2020(S11) Lecture:week 7

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=<center>Week 7 Studio</center>=
=<center>Week 7 Studio</center>=
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==<font color = blue> '''Homework'''</font color>==
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Are there tools or methods for breaking down a complicated problem into simpler parts?
 +
*Watch the [http://www.biobuilder.org/animations/ Abstraction animation] from BioBuilder
 +
*Walk through one sample abstraction hierarchy that may guide synthetic biology<br>
 +
This abstraction hierarchy is modified from one of [[Drew Endy | Drew Endy's]] slides. It gives us a framework for how to intentionally engineer various aspects of biological systems.
 +
<br style="clear:both" /><center>[[Image:Hierarchy def.png]]
 +
[[Image:Abstraction redrawn.png]]</center>
 +
 
 +
==<font color = blue> Abstraction in action: Systems to Devices</font color>==
 +
<center>'''Three quick examples to put the abstraction hierarchy in action'''</center>
 +
===First up: Arsenic detector===
 +
[[Image:Arsen Dev-level.png|450px|left]]Recall the University of Edinburgh 2006 iGEM project that was described as an Arsenic Detector in the "abstraction" BioBuilder video. The system was designed to sense arsenic and result in a color. Two devices were used to build this system. The first device sensed arsenic and gave rise to a signal when arsenic was detected. And if the second device sensed the signal from the first device, then it gave rise to a color. The device-level system diagram is pretty straightforward, but makes clear that you could swap out the first device for a different sensor, as long as the output could still be interpreted by the second device. Similarly you could change the output from color to anything, as long as the input to that color-generating device was paired to the output of the arsenic sensor. <br style="clear:both" />
 +
 
 +
===Next: Polkadorks===
 +
Let's try a more dynamic system. The 2004 IAP team wanted their engineered cells to "form, diffuse, and form again in random areas on the plate. Our system should thus form time-varying patterns based on local random time-varying symmetry breaking." Check out the Polkadorks [http://parts.mit.edu/wiki/index.php/Image:Intro1-EcolibratorMovie.gif animation].
 +
*'''As a class''' we'll
 +
**describe the system in plain language, then
 +
**list the devices needed to implement the system
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*Then '''as a team''' you'll have '''10 minutes''' to draw a device-level system diagram.
 +
*Finally, '''as a class''', we'll look at the timing diagram that the 2004 IAP team wrote.
 +
<center>[[Image:Ecolibrator TimingDiagram.png|center|650pxl| timing diagram for the Polkadork's Ecolibrator project]]</center>You'll see that the devices (or the named connections between these devices) are listed on a y-axis and time is shown on an x-axis. The timing diagram indicates the '''timing for operation''' of each device or wire, including the persistence of each device's signal through time--shown as PS (protein synthesis) and PD (protein degradation). '''You and your team''' should take 10 minutes to make a timing diagram for '''EITHER'''<br> the Polkadork's devices that you have wired together<br> '''OR''' <br> the Eau D'coli project that we looked at on week 1. [[Image:Copy of BBa J45200.png| thumb| right| 400px| Eau D'coli]]<br>You can keep a running list of any uncertainties. '''After 10 minutes of work,''' we'll have each team report back to the group to see how we did and what questions still remain.
 +
 
 +
===And finally: Get busy!===
 +
Start applying these ideas to your team's project. You can work on a device list, a device-level system diagram and a timing diagram if you're ready.
 +
 
