Glimpsing the future one A, T, G, and C at a time

The Joint Genome Institute, in Walnut Creek, CA. (DOE)

Recently, I had the pleasure of attending the annual meeting of the Joint Genome Institute out in Walnut Creek, entitled “Genomics of Energy and Environment.” I work in a neurobiology lab with a bent for genomics, so I knew I wouldn’t be too lost as a vertebrate biologist amongst plant, microbe, and fungi experts. I’ve also been working on an article for our magazine about next-generation genetically-modified crop plants (keep your eyes out for it in the next few weeks!), and a good number of the speakers were slated to present research on plant genomics on the last day of the conference. The opportunity was too good to pass up.

But what is the JGI? The JGI was founded in the late 1990’s by the Department of Energy to unify some of the scientists working on the Human Genome Project. Since the completion of the human genome (the JGI was responsible for human chromosomes 5, 16 and 19), the JGI has moved on to other projects of interest for the DOE. Having invested in a good number of DNA sequencing machines (which can cost up to a million dollars each),  the JGI began to specialize in the genomes of microorganisms and plants, betting that biology might be used to clean up the environment, or even provide sustainable energy.

A bank of DNA sequencers.

Over a decade since embarking on this newfound course, the talks I heard validated the JGI’s decision to focus on the genomics of non-animal life. Using insights from genetics (the study of genes and heredity) and genomics (the more specific study of all the genes of a given organism), the JGI has provided scientists with the ability to sequence many genomes efficiently and cheaply, allowing those scientists to harness this data for any project of interest.

The morning kicked off with June Medford of Colorado State University. Her lab is pioneering the development of “plant sentinels” that could improve our ability to detect human or environmental threats. By engineering plants to contain genes encoding proteins that detect certain substances, and partner genes that promote a reaction to such detection with a change in the plant’s color, these plants could provide early warning of something like a minute natural gas leak. Natural gas pipelines run thousands of miles through extremely rural regions, and are rarely, if ever, inspected for leaks unless a large (and dangerous) leak has already developed. Aerial monitoring for color changes in the miles of bushes lining those pipes could cue engineers to double-check the integrity of that segment of pipeline.

Medford’s talk was a great example of a real-world application of synthetic biology, a field that attempts to reconstruct genetic pathways for experimental or functional purposes. I’ve mostly heard of using synthetic biology to manipulate genomes, or reconstruct chromosomes from scratch, but plant sentinels provide the intriguing possibility of a living threat-detection system. Medford has partnered with a company, Phytodetectors, to bring her lab’s inventions to market. For a 9am talk, I was wide awake.

The next few talks got into the details of how scientists might use large amounts of genomic data to improve agriculture or energy. Steve Rounsley, of Dow Agrosciences, has been working with cassava breeders across Africa to help them battle cassava brown streak disease (CBSD), a hard-to-detect scourge on one of the most important food resources in the world. By uniting the DNA sequencing capabilities of centers such as the JGI, with the on-the-ground experience of African farmers, Rounsley, along with dozens of other scientists, has made serious headway into characterizing the diversity of cassava variants in Africa, some of which are resistant to CBSD. Some of these resistant cassava variants had even taken up swaths of DNA from other plant species – an example of gene transfer that could only be picked up by analyzing and comparing entire genomes. In addition to honing in on CBSD resistance, Rounsley and his colleagues hope to isolate other improved cassava variants, perhaps those that are faster-growing or resistant to herbicides, and is also considering using transgenic techniques to speed these improvements (something that is currently being pursued here at UC Berkeley).

Populus trichocarpa, also known as the California poplar.

Gerald Tuskan, working out of the Oak Ridge National Laboratory, next showed how genomics might be used to improve energy production, as opposed to food production, by analyzing natural populations of poplar trees. Trees are a great resource for energy, as well as (obviously) for wood and paper, but much of its energy is tightly packed into a molecule called lignin, useful for structural applications but hard to break down for paper or fuel. Scientists have been trying to develop trees with lignin that can be more easily broken down, and some have recently succeeded with genetically-modified poplar trees that might make paper production cleaner. Tuskan, on the other hand, wondered whether natural poplar variants might, by default, produce less lignin, and thus be more easily used as a precursor to ethanol. By analyzing the genomes of thousands of poplar trees in the Pacific Northwest, Tuskan and his team identified poplar variants that produced up to 30% less lignin without any detriment to their health. Indeed, with less lignin, more ethanol could be produced from these trees. You might be skeptical that trees would be a useful, sustainable ‘crop,’ but poplar in particular holds promise – many poplars grow to over 20 feet in just three years.

Pamela Ronald, a renowned rice geneticist from UC Davis, next described similar work attempting to turn her favorite plant into an energy resource. Taking a forward-genetics approach in which she and her colleagues irradiated rice to create random mutations throughout the rice genome, her lab was able to isolate a handful of rice varieties that produced more sugars, making them better-suited for ethanol production. While this sort of approach has been around since the first half of the 20th century, DNA sequencing has allowed the Ronald group to identify all mutations caused by irradiation in a given rice strain, taking out the ambiguity of breeding mutant rice lines without knowledge of the underlying genetic changes. She has also used this approach to develop virus-resistant rice lines, and is consolidating the genomes of her mutant rice strains to provide a foundation for future reverse-genetics approaches, in which scientists target a specific gene to improve a crop. With the resources of the JGI, mutation breeding, not to mention good old selective breeding, has been brought into the future.

Extent and timing of large extinction events in the past 542 million years (the Phanerozoic era is the most recent, and longest-lasting, era of biological diversity on Earth). For each of the “Big 5” mass extinctions, although many genera survived (allowing life to continue on), at least 70% of all species were lost.

There were a few other interesting talks, including one on the future of gene editing in crops, but I’ll let you read about that in my upcoming BSR piece. The keynote address, by Annalee Newitz, of the science and technology blog io9, was a fitting end to the conference.  Newitz recently released a book, entitled “Scatter, Adapt, and Remember: How Humans will Survive a Mass Extinction,” and her talk put a hopeful spin on the challenges humanity is likely to face in the near future. Newitz described how life on Earth underwent multiple mass extinctions, in which over 70% of all life perished, only to see life persist and flourish again – one of those extinctions, it turns out, was due to an ancient microorganism inheriting a gene from another species, devouring the carbon excess being released by volcanoes, and then taking over the planet.

That extinction, however, was the backdrop to Newitz’s message. From the plant sentinels of Medford, to the improved understanding of wood formation and composition by Tuskan, Newitz envisioned a future in which humans would use biology to protect themselves from extreme variation in their natural environment. Buildings made strong with biological materials. Plants, fungi, and microbes that could keep our air breathable, our water clean, our energy abundant. Would surviving a fossil-fuel-driven extinction be easy? Unlikely. But given the promise of the conference’s talks, and the ongoing ingenuity of scientists and dreamers, Newitz was betting that humans would make it. It’s not often a crowd of scientists can be pulled from their microscopes and DNA sequences to consider their roles in shaping the future. But on a sunny afternoon in the shadow of Mount Diablo, as a neuroscientist amongst plant and microbiologists, this writer smiled at the possibility of a happy future for humanity, thanks to science.

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  1. ruth rischin

    To Levi Gadye.
    Re roles of scientists in shaping the future of Our? world,
    Cogent and accessible to the non-specialist, this article indicates that promise begins with communicators of the mindset and the skill of its author. Give us ore!!!