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Archive for the ‘Plant Science’ Category

Anthers pollenEscape of the Transgenes?

Last week, I was a bit startled as I listened to a podcast of NPR’s Science Friday program.

In this episode (2/18/2011), host Ira Flatow was interviewing the new president of the American Association for the Advancement of Science (AAAS) Dr. Nina Fedoroff (a distinguished plant molecular biologist, by the way).

She shocked me (and, apparently, Ira Flatow) by flatly denying that there were any cases of transgenes “leaking” into the environment from genetically-engineered (GE) crop plants.

To Ira’s credit, he challenged her on this somewhat preposterous statement. (See below why it was indeed such a surprising remark.)

Because this episode elicited a “storm” of letters and e-mails, Ira Flatow did a follow-up interview (which you can listen to here) with Fedoroff and plant ecologist Dr. Allison Snow.

Briefly, Dr. Snow provided several examples of transgenes being acquired by wild relatives of genetically engineered crop plants, particularly canola. Dr. Fedoroff seemed to dismiss these examples as merely “management” problems.

It’s Hard To Corral A Transgene In The Wild.

Contrary to Dr. Fedoroff’s statement on Science Friday, there is ample evidence that transgenes have “leaked” from GE crops to other plants.

Escape plantFor example, in a previous post regarding the herbicide Roundup® (glyphosate), I noted how a transgene conferring resistance to Roundup® had escaped from a test plot of genetically-engineered turfgrass to adjacent populations of a related native grass.

There certainly are other published examples (see ref. 1, e.g.) of gene flow from GE crops to other non-GE crops and to weedy or wild relatives. And, as genetically-engineered organisms (GEOs), such as crop plants, proliferate, there will likely be more.

It’s not hard to imagine the ecological and agricultural implications if so-called “weedy” plants acquire transgenes conferring herbicide tolerance and pest resistance, for example, from related GE crop species.

But, although gene flow from GE plants to wild relatives has been well documented, the ecological significance of these occurrences is much less well understood.

Overall, there are relatively few data available with which to evaluate the potential for increased weediness or invasiveness in a crop species with fitness-enhancing abiotic and biotic GM traits. A better understanding is needed of the factors that presently control population size and range limits of either the crop volunteers or wild recipient populations, and the degree that survival or reproduction in the field is presently affected by the relevant biotic or abiotic stress-tolerance trait.” – from Ref. 1 below.

In a sense, Dr. Fedoroff is correct in stating that this is a “management” issue. But perhaps such management of GE crops should be conducted primarily by plant ecologists, such as Dr. Snow (see ref. 2, e.g.), rather than by plant genetic engineers.

Re. DIY Biotechnologists: This is certainly one of the serious drawbacks of GEOs that all of you DIY genetic engineers must seriously consider before releasing your creations into the wild.

References

1. Warwick, S.I., H.J. Beckie and L.M. Hall (2009) “Gene Flow, Invasiveness, and Ecological Impact of Genetically Modified Crops”, Annals of the New York Academy of Sciences, Vol. 1168, pp. 72–99. (PDF)

2. Snow, Allison A. (2010) “Risks of Environmental Releases of Synthetic GEOs”, Invited Presentation for the Presidential Commission for the Study of Bioethical Issues, July 8, 2010 (PDF) The agenda and video of this meeting are available here.

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3081994600 88b5b9f4f7Whither Plant Genetic Engineering?

The first generation of transgenic plants was in its infancy in the 1980’s, came of age in the 1990’s and seems to have settled into staid middle age in the past ten years.

So, what’s next?

A succinct answer is provided here thanks to the Crop Science Society of America (CSSA): “First-generation genetically modified (GM) transgenic crops with novel traits have been grown in a number of countries since the 1990’s. Most of these crops had a single gene that allowed them to tolerate herbicide application, giving them an advantage over wild species.