=<center>Week 7 Thursday</center>=
=<center>Week 7 Thursday</center>=
-
==<font color = blue> </font color>==
+
We've been working hard this week to move between the System and Device levels of an abstraction hierarchy and today we'll drop down one more level to think about the parts that make up a device. The device you'll design is one we've talked about already, namely a bistable toggle, but first we'll look at a "classic" device that's a little simpler, namely an inverter, and the parts that make it up.
-
==<font color = blue>Why are we doing this?</font color>==
+
==Challenge:<font color = blue> Abstraction in action: Devices to Parts</font color>==
 +
After some discussion about what makes a [[Media:StdAssembly 031711.ppt| "standard biological part,"]] we'll turn our attention to building devices from parts.
 +
===Part 1: Four-part inverter===
 +
Recall the Eau d'coli project from the 2006 MIT iGEM team. Their goal was to replace the nasty smell of bacteria with <font color = green> '''wintergreen smell''' </font color> during log phase growth and <font color = gold>'''banana smell'''</font color> during stationary phase growth. We talked about the engineering ideas behind the Eau d'Coli project way WAY back in [[2020(S11) Lecture:week 1| Week 1.]] Today we'll focus in on one device within the system, namely the inverter that was used upstream of the <font color = green> '''wintergreen generating device (WGD)'''</font color>, turning it off during stationary phase.  <center>
 +
[[Image:EauD'coli abstraction.png]]</center>
 +
The abstraction hierarchy shown above zooms in on the inverter part that reverses the signal from the stationary phase promoter. This turns the wintergreen generating device off in stationary phase and on in log phase. The inverter part that's shown is a permutation of a natural gene that encodes the tetracycline repressor protein. <center>[[Image:TetRgene.png]]</center><br>
 +
Within this gene, we can define 4 "parts:" a promoter, a ribosome binding site (RBS), an open reading frame (ORF) that encodes the tet repressor protein, and a transcriptional terminator so the RNA polymerase transcribing the gene doesn't continue down to the next sequences downstream. The promoter is repressed by the tetR protein itself, allowing for a simple rearrangement that makes a useful inverter device. You can imagine a family of 4-part inverters that might be made for every repressor protein we know (lac repressor, lambda repressor, etc). For one more example, let's consider [http://www.biobuilder.org/animations/ this inverter animation] that shows us how (and why!) you might build an inverter from the arsenic-inducible operon. The number of inverters that can be built this way will be finite, however, and there will almost certainly be a time when a '''transcription-based device''' will not be optimal.
 +
 
 +
===Part 2: Toggle-away===
 +
Working in your project teams, develop a design for '''a genetically encoded toggle switch that can be flipped with exogenous inputs and that maintains one state (or the other) even in the absence of the input.'''  Your team's design should include
 +
*(a) a high level system diagram,
 +
*(b) a full list of devices and parts,
 +
*(c) timing diagram (time on the x-axis and devices on the y plus some indication of when their activities rise and fall, and
 +
*(d) a plan for testing the most important components of your toggle.<br> '''You have 45 minutes.'''--so we've helped you get started by collecting some parts that you might find useful. These are parts that are documented, to different extents at the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts.]
 +
====Partial Parts List====
 +
You can use parts that are not on this list. Try to find them in the Registry (where you could get them for free) or if you want to get them from another source, please specify and note associated cost, e.g. synthesis cost is $1/base, licensing agreements, needed MTAs etc.
 +
=====Promoters=====
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K113009], [http://partsregistry.org/wiki/index.php?title=Part:BBa_R0040], [http://partsregistry.org/wiki/index.php?title=Part:BBa_R1051],[http://partsregistry.org/wiki/index.php?title=Part:BBa_I1051], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I12001], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I14032]
 +
=====Reporters=====
 +
[http://partsregistry.org/wiki/index.php?title=Part:BBa_E0030], [http://partsregistry.org/wiki/index.php?title=Part:BBa_E0020], [http://partsregistry.org/wiki/index.php?title=Part:BBa_E1010],[http://partsregistry.org/wiki/index.php?title=Part:BBa_E0040]
 +
=====RBS=====
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[http://partsregistry.org/Part:BBa_B0034],[http://partsregistry.org/Part:BBa_B0031],[http://partsregistry.org/Part:BBa_B0032],[http://partsregistry.org/Part:BBa_B0033]
 +
=====Transcription Factors=====
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_C0012], [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0040], [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0051], [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0062], [http://partsregistry.org/wiki/index.php?title=Part:BBa_C0080]
 +
=====Terminators=====
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[http://partsregistry.org/wiki/index.php?title=Part:BBa_B1010], [http://partsregistry.org/wiki/index.php?title=Part:BBa_B1006],[http://partsregistry.org/wiki/index.php?title=Part:BBa_B1005],[http://partsregistry.org/wiki/index.php?title=Part:BBa_B1004],[http://partsregistry.org/wiki/index.php?title=Part:BBa_B1003],[http://partsregistry.org/wiki/index.php?title=Part:BBa_B1002]
 +
**NOTE: This activity features an "All questions answered" work environment.  Ask lots of questions.
 +
**HINT: Spend 2 minutes right now thinking about all the things that need to come together over the next 45' for your team to be successful.
 +
**QUESTION: How will you check that everybody on your team understands what is going on?
 +
{| cellspacing="2"
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|- valign="top"
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<div style="padding: .4em .9em .9em">
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<center>'''Homework'''</center>
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1. Think about how you can specify the parts, devices, architecture and operation of your team's system. <br>
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2. Have a great Spring Break.
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</div>
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|}

