Team:Virginia United/Team

From 2010.igem.org

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*''' Adv 7 ''': Jason Papin  
*''' Adv 7 ''': Jason Papin  
*''' Adv 8 ''': Inchan Kwon
*''' Adv 8 ''': Inchan Kwon
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*''' Adv 9 ''': David Ball
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*''' Adv 10 ''': Brad Howard
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== '''What we did''' ==
+
== '''Where we're from''' ==
 +
Virginia United is a regional team between Virginia Tech, University of Virginia, Virginia Commonwealth University, Bluefield State College, and Virginia State University. The team members spent their summer spread between labs at Virginia Tech, University of Virginia, and Virginia Commonwealth University working towards a common project.
 +
===== Regional Team =====
-
Quorum Sensing Amplifiers and a Codesign Approach for Information Processing
+
The Virginia United Team was created as a collaborative effort between five schools, University of Virginia, Virginia Commonwealth University, Virginia Polytechnic Institute and State University (Virginia Tech), Bluefield State College, and Virginia State University. We divided up and worked on separate parts of the project in three different locations in the state and maintained communication through constant emails, Skype calls, and face to face regional meetings.  Collaboration for a project of this magnitude with this many people was in itself an experimental endeavor that challenged us to develop a project and maintain strong communication and organizational skills that are vital to the interdisciplinary component of synthetic biology.  Not only did each individual offer a unique perspective to the team, but each university, based on access to variable resources and instruments, provided different approaches and angles to completing our project.  Perhaps one of the most vital components of this project was learning how to work together as a team in a research environment.  Having gained a better understanding of how research can be conducted in a multi-institutional setting has provided us with an experience that will be instrumental for development of our futures in research and beyond.  As collaborative efforts between universities, states, and even countries becomes a normal part of the research world, our team members are now better equipped to handle and solve future scientific problems.
-
Synthetic biology endeavors to create information processing systems modeled on digital electronics.  The use of quorum sensing can help transform an inherently analog molecular signal into a binary response and simultaneously allow the tuning of input response thresholds and signal amplification.  This project demonstrates these capabilities through experimentation and modeling.  Another candidate for reapplying an electronic engineering technique is the codesign of hardware and software to implement a function.  In synthetic biology, codesign might mean implementing a design specification in different expression control regimes and comparing their relative merits.  Our work examines the codesign concept by constructing an AND gate in three different design domains.  We explore the application of these ideas with an environmental sensor.  A unique aspect of our project is the collaborative nature involving five institutions at three locations, which fostered a codesign-like approach using three distinct assembly techniques.
+
===== Collaborations with Other Teams =====
-
== '''Where we're from''' ==
+
We helped the software team create a program that can analyze a
-
Virginia United is a regional team between Virginia Tech, University of Virginia, Virginia Commonwealth University, Bluefield State College, and Virginia State University. The team members spent their summer spread between labs at Virginia Tech, University of Virginia, and Virginia Commonwealth University working towards a common project.
+
construct's DNA sequence and design oligo primers that can be used for USER
 +
fusion.  Our team helped by explaining how USER fusion works, explaining
 +
optimal length of primers, and explaining optimal melting temperatures for
 +
the primers.  USER fusion is a method for splicing together long strands of
 +
DNA and is convenient for construct assembly.
 +
 
 +
== '''VA United Boot Camp''' ==
 +
[[Image:people-igem.jpg|960px|center]]
 +
 
 +
In order to become acquainted with the members of each sub team, the Virginia United team held a "boot camp" at the beginning of the summer starting June 1 and ending on June 4.  In addition to getting to know one another the team also discussed an overview of our project.  To bring each team member up to speed in the field of synthetic biology, daily laboratory projects were planned including construct assembly, screening, and analysis.  Each day, guest speakers, including advisors from each institution, lectured on important points in the growing field of synthetic biology and instilled excitement in all the students.  The FBI visited the Virginia United students to lecture on safety and discretion while participating in research and provided a workshop to help conceptualize their lecture’s importance.  In summary, the boot camp provided an exciting environment for team bonding and offered an environment conducive for thinking and learning.
 +
 
