Stanford/BIOE44:Module 5:Day2

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M5: Day 2

Design Project Reports

Here's the suggested outline for completing your project reports. Each report should be written by you, but based on the work done with your individual project design partners. Please also see the "Polkadorks" project for ideas about how to best prepare various types of figures.

  1. Project Summary (1 page)
    • problem/opportunity (1 paragraph, what's the purpose of your system?)
    • summary of system (1 para., how does your system work?)
    • current status (1 para., how far did you get?)
  2. System Description (2 or more figures)
    • device level diagram of system (1 figure with caption)
    • parts level diagram of each device with captions (N figures with captions)
  3. New Parts (1 table and online entries, 1 or more parts)
    • summary table providing names, official part numbers, and short descriptions for all parts newly designed by you (1 table)
    • online entries in Registry of Standard Biological Parts; each part's entry must include an annotated sequence, short descriptions, long description, and references (N entries)
  4. Construction & Testing Plan
    • Diagrams of all plasmids needed to build or test your system; drawings should be electronic, show all basic parts, and use standard visual nomenclature/icons (1 or more figures)
    • Construction process for each plasmid: provide an outline of steps needed for its construction, at each step note which standard assembly method is being used or note and explain specific sites if a non-standard physical assembly method is to be used (1 or more outlines).
    • Experiments to be conducted in order to test functioning of relevant parts and devices comprising your system, including positive or negative controls (1 or more brief paragraphs, detailing individual tests or control experiments)
  5. Next Steps (1 page or less)
    • Description of immediate next steps (1 paragraph)

Handling your recently returned designer DNA

OK. Your newly synthesized designer DNA has just returned from DNA2.0. What do you need to do in order to get started using these new materials? Learning how to properly handle newly arrived genetic materials and engineered strains is a simple but essential skill to working in a lab. Read on!

Get ready by noting that the DNA arrived in two forms:

  • 2ug lyophilized plasmid DNA carrying your parts (i.e., naked DNA).
  • bacterial cells containing plasmids carrying your parts (i.e., cell culture as agarose stab).

The "naked" plasmid DNA is ready to use for digestion, PCR, and transformation. You'll need to resuspend the DNA in sterile distilled water. You should split the sample into aliquots so that you only use as much of the DNA as you need.

The cell culture must be streaked on an antibiotic plate (the plasmids carrying your DNA have a KanR marker). We'll eventually pick single colonies from these plates and make permanent -80C freezer stocks so that we have an archive of your new parts.

Plasmid Map

Click here for a DNA 2.0 map of the plasmid


Nothing to read here, just adding enough section on this page to activate the automatic table of contents.