BU06:Reading and Discussion 1

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We've decided to meet at 4:30 in Ingall's on Thursday, June 15

Work in groups to save time and learn from one another!

Don't skim these readings - go in as deep as you can. Do the suggested excercises, because they are exactly what we will be doing for prepraration and in lab. Visit the Registry. Look up concepts that you don't understand and really try to understand the biology. That said, the readings web-labs from a class last semester at MIT, and 1) the Registry has gotten a layover, so some of the instructions concerning it don't make complete sense (they are indicated below), 2) don't worry about actually writing the term paper. DO imagine what it would take to do the lab, because it's closely related to what we will actually be working on in the laboratory.

Don't forget that these will be a great preparation for James Brown's talks on Monday.

Also, remember that you can use the "printable version" link in the "Toolbox" to the left to get a printer-friendly version of this page.

Reading 0 - LuxR, LuxI and Cell-to-cell signaling
The elements of the signaling system described here are naturally how the Lux operon is controlled and have been used as the cornerstone of general signalling systems in many research projects. Additionally the system already has already been reincarnated as Parts in the Registry, as described. Check this page out.
Reading 1 - Tools for systems engingeering
  1. Register as a user on the Registry if you like, but DON'T SUBMIT ANY NEW PARTS!
  2. The Registry's organization has changed; to explore part types, click on the picture + link titled "Browse parts by type" on the Registry's main page.
  3. Questions #7 & #8 are optional as they have become more confusing since the registry was updated.
  4. The same goes for the Composite Parts section - instead, consider why BBa_F1610 might be an interesting part for our team.
  5. Design your own part under the heading Specify a protein generator..., and be prepared to continue developing it in the next reading. Specifically, design a part to express LuxI or LuxR. You may find parts that do this already exist in the Registry. If so, try and identify elements of their design (i.e. subparts) that might make them incompatible with the Lux operon part (i.e. LuxCDABE, but not LuxI or LuxR) our team wants to build, and either modify or keep the current design handy for the next reading.
  6. Try your best to understand the steps outlined in the experimental module, but don't stress.
  7. Absolutely consider each of the bullet points under For next time.
Reading 2 - Adventures in Synthetic Biology
  1. Good thing you already read this while doing Reading 1. For thoroughness (you are rockstar synthetic biologists, and rockstars are always thorough), reconsider how PoPS, the common signal carrier described in the comic, can be applied to the parts you see at the registry. Specifically, use "PoPS" to justify or criticize the following statements:
    1. "a terminator is analogous to a grounding device in electrical engineering"
    2. "BBa_I14032 works just like a battery"
    3. "the closest part I can find to work like a wire is an ORF"
Reading 3 - Basic bacterial photography: black and white
  1. Actually go to the NEB website and find out the information about the restriction enzymes. Record what you determine.
  2. As directed, make a step-by-step protocol to build your protein generator. If you have modified the design of an existing generator, understand that unlike LEGOs, composite parts cannot be "unsnapped" into their subparts (because no known restriction enzyme can cut at the mixed sites), so you'll have to rebuild the generator from it's constituent parts. This is exactly what we'll be doing in lab, so really try to do this and understand it. Work with someone else to save time, if you desire.
  3. Don't worry about Part 3: Black and white photography - we obviously haven't don't have access to the lab or materials.
  4. DO consider question 1. under For Next Time. Evil Co., I mean Codon Devices, specializes in synthesizing long stretches of DNA as cheaply as possible, and as technology progresses, some predict the entire multiday part construction process will become obsolete and replaced by companies like them. It is important context for understanding the present and future direction of Synthetic Biology.
Reading 4 - Advanced bacterial photography: 2 color
It's all a great read! Almost Done!


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