Current revision

Contents

Week 7 Tuesday

Getting Technical

Over the next few weeks we will spend nearly all of our lecture and studio time specifying these aspects of your project:

  • a high level system specification (i.e. a plain language overview of what your project will do)
  • a pseudo-code description of your system (i.e. a series of IF, THEN statements that program your cell)
  • a block diagram showing the system's architecture (i.e. a simple series of squares inside a cell to show functions and their connections)
  • a device/modules list
  • a timing diagram
  • a parts list

Be ready to revise what seemed like completed aspects of your project as you learn more about what's available and how things work. Design/revise/design/revise/design/revise....that's what the next few weeks will be all about...

Project Selection Status?

  • Brief report of each team's project selection status.

System Overview: Bacterial Buoy

  • You and your project team will describe the highlevel a system behavior for an engineered system, namely for the Melbourne 2007 iGEM "coliform" project.
    • The Melbourne team wanted to build a 3D, floating mass of bacteria that adhered to one another when the cells detected both blue and red light. In other words: at the intersection of an incoming red light beam and blue light beam, a solution of bacteria would clump and remain suspended in its growth media.
coliformers from Melbourne's iGEM 2007 team
coliformers from Melbourne's iGEM 2007 team
    • As a class we'll watch the first 5 minutes of the Melbourne team's iGEM presentation.
    • Next your project team should work out a high level overview of the system's behavior for the coliform project and some pseudo-code to program this behavior. Finally write on the white board a block diagram that connects the inputs and outputs for the cell. You should not spend more than 10 minutes on this activity. When you are done, delegate someone to explain what you've done as a team and what questions arose as you worked. Then you and your team can get right to work on the last thing planned for today's lecture.

System Overview: Your Idea Here

Finally, take the rest of today's lecture time to illustrate or specify the system overview of your team's project in plain language, in psuedocode, and in a block diagram. Some version of the system overview you generate today will be included in your Tech Spec Review.

Before you leave today

If there are outstanding issues related to the system overview for your project be sure everyone on your team knows how you'll try to solve the issue(s). Make a plan to come to studio tomorrow with materials for finishing the system overview and getting good work done on the device list and, perhaps the timing diagram.

Week 7 Studio

Are there tools or methods for breaking down a complicated problem into simpler parts?

  • Watch the Abstraction animation from BioBuilder
  • Walk through one sample abstraction hierarchy that may guide synthetic biology

This abstraction hierarchy is modified from one of Drew Endy's slides. It gives us a framework for how to intentionally engineer various aspects of biological systems.


Image:Hierarchy def.png Image:Abstraction redrawn.png

Abstraction in action: Systems to Devices

Three quick examples to put the abstraction hierarchy in action

First up: Arsenic detector

Recall the University of Edinburgh 2006 iGEM project that was described as an Arsenic Detector in the "abstraction" BioBuilder video. The system was designed to sense arsenic and result in a color. Two devices were used to build this system. The first device sensed arsenic and gave rise to a signal when arsenic was detected. And if the second device sensed the signal from the first device, then it gave rise to a color. The device-level system diagram is pretty straightforward, but makes clear that you could swap out the first device for a different sensor, as long as the output could still be interpreted by the second device. Similarly you could change the output from color to anything, as long as the input to that color-generating device was paired to the output of the arsenic sensor.

Next: Polkadorks

Let's try a more dynamic system. The 2004 IAP team wanted their engineered cells to "form, diffuse, and form again in random areas on the plate. Our system should thus form time-varying patterns based on local random time-varying symmetry breaking." Check out the Polkadorks animation.

