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Brave New World


by John S. MacNeil & Meredith W. Salisbury

Scientists who have remained dedicated to progress in genomics, proteomics, or bioinformatics during the last few years may not have noticed that the benefits of the field have slowly been creeping out of basic science labs and into more applied research. Sure, these next-generation genomics teams are sequencing, expressing genes, and altering the structure of DNA. But they’re doing it for products targeted at the consumer market — a whole new realm for this discipline.

The Genome Technology staff scoured through files, press releases, news clippings, and information from sources to track down some of the most fascinating industries and applications where genomics is making an impact. Some of these are the last places you might look (anti-counterfeiting devices, anyone?) and others are things that you might find yourself snatching up when they finally hit the shelves (check out the personalized skin cream).

Most of all, what you’ll read about here are examples of cutting-edge research that build on the genomics foundation laid out by scientists like yourself over the last decade or more. Welcome to the brave new world.


Space Odyssey 2009: Interplanetary PCR?


Gary Ruvkun gets his share of ‘little green men’ jokes. But with a respected cast of supporters, his dream of sending genomics to Mars is gaining attention — and maybe even credibility.

Ruvkun, a molecular geneticist at Harvard Medical School focusing on C. elegans, remembers getting the idea in the early ’90s when Norman Pace started bringing up microbes from hot springs and other unlikely places. The lesson was simple: “You could characterize what life is in places without having to culture it. You just have to PCR it,” Ruvkun says. “As soon as I heard that, I thought this should be applied to life detection on Mars.” People who have signed on to his cause include George Church, Steve Quake, Wally Gilbert, and MIT planetary scientist Maria Zuber.

Basically, his goal is to send a specially engineered thermal cycler to the Red Planet — a simple machine that could amplify DNA if it finds any. After discussing the idea with Mike Finney at MJ Research, which makes thermal cyclers, Ruvkun grew more enthusiastic and wound up writing a position paper. That paper made its way into the hands of the right people, and just recently Ruvkun heard that he’ll get about $750,000 over three years from NASA to do some preliminary work on the project. That amount “is adequate to get started,” he says, “but it’s nowhere near adequate for developing it for a flight.”

And it’s no guarantee that Ruvkun’s thermal cycler will even see a flight. Mars missions tend to take off every other year, and Ruvkun is optimistically targeting the 2009 mission for his PCR project. “But in no way have we been selected for that,” he says. “They like to do experiments there that no matter what, it’ll generate data. Ours is kind of a jackpot experiment: you either see something or you don’t. That could be a reason why it’ll never be selected.”

Ruvkun and his team are working to design an extremely small, automated instrument that could perform PCR with microfluidics. For a Mars mission, he has learned, weight is everything. “What we want to do is make it so light that they can’t say no,” he says. His goal is to get the instrument down to approximately one pound, or one percent of the normal 100-pound scientific payload.

Critics argue the obvious point: what indication is there that even if there is life on Mars it would involve recognizable DNA? Ruvkun’s response is that “there’s nothing sacred” about life on Earth — in his mind, it’s more likely that life on both planets came from another origin entirely, making it probable that an organism on Mars could actually be fairly similar to one on Earth.

Realistically, Ruvkun says there are two scenarios if his project is finally accepted for the Mars trip. One, that he finds something — and then has to “try and argue that it’s not a contaminant.” Two, that “we don’t amplify anything, and people think we’re really stupid,” he says.

But when Ruvkun lets himself imagine success for a moment, he says that “the dream result would be to be able to do the DNA sequence of what [we] find, and then do a phylogenetic tree compared to life on earth.”

— Meredith Salisbury


With DNA structure, there’s nothing better than the real thing


Just when it looked like those $10 knockoff Prada handbags sold on the streets of New York City were indistinguishable from the real thing, here comes genomics to remedy the situation.

Or at least that’s the hope of Applied DNA Sciences, a startup company that has licensed DNA-based anti-counterfeiting technology developed by scientist Jin Sheu at Taiwan’s Biowell.

Julia Hunter, a spokeswoman for Applied DNA Sciences, says the technology was licensed about two years ago when the company was formed, and the first product line was officially rolled out last November. Counterfeiting, she says, is a problem plaguing any number of industries, such as electronics, medical drugs, cigarettes, textiles, and even airplane components. If you ask her, Applied DNA’s tag could work for all of these.

Boiled down to basics, the technology is based on the idea that since DNA is such a complex structure, it would be pretty hard for someone to replicate it. Sheu discovered a way to stabilize the structure of DNA so that it could last a predicted 100 years or more and withstand various manufacturing processes.

