Category: Organisms

Modifying Yeast for Drug Production in Beer – BioBeer

Posted by – November 13, 2008

How synthetic biology gets done in iGEM competition:

Jam08 Live: Rice – BioBeer from mac cowell on Vimeo. [1]

Before getting too excited though, keep in mind:

  • The experiment hasn’t been verified to work. The yeast “seems to be consuming some intermediate products” however the drug production hasn’t been verified.
  • The benefits of resveritrol may be dramatically overstated. It may take very large quantities of resveritrol to have any health benefits [2].
  • The public-at-large has responded very enthusiastically to this idea (same with the modified yeast for Bio Yogurt) — which may signal the tempering of the typical U.S. “No GMO!” paranoia. Random people have proclaimed: “I want to drink this beer!”, casting aside concerns of consuming genetic engineered products.
  • The most remarkable health benefits in both wine and beer may be due to the alcohol (reducing psychological stress); it seems no one (?) has a good study on this because no one studies non-alcoholic wine or non-alcoholic beer.
[1] Jam08 Live: Rice – BioBeer from mac cowell on Vimeo. Filmed by
[2] Beer: The Best Beverage in the World. Charlie Bamforth, Ph.D., D.Sc. of University of California, Davis, at PARC Forum. March 22, 2007. Watch the Video as wmv  Charlie Bamforth is Fellow of the Institute of Brewing & Distilling and Fellow of the Institute of Biology, Editor in Chief of the Journal of the American Society of Brewing Chemists and has published innumerable papers, articles and books on beer and brewing.

Creating beneficial biological systems without cells

Posted by – October 19, 2008

In general terms, synthetic biology brings to mind using “BioBricks”, which are engineered genetic parts used to modify an organism, such as bacteria or yeast. The idea is to modify the organism to work to our advantage; for example, to eat sugar and produce biofuel — a pretty good tradeoff, considering the cost of gasoline and the cost of sugar. This is a top-down methodology: take an existing organism, modify it’s DNA, measure it’s behavior, and repeat the modification process until the desired “behavior” is measured.

Some synthetic biology research, however, doesn’t use traditional organisms at all. In fact, doesn’t even use “cells”. This might be called cell-free synthetic biology, or in vitro synthetic biology. This is a bottom-up approach: create the desired “behavior” from scratch. The idea has existed for some time; a good summary is Synthetic biology projects in vitro, Anthony C. Forster and George M. Church, Genome Res. 17:1-6, 2007: “Many biopolymer syntheses are already better scaled up in cell-free systems, such as linear DNAs by oligo synthesis and PCR, unmodified RNAs by in vitro transcription, and peptide libraries by in vitro transcription/translation. And engineering flexibility is much greater in vitro, unshackled from cellular viability, complexity, and walls.”

Synthetic Life

“How can I hack biology without using cellular organisms?”, you’re probably asking.

One proposed method for creating such cell-free synthetic biology projects (meaning: no bacteria, no yeast…  just… chemistry) is An integrated cell-free metabolic platform for protein production and synthetic biology, Michael C Jewett, Kara A Calhoun, Alexei Voloshin, Jessica J Wuu & James R Swartz, Molecular Systems Biology 4:220. These fully synthetic systems have significant environmental interactions in common with traditional bacteria:

It is striking to note that the Cytomim system closely mimics E. coli cellular metabolism. It is homeostatic in pH and [Pi], uses natural, non-phosphorylated energy substrates, provides a long-lasting ATP source, and fuels highly productive protein synthesis (up to 600 mg protein/l/h). In addition, each ribosome can polymerize approximately 10 500 amino acids (42 copies of chloramphenicol acetyl transferase, CAT), indicating that the Cytomim system is not limited by enzyme turnover (e.g. only one protein, or fraction of a protein, produced per ribosome). Furthermore, the specific oxygen uptake rate in the Cytomim system is on the same order as for intact E. coli cells.

As can be seen from the date of this publication (2008), this research is cutting edge. Prior work by the same primary author established this Cytomim system.

Digital-logic-like bistable circuit using synthetic biology without using organisms has previously been described in Construction of an in vitro bistable circuit from synthetic transcriptional switches, Jongmin Kim, Kristin S White & Erik Winfree, Molecular Systems Biology 2:68

The question by now might have changed.  Maybe at this point, you are asking, “Why should I use extensive trial-and-error while attempting to modify existing bacteria, when I can create exactly the proteins I need, from the ground-up, instead?”

That’s a good question for further research.

The World’s Smallest Organisms & Their Importance

Posted by – March 30, 2008

Biology is faced with the problem:  the field in general does not understand much of what it studies.  One method of solving this is to study the smallest organisms known, in an effort to “understand 100% of something small.”  This is a typical engineering approach, to understand the smallest system first, then work up to attempting to understand larger systems.  After understanding the organisms, of course, we have a better chance at modifying them (their DNA) into something useful (or, rather, something that actually lives at all).