Before getting into the how, let’s talk about why this research is important. According to Enhancement of fruit shelf life by suppressing N-glycan processing enzymes in this week’s PNAS, post-harvest fruit and vegetable softening is a big problem, with losses accounting for almost 50% of all produce in developing countries. India, the country that funded the research, and the world’s 2nd largest fruit and vegetable producer, loses 35-40% of produce to softening.

Squished tomato by limaoscarjuliet via Flickr.

We all know that post-consumer food waste is a big problem, and we can alleviate this somewhat in our homes and by choosing restaurants that try to reduce waste. But there isn’t much we can do about pre-consumer waste – from grain that rots in the silo due to fungus to tomatoes that rot in transit due to ripening. By reducing pre-consumer food waste, we can reduce the number of acres needed to produce the same amount of food. In India, preventing all fruit and vegetable softening would be like reducing the amount of land needed to grow fruits and vegetables by 35-40%!

So, how could that softening be prevented?

Researchers have been working for a long time on different parts of the ripening and spoiling process, trying to find ways to slow it down. Nothing has been really effective in getting produce to last longer, and we’ve ended up with produce that is more bland than it used to be, especially when it comes to tomatoes. In short, neither breeding nor genetic engineering has been successful… until now.

In Enhancement of fruit shelf life by suppressing N-glycan processing enzymes, Meli* and fellow researchers found two enzymes that contribute to fruit softening. The enzymes are α-mannosidase and β-D-N-acetylhexosaminidase, α-Man and β-Hex for short. Both of these enzymes break the glycosidic bonds between carbohydrates, as well as between carbohydrate and noncarbohydrate. The role of these enzymes in ripening and softening is to help break down the cell walls that keep the fruit firm. If the enzymes are stopped from breaking down the cell walls, the tomato stays fresh!

Meli and fellow researchers turned off the genes that code for these two enzymes α-Man and β-Hex with biotechnology, but they didn’t use any whole genes from tomatoes or any other species. Instead, they used some pieces of the tomato α-Man and β-Hex genes. These gene fragments are transcribed into RNA under control of the constitutive (always on) CaMV 35S promoter. They then twist and bind with themselves, resulting in double stranded RNA, which activate the RNA interference mechanism that plants and other organisms naturally use to combat double stranded RNA viruses.

The results are pretty striking, as you can see from these pictures. The control tomatoes were unappealingly wrinkly by 20 days, and rotten by 45 days. The tomatoes with α-Man or β-Hex turned off were still firm even at 45 days.

Control and experimental tomatoes over time, from the PNAS article "Enhancement of fruit shelf life by suppressing N-glycan processing enzymes" by Meli, et. al.

RNAi can be used just about any time you want to turn off a gene – it’s even being tested for human use to help combat genetic diseases. For an overview of RNAi that’s a little more detailed than the picture below, check out the RNA Interference interactive video by Nature Reviews (via ERV. Note: the video wouldn’t play on my Mac in Firefox but worked great in Safari).

Overview of RNAi from Huntington's Outreach Project for Education, at Stanford.

The researchers used Agrobacterium to carry the DNA sequences into very young tomato plants, along with a marker gene for kanamycin resistance. Biotech plants can be made without markers but it’s much easier to use them, and there is no risk (for more on antibiotic resistance markers, see GMO Compass).

This work, as far as I can tell, is funded purely by the Indian government – not by private corporations. Specifically, it is funded by the Department of Biotechnology which is part of the Ministry of Science and Technology. They have some pretty impressive goals, as listed in the Plant Biotechnology section, including:

• Genetic engineering and molecular biology tools for forest tree improvement including reduction of generation time, production of horticultural and plantation crops with desired characteristics.
• Transgenics for improved yield, stress tolerance, balanced nutrition, keeping quality of flowers, fruits and vegetables, better nutrient and water utilization capacity should be produced.
• Cataloguing of accessions of wild and land races to study genetic diversity for resolving taxonomic problems.

Tomatoes at Union Square by Lindsay Beyerstein via Flickr.

One of the biggest arguments against biotechnology is that it has been under corporate control. Unfortunately, that’s been true in the United States, where publicly funded research in agriculture has been all but ended. Happily, that’s not the case in India and China. These governments are researching biotech traits for the benefit of their farmers, not for the benefit of shareholders.

If this biotech trait is available royalty-free, then it will presumably be available for breeding by small seed companies and by farmers. I’m imagining beautiful genetically-diverse heirloom tomatoes that have this amazing ability to stay firm on your counter well past the tomato growing season. This means that fewer tomatoes will need to be shipped around the world, and that more can be grown locally. I hope to see some long-lasting tomatoes in my CSA share soon!