The Applied DNA crew manipulates the structure of plant DNA, inserting markers as needed to code for information such as where a product was manufactured or where it was destined to be distributed. “The length is dictated by how much information the customer wants transmitted by the markers,” Hunter says. That structure is stabilized with a DNA envelope — a kind of surrogate for the cell membrane — designed by Sheu and then inserted into some kind of anti-counterfeiting device, such as a microchip. Then it can be read with the company’s proprietary readers.

A microchip, for instance, would be connected to a reader and pulsed with electricity to make the DNA emit an analog signal, which bounces back to the reader as a kind of password verification. “All this happens in less than half a second,” Hunter says. “There’s so much information being loaded onto chips” — she cites ATM cards and credit cards as two examples of where they’re used — “and you want that information to be protected.”

The DNA can be used in other media, too. Converted into a liquid form, it can be sprayed right onto the cotton used to make textiles or currency, Hunter says. “We’ve really reinterpreted the concept of tagging.” Along the way, the company has tested any number of potential processes that might compromise the stability of the DNA, including radiation, pulp processing, petroleum and gasoline, converting to inks, and being printed on — so far, according to Hunter, nothing has harmed the tag.

Readers for the tags come in two varieties: a basic one simply detects the presence of the DNA device; a more complex one reads the DNA to figure out what each marker structure means for a particular customer. The more basic reader also comes in a liquid format that changes colors to indicate whether the DNA is where it should be.

As James Bond-ish as the technology might seem, Hunter contends that it’s not only feasible, it’s cost-effective, too. “Because it’s plant DNA, we’re not dealing with something that we’ve got to pay a lot of money for the actual building blocks of the technology,” she says. “We can undercut significantly security products that have been on the market for a long time, and we can price our marker down to the fractions of a cent level.”

— Meredith Salisbury


SNP and tuck? From GeneLink, personalized skin care

Bet you never expected to hear this statement when teams were scurrying to complete the human genome sequence: “We see the mapping of the human genome as a starting point for true customization of cosmetic and personal care needs.”

Sure enough, though, that sentence was uttered by Andy Banham, business director of Arch Personal Care Products, a division of Arch Chemicals that has been working with genomics-based firm GeneLink to develop personalized cosmetics and creams based on a customer’s genotype. GeneLink develops ingredients using the SNP data and sells them to larger chemical and cosmetic companies that actually manufacture and distribute the lotions. The products closest to commercialization are expected to launch soon.

John DePhillippo, CEO of Margate, NJ-based GeneLink, says the company already has 13 patents for such products. The closest products to the shelves are in the skin-care line. Scientists at GeneLink have culled through published studies and run their own to come up with a catalog of skin-related SNPs that code for “how your skin behaves, how it ages, how it wrinkles, and so forth,” DePhillippo explains.

Customers wanting the cream would take GeneLink’s test, and the company would then use the results to identify each person’s particular skin deficiencies. Then a cream is designed for that genetic makeup using a targeted algorithm built by DePhillippo and his team. “The creams are skewed to match your particular issues,” he adds.

“Putting the smoking and the drinking and the sunlight aside,” DePhillippo says, “the genetics lead the way” in how a person’s skin behaves as it ages.

These products aren’t avail-able yet, but DePhillippo says the creams are in clinical trials right now and at least one corporation is planning to launch the skin-care line in another country selected as a test market.

This wasn’t how GeneLink started out — the company kicked off in 1994 as a DNA banking facility. After raising money and going public in 1998, the GeneLink team realized that pharmacogenomics was leading the way for genetic applications. “Our little company does not have the money to create drugs,” DePhillippo says. His company got involved in skin-care and other products after meeting Arch and realizing that SNP research could be useful in that arena, too.

— Meredith Salisbury


And the genes say: Mmm, salty


Clint Brooks spent 16 years in pharma working with the drug discovery process, so in a way it makes sense that he’s the one thinking about how to implement high-throughput biology at corporate giant International Flavors & Fragrances.

Brooks, senior vice president of R&D at IFF, came from building molecules at Abbott Laboratories and now helps IFF develop new ways to build molecules, too. When he joined the company, he looked into whether genomics could be used to accelerate research in much the way it has been used to create a faster, more accurate way of choosing targets at pharmas. “Can we move this interesting industry of flavor and fragrance from its current, old-world way of doing research where you make molecules and you have people taste them and smell them,” Brooks says, “to the world of modern, high-throughput receptor biology screening?”

