It's kind of fun to do the impossible.
BIOC 313 Introductory Synthetic Biology
Synthetic Biology in Complex Settings
Time and Location: Scheduled meetings
on Monday and Wednesday in the 2nd half
of fall semester from 1 - 5 p.m. in ABL B03 and B06 (Biology basement classroom and labs); self-scheduled at other times
Oct. 12: Workshop on Journal Article Presentations, Center for Written, Oral, and Visual Communication; framework for course
Oct. 17: Day 1 DNA manipulation
Oct. 19: Day 2 DNA verification and DNA
Oct. 24: Day 3 DNA verification
Oct. 26; Nov. 2, 7, and 9: DNA assembly of own project
Nov. 14 and 16: Testing of DNA
BIOS/BIOC 211: Intermediate Experimental Biosciences or permission
Registration: You may register on Esther. Enrollment
is limited to 18 students.
General Course Description: This course is intended to introduce students to the emerging field of synthetic biology. Students will present current literature that focuses on genetic parts that are currently used to program bacteria (sensors, logic functions, and actuators) and bacteria that have been successfully programmed to exhibit novel functions. The laboratory will expose students to molecular biological procedures that are routinely used in building and characterizing synthetic genetic circuits. Teams of students will choose, design, and test projects using synthetic biology in complex settings.
In preparation for class discussions and student presentations,
everyone is expected to read appropriate background material
and assigned paper(s) (available
in OWL-Space Resources). See How
to Read a Scientific Article (in OWL-Space Resources) for tips on reading
research papers. Additionally, you
must come to lab prepared--this requires
you to READ the
experimental protocols BEFORE coming
to lab, not just print a copy and bring it with you.
AIMS of course:
There are three threads in this lab course:
- Literature: you will read and present classic journal articles in synthetic biology as well as current articles with approaches and strategies for complex settings
- Basic Methods: in the first three lab sessions, you will gain experience with fundamental methods of DNA assembly
- Creative Outlet:
you will work as a team to design, assemble, and test a microbial biosensor
I) Fundamental DNA Assembly (purification
of plasmid DNA, DNA fragmentation, size analysis of DNA fragments,
classic assembly of DNA fragments)
Build a simple genetic circuit using
the following BioBricks and BioBrick
II) DNA Assembly of Project DNA
negative (part = 54 bp) [in pSB1A2, AmpR]
reporter with strong RBS (part = 878 bp) [in pSB1A2, AmpR]
- Day 1: isolate plasmid DNA, digest BioBricks,
- Day 2: analyze DNA fragments on agarose
gel, purify DNA fragments from gel, ligate insert and vector,
transform bacteria with ligated DNA
- Day 3: PCR screen bacterial colonies
for those with desired inserts and analyze PCR products on agarose
III) Testing of Assembled DNA
- Lab Days 4-6: procedures to be determined
Presentation: You and a partner will give a 20 minute presentation on a selected scientific article in synthetic biology.
- Lab Days 7-8 and beyond: procedures to be determined
Team Project: On the first day of class, teams will start working on a "Reflection on the synthetic biology challenge." The following week, teams will 1) pick a unique set of genes and design PCR strategies and 2) submit a one page proposal (TEAM document) about their project. After the lab ends, you will submit a short paper in the format of a RESEARCH PROGRESS REPORT (individual effort).
Assignments & Grading: Your
final grade will be determined from your lab notebook, lab performance and class participation, Journal Club
Presentation,and Project Proposal and Paper.
We would like to thank New England Biolabs for their generous support of this laboratory course
This project was supported in part by a grant to Rice University from the Howard Hughes Medical Institute through the Precollege and Undergraduate Science Education Program.
and Intended Use
Created by B. Beason (email@example.com),
Rice University, 10 January 2008
Updated 4 October 2016