* You may have noticed that I usually use the name of the first author rather than the name of the last author when I’m referring to a peer-reviewed paper. In biology-related papers, the first author is the graduate student, or sometimes post-doctoral researcher, who did most if not all of the labwork and writes most if not all of the paper.The last author is the PI (Primary Investigator), who generally provides guidance, helps with experimental design, and edits the paper. The authors in the middle are usually other grad students and their PIs who helped with the project. While all of the authors usually have put in a lot of time and effort, it’s that first author who worked the hardest, and I like to recognize that.

Meli V, Ghosh S, Prabha T, Chakraborty N, Chakraborty S, & Datta A. (2010). Enhancement of fruit shelf life by suppressing N-glycan processing enzymes Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0909329107

In the coming weeks, I plan to give the blog a much-needed visual and functional update. Biofortified is run with WordPress, which allows for an enormous set of possibilities. I plan to replace the blog’s current theme with a more functional updated one that will look similar. The fading features gallery seen before on the blog will return, which was lost because of a conflict between the current theme and a recent wordpress update. Along the sidebar, we have added Frank’s Twitter widget, an awards section (hopeful for more!), and a Networked Blogs widget that shows who is following the blog in Facebook. With the updated theme, I will also add a much-needed “Latest Forum Posts” section so that you don’t have to sift through the forum categories to see if people are talking about things. Of course, the recent comments and calendar are good things to have, and the tabs full of information will stay, too.

What other kinds of sidebar features have you seen on the blogs that you read that you would like to see here? (Tag cloud, Similar Posts, Google news feed…)

Now on to the other special functions and doodads we are going to include in the blog. Another great thing about WordPress if that we can quickly upload and activate plugins that give the blog new functions. There are thousands of such plugins to choose from.

As has been mentioned before, we are going to include a plugin that will enable contributors who have their own blogs to have new posts automatically (or near-automatically) syndicated on Biofortified. So for those of us who blog in more than one place, this will make life easier. But for readers who have their own blogs and would like to contribute from time to time, we will be able to set you up in the plugin to be able to do so. This has the potential to greatly expand the number of bloggers who can be a part of this group blogging effort. In fact, it might make us not only a group blog but also a blogging network! We are trying to see if the author of the Feedwordpress plugin will be able to modify the plugin to suit a few special needs we have that could make this process go more smoothly. Contributors could advertise their involvement with a special banner, and readers and fans could have one too. Here is one mockup.

Next, it would be great if we could make it possible for other bloggers to be able to show the latest posts on Biofortified on their sidebars. For wordpress, this is easy, as there are many feed-reading sidebar plugins to choose from, and we could even customize our own if we wanted to. But this leaves out bloggers without a wordpress blog. It would be great if we could make (or modify) some javascript code that will allow the latest posts (and last comment?) from the posts and comments rss feeds to be displayed on the sidebars of other sites. Here’s a mockup of what I thought it might look like. Anyone know any javascript or know someone who does? A feature like this would greatly enhance our ability to show that there is an ongoing discussion to attract readers from other blogs. Sure, we could just encourage people to subscribe to the feeds… but this would be so much cooler! Note the optimistic blog post titles in the example image!

Next, if the page on Genetic Engineering Companies is any indication, there is great potential in getting help from readers in adding content to the pages of the site. The quintessential model of group participation on the web is a wiki, would that be a good addition to Biofortified? Perhaps it could be used to build a database of terms and concepts often discussed on the blog, or going whole-hog and building a comprehensive information resource from the ground-up. The wiki could be hosted internally or on the free Wikispot site, which I have been involved with. Here is an example of a wiki on genetics that I started a couple years ago, but only got so far as to build a few basic pages and 500 placeholders for terms and concepts. A external wiki could be very useful, but it means more time spent managing the wiki and less time spent writing  posts.

Then again, there is also a wikifying plugin for wordpress that will allow us to open up certain pages for registered users to edit on their own and build content. We could do a ‘project of the month’ or something to try to add batches of pages to the blog. As with all wikis, there are issues with vandalism, however, there are ways to deal with that. Do either of these wiki ideas sound like a good idea?

Speaking of adding pages, Anastasia is working on a list of books for the blog, and proceeds of sales will go to supporting the blog.

Anything else? Video in the sidebar? Related Posts plugin? Enhanced user profile pages? I’m open to suggestions! Feel free to get lost in the WordPress plugin directory – people have all kinds of interesting ideas expressed in widget form.

Thumpetty thump thump,
Thumpety thump thump,
Look at Franky grow.
Thumpetty thump thump,
Thumpety thump thump,
In all the farmers rows.

