2020(S11) Lecture:week 1

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=<center>Week 1 Tuesday </center>=
=<center>Week 1 Tuesday </center>=
-
==<font color = blue> GOT DNA? </font color>==
+
==<font color = blue> Got DNA? </font color>==
After a short introduction to the who/what/why for this class, we'll start handling the programming material that's at our fingertips...in our fingertips, even! As you work through this DNA isolation protocol below, be mindful of your questions and your own reactions to this activity. Is this the first time you've ever handled a lump of DNA? How hard is it to isolate DNA, both technically speaking and in terms of the needed equipment? What surprised you? What did you learn and what questions do you still have? What could you do next with this material you've isolated?  
After a short introduction to the who/what/why for this class, we'll start handling the programming material that's at our fingertips...in our fingertips, even! As you work through this DNA isolation protocol below, be mindful of your questions and your own reactions to this activity. Is this the first time you've ever handled a lump of DNA? How hard is it to isolate DNA, both technically speaking and in terms of the needed equipment? What surprised you? What did you learn and what questions do you still have? What could you do next with this material you've isolated?  
===DNA from a Strawberry===
===DNA from a Strawberry===
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=<center>Week 1 Studio</center>=
=<center>Week 1 Studio</center>=
==<font color = blue>Wednesday matinee</font color>==
==<font color = blue>Wednesday matinee</font color>==
-
'''Instructions:''' Today you will have the opportunity to watch a video showcasing completed [http://ung.igem.org/Results iGEM projects]. "iGEM" stands for the "international Genetically Engineered Machines" competition. It is a summer-long opportunity for teams of students working at colleges and universities around the world to design and build genetically engineered machines, many of which use standard biological parts from the [http://parts.mit.edu Registry of Standard Biological Parts.] The video will orient you to the kinds of accomplishments realized in a summer by teams of undergraduates and their advisers.  
+
'''Instructions:''' Today you will have the opportunity to watch a video showcasing completed [http://2010.igem.org/Main_Page iGEM projects]. "iGEM" stands for the "international Genetically Engineered Machines" competition. It is a summer-long opportunity for teams of students working at colleges and universities around the world to design and build genetically engineered machines, many of which use standard biological parts from the [http://parts.mit.edu Registry of Standard Biological Parts.] The video will orient you to the kinds of accomplishments realized in a summer by teams of undergraduates and their advisers.  
===Our feature presentation===
===Our feature presentation===
[[Image:EauD'coli.jpg|thumb|left| Eau D'coli]] Our featured presentation will emphasize some of the "engineering" that can be accomplished in a summer by a talented group of undergrads much like yourselves. We'll listen to  
[[Image:EauD'coli.jpg|thumb|left| Eau D'coli]] Our featured presentation will emphasize some of the "engineering" that can be accomplished in a summer by a talented group of undergrads much like yourselves. We'll listen to  
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Their project will allow us to focus on
Their project will allow us to focus on
** '''programming genetic logic, growth phases of bacterial cultures, ethical questions of human experimentation'''
** '''programming genetic logic, growth phases of bacterial cultures, ethical questions of human experimentation'''
-
***our ppt review of these processes is [[Media:20.20(S09) review EauD'coli.ppt| here]]<br><br>
+
***our ppt review of these processes is [[Media:20.20(S11) review EauD'coli.ppt| here]]<br><br>
 +
 
