signalsmag.com
Space-Age Genomics -- And Beyond
If carbon-based life forms ever existed on Mars, NASA researchers will find them -- thanks to far-out technology being developed at the NASA Ames Research Center in California. Viktor Stolc and others at Ames' Center for Nanotechnology are developing exquisitely sensitive devices for DNA and RNA sequencing.
These nanopore sensors will be capable of sequencing single molecules of nucleic acid at a rate of one million bases per second by electrophoresis of the charged polymers through the solid-state nanopore channel, whose diameter is only slightly wider than that of DNA. Ultra-sensitive, fast, and reagent-free: Nanopores are the perfect sensors to detect life on Mars -- or any other planet -- by cataloging the tantalizing wisps of genetic material that might have been left behind by organisms as yet unknown. NASA's first mission to return samples of Martian rock and soil to Earth is currently slated for launch in 2014.
In the meantime, these slick sensors will also prove eminently useful right here on Terra Firma -- for scientists will soon be able to analyze the DNA sequences of all organisms on Earth. As a start, they're investigating the DNA sequence diversity of microbes found above the Arctic Circle -- specifically, those living at the Haughton impact crater on Devon Island in Nunavut, Canada. Unlike the familiar genetic workhorses E. coli and S. cerevisiae, more than 99 percent of all microorganisms that inhabit the Earth and its oceans can't be cultivated in the lab -- including those living in extreme environments such as the Arctic desert. However, their genetic material can be extracted, cloned and sequenced. Stolc, who is a research scientist at NASA Ames Research Center, was a project leader for the NASA Houghton-Mars Project. Not only will data gleaned from the Houghton project be illuminating per se, but, because the Houghton crater is considered an analog to the planet Mars, the researchers hope to learn how to best conduct their search for signs of life on the Red Planet.
High-throughput DNA sequencing is one approach to whole genome analysis; investigating gene expression in vivo is another. To this end, Stolc is conducting genome-wide functional analyses of microbes -- with S. cerevisiae as a model for human physiology and genetics -- in multiple environments, including the microgravity found in space. Genome-wide scans are best done on high-density DNA chips, which allow hundreds or thousands of experiments to be conducted simultaneously. And chips have one other attribute that makes them especially useful for space-based experimentation: They're lightweight and small.
The first microarrays that could find their way aboard the International Space Station might be CombiMatrix Corp.'s biochips. In early August, the Mukilteo, WA-based company and NASA Ames Research Center signed a formal agreement under which Ames will license, buy and use CombiMatrix's chips and related technology to conduct experiments aboard the space station, as well as here on Earth. "CombiMatrix's technology will enable NASA to conduct genome-wide functional analysis of any organism under any condition, including in a microgravity environment," Stolc explained. For, one of NASA's goals is to understand the effects of low gravity on gene function -- especially as it applies to humans who will be living on the space station for long periods of time or even traveling to distant planets.
CombiMatrix uses electrochemistry and semiconductor technology to synthesize biological materials -- DNA or RNA probes, even proteins -- right on the surface of its chips. The chip consists of thousands of tiny "virtual flasks," each the diameter of a human hair. These flasks are actually electrodes, arranged in a grid pattern on the semiconducter wafer -- and, importantly, each electrode is wired to a computer, which can direct it to construct a specific chemical compound. End-users can access this computer from the Internet -- allowing them to design their own chips from afar. (For a more detailed explanation of CombiMatrix's chips, please refer to the Signals article, "Protein Chip Challenges.")
"We'll use the CombiMatrix system to synthesize oligonucleotide arrays for gene function monitoring in the yeast project [which uses the complete set of yeast deletion strains to assign functions to genes]," Stolc explained. In this collection of strains, "every gene in the yeast genome has been deleted and replaced with two marker tags, which can be amplified and their relative abundance measured via oligo arrays. The CombiMatrix system allows us to change the sequences on the chip to monitor all gene functions simultaneously."