Franky the Snowmaize knew
That Greenpeace was out that day,
So he said “Let’s run and
We’ll have some fun
Now before I’m plucked away.”
Down from the city,
With pitchforks in their hands,
Running here and there
Carving circles in his hair saying
Donate if you can.
He led them down the streets of town
Right to U.S.D.A.
And he only paused a moment when
He heard a judge say “Political Hay!”
Though Franky the Snowmaize
Eliminates some sprays,
But he waved goodbye saying,
“Don’t you cry,
I will grow again someday.”

Thumpetty thump thump,
Thumpety thump thump,
Look at Franky grow.
Thumpetty thump thump,
Thumpety thump thump,
In all the farmer’s rows!

Merry Frankmas and a Happy New Year!

We have won a $1500 grant which we will use to bring more good stuff to the site, a conversation with Michael Pollan which will be sure to be enlightening for all, and an enhanced social media training session. Specific details of the last two have yet to be worked out, but what was conjecture last week is truly official now!

We will also be featured in a one-page ad in the Stanford Social Innovation Review magazine. Start the presses!

The runners-up were the Non-GMO Project and “The Campaign for Healthier Eating in America.” Although vote totals are not visible on the site, our unofficial count put us at over 800 votes, more than twice the number of votes of each of these two entries. The most-voted Latin American entry, Healthy Kids, Healthy Forests, has also won a round-trip ticket to anywhere in South America.

In what was a phenomenally exciting final few days of the contest, science bloggers and more came out of the woodwork to support us, and we would like to thank each and every one of you again for your help in promoting us and voting for us. A lot of people should deservedly share in this victory.

Not only is it a victory for science communication, but also for dialogue, honesty, and independence. There are a lot of vested interests on both sides of the debate over genetic engineering, and it is heartening to see that an independent group blog such as ours could muster support from the blogosphere and get people talking about the genetics of food like never before. I would like to see this continue, through the posts we will continue to write, more guest commentaries, interviews, videos, and conversations with each other in the new forum. We’ve been getting suggestions for new ideas, and we welcome more.

I would like to commend the Non-GMO Project and in particular their Executive Director Megan Westgate for supporting honest dialogue when things got a little ugly and accusations were flying around. And the Ashoka Changemakers people behind the scenes had to sift through almost two thousand votes to certify the contest – not a small feat so pat them on the back. I would like to thank them for hosting this contest and helping to facilitate more discussion on this important topic.

We’re now Change-Makers, so lets go out there and make some real change in the discussion about changes in the genetics of our plants. I hope you will stick around here awhile longer and help make a few changes yourselves. Let’s make our second year blogging here better than the first!

Last week, James and the Giant Corn gave us a plug with Putting Prejudice over Science. The Council for Biotechnology Information gave us a plug on Twitter, as well as Mica from Monsanto on her twitter account. Thanks for helping! We enjoyed an early lead of a dozen votes at the beginning, but when Monday morning rolled around, we were behind the Non-GMO Project by about 100 votes. They gathered an impressive number of votes from Friday through the weekend, networking through facebook and other places.

But then at a little after 8 in the morning PZ Myers of the popular blog, Pharyngula, boomed Yum, Genetically Engineered Plants! An hour later, we overtook the competition and took the lead! PZ is an immensely popular blogger, and the pulse of his endorsement was felt across the world, from California to the UK! It was almost inexplicable! Thanks for your help!

Later that day, the indomitable ‘Mean Girl’ Abbie Smith at Endogenous Retrovirus joined in with Vote for Biofortified! and chimed “DOO EEEEEET FOR THE PAPAYAS!!!!” She also liked the discussion going on at the changemakers site on our entry, and anyone that sticks up for the papayas gets an AA in their punnett square as far as I’m concerned. Thank you ERV!

With A Science-based blog about GMO, Tim Kreider at Science Based Medicine gave us a shining endorsement and sent a new army of voters our way. We are happy they like what we are doing over here, we love what you do for medicine over there! Thanks Tim!

Apparently, our quick influx of voters made a few people upset, and they started saying not-so-nice things about who must be supporting us. Cries of “Fixing the Competition” by the ‘biotech industry’ were flying around thanks to my newest bestest buddy GM Watch. And PZ Myers jumped back into the fray with a second post on his blog, saying …and those cheapskates at Monsanto haven’t given me a penny! Thanks PZ for the double-plug, and thanks GM Watch for keeping the attention on us! They must have thought we made a Deal with the Devil… they just didn’t know what kind. We were Pharyngulated.