 +
=== Here is a basic outline of the days ===
 +
 
 +
=== June 1 ===
 +
11:00-12:00: Welcome, Introductions, Outline of Week (VBI Conference Center)<br>
 +
12:00-1:00: Lunch provided (Pizza Hut) (VBI Lobby)<br>
 +
1:00-2:00: Lecture: Steve Fong (VCU) - synthetic biology (Fralin)<br>
 +
2:00-3:30: Discussion: Review and Discuss Project (Fralin)<br>
 +
3:30-4:00: Discussion: Outline of Labwork (Fralin)<br>
 +
4:00-4:30: Labwork: Start overnight cultures (Fralin)<br>
 +
4:30-6:00: Students Find, Read, and Summarize Papers in pairs (Fralin)<br>
 +
6:00-8:00: Group Dinner (not provided)<br>
 +
8:00-10:00: Student Literature Presentations and Discussion (Fralin)<br>
 +
 
 +
=== June 2 ===
 +
8:00-8:30: Breakfast provided (Muffins and Fruit) (Fralin)<br>
 +
8:30-12:00: Labwork: Minipreps, assembly, transformation (Fralin)<br>
 +
12:00-1:00: Lunch provided (Jimmy Johns) (Fralin)<br>
 +
1:00-2:00: Inchan Kwon (UVA) (Fralin)<br>
 +
2:00-4:00: Continue Labwork<br>
 +
4:00-5:00: Campus Tour (Weather Permitting) (Fralin)<br>
 +
5:00-6:00: Project Discussion/Parts Sequence Collection Continued (Fralin)<br>
 +
6:00-8:00: Group Dinner (not provided <br>
 +
8:00-10:00: Research Past iGEM Projects and Discussion (Fralin)<br>
 +
 
 +
=== June 3 ===
 +
8:30-9:00: Breakfast provided (Panera bagels) (Fralin)<br>
 +
9:00-10:00: Lecture: John Tyson (VT) - modeling of cellular processes (Fralin)<br>
 +
10:00-11:00: Workshop: Mathematical Modeling (Matt Lux) (Fralin)<br>
 +
11:00-12:00: Continued project discussion or campus tour (alternate time) (Fralin)<br>
 +
12:00-1:00: Lunch provided (Kroger) (Fralin)<br>
 +
1:00-2:00: Lecture: Jean Peccoud (VT) (Fralin)<br>
 +
2:00-3:00: GenoCAD Workshop - Introduction to Grammars (Laura Adam) (Fralin)<br>
 +
3:00-3:30: GenoCAD Workshop - GenoCAD Tutorial (Matt Lux) (Fralin)
 +
3:30-5:00: GenoCAD Workshop - iGEM Project in GenoCAD (Matt Lux) (Fralin)<br>
 +
5:00-6:00: LABWORK: Pick colonies, grow in 96-well plates w/ and w/o aTc (Fralin)<br>
 +
6:00-8:00: Dinner (not provided)<br>
 +
8:00-10:00: Present Past iGEM Projects and Discussion (Fralin)<br>
 +
 
 +
=== June 4===
 +
8:30-9:00: Breakfast provided (Doughnuts) (VBI Lobby)<br>
 +
9:00-10:00: Biosecurity aspects of synthetic biology, Edward You, Supervisory Special Agent, Federal Bureau of Investigation (VBI Conference Center)<br><br>
 +
==== Abstract: ====
 +
Amidst the increased attention and the diversity of views within the U.S. Government on biosecurity, the FBI Weapons of Mass Destruction Directorate has proactively engaged in outreach activities to promote science, safety and security within academia. Supervisory Special Agent Edward You will provide a presentation which will explore the nature of risk, review current policy discussions to minimize those risks, and suggest actions to improve the collaborative environment to promote research and education in the biological sciences while minimizing potential national security risks.<br>
 +
10:00-12:30: Biosecurity Table Top Exercises (simulating biosecurity incidents through discussions guided by FBI agents) (VBI various)<br>
 +
12:30-1:30: Lunch provided (Macadoos) (VBI Lobby)<br>
 +
1:30-2:30: Ryan Senger (VT) - whole-cell modeling (Fralin)<br>
 +
2:30-5:00: LABWORK<br>
 +
Measure fluorescence using flow (Melissa Makris) (Vet School)<br>
 +
Measure fluorescence using plate reader (Matt Lux) (VBI)<br>
 +
Measure fluorescence using microscope (Dave Ball) (VBI)<br>
 +
5:00pm: Dinner at Matt's <br>
 +
 
