Synthetic Biology Seminar

Reengineering Life: Synthetic Biology Seminar

Fall, 2007 (Tuesdays: 1 - 4 pm, Dana 153)

A. Malcolm Campbell

Reengineering Life: Synthetic Biology Seminar
(jump to weekly schedule)

Prerequisites

Must have taken at least one of the following courses at Davidson: Genetics, Microbiology, Immunology, Genomics, Development, Biochemistry, or Bioinformatics. If you have not taken these biology courses (e.g., your are a younger Biology major, Chemistry, Math, or Physics majors, etc.) and are still interested, you can seek permission from the instructor.

Overview articles to see if you might like this course:

Dan Ferber. 2004. Microbes Made to Order. Science. Vol. 303: 158 - 161. (Good general overview)

Philip Ball. 2004. Starting from Scratch. Nature. Vol. 431: 624 - 626. (Good general overview)

Editors of Nature. 2004. Futures of Artificial Life. Nature. Vol. 431: 613. (Editorial that addresses ethical considerations)

A. Malcolm Campbell. 2005. Meeting Report: Synthetic Biology Jamboree for Undergraduates. Cell Biology Education. Vol. 4: 19 - 23. (Explanation of friendly competition for students who design and build synthetic biological devices)

Baker, et al. Engineering Life: Building a FAB for Biology. Scientific American. June 2006. 44-51.

2006 Scientist of the Year. Jay Keasling - synthetic biologist. Discover. December, 2006.

Course Goals

1) Learn the various areas within the new and rapidly evloving field of synthetic biology.

2) Produce an integrated understanding of life blending math, computer science, biology, and engineering.

3) Discover biological principles and characteristics revealed through experimentation.

Course Design

1) Read research papers and reviews that cover diverse areas within synthetic biology.

2) Students will lead 2 discussions based on papers they have chosen.

3) Other students will be assigned as support personnel to a primary presenter.

4) Other students will be designated as "official skeptics" for each paper.

5) Each student will pick an area of enquiry and write a paper describing the state of the field. This paper will be posted on the course wiki (see #7).

6) Entire class will invite to campus a guest speaker in the area of synthetic biology.

7) Entire class will produce a Synthetic Biology web site (using wiki) that summarizes the field and links to each of their papers.

Required Reading

Many papers from recent literature.

Tipping Point by Malcolm Gladwell.

Grading
Grades will be based on lead presentations (30%), supporting roles (15%), skeptic roles (15%), wiki site (10% - group grade), term paper (20%), and speaker visit (10%). Assignments turned in late will be docked 1 letter grade for each 24 hour period.

Logistical Details
Ceiling will be capped at 12 students. Order of student presentations will be organized the first day of class, as will assignments for inviting a speaker and producing a Synthetic Biology web site. Instructor will lead the first session with students serving in other roles.

Honor Code
Work presented by you (in oral or written format) is to be original work produced by you. It is considered an Honor Code violation if someone takes credit for work he or she does not deserve. Clearly, you will rely heavily on the written work of others, but you need to balance the number and amount of direct quotes with a synthesis of their work written in your own words. You should consult the Biology Department's plagiarism web site for additional help.

Schedule (tentative)

Week 1 (August 28)

1) Define synthetic biology *

2) Read one review paper for lay audiences (during class for 20 minutes and report back)

3) Discuss iGEM Jamboree 2007 – share some past projects from 2006

4) Find some newspaper stories (search for 15 minutes and report back)

5) Each person report on one lab doing synthetic biology – possible speakers

6) Discuss wiki project

* Good starting places: SyntheticBiology.Org , Implications and Applications of Synthetic Biology , iGEM Educational Resources.

Week 2 (September 4)

Campbell leads discussion of

1) A synthetic oscillatory network of transcriptional regulators
Michael B. Elowitz & Stanislas Leibler

Origins of Replication (The GFP reporter has ColE1 and the oscillator has pSC101.)

Fourier Analysis: "In signal processing and related fields, Fourier analysis is typically thought of as decomposing a signal into its component frequencies and their amplitudes." (from Wikipedia)

Hysteretic behavior: "Hysteresis is a property of systems (usually physical systems) that do not instantly follow the forces applied to them, but react slowly, or do not return completely to their original state: that is, systems whose states depend on their immediate history. For instance, if you push on a piece of putty it will assume a new shape, and when you remove your hand it will not return to its original shape, or at least not immediately and not entirely. The term derives from an ancient Greek word υστ?ρησις, meaning 'deficiency'. The term was coined by Sir James Alfred Ewing." ( from The Free Dictionary)

stochastic vs. chaotic: "Stochastic, from the Greek "stochos" or "aim, guess", means of, relating to, or characterized by conjecture and randomness. A stochastic process is one whose behavior is non-deterministic in that a state does not fully determine its next state." (from Wikipedia)
"In mathematics and physics, chaos theory describes the behavior of certain nonlinear dynamical systems that under specific conditions exhibit dynamics that are sensitive to initial conditions (popularly referred to as the butterfly effect). As a result of this sensitivity, the behavior of chaotic systems appears to be random, because of an exponential growth of errors in the initial conditions. This happens even though these systems are deterministic in the sense that their future dynamics are well defined by their initial conditions, and with no random elements involved. This behavior is known as deterministic chaos, or simply chaos.The butterfly effect is a phrase that encapsulates the more technical notion of sensitive dependence on initial conditions in chaos theory. Small variations of the initial condition of a nonlinear dynamical system may produce large variations in the long term behavior of the system. So this is sometimes presented as esoteric behavior, but can be exhibited by very simple systems: for example, a ball placed at the crest of a hill might roll into any of several valleys depending on slight differences in initial position.
The phrase refers to the idea that a butterfly's wings might create tiny changes in the atmosphere that ultimately cause a tornado to appear (or prevent a tornado from appearing). The flapping wing represents a small change in the initial condition of the system, which causes a chain of events leading to large-scale phenomena. Had the butterfly not flapped its wings, the trajectory of the system might have been vastly different." (from Wikipedia)

2) Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro et al.

