Photo: Courtesy of NASA
Researchers at the National Space Biomedical Research Institute (NSBRI) are developing technologies to identify and monitor anticipated and unanticipated microorganisms in space--technologies, they suggest, that could also help to more efficiently diagnose medical conditions down here on Earth, as well as help detect biological hazards in this post-Sept. 11 world.1-3
George E. Fox, professor of biology and biochemistry, and Richard Willson, associate professor of chemical engineering and biochemistry, both at University of Houston, have been working together for nearly a decade on projects involving microbial detection and environmental monitoring. As part of the immunology, infection, and hematology team of NSBRI, a consortium of institutions researching health risks related to long-duration space flight, they have been studying techniques to detect, rapidly identify, and monitor bacteria and other microorganisms in space, as well as investigating the effects of microgravity on bacteria.
Fox and Willson have created a 'universal classifier,' a kind of lab on a chip to spot and generally identify microbial pathogens. Featuring a typical checkerboard array with probes hybridized to target the input DNA, the universal classifier chip will reveal "approximately" what almost anything is ..., "distinguishing DNA sequences unique to small groups of bacteria," explains Fox.
"Typically, in the space application we're looking at, we don't necessarily know what the problem organism is going to be, so the key thing that we're doing that is different ... is trying to identify not what a particular organism actually is, but how it relates to the tree of life," elaborates Fox, who with Carl Woese at University of Illinois, discovered Archaea and revolutionized the field of bacterial taxonomy.
Astronauts on long space flights spend months in a closed environment, "in the same quarters, breathing recycled air, and drinking recycled water, conditions that create a microbial breeding ground;" therefore, understanding the microbial environment is critical to the health of astronauts and the success of the mission, says Fox. "Not only are there a whole series of regenerative life-support systems that are dependent on living systems which can get sick or get infected ..., the astronauts also have everything from microgravity to stress to low-level radiation to contend with, and they do get immunosuppressed," adds Willson.
Previous research has shown that the conditions of microgravity may suppress the human immune system, as stress does, making the body more susceptible to infection. There are also indications that, along with higher levels of radiation, the conditions of microgravity may stimulate mutation in bacteria.
In one scenario, elaborates Willson, "Organisms brought onto the spacecraft from Earth may not be a problem when the astronauts are healthy and well-rested, but when [the astronauts] become stressed or perhaps just by being in microgravity for long periods of time, that picture may change." A radically different, extraterrestrial microbe could also change the picture. Fox and Willson do not foresee finding any such oddity.
The objective of their research is to develop better ways of keeping bacterial levels low and avoiding infections. "The basic countermeasure NASA employs for contamination is to keep the levels reasonably low," informs Fox. "They can't keep the environment sterile. We developed this classifier technology to allow astronauts to pinpoint an organism's family and significantly narrow down the possibilities of its identity quickly," enabling them to track down the source more efficiently.
Photo: Courtesy of Sandra Silvers, Agricultural Research Service
Fox and Willson are designing a prototype signature array DNA chip that will distinguish about 16 different organisms or groups of organisms. "We hope to ... test it sometime after the first of the year," says Fox. "If that's functional, then we will go to a chip that could distinguish 1,000 or 5,000 different things."
The two are also working on new methods of DNA and RNA purification, and a routine bacterial monitoring system. The monitoring system utilizes specially designed molecular beacons, "hairpin probes that are self-quenching until they hybridize to their targets," offers Willson. This device will enable astronauts to keep detected bacteria under watch and in check, and provide an early warning for malfunction of onboard systems, such as air filters and water purification devices.
No one knows for sure how Earth microbes might behave in microgravity, so research in this area is critical. "A bacterium might do something it normally doesn't, or you may develop consortia of organisms that don't normally develop on the Earth, and that may result in behavior that's different," points out Fox. Early studies on eukaryotic cellular response in microgravity strongly suggest that the space environment can effect change. Now, in collaboration with Duane Pierson, director of microbiology at NASA's Johnson Space Center, Fox and Willson are conducting microgravity studies with Escherichia coli in the space agency's bioreactor, a rotating cell-culture system that models conditions of microgravity,4 and allows observation of E. coli's general behavior.
The long-term goal is for the results to be used in the space shuttle and/or the international space station, but these future technologies also have immediate applications on Earth. The knowledge gleaned from the microgravity studies, for example, could lead to new treatments for microbial infections. New methods for nucleic acid purification "seem very directly applicable to ground-based use for genetic diagnostics, large-scale sequencing or gene therapy vectors," proposes Willson. The universal classifier could work in hospitals to aid in rapid diagnosis of patients' infections and to identify biohazards.
Not surprisingly, the homeland security officials have shown "a significant amount of interest" in the universal classifier technology, admits Willson. "The high-adrenalin scenario is that someone dumps a bunch of brown powder in the air at the Pentagon, or on a public street or subway, and authorities need to know what that organism is as fast as possible. This technology can give them some degree of information very quickly, which, for one thing, will help eliminate false alarms so that things like granulated sugar don't wind up being the cause for evacuating buildings," he expounds. Or, adds Fox: "If somebody were to somehow weaponize a bacterium that wasn't anticipated, it could pick that up."
A.J.S. Rayl is a contributing editor.
1. Z. Zhang et al., "Identification of characteristic oligonucleotides in the 16S ribosomal RNA sequence dataset," Bioinformatics, 18:244-50, 2002.
2. K.D. Kourentzi et al., "Microbial identification by immunohybridization assay of artificial RNA labels," Journal of Microbiology Methods, 49:301-6, 2002.
3. J.C. Murphy et al., "Structured RNA isolation and fractionation with compaction agents," Analytical Biochemistry, 295:143-8, 2001.
4. A.J.S. Rayl, "The spin on rotary culture: NASA project launches researchers into the realm of three-dimensional cell structures," The Scientist, 16:36, Oct. 28, 2002.