasmids in a similar way.

Cadets2Vets had a Skype call with Dallas McDonald from the Lab Pats team.

The results obtained from the Lab Pats Interlab study were different from Cadets2Vets. At the 6 hour time point, the plasmids with highest to lowest GFP fluorescence were:

LB + Chloramphenicol
Negative Control
Device 6
Positive Control
Device 1
Device 4
Device 5
Device 3
Device 2

After sharing these results, Cadets2Vets were curious why the results were so different. The Lab Pats team speculated that the difference may have been due to pipetting errors or differences in the instruments. Te Lab Pats used a SpectraMax M5, which uses monochromators to excite the GFP instead of filters, which is what Cadets2Vets had in their FilterMax F5 instrument. Cadets2Vets went back to their transformation plates and tried to assess whether the bacterial colonies sill expressed GFP and if the intensity was similar to the pattern gain from the plate reader.

Cadets2Vets’ one-month old transformation plates were still fluorescent, and we used a hand-held blacklight to qualitatively observe the colonies. The order of highest to lowest fluorescence using this method was:

Positive Control
Device 2
Device 4 = Device 1
Device 6 = Device 3
Negative Control.

Device 5 was omitted due to the few colonies present were on the edge of the plate and difficult to see clearly.

The sensitivity of using a blacklight was much lower than using a plate reader, and so it was hard to see the differences between some of the plates. However, it appears that the pattern of fluorescence we observed in the plate reader is consistent with the bacteria in the plates. Washington also shared the results of their Interlab study. Summarizing their data in the same way we looked at ours and Lab Pats, the ranking of high to low GFP for Washington was:

Device 2
Positive control = Device 4
Device 5 = Device 1
Negative control = Device 3 = Device 6 = LB + Chloramphenicol

Difference between revisions of "Team:Cadets2Vets/Collaborations"

Latest revision as of 20:01, 28 October 2017

WELCOME TO OUR COLLABORATION PAGE

CONTRIBUTORS TO THE CAUSE

First Inter-Team Meeting (07/14/2017)

iTesla-soundbio team meeting (09/28/2017)

Lab Pats First Interlab Meeting (10/05/2017)

FOURTH INTER-TEAM MEETING (10/05/2017)

Interlab collaboration with lab pats air force research lab

Follow us on Social Media!