Second-generation transgenic crops are now being tested in confined field trials around the world. Some of these traits will allow crops to tolerate environmental stress such as drought, cold, salt, heat, or flood. Other traits being developed may lead to increased yield or lower nutrient requirements, or increase tolerance to disease and pathogens.”

New generations of transgenic plants are being produced, as, perhaps, a way to counter potential “mid-life crises” of current GM crops.

Such “crises” include the emergence of “superweeds”, the ineffectiveness of insect resistance in some GM cotton, e.g., and the “contamination” of agricultural and natural landscapes by GM crops or by “transgene pollution” via horizontal gene transfer.

(FYI – Monsanto responds to ineffectiveness of Bt cotton in India)

But how does one go about making such “second generation” GM plants?

More Is Better: “Trait-Stacking” & Multigene Transfer

3967341366 b02cc2d99dOne way to make the “next generation” of GM crop plants is to simply add two or more “commercially-desirable” traits, such as herbicide tolerance and insect resistance, to one plant.

According to the GMO Compass website: “Herbicide tolerance (HT) continues to be the most common transgenic trait in GM crops worldwide.” And “Insect resistance (mostly Bt) is the second most common genetically modified trait. Herbicide tolerance and insect resistance (Bt) often are introduced simultaneously to a crop in one transformation event. This is called trait stacking. The third most commonly grown transgenic crop was stacked insect resistant/herbicide tolerant maize. Combined herbicide and insect resistance was the fastest growing GM trait from 2004 to 2005, grown on over 6.5 million hectares in the US and Canada and comprising seven percent of the global biotech area.”

(FYI – Monsanto’s take on “gene stacking”)

Another class of second generation GM plants is more complex phenotypically than “stacked” GM plants. Such “ambitious” phenotypes may result from the insertion of multiple genes – even artificial chromosomes called minichromosomes – into GM plants.

“Instead of attempting to generate useful transgenic plants by introducing single genes, we now see an increasing number of researchers embracing multigene transfer (MGT) as an approach to generate plants with more ambitious phenotypes. MGT allows researchers to achieve goals that were once impossible – the import of entire metabolic pathways, the expression of entire protein complexes, the development of transgenic crops simultaneously engineered to produce a spectrum of added-value compounds. The potential appears limitless.” (from reference 1 below)

So, whither plant genetic engineering? – “The potential appears limitless”!

References

1. Shaista Naqvi, Gemma Farré, Georgina Sanahuja, Teresa Capel, Changfu Zhu and Paul Christou (2010) “When more is better: multigene engineering in plants.” Trends in Plant Science Vol. 15, pp. 48-56. (Abstract)

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3554315659_58ffc0bbda.jpg“Apple, Peaches, Pumpkin Pie….”

After the initial reports in 1983 of successful genetic transformation of tobacco, petunia and sunflower plants using Agrobacterium to mediate gene transfer, this technique was tried on many other crop plants.

By 1989, a colleague at the time summarized a “Plant Gene Transfer” meeting he’d attended by singing the line “Apple, Peaches, Pumpkin Pie….” from the 1967 hit song by Jay & The Techniques.

It was almost easier to name the crop plants NOT reported as being genetically modified using Agrobacterium.

There were, however, a very important group of crop plants not amenable to this transformation technique. The cereals.

Corn (maize), wheat, barley, oats, etc., all resisted efforts at genetic transformation using the Agrobacterium-based technology. The reasons are complex, but suffice it to say here that it was mainly due to the fact that they are all monocots. The cereals not only don’t serve as good hosts for Agrobacterium, but also can’t be regenerated very easily via tissue culture, which is a critical step in Agrobacterium-mediated genetic transformation.

So, what were the poor cereal breeders to do?

Shotgunning DNA

In 1988, it was reported (see ref. 1 below) that maize could be genetically transformed by bombarding maize embryos (isolated from seeds) with extremely small tungsten micro-projectiles (0.6 or 2.4 microns in diameter) coated with DNA. Thus, these researchers avoided having to use Agrobacterium to deliver the foreign DNA into plant cells and, by using maize embryos, the necessity of generating plants from somatic cells.