Though the jury’s still out on fragrances — a far more complex set of olfactory receptors means that “the science just isn’t there yet, and probably won’t be there for another five years” — Brooks says genomics has definite promise for creating flavors.

“When we talk about genomics for flavor, we’re talking about the genes that code for taste receptors and also the genes that code for … what we call ‘mouth feel’” — that is, tactile receptors that distinguish hot or cold or tingly sensations, he adds.

Most of the taste-receptor genes have been identified in academia, Brooks says. Now, companies like IFF and startups such as Linguagen and Senomyx are working on assays that would use a cell host to express those particular genes. In theory, any molecules developed by scientists would be screened against these cell assays to find which receptors — sweet or salty, for instance — turned on. That system would be far more sensitive and accurate than relying on the trained human tasters who currently test new molecules.

One goal of this type of assay would be to develop flavor-enhancing molecules, rather than just flavor molecules, Brooks says. A salt enhancer is one of the most highly sought: this would upregulate the salt receptors, making them far more sensitive to salt. That would mean food manufacturers could make healthier products with far less sodium, but consumers wouldn’t notice a difference in taste.

IFF has invested in this internally, and is also looking to license technologies from genomics-based flavor companies, Brooks says. “We fundamentally believe [this] can change the food industry.”

— Meredith Salisbury


The art of the enzyme: Diversa’s screening campaign


While a few public-sector initiatives are starting to look into ecosphere genomics — the genomes of an entire environmental community — San Diego’s Diversa has already collected some 3 million genomes and counting. Diversa’s goal isn’t to study the environment, though. It’s to find and build enzymes for various types of industrial applications, such as improving oil and gas wells or creating better animal feed.

The old school of thought, explains Dan Robertson, senior research fellow at Diversa, was to go into an environment and culture organisms like crazy. “That ends up being a very time- and labor-intensive activity that’s probably only successful about one percent of the time,” he says. “We just leapfrog that whole culturing idea and isolate all the DNA in a sample.” The Diversa team then clones and expresses the genes they find, building libraries of both small inserts (to help find individual genes with a particular function) and larger inserts (to try to isolate pathway data).

When Robertson and his colleagues need to find a particular enzyme that might, for instance, function in the gut of a chicken, they design an assay for that condition and do expression- or sequence-based screening of the libraries. “That allows us to find candidate enzymes,” he says.

That resulting list of potential enzymes is studied for phenotypes to find the best possible enzyme. If there are some good candidates but no perfect one, the Diversa team uses genomic tools to engineer improved enzymes. One way is what Robertson calls “gene site saturation mutagenesis” — that is, going through a gene and changing each and every codon to all 64 codon possibilities to comprehensively study the effect of every possible point mutations. “Nature herself makes point mutations,” Robertson says. “What she can’t do is parse all of those variabilities.” Afterward, the best mutants are selected and combined to form an enzyme with the best possible phenotype for a given application.

Alternatively, the Diversa crew can also utilize gene reassembly tools. They’ll take a handful of the best-performing enzymes “and then create recombination points, or break points, in those genes. Then combinatorially we put the pieces back together again,” Robertson says. “We create huge libraries of stochiastic variations on those gene pieces.” The best part, according to Robertson, is that break points can be created and reassembled anywhere in the gene — “we can recombine those without regard to homology,” he notes.

To accomplish all of this research — screening across a library of 3 million genomes understandably takes more than a few experiments — Diversa has come up with new formats for microtiter plates, increasing the number of wells to 100,000 in a well-proven version and 1 million in a new prototype. That allows for up to 1 billion screening events each day, Robertson says.

Ultimately, the enzymes are used by various industries for a number of improvements. Diversa is currently working to find an enzyme that would remove the color from paper pulp so companies can stop using environmentally harmful bleach. Past products have included enzymes to help animals absorb more vitamins and to make oil wells easier to access.

— Meredith Salisbury


Migrating eyeballs and other reasons to study halibut


In Nova Scotia, researchers are putting genomics to work for another industry: fish farming. In recent decades, overfishing has depleted fishing stocks, and Canada’s Maritime Provinces have turned to farming halibut, among other types of fish, as a means of resurrecting an otherwise endangered industry.

But the field is hampered by the lack of basic biological knowledge about raising halibut in these farms, a process that occurs on land in giant tanks with recirculating water systems. “There’s very little known about halibut development, period,” says Susan Douglas, a marine biologist at the National Research Council’s Institute for Marine Biosciences in Halifax, Nova Scotia.