Dr. ‘Orac’ at Respectful Insolence couldn’t stand to have PZ be the only one getting “all that filthy Monsanto lucre” so he posted, I may be late to this party, but I want my big Monsanto check anyway! You won’t be late in our thanks, oh acrylic-encased one. Thank you!

Thank you everyone who passed on our message through email, facebook, over the phone, etc. Your efforts are not forgotten, pat yourselves on the back – you know who you are!

And thank you Anastasia, Pam, Karl, and David for your tireless efforts to get out the vote and welcome people to the site! You’re all heavyweight science bloggers now. We have only one week to wait as the votes are tallied officially and the winner is announced next Wednesday. The votes are not visible on the entries anymore, but the last tally we had that was just minutes before the contest was closed placed the top three entries in this order:

Biofortified: 830 votes

The Campaign for Healthier Eating in America: 379 votes

The Non-GMO Project: 347 votes

These results are by no means final, as the changemakers team still has to verify that each vote came from a registered user, and we have undoubtedly made their job a lot harder. But it looks like we may have won by more than a 2-to-1 margin. Thanks for your support, everyone who managed to make it through their site to register – I know how hard it was so it means a lot to this little ear. We made a really good showing in this contest, and I hope you will stick around and read what else our bloggers have to say in the future, and check back on Wednesday for the results! Thanks again for everyone who supported us!

Enjoy this nifty graph of the voting progress:

Science is so cool!

And a good time was had by all!

Look, we just passed 600 votes!

I heard that their site was a little awkward and people were having trouble navigating around and voting, so let me show you how to do it step-by-step!

1. First, go to the changemakers registration page. (Try opening the link in a new window or a new tab with a right click so you can refer back to here.) Fill out your name, email, and username. If you are concerned about getting unwanted emails in your inbox, check the box on the right and you won’t be bothered by any. Finally, enter the words you see in the ‘captcha’ box on the bottom – if they look too confusing just click on the little circle of arrows and it will give you another one.

2. You are now registered for the site, and you will get an email in your inbox. In this email will be a random password and a link that takes you back to the changemakers site. Click on it. When you get there, there will be a login button that will automatically log you into the site. The first place it will take you after you click on it is your profile page where you can change your password to something you can remember more easily. Feel free to change it, but if you are just quickly registering to vote it won’t matter. Leave the window open and come back here.

(If you accidentally click off the site, the auto-login link will not work again, so you’ll have to use the username and password sent to your email to login again.)

3. Now that you are registered and logged in, open the Biofortified contest entry page in another window like you did before. (If you go to this page without logging in first you will not be able to vote.) On the right hand side is a Thumb’s Up that shows how many votes we have. Click on it and watch your vote be tallied up!

4. You are done! Wasn’t that easy? Pat yourself on the back for helping us out. Or leave a comment on this post saying you voted so we can pat you on your back, too!

Thank you for your vote, from the center of my pithy stalk. Check back before the 28th to see how well we are doing, and don’t forget to tell your friends!

My flight was delayed, so I missed the first part of the conference. Luckily someone filled me in on what happened. Apparently I’m 1.4 percent Helitron! Good deal.

I managed to get there just in time for the first viewing session for posters. But three geneticists barred my way saying “Is this guy legit?” I thought they didn’t recognize me, but they were pulling my leg, I was expected!

That was a relief! I wouldn’t want to miss these posters. This is my favorite part of scientific meetings. Meeting people, seeing what cool stuff they’re working on. Like Patrice, here, who was comparing the chromosomes of some of my cousins by FISH mapping repeat sequences. That means that wherever there were repetitive segments of DNA of different kinds, she made them glow different colors under the microscope! I wish I could show them to you but this stuff is unpublished. And she was simply glowing to see me.

Later that evening, I listened to a big presentation by Pam Johnson from the National Corn Grower’s Association. My favorite part was when she talked about how the connection between corn geneticists, breeders, farmers, and the consumer was the strongest of any crop grown in the states. It was also neat to know that studying me will help them understand switchgrass and more exotic plants like miscanthus.

Saturday I had a blast in the morning talks. All about how I release Jasmonic Acid when I’m injured, or some mutant relatives of mine that look more like a grass than proper corn. And I learned that even though two corn plants may be hybrids of the same parents, it matters which parent is the mom and which one is the dad!

At the second and final poster session, I got to talk to a few people who run websites about plants. Ann, here, works on the iPlant Collaborative, a center for organizing plant biologists to answer the BIG questions in the field.