  • As a class we'll
    • describe the system in plain language, then
    • list the devices needed to implement the system
  • Then as a team you'll have 10 minutes to draw a device-level system diagram.
  • Finally, as a class, we'll look at the timing diagram that the 2004 IAP team wrote.
timing diagram for the Polkadork's Ecolibrator project
You'll see that the devices (or the named connections between these devices) are listed on a y-axis and time is shown on an x-axis. The timing diagram indicates the timing for operation of each device or wire, including the persistence of each device's signal through time--shown as PS (protein synthesis) and PD (protein degradation). You and your team should take 10 minutes to make a timing diagram for EITHER
the Polkadork's devices that you have wired together
OR
the Eau D'coli project that we looked at on week 1.
Eau D'coli
Eau D'coli

You can keep a running list of any uncertainties. After 10 minutes of work, we'll have each team report back to the group to see how we did and what questions still remain.

And finally: Get busy!

Start applying these ideas to your team's project. You can work on a device list, a device-level system diagram and a timing diagram if you're ready.

Week 7 Thursday

We've been working hard this week to move between the System and Device levels of an abstraction hierarchy and today we'll drop down one more level to think about the parts that make up a device. The device you'll design is one we've talked about already, namely a bistable toggle, but first we'll look at a "classic" device that's a little simpler, namely an inverter, and the parts that make it up.

Challenge: Abstraction in action: Devices to Parts

After some discussion about what makes a "standard biological part," we'll turn our attention to building devices from parts.

Part 1: Four-part inverter

Recall the Eau d'coli project from the 2006 MIT iGEM team. Their goal was to replace the nasty smell of bacteria with wintergreen smell during log phase growth and banana smell during stationary phase growth. We talked about the engineering ideas behind the Eau d'Coli project way WAY back in Week 1. Today we'll focus in on one device within the system, namely the inverter that was used upstream of the wintergreen generating device (WGD), turning it off during stationary phase.
Image:EauD'coli abstraction.png
The abstraction hierarchy shown above zooms in on the inverter part that reverses the signal from the stationary phase promoter. This turns the wintergreen generating device off in stationary phase and on in log phase. The inverter part that's shown is a permutation of a natural gene that encodes the tetracycline repressor protein.
Image:TetRgene.png

Within this gene, we can define 4 "parts:" a promoter, a ribosome binding site (RBS), an open reading frame (ORF) that encodes the tet repressor protein, and a transcriptional terminator so the RNA polymerase transcribing the gene doesn't continue down to the next sequences downstream. The promoter is repressed by the tetR protein itself, allowing for a simple rearrangement that makes a useful inverter device. You can imagine a family of 4-part inverters that might be made for every repressor protein we know (lac repressor, lambda repressor, etc). For one more example, let's consider this inverter animation that shows us how (and why!) you might build an inverter from the arsenic-inducible operon. The number of inverters that can be built this way will be finite, however, and there will almost certainly be a time when a transcription-based device will not be optimal.

Part 2: Toggle-away

Working in your project teams, develop a design for a genetically encoded toggle switch that can be flipped with exogenous inputs and that maintains one state (or the other) even in the absence of the input. Your team's design should include

  • (a) a high level system diagram,
  • (b) a full list of devices and parts,
  • (c) timing diagram (time on the x-axis and devices on the y plus some indication of when their activities rise and fall, and
  • (d) a plan for testing the most important components of your toggle.
    You have 45 minutes.--so we've helped you get started by collecting some parts that you might find useful. These are parts that are documented, to different extents at the Registry of Standard Biological Parts.

Partial Parts List

You can use parts that are not on this list. Try to find them in the Registry (where you could get them for free) or if you want to get them from another source, please specify and note associated cost, e.g. synthesis cost is $1/base, licensing agreements, needed MTAs etc.

Promoters

[1], [2], [3],[4], [5], [6]

Reporters

[7], [8], [9],[10]

RBS

[11],[12],[13],[14]

Transcription Factors

[15], [16], [17], [18], [19]

Terminators

[20], [21],[22],[23],[24],[25]

    • NOTE: This activity features an "All questions answered" work environment. Ask lots of questions.
    • HINT: Spend 2 minutes right now thinking about all the things that need to come together over the next 45' for your team to be successful.
    • QUESTION: How will you check that everybody on your team understands what is going on?
Homework

1. Think about how you can specify the parts, devices, architecture and operation of your team's system.
2. Have a great Spring Break.

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