===After the presentation===
===After the presentation===
You will have 10 minutes to gather with your fellow moviegoers and discuss what you saw, using these "iGEM review questions" as a guide for your conversations:
You will have 10 minutes to gather with your fellow moviegoers and discuss what you saw, using these "iGEM review questions" as a guide for your conversations:
Line 53: Line 54:
# are there aspects of the work that are unclear to you?
# are there aspects of the work that are unclear to you?
# if you could ask this team one question what would it be?
# if you could ask this team one question what would it be?
 +
===At 3PM we'll have a short presentation from MIT' EHS===
 +
This will help us prepare for tomorrow's hands-on activity!
===Our second feature===
===Our second feature===
-
There have been many wonderful projects from teams over the years, but to narrow down the number of possible choices, let's look at the MIT team projects. As a class we'll choose to watch and discuss one more video,
+
There have been many wonderful projects from teams over the years, but to narrow down the number of possible choices, let's look at the projects from recent MIT teams. As a class we'll choose one of the following videos to watch and discuss:
-
*MIT 2007
+
*[http://2008.igem.org/Team:MIT MIT 2008]: Biogurt, fighting tooth decay since 2008,[http://2008.igem.org/files/video/MIT.mp4 presentation video]
-
*[http://2008.igem.org/Team:MIT MIT 2008]
+
*[http://2009.igem.org/Team:MIT MIT 2009]: Phycocyanobilibuddies, photolocalizer project,[http://2009.igem.org/files/video/MIT.mp4 presentation video]
-
*[http://2009.igem.org/Team:MIT MIT 2009]
+
*[http://2010.igem.org/Team:MIT MIT 2010]:Programmable, self-constructing biomaterials, [http://2010.igem.org/files/video/MIT.mp4 presentation video]
-
*[http://2010.igem.org/Team:MIT MIT 2010]
+
===After the presentation===
-
As homework you were asked to draft a letter describing a real world problem or opportunity you have inherited that could be addressed in the near term. You should discuss these letters at your team tables and make some notes about them on the white boards. For example,
+
Take time again with your fellow movie goers to discuss what you saw
-
*who were they addressed to?
+
# what was the problem this team chose to address and why?
-
*how many problems/opportunities did each letter address?
+
# is this an important problem and why or why not?
-
*what areas were tackled?
+
# did they succeed in part or in total?
-
*how many also proposed solutions to these problems?
+
# are there aspects of the work that are unclear to you?
-
After about an hour of discussion at your tables, you'll have a chance to hear from the other groups. Be sure to take notes on your letter about any new ideas, clarifications, or thoughts you have from the discussion. You will turn in a revised letter before tomorrow. (and note that if you've finished your discussion about the letters early you can get to work on the homework below). 
+
# if you could ask this team one question what would it be?
 +
===After the show===
 +
Before you leave today, consider the topic areas that are prized by iGEM judges. In 2010, prize areas were:
 +
{| border="1"
 +
|-
 +
| '''Area'''
 +
| '''Challenge'''
 +
|-
 +
|Food or Energy
 +
|People need to eat. Planes, trains, and automobiles need to eat too. Can biotechnology be responsibly used to produce food or energy without causing widespread shortages of either, and without harming the environment that future generations will inherit?
 +
|-
 +
|Environment
 +
|The quality of the air, water, and land, both on Earth and other heavenly bodies, limits the happiness of humans and other creatures. Can biotechnology be used to help clean the air, provide fresh drinking water, restore or enhance soil quality, terraform a near-Earth asteroid, or protect, preserve, or enhance natural biological diversity?
 +
|-
 +
|Health or Medicine
 +
|Many health and medical problems might best be addressed by improved biological technologies. What can synthetic biology do?
 +
|-
 +
|Manufacturing
 +
|Have you ever heard of nanotechnology? Well, biology is a nanotechnology that already exists, and that actually works. The ribosome is a programmable nanoassembler embedded within a reproducing machine. Forget grey goo, we've got green goo, and it has already taken over the planet! Thus, could we responsibly use biology to manufacture useful products, from the nanoscale (atoms) to the decascale (buildings and bridges). What can biology be programmed to manufacture?
 +
|-
 +
|New Application Area
 +
|We're guessing that you have great ideas that nobody has ever thought about, or if they have they forgot to tell somebody else. Can you imagine an entirely new application area for biological technology? Go for it. We'll celebrate you in front of the entire world
 +
|-
 +
|Foundational Advance
 +
|Modern biotechnology dates back to the invention of recombinant DNA technology, which lets people cut and paste pre-existing fragments of genetic material. That was only 35 years ago. In other words, biotechnology is a young adult, just entering its prime years. One thing that desperately needs doing is to develop improved tools and technologies that help to make the entire process of engineering biology easier. What foundational advance can you contribute that will take everybody's work forward?
 +
|-
 +
|Information Processing
 +
|
 +
|} 
-
*The MIT team made some "on the fly" adjustments to their project based on early data collected. For instance they decided to control the banana smell for expression in stationary phase since the smell overwhelmed the wintergreen. Could they have used a computer simulation of their system to make this decision? Why or why not?
+
===<center>BEFORE YOU LEAVE TODAY</center>===
-
When you are finished, please upload your assignment to your "Personal Design Portfolio" in the [https://stellar.mit.edu/S/course/20/sp09/20.020/homework/index.html homework dropbox.], calling your assignment: FirstInitial_LastName_PDP_1.doc, for example: <font color = red> B_Obama_PDP_1.doc </font color><br>
+
Put your name on a piece of paper or index card and list your top 3 areas of interest. Hand in this list before you leave. <br>This term you'll be on a team of 20.020 students and work with 20.385 mentors to design and specify an iGEM-like system in one of these areas. You won't get to build it unless you sign on for the iGEM summer, but many 20.020 students have gone on to do just that...
-
 