And the nice folks at the Maize Genome DataBase told me all I wanted to know about my genome and how to access it from anywhere in the world. They even created a database of my weird looking cousins. Here’s to MaizeGDB! (Always jokers, those database types)

Apparently my fans are everywhere, look at this next guy – he dressed up as a giant… me! He even got the glasses right! And who is this other scientist with you?

Oh of course, it was Karl and Anastasia from Biofortified, promoting their stuff. And lo and behold, James from James and the Giant Corn was here too, so we grabbed him for a group shot.

After dinner, it was time for my keynote address. I was pretty nervous, but I think I managed to move the audience. I felt like they could all see through me, so I tried to imagine them without their husks. I sprinkled in a few, heh, corny jokes to get them started, and then I was off! “Compost! Compost alone moves the wheels of history!” I pounded my fists. I think I had an impact.

After that was over, it was time to party. And corn geneticists know how to do that. They tore open the curtain between the posters and the dining area, cleared out a dance floor, and brought forth the ethanol. These two ladies sure knew how to get down.

I’m not much of a dancer, but I play a good game of Euchre. So while everyone was grooving I was winning the kernels off of some grad students.

The next morning there were a few more talks, and then we all adjourned to go our separate ways. Just when I thought I could slip away un-noticed, a fan called down the hallway asking for a photo op. Sure, I can do a favor for last year’s chairman. Heck, Tom was probably the matchmaker that brought one of my ancestors together!

I had a fun time at Maize Genetics. These are definitely my kind of people. They grow hard, and they yield hard. I hope to see them all again in Italy next year.

Oh, the things I’ve seen!

]]> http://www.biofortified.org/2009/03/frank-n-foode-at-maize-genetics/feed/ 1 http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/ http://www.biofortified.org/2009/03/transposons-browsers-and-annotation-oh-my/#comments Mon, 16 Mar 2009 22:29:33 +0000 Karl Haro von Mogel http://www.biofortified.org/?p=231 Friday was the first full day of the 51st Maize Genetics Conference, and it was filled with all kinds of genetic fun. When I saw the program, I knew I would be up for the first talks of the morning at 8 am, because they were about transposons. The rest of the day was filled with poster presentations, talks about online genetic resources, and a discussion of gene annotation. Anastasia was there with me,

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Friday was the first full day of the 51st Maize Genetics Conference, and it was filled with all kinds of genetic fun. When I saw the program, I knew I would be up for the first talks of the morning at 8 am, because they were about transposons. The rest of the day was filled with poster presentations, talks about online genetic resources, and a discussion of gene annotation. Anastasia was there with me, and she’ll have all sorts of good stuff to talk about as we give the 51st MGC the exposure it deserves!

Transposons are really neat. Also known as Mobile Genetic Elements, Transposable Elements, or just “jumping genes,” they are sequences of DNA that are capable of popping out of a chromosome and inserting themselves into another. The most well known kind of transposon contains a gene that encodes for an enzyme called Transposase, which physically chops the transposon out of the DNA strand it is in, and puts it in another. The result is a gene that does not remain in a fixed location, and ‘jumps’ around the genome from Chromosome to chromosome, turning other genes on and off if it inserts in them or near them. Transposons were first described in Maize, by the famous Cornell biologist Barbara McClintock, and are thought of as some of the source of genetic variations that fuel evolution. Sometimes they can incorporate bits of other genes and move them around, causing all sorts of genetic modifications.

The morning talks were full of transpositional goodness. We had one talk about using transposons to help in genetic studies where you try to connect genotypes to phenotypes, and one on studying the relationships between different transposons. One very interesting one described a pair of transposons near each other, that could actually pull an entire gene out (between them) to move them somewhere else. Titled Paired Transposons: Natural genetic engineers – it really makes you wonder what the difference is between genes moved around by the plants themselves or by people intending to move them around?

One transposon talk was truly the highlight of the day for me. It described a newer, quite interesting kind of transposon called a Helitron. It sounds cool, and it is. Helitrons are transposons that have sequence that complements part of itself near one of its ends. What this does is forms a couple “hairpin loops,” which look like little twisty knots that stick out of the DNA strand. Here is a picture of a Helitron (with an ear of corn behind it).

Helitron superimposed over an ear of maize

Helitrons are a little different from other transposons in how they operate. Rather than being snipped out of a chromosome by transposase and re-incorporated elsewhere, they actually “roll” into another strand, making a copy of themselves (Leaving a copy behind as well.) It’s called “Rolling Circle” replication, and here’s a picture of how it works.

Pretty neat, huh? Helitrons have been found with all sorts of pieces of genes inside them. Genes are made up of coding Exons and non-coding Introns that are spliced out of the mRNA before it is used to make a protein. Helitrons have been found carrying one or more Exons that they captured from other genes. We don’t know at this point whether they can contain entire large genes, but they demonstrate a clear mechanism by which parts of genes get shuffled around the genome, providing more mutational fuel for natural selection.