 +
=== Assembling ===
 +
The goal is to assemble a simple device using BioBricks. Since we only have 1 week, the BioBrick parts have already been transformed and grown on plates. During the week, students will start liquid cultures for each part, miniprep the plasmids, digest the plasmids, ligate the digested DNA, transform the assembled device, grow the new cells, and measure their results.<br>
 +
 
 +
The device contains three BioBrick parts: a TetR generator (BBa_I732084), a Ptet controlled GFP (BBa_I13522), and a vector expressing RFP (BBa_J04450). The TetR generator expresses the TetR transcription factor, which represses the Ptet promoter. The inducer aTc can be added to the growth media and block TetR from repressing the Ptet promoter. Thus, the Ptet controlled GFP will show a response in GFP level based on the presence or absence of aTc. The RFP expressing vector provides a positive control for the assembly because those vectors that do not properly digest can be identified by their expression of RFP, which can be seen by eye.<br>
 +
 
 +
[[Image:boot_camp_chart.jpg|517 px|center]]
 +
 
 +
===== June 1 =====
 +
Start liquid cultures from pre-made plates (Inoculation protocol)<br>
 +
===== June 2 =====
 +
Perform miniprep on liquid culture to prepare the plasmid DNA (miniprep protocol)<br>
 +
3A BioBrick assembly (BioBrick Assembly Manual)<br>
 +
Restriction Enzyme Digestion<br>
 +
Ligation<br>
 +
Transform cells and plate (Transformation protocol)<br>
 +
===== June 3 =====
 +
Pick colonies and start liquid cultures (Inoculation protocol)
 +
Create cultures of <br>
 +
(a) non-transformed cells (control),<br>
 +
(b) transformed cells w/ aTc (+aTc),<br>
 +
(c) transformed cells  aTc (-aTc).<br>
 +
 
 +
===== June 4 =====
 +
Make glycerol stock (Glycerol stock protocol)<br>
 +
Measure fluorescence in 3 rotating groups:<br>
 +
Station 1: Melissa Makris: flow cytometer (VT Vet School)<br>
 +
Station 2: David Ball: fluorescent microscopy (VBI)<br>
 +
Station 3: Matt Lux: plate reader (VBI)<br><br>
-
[[Image:banner-vt-960.jpg|960px|center]]
+
Not only did we have the opportunity to meet all the team members at the boot camp, but we also learned a lot of important elements that helped us throughout the summer. Each speaker helped us understand a different aspect of the field, and each day we worked in the lab we became more familiar with the techniques that we were using throughout the summer.<br>
-
[[Image:banner-bfs-960.jpg|960px|center]]
+
[[Image:banner-vcu-vt-uva-2.jpg|960px|center]]
-
[[Image:banner-vsu-960.jpg|960px|center]]
+
-
[[Image:banner-uva-960.jpg|960px|center]]
+
-
[[Image:banner-vcu-960.jpg|960px|center]]
+

Latest revision as of 21:43, 27 October 2010

igem

Virginia United 3.jpg

Contents

Who we are

Advisors:

  • Inst 1: Jean Peccoud
  • Inst 2: Martha Eborall
  • Grad 1: George McArthur
  • Grad 2: Matt Lux
  • Adv 1 : Daniel Tarjan
  • Adv 2 : Erik Fernandez
  • Adv 3 : Stephen Fong
  • Adv 4 : Brian Sayre
  • Adv 5 : Ryan Senger
  • Adv 6 : Keith Kozminski
  • Adv 7 : Jason Papin
  • Adv 8 : Inchan Kwon
  • Adv 9 : David Ball
  • Adv 10 : Brad Howard

Undergrads:

  • Student 1: Rohini Manaktala
  • Student 2: Yong Wu
  • Student 3: Megan Barron
  • Student 4: Arjun Athreya
  • Student 5: Austin Chamberlin
  • Student 6: Sara Brickman
  • Student 7: Adam Bower
  • Student 8: Brett Tolliver
  • Student 9: Daniel Chique
  • Student 10: Dasha Nesterova
  • Student 11: Jane Carter
  • Student 12: Joe Edwards
  • Student 13: Karis Childs
  • Student 14: Priscilla Agyemang
  • Student 15: Maria McClintock

Where we're from

Virginia United is a regional team between Virginia Tech, University of Virginia, Virginia Commonwealth University, Bluefield State College, and Virginia State University. The team members spent their summer spread between labs at Virginia Tech, University of Virginia, and Virginia Commonwealth University working towards a common project.

