MICROBIOLOGY


Water Works

USC scientists plot a stealth-network of microscopic robots designed to snitch on ocean pathogens.


Safe to swim? Rather than consult chemical test kits, public health officials may someday look to swarms of microscopic robots for the answer.

In research spanning nanotechnology, robotics, computer science and marine biology, USC scientists plan to build and deploy water-borne nanosensors capable of detecting and instantly warning of dangerous micro-organisms in the ocean.
“The idea that we’ll have swarms of nanorobots in the ocean is no more far-fetched than the idea of connecting millions of computers was in the late ’60s,” says USC computer scientist Ari Requicha.

Requicha directs the USC School of Engineering’s Laboratory for Molecular Robotics, where his team has experimented with nanometer-scale structures for nearly seven years. (At one-billionth of a meter, a nanometer is to a meter what a grape is to the entire Earth.)

The group has built a nanoscale single-electron transistor and an optical waveguide, and they are now working on a switch and beginning to fabricate more complex nanostructures. Still to come: nanoscale devices with electrical and mechanical components capable of propelling themselves, sending electronic signals and even computing.

Ocean robots needn’t be terribly complicated or powerful, says co-investigator and USC biologist David Caron. A single robot might, for example, sense whether the water is fresh or saline and communicate that information by a faint radio signal to other robots nearby, which would relay the data to other robots, and so on, all the way up to robots communicating with the Internet.

The beauty of such a network is speed. Caron recently created an antibody that binds to Aureococcus anophagefferens, the toxic algae also known as “brown tide.” With advanced lab techniques, he can reliably test water samples for the algae in a day, but “it’s still not fast enough,” he says. Nanosensors carrying the antibody could detect the algae and send a warning the moment a microorganism binds to it.

It’ll be a decade before the researchers can build and deploy nanoscale robots capable of that kind of instant and specific test, says Requicha. For now, they’re building small robots that move, sense and communicate while tethered in a tank of water. From there they’ll progress to larger numbers of increasingly tiny free-moving robots. The ultimate goal: create robots as small as the micro-organisms they monitor.

The nanosensor research is supported by a $1.5 million grant from the National Science Foundation.

– Bob Calverley
Illustration by Regan Dunnick


Friendly Bacteria
Pros of Probiotics


While bacteria are often maligned as the cause of human and animal disease, “friendly bacteria” actually far outnumber pathogenic ones in the human body. Especially prevalent in the gastrointestinal (or GI) tract, they help us digest food and absorb essential vitamins. “More important, these friendly bacteria may modulate our body’s immune system in order to ward off potential infections,” says Roger Clemens of the USC School of Pharmacy.

One’s “microflora profile” is determined shortly after birth, during the first feeding and throughout the first week of life (the GI tract is sterile in utero). This early colonization of friendly bacteria is unique to each person and remains relatively constant throughout life, says Clemens.

However, research suggests that taking probiotics – health-promoting live organisms – may work as well as traditional medicines against common GI disturbances, Crohn’s disease, bacterial vaginosis and even constipation – all conditions associated with an imbalance of specific bacterial strains in the body. Probiotics are commonplace in Japan, Sweden, Finland and elsewhere in Europe and are gaining credibility in the United States. Scientists and dietitians alike are looking to discover new ways to incorporate friendly bacteria (such as lactobacilli and bifidobacteria) into adult diets, either through dietary supplements or natural food sources.

“Many fermented foods such as yogurt, kefirs and other products containing live and active cultures may be helpful in increasing levels of friendly bacteria in the GI tract,” says Clemens.

– Alexis Bergen



A Microbe’s Moveable Feast

Who’s been dining on DNA? New research suggests bacteria such as E. coli gobble up the genetic treats.


Scientists have long divided microbes into two camps: those that can absorb free-floating DNA into their own genomes, and those that can’t. The ubiquitous E. coli is among the latter. Yet it turns out it can absorb free-floating DNA – as food. A USC team led by molecular biologist Steven Finkel has documented this surprising ability in E. coli and found the same genes responsible in numerous other microbes.

“If you think about it,” says Finkel, “DNA is a pretty good nutrient source for a bacterium. Broken down, it’s just sugar, nucleotides and phosphoric acid.” While genetic material isn’t the very best repast a bacterium could wish for, nature rarely offers up pure sugar. But free-floating DNA abounds in seawater, soil, lung mucus and feces.

Focusing on E. coli, the researchers identified eight genes that seemed to underlie the bacterium’s DNA-eating ability. They then looked for similar genes in other microbes – and found them in abundance.

“We looked at two dozen different species – including bugs that are medically relevant, like Salmonella, the plague bacterium, the primary cystic fibrosis pathogen, one of the bugs involved in tooth decay – and they all had [these genes],” says Finkel. Their findings were published in the Journal of Bacteriology.

E. coli is possibly the best studied organism in the history of modern biology. “We know more about it than we know about any other living thing,” says Finkel. “Its genome has been sequenced. We know it has a chromosome of about 4.6-million base pairs and about 4,300 genes. And we don’t have the vaguest idea what more than a third of those genes do.”

Chalk up eight more on the list of known genes. And admit one more piece in the evolutionary puzzle of single-celled life’s 3.5-billion-year history.

– Matthew Blakeslee


Illustration by A. J. Garces


Tidewater Trails
Aqua Sleuth

Jed Fuhrman (left) is on the trail of an elusive predator. It lurks, invisible to the eye, in contaminated ocean waters, infecting humans upon contact: the harmful marine virus.

While searching for marine viruses may sound like an easy enough task with the right tests, it’s much like looking for a needle in a haystack. Less than a teaspoon of pristine seawater contains about 10 million naturally occurring viruses – microscopic workhorses that help keep the ocean clean. The question is, when a handful of harmful viruses get in the mix, how do you detect those?

The USC marine microbiologist has developed a sophisticated test that may one day become a standard in the water-quality industry. Taking the polymerase chain-reaction technique to the next level, he makes DNA copies of virus RNA and then looks for the type and the quantity of the organisms.

In two coastal areas plagued by beach closures, Fuhrman is currently searching for “the fingerprints of contamination.” In Avalon Harbor, on the north shore of Santa Catalina Island, he collected water samples testing for a whole family of organisms, including echoviruses and the coxsackie viruses. “Most people don’t recognize them, but they would not be happy getting them,” Fuhrman quips.

Identifying viruses is only half the trick, however. At oft-closed Huntington Beach, finding the contamination’s origin is the challenge. It could be the Santa Ana River with its dairy farms upstream. Or a marsh that serves as a rest stop for migrating birds. Plus there’s a power plant, a sewage treatment plant and the San Gabriel River feeding into the ocean.

“Any of those are possible sources of the contamination that comes to the beach,” Fuhrman says. “We are looking for a smoking gun.”

– Usha Sutliff


Photo by Irene Fertik






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