Douglas and her NRC colleague Michael Reith are hoping their genomics work will help change that. With several million in funding from Genome Canada, the two plan to sequence halibut ESTs, and then use that data to build microarrays with the help of colleagues at the NRC’s Biotechnology Research Institute in Montreal. The microarrays will also include EST data collected by collaborators in Spain working with Senegal sole, a species closely related to Atlantic halibut.

Reith and Douglas say their work will focus on trying to understand the development of the immune and digestive systems, as well as a phase of development known as metamorphosis, when the fish go from swimming upright to turning on their side.

A number of physiological changes occur during metamorphosis, including one eye migrating from one side of the head to the other, “and that’s when [growers] tend to see a lot of the problems with the fish in terms of deformities of the skeleton or pigmentation,” Reith says. “There’s quite an array of problems that we’re interested in looking at, and hopefully we’ll make some progress in terms of helping agriculturists grow their fish more efficiently.”

— John S. MacNeil


Genomic scientists fight flabby wine


Out of the 14-week growing season for grapes in the Okanagan wine growing region of British Columbia, there are just one or two days during which the berries’ biochemistry undergoes changes that dramatically affect what kind of wine the grapes will produce. So for a viticulturist trying to optimize the quality and consistency of a particular wine, knowing how and exactly when these changes occur is significant.

“There are things that viticulturists do to affect quality,” says Steven Lund, a plant biologist at the University of British Columbia, “but the problem is they don’t understand when you do X and you get Y — why did that happen, how did that happen?”

Together with his colleagues at UBC, and with $3.1 million in funding from Genome Canada, Lund is planning to apply genomics to help solve some of these wine-making mysteries. One part of the project involves collecting cDNA sequence data from Cabernet Sauvignon berry tissue and seed samples, and then contracting with Affymetrix to produce custom microarrays for gene expression analysis. Much of the grape genome data currently available is assembled as a mixture of different cultivars, and focusing strictly on Cabernet berries as a model system would do much to aid viticulturists, Lund says.

“What we’re going to do is [first] look at the berries under standard or optimal growth conditions to make the libraries for the expression profiling,” Lund says. “These would be well-watered, well-fertilized, very well sun-exposed berries, and then we’re going to see what expression profiling, biostatistics, and biocomputing can do to identify important pathways that are responding to environmental variables.”

Another element of the project is to develop diagnostic tools that viticulturists can use in the field to determine what’s happening biochemically in grapes at a given point in their maturity. Of particular interest to wine growers in colder climates like British Columbia is the level of acids in the grapes, Lund says.

“The environment seems to have a big effect on the timing and the extent to which the acids go down by the time the harvest comes,” he says. Wine with too much acid tastes sour, and wine with too little acid is said to be “flabby, or lack backbone,” Lund adds. His efforts to help viticulturists optimize these processes might just keep that flabby wine off your table.

— John S. MacNeil


Chocolate under fire, and cacao in the spotlight


What do witches’ broom and Hurricane Andrew have in common? Both have been major threats to the chocolate industry.

Witches’ broom, a fungal disease that attacks the cacao tree, turned Brazil from the world’s second-largest exporter of cocoa to a net importer, according to John Lunde, director of international environmental programs for Masterfoods USA, a division of chocolate giant Mars. Now, most of the world’s supply of chocolate comes from west Africa, Lunde says — but most of the cacao trees there came from Brazil, which has scientists worried that the disease could jump continents and continue its decimation of the plant.

USDA researchers had begun studying the genetics of cacao by the late ‘80s, says the agency’s research geneticist Ray Schnell. But Hurricane Andrew in 1992 wiped out much of the Miami research facility and “the project came to an end in early 1993 because there was just nothing left,” he says.

Chocolate lovers, take heart. Genomics has its place here, too. Thanks to a major collaboration between Mars and the USDA — as well as cooperative agreements with countries including Costa Rica, Ecuador, Brazil, and Trinidad for field research — scientists are hard at work studying the cacao genome for ways to improve disease resistance and speed up the breeding process. “This is at least a 10-year-long commitment from Mars,” Lunde says.

Schnell, who’s leading the Miami-based research for the program, says his team of 15 scientists and technicians are busy mapping the genome, looking for QTLs for resistance. So far, they’ve already produced a linkage map based on SSR markers. “We’ve identified two QTLs for witches’ broom,” Schnell says. “One accounts for about 40 percent of the variation [and the other] accounts for only about 10 percent of the variation.”