And, the company's system is small, making it ideal for tucking into a nook aboard the space station. According to Siavash Ghazvini, CombiMatrix's VP of strategic corporate development, the synthesizer modules for making the microarrays are about the size of a hard-back book, and a cassette containing several biological array processors (up to roughly 1,000 test sites per chip) is about the size of a credit card. Plus, due to the system's computerized aspects, researchers could conduct experiments here on Earth and upload the data to the space station -- where the experiment would then be duplicated. As well, scientists in space will be able to design and produce customized biochips, which they can then modify in an iterative fashion depending on experimental results.
Being able to analyze the results of an experiment conducted on the space station immediately -- rather than sending it back to Earth -- is a real bonus: It gets around the problem of preserving specimens in some fashion until they can be returned to Earth. According to Ghazvini, NASA could start using the CombiMatrix system on the space station within the next few years.
Customized chips can also be used to study protein crystal growth in microgravity -- which is why NASA's teamed up with Caliper Technologies Corp. Caliper's microfluidic-based chip is capable of performing multiple experiments simultaneously; it's essentially a miniaturized laboratory that can fit into the palm of a child's hand. That's a perfect size for the space station, too, although the initial experiments will be conducted on Earth.
NASA's joined Caliper's applications developer program (ADP), which offers the company's customers the opportunity to establish their own in-house microfluidics research program and develop specific chip-based applications. For NASA, that means taking the chips into space to study protein crystallization, explained Jane Green, Caliper's senior director of corporate communications. The agency's already determined that it's feasible to grow high quality crystals in the chip's micro-channels on Earth, she added. Now, "The goal is to send the system into space and perform experiments with investigators on Earth manipulating the conditions."
Hundreds of protein chemists and crystallographers can attest to the fact that it's not easy to grow crystals, much less perfect ones -- and some proteins won't cooperate at all. Yet, if one wishes to determine the three-dimensional structure of a protein -- the Holy Grail of many proteomics researchers today -- having a crystal is imperative. As it turns out, gravity can cause buoyancy and sedimentation effects that are detrimental to crystal growth -- which is where NASA comes in. In fact, the agency has been sponsoring experiments on crystal growth (initially inorganic crystals) in microgravity for decades. Not only should it be possible to improve the quality of existing protein crystals by growing them in space, but also it might provide the perfect environment for producing crystals from macromolecules that no-one's been able to crystallize on the ground.
Biological experiments in microgravity are nothing new to NASA, either -- cell-growth experiments in bioreactors (on Earth and in space), for instance, started in the 1980s. And these experiments continue, spurred on by advances in technology that enable researchers to ask ever more sophisticated questions. For instance, NASA just awarded $27 million in grants to 43 academic researchers to conduct biotech research on Earth and in space -- covering tissue engineering, gene expression, biosensor technology, structural biology, membrane proteins and artificial biomembranes -- as well as cell cultures and protein crystals. (Click here for a list of the selected principal investigators, institutions and research titles.)
According to Stephen Davison, biotechnology enterprise scientist in NASA's Washington, D.C.-based physical sciences research division, the overall biotech effort can be divided into two major categories: the cellular program (which is based at the Johnson Space Center) and the macromolecular program (at Marshall Space Flight Center). "All of these programs have an extensive ground base, which provides the intellectual foundation for research in space."
The individual experiments -- past, present and future -- are far too numerous to mention here. But, as an example, one experiment that's scheduled to go up fairly soon will focus on using bioreactors to cultivate cells that retain the three-dimensional form and normal function of natural tissue. On the ground, cultured cells form flat, thin layers -- which doesn't really shed much light on the way that cells relate to each other in an organ. But space station experiments might provide answers to how cells form three-dimensional structures and how they differentiate, Davison explained.
The space-bound cells are not necessarily "normal," however: They include an ovarian tumor cell line, colorectal carcinoma cells, renal cells and PC12 cells (a secondary rat cell line that's been grown in culture for over 20 years). However, "All of these cells lines are particularly well understood and characterized biochemically," making them ideal candidates for in-depth microgravity studies, Davison said. "We can ask questions for which there's an answer."
But, ultimately, these experiments are intended to do more than answer basic biological questions: Microgravity's long-term effects on humans are not yet known. "NASA's trying to form a foundation in space cell biology in order to understand the implications for long-duration manned space flights," Davison explained. |