In Maize, Helitrons make up 1.4% of the genome. It’s already half transposon as it is, but just imagine that every 70th bite of sweet corn you’re eating a mouthful of helitron DNA. Mmm, delicious.

David Tribe has also talked about Helitrons before at the GMO Pundit.

It is clear that genomes engineer themselves. Not in a purposeful fashion, mind you, but the random moving and shuffling of genes that has constantly occurred in the evolution of our crops plants makes tweaking or adding one or two genes sound like nothing at all. The analogy between mobile genetic elements and human genetic engineers is not only getting stronger, but was also reflected in the titles of some of these talks.

After lunch, we had the first poster session, displaying grad student posters on topics everywhere from more transposons, to carotenoids (Vitamin A precursors) in maize, database resources, chromosomal variations, outreach efforts, and even a few on switchgrass. Unfortunately for you, the reader, we couldn’t take pictures of the cool posters, because it represents unpublished ongoing research being conducted by grad students, undergrads, and their research groups. But we have heard that poster presenters have the option of submitting their posters to be published online, and when that happens we’ll point out some of the good ones.

This year, I did not have a poster to present, as I already showed off my corn videos last year, and I didn’t have enough evidence in my research to submit an abstract by the deadline in January. (Oh, I will have a lot of sweet sugar enhanced evidence for next year’s conference!) So I had a lot of time to read other posters and get the zeitgeist of maize genetics research. A few techniques here, some strategies there, and I’ve got a few more ideas for my own research goals.

Anastasia, however, did have a poster at the conference, on her research with Maize Zein proteins. Here she is showing off her research… who is that posing with her in the picture? I’m sure she’ll be telling us all more about her project in the near future.

After the poster sessions, it was time to jump back into the lecture hall to learn about some new genetic resources on the web for scientists. One really cool one, called TARGeT, allows anyone to take the sequence of a gene, search for similar gene sequences to find related genes, and then also assemble an evolutionary tree from those sequences. I have been wondering (for years) where I could do this without buying a proprietary program, and rest assured I’ll be trying this out soon. It appears that TARGeT, (originally named TERT in the conference abstract book) was intended as a teaching tool for high schools and college classes, but has since morphed into a research platform as well. If you make it easy to assemble genes in a tree based on sequence similarity, you’ll find scientists flocking to it.

There were also some improvements to MaizeGDB, MaizeSequence.org, and some other resources that maize geneticists use to do their research.

After dinner, we listened to a talk by Pam Johnson, Chair of the Research and Business Development Action Team of the National Corn Growers Association. I will talk about her presentation in a separate post.

Finally, we come to the last event of the day, a panel discussion about Community Gene Annotation. Here’s the problem: We have the sequence of the corn genome in-hand, and there may be upwards of 50,000 genes in it. We have evidence of these genes through sequence analysis, expressed genes discovered through research, and more. But our computer gene-processing algorithms aren’t very good at annotating them, and well-assembled genes in the database will be very helpful for future research.

So the panel discussion set out to get input from the Maize Genetics community. They wanted to Wikify it, allowing researchers to log in, edit, and have their annotations proof-read by others. Bit by bit, with hundreds of people contributing a little, we could complete this task in a few years.

Well, that’s what the panel set out to do, but in my opinion, it was an unsuccessful exercise. The conversation happened between two panelists on the right side, and a member of the audience. More time was spent discussing minor details about how it would work in a technical sense, and those on the left hand side hardly had a chance to contribute. Maybe the one or two scientists in the audience who dominated the discussion should have been on the panel, and the panel should have had a little more direction.

When it came to how to encourage scientists to voluntarily contribute to the maize gene annotation semi-wiki, the emphasis was on the stick rather than the carrot. I felt like going to the microphone to suggest “fabulous prizes” or “fame and glory in the community” for top annotation editors, if I didn’t feel so bored and annoyed. It also went on too long.

Later, I talked to my roommate from Oregon about it and my experience with wikis such as the Davis Wiki. And in a tight-knit-enough community, the social incentive to be a [top] contributor was a pretty powerful motivator that built over 10,000 pages. The Maize Genetics community is pretty tight-knit, and that seems like a good starting point for a massively collaborative project like this. Perhaps with prizes, recognition at the meeting, or dangling other carrots (rather than thwacking potential annotators with sticks), it could get done. Wikis are a ground-up kind of community, and I don’t think top-down requirements will be as helpful. Truth be told, I think I had a better chat with my roommate about the issue than the panel did. There, I said it.