And so the gene gun was born.

Information about the Biolistic®-PDS-1000/He Particle Delivery System, e.g., can be found here. (And you may even be able to buy a used one for $100!)

So, by 1990, there were multiple ways to genetically transform plants. And the race was on to develop commercially available (and profitable) GMOs.

genengcrops.gif

The first GMO approved by the USDA for human consumption was the “Flavr Savr” tomato in 1992. And by 1996, Roundup Ready® soybeans were sold by Monsanto. As indicated in the graph above, both herbicide-tolerant (HT) and insect-resistant (Bt) genetically engineered (GE) crops have been widely adopted by U.S. farmers. (For more info click on figure.)

Though their GE crops have sold well, biotech companies want to protect their investments by limiting or preventing the ability of growers to save seeds from GE crops. One way is through litigation. Another way is through technology.

“Terminating” Seed Germinationthe-terminator.jpg

Officially called the Technology Protection System (TPS), a way was found to block the germination of seed produced by GE plants.

Briefly, this so-called “terminator” technology incorporates genes into GE plants that, when expressed, are lethal to seed embryos. (see ref. 2 below for more information)

T-GURTs Are “Traitors”

Another technological way to prevent farmers from saving and replanting seeds from GE crop plants would be to incorporate traits into the GE plants that would require a special chemical for second-generation seeds to germinate. Sort of like a special key for the lock.

Officially known as Trait-specific Genetic Use Restriction Technology or T-Gurt (a.k.a., “Traitor” technology), this method incorporates a genetic control mechanism that requires yearly applications of a proprietary chemical to activate desirable traits. (see ref. 2 below for more information)

Bottom Line: These days, the genetic transformation of plants, even cereals, has become routine. And there are even ways to insert “locks and keys” into your GE plants.

References

1. Klein, T.M., Fromm, M.E., Weissinger, A., Tomes, D., Schaaf, S., Sleeten, M. & Sanford, J.C. (1988) “Transfer of foreign genes into intact maize cells with high-velocity microprojectiles.” Proceedings of the National Academy of Sciences (USA) Vol. 85, pp. 4305-4309. (PDF)

2. “Terminator” Technology, Department of Soil and Crop Sciences, Colorado State University.

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Animal, Vegetable, Miracle - Vegetannual.jpgWhere Do New Plants Come From?

Well, new plant species arose (and still arise) through plant evolution, that is, as a consequence of hundreds of millions of years of natural selection.

About 12,000 years ago, however, humans got involved.

Early examples of humans trying to manage plants for their benefit likely included burning of forests to encourage herbaceous plants, the vegetative propagation of plants using tubers (think yams, e.g.), and, of course, the saving and sowing of seeds from “desirable” plants.

After people began domesticating plants, things got a bit more interesting. They began producing so-called “cultigens”, that is, plants that have been deliberately selected by humans, a.k.a., “artificial selection”.

1761o.jpg Thus, the field of plant breeding commenced. (An excellent book on this subject is Hybrid: The History and Science of Plant Breeding)

On the left is shown an Assyrian relief carving from 870 B.C. depicting the artificial pollination of date palms.

So, even though they didn’t know the scientific basis of plant breeding, humans were apparently actively engaged in it nearly 3,000 years ago.

Remarkably, this lack of understanding of the genetic basis of plant breeding was true even up to the early twentieth century, until, of course, the experimental results of Gregor Mendel were discovered and disseminated.

Besides the production of plant hybrids via cross pollination, new plants can also be made by the ancient art of grafting and the relatively new technique called transgenics, a.k.a., plant genetic engineering. (Since I’d like to focus on transgenics, I’ll refer you to an excellent introduction to grafting here.)

1977 – The Genie Emerges From The Bottle

Though humans have been making new plants for thousands of years, they’ve only been making transgenic plants for about 30 years.