+
{| cellspacing="2"  
{| cellspacing="2"  
|- valign="top"
|- valign="top"
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<div style="padding: .4em .9em .9em">
<div style="padding: .4em .9em .9em">
<center>'''HOMEWORK'''</center>
<center>'''HOMEWORK'''</center>
 +
Next time we will work with the banana-smell generating system. In advance of this activity, please
 +
* read this [[Media:BuildingLife Nat10.pdf| 2 pg review article]] that explicitly addresses the interplay between engineering and science
 +
* review the set up of tomorrow's challenge by looking at the BioBuilder [http://www.biobuilder.org/activities/bioprimer-1.html BioPrimer #1].
 +
* If you need a refresher on some of the terminology (inverter?? stationary phase promoter??), then you can watch the animations that are linked to the BioPrimer from the [http://www.biobuilder.org/animations/ BioBuilder website.] 
</div>
</div>
|}
|}
=<center>Week 1 Thursday</center>=
=<center>Week 1 Thursday</center>=
-
==<font color = blue> </font color>==
+
==<font color = blue> Eau that smell!</font color>==
-
==<font color = blue>Why are we doing this?</font color>==
+
Today you will compare 2 competing designs that are based on the Eau d'coli project you learned about last time.
 +
[[Image:Copy of BBa J45200.png| thumb| left| 300px| Eau that smell!]]
 +
======Acknowledgments: A longer version of this activity is housed at [http://openwetware.org/wiki/BioBuilding:_Synthetic_Biology_for_Students:_Lab_1 BioBuilder.org]. It was developed with materials and guidance from the MIT 2006 iGEM team, as well as technical insights and help from Ginkgo Bioworks======
 +
===Procedure===
 +
#Begin by reviewing BioPrimer 1. Is it clear the differences are between the 4 strains of bacteria well be studying?
 +
#Next we'll watch the animation about cell growth and division. Is it clear how log, lag, and stationary phase differ? Is it clear how you'd know what phase of growth the cells are in?
 +
#Finally, you'll work in small groups to compare the turbidity and the banana-smell intensity for the four strains at each stage of growth. Give each strain a smell value and a density value.
 +
#When you are done collecting your data, please wash your hands.
 +
#Next, upload your data to the [http://www.biobuilder.org/submit-your-data/ BioBuilder website]
 +
#Before you leave today, we'll consider these questions:
 +
**Were we able to measure the population growth?
 +
**Were we able to smell bananas?
 +
**Did each device produce the same results?
 +
**Did the genetic systems affect the growth curve of the bacteria? Explain your answers.
 +
**How confident are you in the results?
 +
**Are you equally confident in both the growth data and the smell data?
 +
**Is using smell to measure the banana smell valid? Why or why not?
 +
**What methods did you use to try to increase your confidence in the results?
 +
**How might we try to change this system so that we can quantify the banana smell? Would we be better off using a different kind of signal? If so, what would you suggest?
 +
**If you could construct a different genetic system, what might you construct? What would you need to do? 
 +
{| cellspacing="2"
 +
|- valign="top"
 +
|width="670px" class="MainPageBG" style="border: 1px solid #336600; color: #000; background-color: #FFFFFF"|
 +
<center>'''Why are we doing this??'''</center>
 +
<div style="padding: .4em .9em .9em">
 +
You've now had some first hand experience with an engineered biological system. We'll return to this experiment a number of times during the term for different reasons but it's hoped that this first week has given you a taste (not literally!) of the kinds of creative solutions that are possible in biological engineering design.
 +
</div>
 +
|}

Current revision

Contents

Week 1 Tuesday

Got DNA?