I’m looking forward to being able to contribute to the annotation process, as in my own research I have assembled a few candidate genes for my own gene, only to find out that they were excluded by my latest mapping data. That information is lost and would have to be re-done by someone else, so I plan to enter it in this system when it is ready. This kind of system will be good, because there’s nothing that a few hundred knowledgeable and experienced geneticists can’t do with the maize genome.

At 9:30, we broke for some casual socializing, poster viewing, with a few free drinks sprinkled in. Anastasia and I both had some good conversations with researchers, including one very fortuitous meeting, where we got a lot of good info about resources to look up. We also had a chance to promote the Biofortified blog and make plans for the next day at the Maize Genetics Conference. Stay tuned for more!

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By Melinda Yerka

This is a painting done by Sir Charles Bell in 1809 of a soldier dying of tetanus.  Doesn’t look too comfortable, hmm?  Tetanus is a condition brought on when certain bacteria, called Clostridium tetani, enter deep puncture wounds, such as the proverbial rusty nail, or in this soldier’s case, a dirty sword in battle.  Once inside the wound, C. tetani bacteria produce the tetanus toxin, which then migrates to the body’s central nervous system where it causes tetanus disease, characterized by intense muscle spasms.  70% to 80% of the people who contract tetanus die.  Unfortunately, many of these people today are newborn infants and their mothers.  Infection by C. tetani bacteria occurs in these cases when unclean instruments are used to cut umbilical cords or remove a fetus from the mother’s womb during live birth or abortion.  If the mother had been immunized against tetanus toxin, she and the infant (who would be born with some of its mother’s immunities) would have survived.

You may wonder why the mother was not immunized when vaccines against tetanus have been readily available for more than a generation.  In fact, it is because vaccinations are far less prevalent in poor countries than in wealthier nations such as the United States and much of Europe.  Furthermore, despite growing humanitarian interest in providing vaccines, the infrastructure of many developing nations is not sufficient to safely synthesize, transport, or store them.  Lack of pharmaceutical companies, efficient transportation systems, refrigerated warehouses, and knowledgeable physicians all play a role in the continued fight against tetanus.  Nevertheless, progress has been made since the early 1980′s, as depicted below in a graph from the World Health Organization (WHO).

On the left y-axis is the number of tetanus cases per year from all around the world.  The blue bars represent the number of cases for each year listed on the x-axis, from 1980 to 2007.  On the right y-axis is the percent of the population that has been immunized against tetanus via the DTP3 vaccine for each year.  The blue line represents the percent of people who “officially” received the vaccine, and the red dotted line represents the percent of people who WHO and UNICEF estimate actually received it.  Note the sharp decline in the number of tetanus cases between 1980 and 1995.  This is largely due to a tremendous humanitarian undertaking by UNICEF to stamp out the disease.  However, even as recently as 2007, nearly 20,000 cases per year still occur.  Clearly more work remains to be done.

A novel approach to vaccination has been suggested since the mid-1990′s when genetically engineered plants began to gain rapid adoption on farms.  Genetic engineering’s first really big commercial success came in the form of incorporating herbicide resistance by way of a human-created transgene into crop plants.  As a result, a farmer could sow (for example) soybeans resistant to a particular herbicide, and then when weeds became a problem throughout the year, (s)he could simply spray that herbicide.  All of the plants in the field except her/his soybeans would die; hence, the birth of much simplified weed control.  But then came a leap of insight:  why not breed vaccines into plants, too?  Seeds do not require refrigeration to transport and store, nor a pharmaceutical company to produce them.

Researchers in Europe studied the possibility of incorporating a gene from C. tetani bacteria themselves, bearing resistance to the tetanus toxin, into plants.  A series of feasibility studies have been conducted and their results were published by Tregoning et al. in 2005 in the European Journal of Immunology, volume 35, pp. 1320-1325.  The title of their paper was “Protection against tetanus toxin using a plant-based vaccine.“  In it, they report transforming the chloroplasts of tobacco plants with a gene that codes for a fragment of a protein from C. tetani that can elicit an immune response. In other words, biotechnology was used to produce a vaccine against tetanus inside tobacco plants.  Tregoning et al. then immunized mice via a nasal spray (previously shown to be the most effective means of delivery) with a protein extract from transformed tobacco plants, and subsequently subjected them to a lethal dose of tetanus toxin.  All mice that received the plant-based vaccine survived, while all mice that did not receive the vaccine died.

Their results are shown in the graph below.

