Fwd: The recent multiplex automated genome engineering (MAGE) machine from George Church's lab

[Bryan Bishop]

---------- Forwarded message ----------
From: JonathanCline <jnc...@gmail.com>
Date: Fri, Aug 7, 2009 at 6:35 PM
Subject: The recent multiplex automated genome engineering (MAGE)
machine from George Church's lab
To: DIYbio <diy...@googlegroups.com>



The recently posted video of EDGE296 seminar had George Church
explaining an interesting synthetic gene testing machine, which came
out of his lab; recently published in Nature (Jul 09).   The EDGE
video showed a brief picture of the machine.  The Technology Review
web page shows a similar picture:
http://www.technologyreview.com/biomedicine/22299/


Nature Ref:
Programming cells by multiplex genome engineering and accelerated
evolution. Harris H. Wang, Farren J. Isaacs, Peter A. Carr, Zachary Z.
Sun, George Xu, Craig R. Forest7  &  George M. Church.  Nature advance
online publication 26 July 2009 | doi:10.1038/nature08187



"... we constructed prototype devices [i.e. a machine] that automate
the multiplex automated genome engineering (MAGE) technology to
facilitate rapid and continuous generation of a diverse set of genetic
changes (mismatches, insertions, deletions). ... Detailed schematic
diagram of MAGE prototype including climate-regulated growth chambers
with real-time cell density monitors (green), anti-fouling fluidics
for transfer of cells between growth chambers and exchange of media
and buffers (blue), and real-time generation of competent cells for
transformation with synthetic DNA (yellow). Cultures are carried
through different chambers at different temperature regimes (30 °C, 42
°C, 4 °C) depending on the necessary MAGE steps (that is, cell growth,
heat-shock, cooling). Cells are made electrocompetent by concentration
onto a filter membrane and resuspension with wash buffer. Oligos are
delivered into cells by electroporation. b, Step-by-step diagram of
MAGE cycling steps at a total run time of 2–2.5 h per cycle. Owing to
high voltage (18 kV cm-1) electroporation, approx 95% of cells are
killed at each cycle. Hence, the electroporation event serves to both
introduce oligos into cells and to dilute the cell population, cells
are then recovered and grown to mid-log phase (7 times 108 cells ml-1)
in liquid medium for the subsequent cycle. "


One principal scientist I talked to described this machine as "great
for the particular niche application he was using it for, though not
useful otherwise, and the same thing could be done by an undergrad in
three days".  (I mention this to keep things in perspective for the
journalists out there.)   From my viewpoint, this is another cool step
in the integration of various bio equipment to streamline a time-
consuming process -- getting rid of the human element (contamination
and error and manhours) = scalability for hardware-software control
over bio engineering.   Scalability is needed because there's a ton of
genomic information out there needing characterization in parallel
with synthesis tech.


Parts of the machinery (from paper's supplementary info):

"MAGE Automation

Automation instrumentation was constructed using the following major
components:
Electroporator: ECM 630  BTX Technologies Inc (MA, USA)
Digital controllers: RS-232 serial modules Superlogics Inc. (MA, USA)
Syringe pumps: Cavro XLP600 9-port Tecan Group Ltd. (NC, USA)
Solenoid valves: Miniature Rocker Isolation Valves Central
Distribution Sales (NH, USA)
Temperature controller: CNI-3233-C24 Omega Engineering Inc. (CT, USA)
Orbital shaker: Advanced 3500 Orbital Shaker VWR International LLC
(PA, USA)
Control system software: LabView  National Instruments (TX, USA)
Growth chamber system: custom manufactured David Breslau Design Inc.
(NH, USA) "


I know some of the items listed above could be replaced by DIY / open
source or refurbished components.

A web search of MAGE turned up another technical talk on the device,
here:

"Reading & Writing Genomes" - George Church @ '09 DOE JGI User Meeting
http://www.scivee.tv/node/10578


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################






--
- Bryan
http://heybryan.org/
1 512 203 0507