Most agree that the era of plant genetic engineering began when a scientific paper was published in 1977 showing that a pathogenic bacterium by the name of Agrobacterium tumefaciens was able to insert some of its own genes directly into the genome of its plant hosts.

This research was conducted at the University of Washington (UW) in Seattle primarily by Dr. Mary-Dell Chilton, who was then a postdoc, working with Prof. Milton Gordon and Prof. Eugene Nester, in the departments of Biochemistry and Microbiology, respectively. (Among her honors, in 2002, Dr. Chilton was awarded Franklin Institute Award in Life Science, and, in 2008, was profiled in Scientific American.)

As a graduate student in the Botany Department at UW at the time, I remember attending a seminar by Dr. Chilton reporting this discovery. As I recall, the implications of this finding regarding the potential genetic transformation of plants was certainly recognized at the time. That is, that Agrobacterium could potentially be used as a means to deliver foreign DNA, i.e., a genetic vector, into plant cells, thus genetically altering them.

Remember that by 1977 scientists knew how to cut and paste genes (recombinant DNA) and regenerate whole plants starting with only a few plant cells using plant tissue culture. So the implications of this 1977 paper were enormous.

Fast-forward to 1983 –

Transgenic plants were first created in the early 1980s by four groups working independently at Washington University in St. Louis, Missouri, the Rijksuniversiteit in Ghent, Belgium, Monsanto Company in St. Louis, Missouri, and the University of Wisconsin. On the same day in January 1983, the first three groups announced at a conference in Miami, Florida, that they had inserted bacterial genes into plants. The fourth group announced at a conference in Los Angeles, California, in April 1983 that they had inserted a plant gene from one species into another species.” (from ref 2 below)

To be continued….

References
1. Three Ways to Make a New Plant, The Exploratorium, San Francisco, California.

2. Transgenic Crops: An Introduction and Resource Guide – History of Plant Breeding, Colorado State University.

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DIYbio.jpgBiotech in Your Garage.

Is it possible that the kids across the street could someday soon be creating genetically engineered plants in their garage or greenhouse? (Now there’s a scary thought.)

This may be more feasible than you think.

An article called Garage Biology in a recent issue of Nature magazine (see ref. 1 below) attracted my attention to the burgeoning field of “do-it-yourself” (DIY) biotech.

For relatively modest amount of money, a person can set up a reasonably functional molecular biology lab, in part, by acquiring used lab equipment in places such as eBay. See, for example, this garage biology lab in Silicon Valley.

The above article is mainly about Dr. Rob Carlson, a pioneer in the field of “garage biotech” (see refs. 2 & 3 below). He has recently published a book called Biology Is Technology: The Promise, Peril, and New Business of Engineering Life. According to one prominent reviewer: “Since Rob Carlson is THE authoritative tracker of progress in biotech, this book is the most complete – and exciting – chronicle of the technological revolution that promises to dominate this century.” –Stewart Brand, Author of Whole Earth Discipline: An Ecopragmatist Manifesto.

fruit_helix.jpgInformation regarding “biohackers” can, of course, be found online (e.g., see ref 4 below).

But even if you don’t have the money or knowledge to do such science yourself, there may actually be community biotechnology labs in your city (e.g., see ref. 5 below) that provide the training and equipment. A DIY Biotech hacker space has recently opened in NYC.

So, similar to open source computer software, does there exist a growing field of “open source biotechnology”. Some say yes, but others say no.

Regardless, the recombinant DNA genie is out of the bottle (so to speak), and the knowledge and equipment required to perform gene splicing can easily be acquired (or built).

And getting such recombinant DNA (artificial genes) transferred into plants is relatively easy (compared to animals).

How?

See here and/or here, for example.

But for a sobering look at the current limitations of so-called “synthetic biology“, please see reference 6 below.