2304 Jefferson Ave, Tacoma, WA 98402

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-		<p><span style="line-height:2em;"><span style="font-size:16px;">Cadet Mitchell and Cadet Buehrer are sophomores at West Point. During the summer of their freshman year, they traveled to Tacoma, WA to work with members of the Cadets2Vets team to design the project that will be presented at the iGEM Jamboree in November of 2017.</span></span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">The United States Military Academy's mission is to educate, train, and inspire the Corps of Cadets so that each graduate is a commissioned leader of character committed to the values of duty, honor, and country, and prepared for a career of professional excellence and service to the nation as an officer in the United States Army.</span></span></p>
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-		<p><span style="font-size:16px;"><span style="line-height:2em;"> ECBC is currently developing better ways to remotely detect chemical and biological materials - before the warfighter or first responder ever enters the threat zone. ECBC is also developing a new generation of technologies to counter everything from homemade explosives to biological aerosols and non-traditional chemical hazards.</span></span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">ECBC possesses an unrivaled chemical and biological research and development infrastructure with scientists, engineers, technicians, and specialists located at four different sites in the Unites States: the Edgewood Area of Aberdeen Proving Ground, Maryland; Pine Bluff, Arkansas; Rock Island, Illinois; and Dugway Proving Ground, Utah.</span></span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">The Readiness Acceleration &amp; Innovation Network is a 501(c)(3) nonprofit organization based out of Tacoma, Washington. Working to unlock local innovation in the biotech and biomedical fields, RAIN was founded as a collaboration between the University of Washington Tacoma, MultiCare Health System, and Madigan Army Medical Center.</span></span></p>
+		<p><span style="letter-spacing: 1.2px; text-align: center; background-color: transparent; font-size: 12pt; vertical-align: baseline; white-space: pre-wrap;">In an attempt to learn the methods used by other iGEM teams we participated in an inter-team Skype call. We chose to meet with the other teams sponsored by the United States Armed forces, because we share many of the same challenges. These teams are Lab Pats Carroll High School and the US Naval Academy.</span></p><p><br></p><p><span style="letter-spacing: 1.2px; text-align: center; background-color: transparent; font-size: 12pt; vertical-align: baseline; white-space: pre-wrap;">Our team took many notes over the course of the hour-plus long Skype call that helped us to prepare for the upcoming challenges that iGEM poses. </span></p>
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-	<h2 id="vbid-32185b27-8p5iyghv" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu   allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >Readiness acceleration and innovation  network<br></h2>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">Thinking many years ahead to what we are working to achieve, we envision our city and region as a major industrial and commercial player in the Pacific Northwest life-science sector with a reputation for being the best in the world at what we do. By helping to build a local innovation-commercialization pipeline, RAIN is inclusive, empowering, and inspiring to our community, friends, and neighbors.</span></span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">Together, we provide startups with significant support for ideation, research and development, prototyping, business development, and launch. In addition, the people and City of Tacoma are core partners in our efforts as we work together to create prosperity and well-being in our community.</span></span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">The Center for Urban Waters brings together environmental scientists, analysts, engineers, and policymakers who are developing creative and sustainable solutions to restore and protect Puget Sound. It</span><span style="font-size: 16px; letter-spacing: 0.6px; background-color: rgb(97, 82, 39);"> is the result of years of work by community leaders who dreamed of a world-class research center on Commencement Bay dedicated to finding solutions for urban bay communities.</span></span></p>
+		<p><span style="font-size: 16px; letter-spacing: 1.2px; text-align: center; white-space: pre-wrap;">Cadets2Vets Adviser Judy Nguyen and Cadets2Vets Collaborator from Center for Urban Waters Joel Baker had a conference call with two team members from iTesla-SoundBio: Anna Vasyura and Advisor Zach Mueller. They shared information about each others’ projects and the status of their experiments.</span></p><p><br></p><p><span style="font-size: 16px; letter-spacing: 1.2px; text-align: center; white-space: pre-wrap;">Anna and Zach are looking for help regarding the analysis of the degradation of polychlorinated biphenyls (PCBs). Joel had previously collaborated with a lab that performed this type of research and had a lot of valuable information to share. One of the significant bits of advice was to pivot the analysis from PCBs to PCEs (tetrachloroethene). </span></p><p><br></p><p><span style="font-size: 16px; letter-spacing: 1.2px; text-align: center; white-space: pre-wrap;">PCBs take a really long time to degrade and the analysis is not fast or easy to do. PCEs degrade a little quicker and make more sense to measure for the iGEM timeline. Joel will meet face to face with iTesla-SoundBio to work out more details of what the analytical experiments would involve. Judy has also joined the team’s Slack workspace and is available to help with any other technical questions or assistance with laboratory space. </span><span style="letter-spacing: 1.2px; text-align: center; font-size: 12pt; vertical-align: baseline; white-space: pre-wrap;"> </span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">The founding partners - the City of Tacoma, the University of Washington Tacoma, and the Puget Sound Partnership - are committed to providing a collaborative environment where the best-available science forms the basis for policy development and implementation.</span></span></p>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">Charles Wright Academy is a private school in the greater Tacoma area that serves students K-12. The school features small classes, a safe campus, and a preparation center for college and life skills.</span></span><span style="line-height:2em;"><span style="font-size:16px;"></span></span></p>
