Researchers create living 'neon signs' composed of millions of glowing bacteria

In an example of life imitating art, biologists and bioengineers at UC San Diego have created a living neon sign composed of millions of bacterial cells that periodically fluoresce in unison like blinking light bulbs. 

Thousands of fluorescent E. coli bacteria make up a biopixel [Credit: Hasty Lab, UC San Diego]

Their achievement, detailed in this week's advance online issue of the journal Nature, involved attaching a fluorescent protein to the biological clocks of the bacteria, synchronizing the clocks of the thousands of bacteria within a colony, then synchronizing thousands of the blinking bacterial colonies to glow on and off in unison. 

A little bit of art with a lot more bioengineering, the flashing bacterial signs are not only a visual display of how researchers in the new field of synthetic biology can engineer living cells like machines, but will likely lead to some real-life applications. 

Using the same method to create the flashing signs, the researchers engineered a simple bacterial sensor capable of detecting low levels of arsenic. In this biological sensor, decreases in the frequency of the oscillations of the cells' blinking pattern indicate the presence and amount of the arsenic poison. 

The smaller chips contain about 500 blinking bacterial colonies or biopixels [Credit: Hasty Lab, UC San Diego]

Because bacteria are sensitive to many kinds of environmental pollutants and organisms, the scientists believe this approach could be also used to design low cost bacterial biosensors capable of detecting an array of heavy metal pollutants and disease-causing organisms. And because the senor is composed of living organisms, it can respond to changes in the presence or amount of the toxins over time unlike many chemical sensors. 

"These kinds of living sensors are intriguing as they can serve to continuously monitor a given sample over long periods of time, whereas most detection kits are used for a one-time measurement," said Jeff Hasty, a professor of biology and bioengineering at UC San Diego who headed the research team in the university's Division of Biological Sciences and BioCircuits Institute. "Because the bacteria respond in different ways to different concentrations by varying the frequency of their blinking pattern, they can provide a continual update on how dangerous a toxin or pathogen is at any one time." 

"This development illustrates how basic, quantitative knowledge of cellular circuitry can be applied to the new discipline of synthetic biology," said James Anderson, who oversees synthetic biology grants at the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research. "By laying the foundation for the development of new devices for detecting harmful substances or pathogens, Dr. Hasty's new sensor points the way toward translation of synthetic biology research into technology for improving human health." 

The larger chips contain about 13,000 biopixels [Credit: Hasty Lab, UC San Diego]

The development of the techniques to make the sensor and the flashing display built on the work of scientists in the Division of Biological Sciences and School of Engineering, which they published in two previous Nature papers over the past four years. In the first paper, the scientists demonstrated how they had developed a way to construct a robust and tunable biological clock to produce flashing, glowing bacteria. In the second paper, published in 2010, the researchers showed how they designed and constructed a network, based on a communication mechanism employed by bacteria, that enabled them to synchronize all of the biological clocks within a bacterial colony so that thousands of bacteria would blink on and off in unison. 

"Many bacteria species are known to communicate by a mechanism known as quorum sensing, that is, relaying between them small molecules to trigger and coordinate various behaviors," said Hasty, explaining how the synchronization works within a bacterial colony. "Other bacteria are known to disrupt this communication mechanism by degrading these relay molecules." 

But the researchers found the same method couldn't be used to instantaneously synchronize millions of bacteria from thousands of colonies. 

Tiny microfluidic chips allow the researchers to synchronize the bacteria to fluoresce or blink in unison [Credit: Hasty Lab, UC San Diego]

"If you have a bunch of cells oscillating, the signal propagation time is too long to instantaneously synchronize 60 million other cells via quorum sensing," said Hasty. But the scientists discovered that each of the colonies emit gases that, when shared among the thousands of other colonies within a specially designed microfluidic chip, can synchronize all of the millions of bacteria in the chip. "The colonies are synchronized via the gas signal, but the cells are synchronized via quorum sensing. The coupling is synergistic in the sense that the large, yet local, quorum communication is necessary to generate a large enough signal to drive the coupling via gas exchange," added Hasty. 

Graduate students Arthur Prindle, Phillip Samayoa and Ivan Razinkov designed the microfluidic chips, which for the largest ones, contain 50 to 60 million bacterial cells and are about the size of a paper clip or a microscope cover slip. The smaller microfluidic chips, which contain approximately 2.5 million cells, are about a tenth of the size of the larger chips. 

Each of the blinking bacterial colonies comprise what the researchers call a "biopixel," an individual point of light much like the pixels on a computer monitor or television screen. The larger microfluidic chips contain about 13,000 biopixels, while the smaller chips contain about 500 pixels. 

Hasty said he believes that within five years, a small hand-held sensor could be developed that would take readings of the oscillations from the bacteria on disposable microfluidic chips to determine the presence and concentrations of various toxic substances and disease-causing organisms in the field.

Source: University of California - San Diego [December 18, 2011]

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DNA origami

In the emerging field of synthetic biology, engineers use biological building blocks, such as snippets of DNA, to construct novel technologies. One of the key challenges in the field is finding a way to quickly and economically synthesize the desired DNA strands. Now scientists from Duke University have fabricated a reusable DNA chip that may help address this problem by acting as a template from which multiple batches of DNA building blocks can be photocopied. The researchers have used the device to create strands of DNA which they then folded into unique nanoscale structures. They will present their findings at the AVS Symposium, held Oct. 30 – Nov. 4, in Nashville, Tennessee. 

Many different methods of DNA synthesis have been developed, but each method has its drawbacks. Bulk DNA synthesis, which makes use of separate columns to house the reactions, can produce large amounts of material, but is costly and limited in the number of different DNA sequences it can create. The Duke researchers, by contrast, used an inkjet printer head to deposit small droplets of chemicals on top of a plastic chip, gradually constructing DNA strands of mixed length and composition on the surface. The team then used a biological photocopying process to harvest the DNA from the chip. To the researchers' surprise, they found they could reuse the chip to harvest multiple batches of DNA. "We found that we had an "immortal" DNA chip in our hands," says Ishtiaq Saaem, a biomedical engineering researcher at Duke and member of the team. "Essentially, we were able to do the biological copying process to release material off the chip tens of times. The process seems to work even using a chip that we made, used, stored in -20C for a while, and brought out and used again." 

After releasing the DNA from the chip, the team "cooked" it together with a piece of long viral DNA. "In the cooking process, the viral DNA is stapled into a desired shape by the smaller chip-derived DNA," explains Saaem. One of the team's first examples of DNA origami was a rectangle shape with a triangle attached on one side, which the researchers dubbed a "nano-house." The structure could be used to spatially orient organic and inorganic materials, serve as a scaffold for drug delivery, or act as a nanoscale ruler, Saaem says. 

Going forward, the team intends to produce larger DNA structures, while also testing the limit of how often their chip can be reused. In the near-term, the research has applications in the spatial positioning of biomolecules, such as proteins, for research purposes. Long-term, it might even transform information technology: "I would not be surprised if this methodology is used to fabricate the next generation of microprocessors that can push Moore's law even further," Saaem says. 

Source: American Institute of Physics [October 31, 2011]

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