After a short introduction to the who/what/why for this class, we'll start handling the programming material that's at our fingertips...in our fingertips, even! As you work through this DNA isolation protocol below, be mindful of your questions and your own reactions to this activity. Is this the first time you've ever handled a lump of DNA? How hard is it to isolate DNA, both technically speaking and in terms of the needed equipment? What surprised you? What did you learn and what questions do you still have? What could you do next with this material you've isolated?

DNA from a Strawberry

  1. Pair up and pick up a ziplock baggie with a strawberry in it. IF YOU ARE ALLERGIC TO STRAWBERRIES, please don't do this part.
  2. Push the air out of the baggie as best you can and reseal it.
  3. Being careful not to break the baggie, mash the strawberry with your fingers for ~2 minutes.
  4. Using a medicine cup to measure it, add 10 ml of extraction buffer to the baggie. Extraction buffer is a mixture of 20 ml dish soap, 1.5 tsp of table salt, a sprinkle of meat tenderizer, and 380 ml of spring water.
  5. Mash the strawberry for one minute more.
  6. Place a funnel over a 3oz. bathroom cup.
  7. Fold a piece of cheesecloth into a ~4 inch square and place it in the funnel.
  8. Pour the strawberry mush into the funnel and allow gravity to do its work. You'll throw away the strawberry mush and cheesecloth into the trash, and return the funnel to the kit.
  9. Carefully pour 2 ml of the filtered strawberry juice into a clean, conical tube, using the markings on the side of the tube to know how much to transfer.
  10. Hold the tube at an angle and, using an eye-dropper, carefully DRIBBLE a 5 ml layer of cold 95% Ethanol or 70% isopropanol (your choice) onto the strawberry goop. DO NOT MIX the layers.
  11. Now watch...after a few minutes you should start to see some bubbles, then some white stringy stuff, which is the DNA.
  12. There will be coffee stirrers to remove the DNA from the tube if you'd like to do that. The DNA is best removed by "spooling"--i.e. winding the DNA around the stick with a gentle twirl of stick.
Why are we doing this??

Let's return to the questions from the start of the day:

  • Was this the first time you've ever handled a lump of DNA?
    • Is it what you thought it would look like?
    • Is there more or less than you thought there'd be?
  • How do you know it's DNA?
  • How hard was it to isolate DNA,
    • technically speaking?
    • needed equipment?
  • What surprised you?
  • What did you learn and what questions do you now have?
    • Where did you finally put the DNA you isolated?
    • What did you do with it after you isolated it?
    • Is it OK to just throw it away?

Week 1 Studio

Wednesday matinee

Instructions: Today you will have the opportunity to watch a video showcasing completed iGEM projects. "iGEM" stands for the "international Genetically Engineered Machines" competition. It is a summer-long opportunity for teams of students working at colleges and universities around the world to design and build genetically engineered machines, many of which use standard biological parts from the Registry of Standard Biological Parts. The video will orient you to the kinds of accomplishments realized in a summer by teams of undergraduates and their advisers.

Our feature presentation

Eau D'coli
Eau D'coli
Our featured presentation will emphasize some of the "engineering" that can be accomplished in a summer by a talented group of undergrads much like yourselves. We'll listen to

Their project will allow us to focus on

    • programming genetic logic, growth phases of bacterial cultures, ethical questions of human experimentation
      • our ppt review of these processes is here

After the presentation

You will have 10 minutes to gather with your fellow moviegoers and discuss what you saw, using these "iGEM review questions" as a guide for your conversations:

  1. what was the problem this team chose to address and why?
  2. is this an important problem and why or why not?
  3. did they succeed in part or in total?
  4. are there aspects of the work that are unclear to you?
  5. if you could ask this team one question what would it be?

At 3PM we'll have a short presentation from MIT' EHS

This will help us prepare for tomorrow's hands-on activity!

Our second feature

There have been many wonderful projects from teams over the years, but to narrow down the number of possible choices, let's look at the projects from recent MIT teams. As a class we'll choose one of the following videos to watch and discuss:

After the presentation

Take time again with your fellow movie goers to discuss what you saw

  1. what was the problem this team chose to address and why?
  2. is this an important problem and why or why not?
  3. did they succeed in part or in total?
  4. are there aspects of the work that are unclear to you?
  5. if you could ask this team one question what would it be?