+		<p><span id="docs-internal-guid-1b7da29c-f937-736d-d27b-f199a1ff299f" style="letter-spacing: 1.2px; text-align: center;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">The Cadets2Vets team had a Skype call with Dallas McDonald from the Lab Pats (AFRL) team. Our teams had Skype’d previously during the summer and we wanted to talk a little more about the Interlab Measurement Study.</span></span></p><p><br></p><p><span style="letter-spacing: 1.2px; text-align: center;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">We are sharing the results from our Interlab Study and wanted to see if Lab Pats had measured data that was similar to ours. Cadets2Vets had graphed the fluorescence values from the 6 Devices and positive and negative controls, and found that the Devices all had variable performance, although there were a few Devices that had very low GFP fluorescence. We also found that some Devices performed at or below the LB+Chloramphenicol blank, which means that the previously known autofluorescence of LB was being picked up by the plate reader. The Devices that performed worse than LB+Chloramphenicol are promoter/RBS sites that we would want to avoid in the future when trying to express GFP, because the amount of GFP expressed was unable to rise higher than the background autofluorescence under the given experimental conditions. </span><br class="kix-line-break"><br class="kix-line-break"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Cadets2Vets will work with Dallas to establish a collaboration where Cadets2Vets will send Dallas the plasmids we have created so that he can help us characterize the GFP fluorescence. We will base the assay off the InterLab study and we will consider these questions:</span></span></p><ol><li><span style="letter-spacing: 1.2px; text-align: center;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Do our plasmids produce GFP as they are expected to?</span></span></li><li><span style="letter-spacing: 1.2px; text-align: center;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">How does our plasmid compare to the Interlab positive and negative controls?</span></span></li><li><span style="letter-spacing: 1.2px; text-align: center;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">What is the appropriate density of cells and duration of growth to get significant GFP fluorescence?</span></span></li><li><span style="letter-spacing: 1.2px; text-align: center;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Can other labs reproduce our data? </span></span><span style="letter-spacing: 1.2px; text-align: center;"></span><span style="letter-spacing: 1.2px; text-align: center; background-color: transparent; font-size: 12pt; vertical-align: baseline; white-space: pre-wrap;"> </span></li></ol>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;"></span></span><span style="line-height:2em;"><span style="font-size:16px;">The Cadets2Vets team is honored to have four of the Charles Wright Academy's best and brightest serve as Interns on their lab team.</span></span></p>
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-	<h2 id="vbid-b5c93daa-a9tbv8yh" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu   allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >Bellarmine Preparatory School<br></h2>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">The Bellarmine Preparatory School was founded under the leadership of the Jesuits. The school serves as a Catholic college preparatory school, and is the only Catholic high school in the Tacoma area.</span></span><br></p>
+		<p><span id="docs-internal-guid-1b7da29c-f936-c0f2-830a-192b378e7a21" style="letter-spacing: 0.6px; text-align: left;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Members of the Cadets2Vets team had a teleconference with Yoshi Goto from the UW-Seattle iGEM team. The Washington team has a really interesting and complex project that involves the creation of a bioreactor and manipulation and development of a violacein reporter system to monitor metabolite production from chemical reactions made by bacteria or yeast.</span></span></p><p><br></p><p><span style="letter-spacing: 0.6px; text-align: left;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">The violacein pigment is produced through a series of 5 different genes and altering the synthetic pathway can produce different colors. This project is also developing an analytical system that monitors the turbidity and color of the culture in the bioreactor. There are many possible applications of this technology for monitoring metabolic reactions while maintaining affordability. </span></span></p><p><br class="kix-line-break"><span style="letter-spacing: 0.6px; text-align: left;"><span style="font-size: 12pt; background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">We discussed the possibility of sharing some reagents to help each other characterize some Parts. Cadets2Vets is looking for collaborators to measure the GFP fluorescence from the plasmids we made and Washington is looking for ways to characterize some of its plasmids in a similar way. </span></span><span style="letter-spacing: 0.6px; text-align: left;"></span></p>
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-	<h2 id="vbid-09af178e-zhnqeuon" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu   allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >Bellarmine Preparatory School<br></h2>
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-		<p><span style="line-height:2em;"><span style="font-size:16px;">The Cadets2Vets team is privileged to have Josh Grace as a Lab Member on their team.</span></span></p>