The research group is working on other forms of gene discovery, and has started up a couple of BAC libraries. They’ve submitted a proposal for sequencing about 100,000 ESTs from the cacao genome to France’s Genoscope, and while there’s no verdict yet, “it looks promising,” Schnell says. A separate group at Penn State is putting together the first UniGene set. That’ll give Schnell’s team a basic starting point for a cacao array, he says.

Lunde says studying the world’s germplasm databanks is a key source of information, and that the USDA has been tremendously useful trying to get access to some of the classified collections for the project.

For Lunde, the best part right now is seeing everyone work together on the effort. “Countries that historically saw themselves as competitors are collaborating in this agreement,” he says.

— Meredith Salisbury


Healthier tobacco on the horizon?


If you’ve seen “The Insider,” starring Russell Crowe as a former tobacco industry executive whose life is turned upside down when he decides to testify against his former employers, you might be forgiven for being cynical about tobacco industry R&D.

But Philip Morris would like to take issue with that assumption. In 2002, the company decided to provide researchers at North Carolina State University with $17.6 million over four and a half years to map tobacco genes in an effort to reduce “levels of components in tobacco and smoke that have been identified as harmful by the scientific and public health community,” the company says.

The NC State research project, also known as the Tobacco Genome Initiative, aims to sequence the majority of tobacco genes, and identify those that control plant traits such as the accumulation of heavy metals like cadmium, a known carcinogen, and the production of precursors of tobacco-specific nitrosamines, carcinogens generated during the curing process. The task is complicated by the fact that most of the tobacco plant’s 5 billion base pair genome does not code for proteins, instead consisting of long stretches of DNA repeats.

To help sift through the junk, NC State researchers led by plant pathologist Steve Lommel are relying on technology from Orion Genomics, a St. Louis, Mo.-based company that specializes in handling DNA methylation. Orion’s GeneThresher technology, licensed from Cold Spring Harbor Laboratory, is designed to remove methylated junk DNA from plant genomic DNA libraries, leaving only gene-rich, unmethylated sections of the genome. Tobacco is thought to contain between 25,000 and 50,000 genes, according to Philip Morris.

In addition to funding gene mapping at NC State, Philip Morris is also engaged in some in-house genomics research of its own. So far, the company says it’s using microarrays for gene expression profiling and 2-D gels to separate and identify tobacco proteins in an internal effort to study the mechanisms controlling the production of carcinogens in tobacco.

“As the project evolves, we envision that the genomics information gained from the program will be employed to guide the development of varieties that potentially reduce constituents that have been identified as harmful by the scientific and public health community,” the company said in a written statement. If “The Insider” were made today, would the character played by Russell Crowe (who in real life, ironically, chain smokes) have to be rewritten?

— John S. MacNeil


Getting ‘buzzy’ with genotyping


There’s nothing new about breeding bees. But thanks to genotyping and the newly available honey bee genome sequence, bee breeding is advancing to unprecedented levels of accuracy and usefulness.

Danny Weaver, who runs the B. Weaver Apiaries, is already taking advantage of the sequence information. “I’ll be making more and more direct use of it as the genome becomes more and more available,” he says. “We’ve just begun to process [the sequence] annotation.”

Next up: large-scale genotyping to identify various genes of interest. In particular, Weaver will be seeking genes that give heightened disease resistance, increase honey production, or even stimulate pollen-gathering in less favorable weather conditions. As a favor to fellow bee investigators, Weaver says, he’s also looking for “genes that would modulate their behavior. I want to breed bees that remain calm despite manipulations by beekeepers.”

In recent years, beekeepers have been contending with new waves of parasites that historically haven’t attacked the honey bee, Weaver says. Finding genes that confer resistance to these parasites is of ever-growing importance. Right now, the only solution is some kind of chemical that kills the parasitic mites. “But most are also insecticides,” Weaver adds, and beekeepers are worried about contaminating or destroying their hives. “I think that undoubtedly genomics will help accelerate progress in that arena.”

— Meredith Salisbury


The Scan

Missed Early Cases

A retrospective analysis of blood samples suggests early SARS-CoV-2 infections may have been missed in the US, the New York Times reports.

Limited Journal Editor Diversity

A survey finds low diversity among scientific and medical journal editors, according to The Scientist.

How Much of a Threat?

Science writes that need for a provision aimed at shoring up genomic data security within a new US bill is being questioned.

PNAS Papers on Historic Helicobacter Spread, Brain Development, C. difficile RNAs

In PNAS this week: Helicobacter genetic diversity gives insight into human migrations, gene expression patterns of brain development, and more.