After the show

Before you leave today, consider the topic areas that are prized by iGEM judges. In 2010, prize areas were:

Area Challenge
Food or Energy People need to eat. Planes, trains, and automobiles need to eat too. Can biotechnology be responsibly used to produce food or energy without causing widespread shortages of either, and without harming the environment that future generations will inherit?
Environment The quality of the air, water, and land, both on Earth and other heavenly bodies, limits the happiness of humans and other creatures. Can biotechnology be used to help clean the air, provide fresh drinking water, restore or enhance soil quality, terraform a near-Earth asteroid, or protect, preserve, or enhance natural biological diversity?
Health or Medicine Many health and medical problems might best be addressed by improved biological technologies. What can synthetic biology do?
Manufacturing Have you ever heard of nanotechnology? Well, biology is a nanotechnology that already exists, and that actually works. The ribosome is a programmable nanoassembler embedded within a reproducing machine. Forget grey goo, we've got green goo, and it has already taken over the planet! Thus, could we responsibly use biology to manufacture useful products, from the nanoscale (atoms) to the decascale (buildings and bridges). What can biology be programmed to manufacture?
New Application Area We're guessing that you have great ideas that nobody has ever thought about, or if they have they forgot to tell somebody else. Can you imagine an entirely new application area for biological technology? Go for it. We'll celebrate you in front of the entire world
Foundational Advance Modern biotechnology dates back to the invention of recombinant DNA technology, which lets people cut and paste pre-existing fragments of genetic material. That was only 35 years ago. In other words, biotechnology is a young adult, just entering its prime years. One thing that desperately needs doing is to develop improved tools and technologies that help to make the entire process of engineering biology easier. What foundational advance can you contribute that will take everybody's work forward?
Information Processing

BEFORE YOU LEAVE TODAY

Put your name on a piece of paper or index card and list your top 3 areas of interest. Hand in this list before you leave.
This term you'll be on a team of 20.020 students and work with 20.385 mentors to design and specify an iGEM-like system in one of these areas. You won't get to build it unless you sign on for the iGEM summer, but many 20.020 students have gone on to do just that...

HOMEWORK

Next time we will work with the banana-smell generating system. In advance of this activity, please

  • read this 2 pg review article that explicitly addresses the interplay between engineering and science
  • review the set up of tomorrow's challenge by looking at the BioBuilder BioPrimer #1.
  • If you need a refresher on some of the terminology (inverter?? stationary phase promoter??), then you can watch the animations that are linked to the BioPrimer from the BioBuilder website.

Week 1 Thursday

Eau that smell!

Today you will compare 2 competing designs that are based on the Eau d'coli project you learned about last time.

Eau that smell!
Eau that smell!
Acknowledgments: A longer version of this activity is housed at BioBuilder.org. It was developed with materials and guidance from the MIT 2006 iGEM team, as well as technical insights and help from Ginkgo Bioworks

Procedure

  1. Begin by reviewing BioPrimer 1. Is it clear the differences are between the 4 strains of bacteria well be studying?
  2. Next we'll watch the animation about cell growth and division. Is it clear how log, lag, and stationary phase differ? Is it clear how you'd know what phase of growth the cells are in?
  3. Finally, you'll work in small groups to compare the turbidity and the banana-smell intensity for the four strains at each stage of growth. Give each strain a smell value and a density value.
  4. When you are done collecting your data, please wash your hands.
  5. Next, upload your data to the BioBuilder website
  6. Before you leave today, we'll consider these questions:
    • Were we able to measure the population growth?
    • Were we able to smell bananas?
    • Did each device produce the same results?
    • Did the genetic systems affect the growth curve of the bacteria? Explain your answers.
    • How confident are you in the results?
    • Are you equally confident in both the growth data and the smell data?
    • Is using smell to measure the banana smell valid? Why or why not?
    • What methods did you use to try to increase your confidence in the results?
    • How might we try to change this system so that we can quantify the banana smell? Would we be better off using a different kind of signal? If so, what would you suggest?
    • If you could construct a different genetic system, what might you construct? What would you need to do?
Why are we doing this??

You've now had some first hand experience with an engineered biological system. We'll return to this experiment a number of times during the term for different reasons but it's hoped that this first week has given you a taste (not literally!) of the kinds of creative solutions that are possible in biological engineering design.

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