Regional Team

The Virginia United Team was created as a collaborative effort between five schools, University of Virginia, Virginia Commonwealth University, Virginia Polytechnic Institute and State University (Virginia Tech), Bluefield State College, and Virginia State University. We divided up and worked on separate parts of the project in three different locations in the state and maintained communication through constant emails, Skype calls, and face to face regional meetings. Collaboration for a project of this magnitude with this many people was in itself an experimental endeavor that challenged us to develop a project and maintain strong communication and organizational skills that are vital to the interdisciplinary component of synthetic biology. Not only did each individual offer a unique perspective to the team, but each university, based on access to variable resources and instruments, provided different approaches and angles to completing our project. Perhaps one of the most vital components of this project was learning how to work together as a team in a research environment. Having gained a better understanding of how research can be conducted in a multi-institutional setting has provided us with an experience that will be instrumental for development of our futures in research and beyond. As collaborative efforts between universities, states, and even countries becomes a normal part of the research world, our team members are now better equipped to handle and solve future scientific problems.

Collaborations with Other Teams

We helped the software team create a program that can analyze a construct's DNA sequence and design oligo primers that can be used for USER fusion. Our team helped by explaining how USER fusion works, explaining optimal length of primers, and explaining optimal melting temperatures for the primers. USER fusion is a method for splicing together long strands of DNA and is convenient for construct assembly.

VA United Boot Camp

People-igem.jpg

In order to become acquainted with the members of each sub team, the Virginia United team held a "boot camp" at the beginning of the summer starting June 1 and ending on June 4. In addition to getting to know one another the team also discussed an overview of our project. To bring each team member up to speed in the field of synthetic biology, daily laboratory projects were planned including construct assembly, screening, and analysis. Each day, guest speakers, including advisors from each institution, lectured on important points in the growing field of synthetic biology and instilled excitement in all the students. The FBI visited the Virginia United students to lecture on safety and discretion while participating in research and provided a workshop to help conceptualize their lecture’s importance. In summary, the boot camp provided an exciting environment for team bonding and offered an environment conducive for thinking and learning.

Here is a basic outline of the days

June 1

11:00-12:00: Welcome, Introductions, Outline of Week (VBI Conference Center)
12:00-1:00: Lunch provided (Pizza Hut) (VBI Lobby)
1:00-2:00: Lecture: Steve Fong (VCU) - synthetic biology (Fralin)
2:00-3:30: Discussion: Review and Discuss Project (Fralin)
3:30-4:00: Discussion: Outline of Labwork (Fralin)
4:00-4:30: Labwork: Start overnight cultures (Fralin)
4:30-6:00: Students Find, Read, and Summarize Papers in pairs (Fralin)
6:00-8:00: Group Dinner (not provided)
8:00-10:00: Student Literature Presentations and Discussion (Fralin)

June 2

8:00-8:30: Breakfast provided (Muffins and Fruit) (Fralin)
8:30-12:00: Labwork: Minipreps, assembly, transformation (Fralin)
12:00-1:00: Lunch provided (Jimmy Johns) (Fralin)
1:00-2:00: Inchan Kwon (UVA) (Fralin)
2:00-4:00: Continue Labwork
4:00-5:00: Campus Tour (Weather Permitting) (Fralin)
5:00-6:00: Project Discussion/Parts Sequence Collection Continued (Fralin)
6:00-8:00: Group Dinner (not provided
8:00-10:00: Research Past iGEM Projects and Discussion (Fralin)

