When the National Science Foundation put out a call to researchers last year to develop sensor technologies that could track the origin and movement of explosives used in terrorist bombings, Paul Millard figured that he and his two close collaborators at the University of Maine were positioned ideally to address the problem. Representing three different, yet complementary fields — biological engineering; electrical and computer engineering; and biochemistry, microbiology and molecular biology — Millard, Mauricio Pereira da Cunha and John Singer worked as a team to develop a unique multidisciplinary project proposal.
For the last few years, engineers Millard and Pereira da Cunha have conducted basic and applied research in molecular sensors to detect pathogenic bacteria, as well as viruses currently threatening fish raised in Maine’s aquaculture industry. With NSF support, they then expanded their research into the human-safety realm, merging DNA-recognition strategies with sensor technology to detect bacterial undesirables, such as salmonella, Vibrio cholerae, and enteropathogenic E. coli O157:H7 in the environment.
To Millard and his colleagues, much of that work seemed to provide a logical lead-up to the NSF’s newest challenge: Devise a method that law enforcement officials could use while investigating a terrorist bombing to determine where the explosive materials were manufactured and the route they traveled to the scene of the attack.
Unique identifying markers incorporated into individual lots of explosives are called taggants. One of the most common explosives taggants in use today consists of tiny multicolored plastic chips bonded to a magnetic material, acting as a bar code of sorts to identify the factory that made the explosive material and on what date, in what batch, as well as its distributor and the places that sold it.
When a material is detonated, the taggants are released and can be collected from the area with magnets. But the technology has its drawbacks. Someone conceivably could fabricate counterfeit taggants, thereby subverting the identification process.
DNA can also be valuable as a taggant, but it, too, has its limitations. One of the biggest flaws of current DNA taggant systems is that the equipment necessary to read the genetic code is fairly expensive, is not portable and requires skilled technicians to operate. So instead of being able to read the code quickly and easily in the field, officials have to send the genetic taggants to a laboratory for analysis that could take days to complete. Besides that, unprotected exposed DNA is susceptible to degradation caused by environmental conditions.
Millard believes he and his colleagues have hit on a method that will allow them to overcome the limitations of the DNA-recognition method. Instead of using naked, vulnerable DNA, the team plans instead to make use of one of nature’s most ingenious little survival mechanisms — bacterial endospores.
NSF has provided nearly $400,000 for the novel three-year explosive tracking project being developed by the UMaine research team, which now includes a multidisciplinary cross section of graduate and undergraduate students.
Bacteria such as bacillus and clostridium are able to ensure their own survival during periods of environmental stress by producing endospores, which are dormant, tough, nonreproductive structures in which the bacterial DNA can be safely stored until conditions become favorable again for growth.
“The endospore is a cell reduced to its minimum — more like a seed — that can withstand extreme heat, desiccation, radiation and other harsh environmental conditions, which makes it an ideal container for DNA,” says Millard. “Before us, no one had proposed using endospores as nucleic acid taggants.”
The clever safeguarding mechanism is a bit like backing up critical system data from a computer onto a flash drive. Provided, of course, that the flash drive is then placed inside a brick, let’s say.
But what is most critical to the making of foolproof explosives taggants that can’t be stolen, replicated or manipulated by terrorists is the genetic material locked in that endospore. That’s where bioengineering comes into play, and where the team will rely on Singer’s expertise in bacterial genetics. The team will use geobacillus, a thermophilic bacterium that is widely distributed in soil, hot springs and sediments. Though it is known to cause spoilage in food, it is nontoxic to humans and animals.
Millard says the project will involve the generation of a number of genetically modified spores, each with a unique DNA sequence or sequences spliced into its genome. In other words, a code so biologically well disguised that terrorists looking to hide their tracks after a bombing could never crack it without the key. They wouldn’t even know where to begin to look.
In a real-world application, the DNA-bearing endospores might be mixed in with a batch of explosive material to uniquely differentiate it and its manufacturer. Should terrorists get their hands on some of that batch and detonate it, the taggants — like their plastic-microchip cousins — would be strewn about the attack site. But unlike nonliving taggants, each endospore would have the capacity to give rise to an unlimited number of growing bacteria, greatly enhancing the potential sensitivity of the method.
As the headlines of 2001 made so chillingly clear, Bacillus anthracis, the bacterium that causes the anthrax disease, can be weaponized because its endospores germinate at body temperature into toxin-producing pathogens. When enough of them are inhaled or ingested, they can multiply rapidly, eventually sickening or killing their hosts.
Geobacillus endospores, on the other hand, favor temperatures closer to 200 degrees Fahrenheit to trigger the reactivation process; 160 degrees F for the nonpathogenic bacteria to grow.
Pereira da Cunha, who recently developed a UMaine-patented sensor for health monitoring of Air Force jet engines, is now working on a new surface acoustic wave (SAW) device that will not only detect the endospores on site, but also create the conditions necessary to end their hibernation, producing dividing bacteria from which DNA can be isolated and screened.
The SAW device, which will be developed and manufactured in UMaine’s Laboratory for Surface Science and Technology, is intended to be an all-purpose tool for law enforcement. Through the recognition of the coded DNA taggants, it will be able to identify the source and transit routes of seized contraband explosives. The complete microsystem will be able to sample the taggants at a bomb site, and then process them for subsequent DNA analysis.
UMaine’s research should give rise to a new class of devices that will serve as a platform for the processing and detection of environmental samples, and provide portability for the sensing microsystem, says Pereira da Cunha.
“That’s the beauty of this system,” says Millard. “You don’t have to send anything back to a lab. You can collect, process and analyze on-site with a single, cheap, handheld device.”
While helping to stem terrorist activity is the primary objective of this research, Millard says, the fundamental advances in bioengineering and sensor science expected to emerge could also be of significant benefit in first-responders services, healthcare, food safety and antipollution efforts.
“This technology is being developed for a specific niche, but the research should also answer some interesting scientific questions along the way.”
by Tom Weber
January – February, 2009