Sweet Wormwood (wikipedia)

farnesyl pyrophosphate (NCBI PubChem)

Asteraceae (wikipedia)

CYP71AV1 (NCBI)

Competing Financial Interests Declaration: J.D.K. is a founder of Amyris Biotechnologies, a company that may eventually use the genes and yeast strains described in this paper for the production of artemisinin. However, neither Amyris Biotechnologies nor the University of California will make any profit from the production and sale of the antimalarial drug artemisinin.

3) Discuss semester assignments and possible speaker

4) How to play each of the roles assigned

5) Assign roles and weeks. Discuss appropriate papers.

Week 3 (September 11)

Presentation by Erin Zwack

Enginnered riboregulators enable post-transcriptional control of gene regulation
Farren Isaacs, et al. 2004.

Official Supporter	Designated Skeptic
Danielle	Laura

YUNR (pyrimidine - uracil - nucleotide - purine) sequence: The IUPAC code for a four nucleotide sequence that has C or U + U + C or U or G or A + G or A.
Dynamic range is a term used frequently in numerous fields to describe the ratio between the smallest and largest possible values of a changeable quantity." (wikipedia)
RNA secondary structure - Examples of bulges and internal loops
(from http://www.biomedcentral.com/1471-2105/8/34)
Competing Financial Interests Declaration: The authors declare a pending patent application whose value may be affected by publication of this paper.

2) Status of letter

3) questions about roles and papers; project clarification

Week 4 (September 18)

Presentation by Hunter Stone

PPT file for assistance

Official Supporter	Designated Skeptic
Samantha	Emma

1) Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production
Hal Alper et al., 2006

gTME method defined
Microarray Method (animation)
Hierarchical clustering (1st PP gives a brief overview of the method and the article explains statistically a couple of methods of creating subsets)
Lycopene biosynethis pathway
Physician's desk reference article on the make-up and benefits of lycopene
A more skeptical acessment of the health benefits of lycopene by the Mayo Clinic

2) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets.
Hal Alper et al., 2005.

Transposons: transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called transposition. In the process, they can cause mutations and change the amount of DNA in the genome. Transposons are also called "jumping genes", and are examples of mobile genetic elements. Discovered by Barbara McClintock early in her career[1], the topic went on to be a Nobel prize winning work in 1983. There are a variety of mobile genetic elements, and they can be grouped based on their mechanism of transposition. Class I mobile genetic elements, or retrotransposons, move in the genome by being transcribed to RNA and then back to DNA by reverse transcriptase, while class II mobile genetic elements move directly from one position to another within the genome using a transposase to "cut and paste" them within the genome. Transposons are very useful to researchers as a means to alter DNA inside of a living organism. Transposons make up a large fraction of genome sizes which is evident through the C-values of eukaryotic species. (wikipedia)
Directed evolution is a method used in protein engineering to harness the power of Darwinian selection to evolve proteins or RNA with desirable properties not found in nature. A typical directed evolution experiment involves three steps:
1. Diversification: The gene encoding the protein of interest is mutated and/or recombined at random to create a large library of gene variants. Techniques commonly used in this step are error-prone PCR and DNA shuffling.
2. Selection: The library is tested for the presence of mutants (variants) possessing the desired property using a screen or selection. Screens enable the researcher to identify and isolate high-performing mutants by hand, while selections automatically eliminate all nonfunctional mutants.
3. Amplification: The variants identified in the selection or screen are replicated manyfold, enabling researchers to sequence their DNA in order to understand what mutations have occurred.

Together, these three steps are termed a "round" of directed evolution. Most experiments will perform more than one round. In these experiments, the "winners" of the previous round are diversified in the next round to create a new library. At the end of the experiment, all evolved protein or RNA mutants are characterized using biochemical methods. (wikipedia)

Week 5 (September 25)

Presentation by Mike Waters

Official Supporter	Designated Skeptic
Erin	Will

Wiki Links to Supplement Readings

1) Tuning genetic control through promoter engineering
Hal Alper et al., 2005

SOM

List of primers
Supporting Figure 5
Fig. 5. The functional promoter library was analyzed by using flow cytometry. The relative average geometric mean fluorescence of the members of the library is illustrated above and exhibited a nearly 3-log fold range after 14 h in a minimal media with 0.1% casamino acids.
Supporting Figure 6
Fig. 6. Above are representative light-field (right) and false-color dark-field (Left) photomicrographs of clones with highly heterogeneous expression of GFP. These promoters were not further analyzed and are not included in the functional promoter library.
Supporting Figure 7
Fig. 7. In contrast, representative clones chosen for further analysis had much more homogenous distributions of fluorescence. Below, two representative sets of photomicrographs are shown. The top two images correspond to a promoter with a relative promoter strength metric of 0.124 and the bottom two to 0.417.

2) Combinatorial promoter design for engineering noisy gene expression
Kevin Murphy et al., 2007

SOM