David Kirkpatrick

October 30, 2008

A molecular clock

This is a cool story from Technology Review.

From the link:

A Fast, Programmable Molecular Clock

The bacteria-based timepiece could be used as a biosensor for changing environmental conditions.
Wednesday, October 29, 2008
By Emily Singer

UC San Diego bioengineers have created the first stable, fast, and programmable genetic clock that reliably keeps time by the blinking of fluorescent proteins inside E. coli cells. The clock’s blink rate changes when the temperature, energy source, or other environmental conditions change. Shown here is a microfluidic system capable of controlling the environmental conditions of the E. coli cells with great precision–one of the keys to this advance.
Credit: UC San Diego Jacobs School of Engineering

A molecular timepiece that ticks away the time with a flash of fluorescent protein could provide the basis for novel biosensors. The clock, or synthetic gene oscillator, is a feat of synthetic biology–a fledgling field in which researchers engineer novel biological “parts” into organisms.

To create the clock, scientists genetically engineered a molecular oscillator composed of multiple gene promoters, which turn genes on in the presence of certain chemicals, and genes themselves, one of which codes for a fluorescent protein. When expressed in E. coli bacteria, the feedback system turns the fluorescent gene on and off at regular intervals.

May 20, 2008

Nanoscale cell spying and bacterial computing

Two Kurzweil AI.net bit with a biological bent today — a 3D light microscope that resolves to 40 nanometers and E. coli engineered to compute a math puzzle.

Looking into Live Cells at Nanoscale Resolution
Technology Review, May 20, 2008

A super-high-resolution 3-D light microscope developed at the Max Planck Institute for Biophysical Chemistry will allow biologists to watch the workings of the tiniest organelles and even individual clusters of proteins in living cells at a resolution of 40 nanometers.


Mitochondrion images (Nature Methods/Stefan Hell)

The Max Planck group developed a way to get around light‘s fundamental wavelength limitations by using two beams instead of one. The first light beam plays the same role–and is the same spot size–as light in a conventional microscope. It moves through the cell under study, exciting fluorescently labeled molecules inside the cell to fluoresce. The second beam “sculpts” the first, says Hell, inhibiting fluorescence created by the edges of the first beam. That reduces the effective spot size to 40 to 45 nanometers in diameter.
Molecular-resolution microscopy is expected to improve patient care and play an important role in advancing personalized medicine in the future.

 
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Engineered bacteria become the first living computer
Science News, May 19, 2008

Davidson College researchers genetically engineered the bacterium E. coli to coax its DNA into computing a classic mathematical puzzle known as the burned pancake problem.

The problem: start with a stack of pancakes of varying sizes burned on one side, and try to get the pancakes into order from largest to smallest — all burned side down — through a series of flips. The figurative spatula can flip at any point in the stack, but has to include all the pancakes above.

The researchers inserted the Hin recombinase enzyme into E. coli. The enzyme could then flip segments of E. coli’s DNA that are marked by genetic flags. The researchers designed these segments so that, when lined up in the correct order like pancakes stacked from biggest to smallest (burned side down, of course), the DNA spells out the code for a gene that gives the bacterium resistance to an antibiotic.

That way, applying the antibiotic to the colony of engineered bacteria killed all of the bacteria that had not yet solved the puzzle. Only those that had “stacked their pancakes” would survive. Measuring how long it took the bacteria to reach the solution indicated how many flips were required.

 
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