Here’s a new book on the subject: Biopunk: DIY Scientists Hack the Software of Life

References

1. Ledford, Heidi (2010) “Life Hackers.” Nature Vol. 467, pp. 650-652. (PDF)

2. Carlson, Rob (2005) “Splice It Yourself: Who needs a geneticist? Build your own DNA lab.” Wired, Issue 13:05. Splice It Yourself

3. Rob Carlson’s Blog

4. DIYbio.org WebsiteDIYbio.org is an organization dedicated to making biology an accessible pursuit for citizen scientists, amateur biologists and biological engineers who value openness and safety.

5. GenSpace – New York City’s Community Lab GenSpace is a nonprofit organization dedicated to promoting education in molecular biology for both children and adults. We work inside and outside of traditional settings, providing a safe, supportive environment for training and mentoring in biotechnology.

6. Kwok, Roberta (2010) “Five hard truths for synthetic biology.” Nature Vol. 463, pp. 288-290. (HTML) (PDF) “Can engineering approaches tame the complexity of living systems? Roberta Kwok explores five challenges for the field and how they might be resolved.

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Ava_Scenery.jpgiPlants: An Introduction

From movies and video games to landscape design to education to scientific research, we are increasingly encountering plants in silico (that is, computer-simulated plants).

Virtual plants fall into three categories: (1) computer-generated images, (2) outputs from computer algorithms, and (3) computer-searchable plant gene and protein databases.

What follows is a summary of my experiences with virtual plants, mainly online. (However, I don’t claim this is a comprehensive review – please let me know via comments what I’ve missed.)

The Botany of Pandora

The alien planet Pandora in the movie Avatar (and also the video game based on the movie) is swathed in a bioluminescent tropical landscape, populated with truly “out of this world” plants and fungi. As a consultant, plant physiologist Professor Jodie S. Holt helped create this computer-generated imaginary world as well-described here.

Virtual Landscaping

Landscape designers have been using cad programs for years. But thanks to web-based apps such as Second Life® and Google Sketchup anyone so-inclined can landscape in silico.

For example, some fantastic examples of such landscapes in Second Life® are presented here. And Google Sketchup has a 3D warehouse full of virtual plants for your virtual landscape.

Virtual Plants For Education

For years I’ve referred students to Virtual Plant Cell to help visualize plants at the cellular level.

At a more macro scale, one can learn some plant anatomy, for example, at The Virtual Plant.

Botany for Computer Geeks

Way back in the day, when I first taught a class in plant development, I introduced the class to the computer modeling of plant growth.

The example I chose was the so-called L-system or Lindenmayer system of the computer modeling of plants. An example of such modeling can be found at Algorithmic Botany, the website of the Biological Modeling and Visualization research group in the Department of Computer Science at the University of Calgary.

As head of this program, Professor Przemyslaw Prusinkiewicz has greatly refined and expanded this system. An illustrated list of their publications can be found here.

Is Plant Research Going To Be Like Shopping On Amazon.com?

One aspect of iPlant-related research involves functional genomics (putting the genetic puzzle pieces together), exemplified by MetNet at Iowa State University.

The VirtualPlant is another web-based software platform to support systems biology research. According to a recent report: “VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology,..”

As shown in this figure, “VirtualPlant follows the e-commerce site logic…users browse and query the database and add products of interest to their shopping cart”, analogous to Amazon.com. (Thanks, by the way, to the journal Plant Physiology for public access to this paper.)

“Big-Ass Science”

The ultimate “iPlant”, however, may be The iPlant Collaborative Project or, in other words, a $50,000,000 US-taxpayer-funded project to do plant research by committee. An excellent summary of this giant project can be found here.

Years ago a colleague referred to such endeavors as “big-ass science”. Personally, I feel that giving 200 young (under 40) plant scientists (profs or post-docs, by the way) $250,000 each to pursue her/his personal research interests would yield much more creative and innovative outcomes. But that’s a discussion for another day….

HowPlantsWork © 2008-2011 All Rights Reserved.

Post-Script:
Inorganic Flora
A couple of weeks after editing the original post, I discovered some amazingly beautiful images of flowers by botanical CG artist Macoto Murayama.

More about Murayama can be found here and here.

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