June 3

8:30-9:00: Breakfast provided (Panera bagels) (Fralin)
9:00-10:00: Lecture: John Tyson (VT) - modeling of cellular processes (Fralin)
10:00-11:00: Workshop: Mathematical Modeling (Matt Lux) (Fralin)
11:00-12:00: Continued project discussion or campus tour (alternate time) (Fralin)
12:00-1:00: Lunch provided (Kroger) (Fralin)
1:00-2:00: Lecture: Jean Peccoud (VT) (Fralin)
2:00-3:00: GenoCAD Workshop - Introduction to Grammars (Laura Adam) (Fralin)
3:00-3:30: GenoCAD Workshop - GenoCAD Tutorial (Matt Lux) (Fralin) 3:30-5:00: GenoCAD Workshop - iGEM Project in GenoCAD (Matt Lux) (Fralin)
5:00-6:00: LABWORK: Pick colonies, grow in 96-well plates w/ and w/o aTc (Fralin)
6:00-8:00: Dinner (not provided)
8:00-10:00: Present Past iGEM Projects and Discussion (Fralin)

June 4

8:30-9:00: Breakfast provided (Doughnuts) (VBI Lobby)
9:00-10:00: Biosecurity aspects of synthetic biology, Edward You, Supervisory Special Agent, Federal Bureau of Investigation (VBI Conference Center)

Abstract:

Amidst the increased attention and the diversity of views within the U.S. Government on biosecurity, the FBI Weapons of Mass Destruction Directorate has proactively engaged in outreach activities to promote science, safety and security within academia. Supervisory Special Agent Edward You will provide a presentation which will explore the nature of risk, review current policy discussions to minimize those risks, and suggest actions to improve the collaborative environment to promote research and education in the biological sciences while minimizing potential national security risks.
10:00-12:30: Biosecurity Table Top Exercises (simulating biosecurity incidents through discussions guided by FBI agents) (VBI various)
12:30-1:30: Lunch provided (Macadoos) (VBI Lobby)
1:30-2:30: Ryan Senger (VT) - whole-cell modeling (Fralin)
2:30-5:00: LABWORK
Measure fluorescence using flow (Melissa Makris) (Vet School)
Measure fluorescence using plate reader (Matt Lux) (VBI)
Measure fluorescence using microscope (Dave Ball) (VBI)
5:00pm: Dinner at Matt's

Assembling

The goal is to assemble a simple device using BioBricks. Since we only have 1 week, the BioBrick parts have already been transformed and grown on plates. During the week, students will start liquid cultures for each part, miniprep the plasmids, digest the plasmids, ligate the digested DNA, transform the assembled device, grow the new cells, and measure their results.

The device contains three BioBrick parts: a TetR generator (BBa_I732084), a Ptet controlled GFP (BBa_I13522), and a vector expressing RFP (BBa_J04450). The TetR generator expresses the TetR transcription factor, which represses the Ptet promoter. The inducer aTc can be added to the growth media and block TetR from repressing the Ptet promoter. Thus, the Ptet controlled GFP will show a response in GFP level based on the presence or absence of aTc. The RFP expressing vector provides a positive control for the assembly because those vectors that do not properly digest can be identified by their expression of RFP, which can be seen by eye.

Boot camp chart.jpg
June 1

Start liquid cultures from pre-made plates (Inoculation protocol)

June 2

Perform miniprep on liquid culture to prepare the plasmid DNA (miniprep protocol)
3A BioBrick assembly (BioBrick Assembly Manual)
Restriction Enzyme Digestion
Ligation
Transform cells and plate (Transformation protocol)

June 3

Pick colonies and start liquid cultures (Inoculation protocol) Create cultures of
(a) non-transformed cells (control),
(b) transformed cells w/ aTc (+aTc),
(c) transformed cells aTc (-aTc).

June 4

Make glycerol stock (Glycerol stock protocol)
Measure fluorescence in 3 rotating groups:
Station 1: Melissa Makris: flow cytometer (VT Vet School)
Station 2: David Ball: fluorescent microscopy (VBI)
Station 3: Matt Lux: plate reader (VBI)

Not only did we have the opportunity to meet all the team members at the boot camp, but we also learned a lot of important elements that helped us throughout the summer. Each speaker helped us understand a different aspect of the field, and each day we worked in the lab we became more familiar with the techniques that we were using throughout the summer.

Banner-vcu-vt-uva-2.jpg
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