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-	<h2 id="vbid-fcbd6c14-pyomoedo" class="preview-element preview-title magic-circle-holder inner-page text-element quick-text-style-menu   allow-mobile-hide" data-menu-name="PREVIEW_TITLE" >University of Washington Tacoma<br></h2>
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-	<div id="vbid-fcbd6c14-vjsg9hwd" class="preview-element preview-body magic-circle-holder text-element quick-text-style-menu   allow-mobile-hide" data-menu-name="PREVIEW_BODY">
+	<div id="vbid-77158560-sxl62tbr" class="preview-element preview-body magic-circle-holder text-element quick-text-style-menu   allow-mobile-hide" data-menu-name="PREVIEW_BODY">
-		<p><span style="line-height:2em;"><span style="font-size:16px;">UW Tacoma is an urban-serving university providing access to students in a way that transforms families and communities. We impact and inform economic development through community-engaged students and faculty. We conduct research that is of direct use to our community and region. Most importantly, we seek to be connected to our community's needs and aspirations.</span></span><br></p>
+		<p><span style="line-height:1em;"><span style="font-size:16px;"><span id="docs-internal-guid-1b7da29c-f937-736d-d27b-f199a1ff299f" style="letter-spacing: 1.2px; text-align: center;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Cadets2Vets had a Skype call with Dallas McDonald from the Lab Pats team. </span></span></span></span></p><p><br></p><p><span style="font-size:16px;"><span style="line-height:1em;"></span><span id="docs-internal-guid-07d9d787-11a4-1efb-f4d4-11ec539fa495"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;"><span style="line-height:1em;">The res</span>ults obtained from the Lab Pats Interlab study were different from Cadets2Vets. At the 6 hour time point, th</span><span style="vertical-align: baseline; white-space: pre-wrap;">e plasmids with highest to lowest GFP fluorescence were:</span></span></span></p><ul><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">LB + Chloramphenicol</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Negative Control</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Device 6</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Positive Control</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Device 1</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Device 4</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Device 5</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Device 3</span></span></span></li><li><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">Device 2</span></span></span></li></ul><p><span style="font-size:16px;"><span><span style="vertical-align: baseline; white-space: pre-wrap;">After sharing these results, Cadets2Vets were curious why the results were so different. The Lab Pats team speculated that the difference may have been due to pipetting errors or differences in the instruments. Te Lab Pats used a SpectraMax M5, which uses monochromators to excite the GFP instead of filters, which is what Cadets2Vets had in their FilterMax F5 instrument. Cadets2Vets went back to their transformation plates and tried to assess whether the bacterial colonies sill expressed GFP and if the intensity was similar to the pattern gain from the plate reader.</span></span></span><span style="font-size: 16px; background-color: transparent; font-family: Arial; letter-spacing: 0.1em; text-align: inherit; vertical-align: baseline; white-space: pre-wrap;"></span></p><p><br></p><p><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Cadets2Vets’ one-month old transformation plates were still fluorescent, and we used a hand-held blacklight to qualitatively observe the colonies. The order of highest to lowest fluorescence using this method was:</span></span></p><ul><li><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Positive Control</span></span></li><li><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Device 2</span></span></li><li><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Device 4 = Device 1</span></span></li><li><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Device 6 = Device 3</span></span></li><li><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Negative Control.</span></span></li></ul><p><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Device 5 was omitted due to the few colonies present were on the edge of the plate and difficult to see clearly.</span></span><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;"> </span></span></p><p><br></p><p><span style="font-size:16px;"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">The sensitivity of using a blacklight was much lower than using a plate reader, and so it was hard to see the differences between some of the plates. However, it appears that the pattern of fluorescence we observed in the plate reader is consistent with the bacteria in the plates.</span></span> <span style="font-size:16px;"><span id="docs-internal-guid-07d9d787-11a4-1efb-f4d4-11ec539fa495"><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Washington also shared the results of their Interlab study. Summarizing their data in the same way we looked at ours and Lab Pats, the ranking of high to low GFP for Washington was:</span></span></span><span style="font-size:16px;"><span><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;"> </span></span></span></p><ul><li><span style="font-size:16px;"><span><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Device 2</span></span></span></li><li><span style="font-size:16px;"><span><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Positive control = Device 4</span></span></span></li><li><span style="font-size:16px;"><span><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Device 5 = Device 1</span></span></span></li><li><span style="font-size:16px;"><span><span style="background-color: transparent; vertical-align: baseline; white-space: pre-wrap;">Negative control = Device 3 = Device 6 = LB + Chloramphenicol</span></span></span></li></ul>
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-		<p><br></p><p><span style="line-height:2em;"><span style="font-size:16px;">A special thanks to UW Tacoma faculty and staff for allowing the Cadets2Vets team the opportunity to utilize their lab, equipment, and facilities.</span></span></p>
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