Laboratory Fundamentals of Synthetic Biology

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Revision as of 22:08, 2 March 2007

Contents

Syllabus

Class Format

The Class will meet twice a week, one 2 hour classroom session, and one 3 hour lab session. Problem sets will be assigned weekly for the first eight weeks. A midterm exam will cover the classroom material and the first several weeks of lab instruction. Lab exercises will be assigned, and cover the lab techniques taught. A small project to assemble and measure a BioBrick system follows the lab instruction. Finally, students will design, build and analyze their own BioBrick system.

Grades

The final grade will be as follows: 20% Problem Sets 30% Midterm Exam 20% Lab Evaluations 30% Final Project

Schedule

  • Introduction - Synthetic Biology: History, current applications and future directions

Assignments: Endy Article and Comic Strip

  • The Biology (4 sessions)
    • Cells, DNA, RNA and Protein
    • DNA - information encoding, structure, sequencing and synthesis
    • RNA - encoding, structure, function (RNA Enzymes, RNA Aptamers)
    • Proteins - Crystallography, functions, scaffolds

Introductory packet about DNA, RNA, Protein. Ron Weiss paper on Vibrio Fischerii quorum sensing (decompose into parts). Artemisnin overview article. Hellinga Paper on protein sensors.

  • Foundational Technologies (4 sessions)
    • BioBricks - Definition of a BioBrick, black-box encapsulation, PoPs and RiPs
    • The Registry of Standard Biological Parts
    • Analytical -omics tools - Proteomics, Genomics, Metabolomics
    • Simulation tools - stochastic simulators, BioJADE, matlab

Create a biobrick out of a sequence (force them to re-optimize a coding region into e. coli and remove a biobrick incompatibility). An introductory packet on PCR and cloning.


  • Basic Lab Techniques (8 sessions)
    • Introductory Lab - PCR Primer Design
    • Lab 2 - PCR, Restriction Digestion, Gel electrophoresis
    • Lab 3 - Insert Preparation, Gel Extraction, Ligation and Transformation
  • BioBrick Discovery and Creation Technique



    • Cloning Basics - restriction enzymes, running analytical gels, QiaPreps
    • Sterile Technique - autoclaving, flaming technique,
    • Competent Cells - Production & QC
    • PCR - About PCR, Polymerases, Primer design
    • Screening - Antibotics, Blue/White screening
    • Growth Curves
    • Metabolite measurement
    • Standardized Measurements for BioBricks
  • Trial Project (2 weeks)
    • Assembly and Measurement of a BioBrick system
  • Final Project
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