On the y-axis is the amount of tetanus antibodies (abbreviated Anti-TetC Ig) in the mice’s blood samples.  On the x-axis are the different groups of mice in the study.  The Tet x1 group received the tetanus vaccine once; the Tet x2 group received it twice, the Tet x2 + CT group received it twice in addition to a cholera adjuvant designed to elicit a stronger immunity response to tetanus; finally the control group did not receive a vaccine.  Where a star is above a particular group of mice’s result, it means that the average performance of that group was significantly different than the average performance of the control group.  Four mice were tested in each group, and as you can see, every mouse that received the nasal spray made from the transgenic tobacco plants survived, while every mouse that didn’t died.

While it is unlikely that such transgenic tobacco plants will be grown in Africa or Southeast Asia anytime soon (no tests have yet been conducted on humans), the implications of this work are nevertheless far-reaching.  They constitute the first clear proof that plants can be used to confer resistance to tetanus in mammals, and continue to push open the door that will hopefully, one day, lead to equal access to basic health care around the world.

Melinda Yerka is a graduate student studying Plant Breeding and Plant Genetics at UW-Madison. When she’s not growing weeds in the greenhouse for her research, she’s plucking weeds in her organic community garden plots.

There are a lot of things on his list, and executive orders are flying out of the Oval Office. Some believe that among his list of things to do is to require mandatory labeling of genetically engineered (GE) foods, but as I will demonstrate below, it is not on his list. First, a bit of background.

Obama has made his policy priorities public, and has made it a point to include people who both agree and disagree with him a part of his administration. Further channeling the memory of Abraham Lincoln, he even rode from Illinois to Washington D.C. on a train. The first 100 days are going to be a very exciting time in the realm of presidential politics.

President Obama has already vetted and selected several people to form his cabinet, which were announced late last year. No doubt the planning went back well into the election season, and his selection of Steven Chu as Energy Secretary gets high marks from me. Including Hillary Clinton as Secretary of State also raises an approving eyebrow. The process has been remarkably free of lobbying and special interests, but plenty of public attention.

There has been quite a bit of attention on his pick for Secretary of Agriculture, Tom Vilsack. Probably more so than any previous Ag Secretary. Many people in this country are hungry for reforms in how we do agriculture, and following the Farm Bill Wars of 2007-2008, Vilsack comes at a time when Ag is in the spotlight.

The Claim

But Jeffrey Smith, anti-GE activist, is not taking Obama’s ag appointments sitting down, in an article titled Obama’s Team Includes Dangerous Biotech “Yes Men.” (repeated here) He criticizes Vilsack, although apparently before the nomination was announced – he seemed to think that Vilsack’s name was withdrawn. He points out that Obama’s transition team includes Michael Taylor, who was involved in some of the early regulation of GE crops, and Sharon Long, who was a scientific advisor to Obama’s campaign, and once worked for the biotech company Monsanto.

He also points out Harold Varmus, a Nobel laureate who authored a key study on GE crops for the National Academy of Sciences. Smith does not explain how Varmus is supposed to be a problematic pick as he did the other people in the list, so it seems all you have to be to be a Biotech “Yes Man” is be in favor of GE crops. (Even if you’re a woman, in the case of Long.)

But two statements of Smith’s seemed rather odd, the first is:

I don’t know Barack Obama’s position on GMOs.

You could say that we all don’t know Obama’s full position on GE crops, but you could also say that Smith didn’t do much research for his article.

ScienceDebate2008 sent a list of questions to then-candidates Obama and McCain, and here is Obama’s GE-focused response in full:

Advances in the genetic engineering of plants have provided enormous benefits to American farmers. I believe that we can continue to modify plants safely with new genetic methods, abetted by stringent tests for environmental and health effects and by stronger regulatory oversight guided by the best available scientific advice.

The article cited in Smith’s article, Obama, like Bush, may be ag biotech ally, bolsters the case that Obama is favorably disposed toward GE crops.

Obama’s official statements on development are “pretty strong on agricultural science,” said Robert Paarlberg, author of the recent book “Starved for Science: How Biotechnology is Being Kept Out of Africa.”

“I certainly haven’t seen any sense of opposition to technology.”

On to the second odd statement by Smith. It was put in BOLD so there’s no possibility of confusing the emphasis with his other, underlined emphases:

There is, however, one unambiguous and clear promise that separates Obama from his Bush and Clinton predecessors.

President Obama will require mandatory labeling of GMOs.

Really? When did he say that? Smith cited no reference, and given the above, it didn’t seem likely. So I decided to put on my skeptical thinking cap and trace this claim to its source.

Tracing the Claim:

After a few repeated searches, I found a few more folks saying the same thing. The OCA claims that Obama made a “campaign pledge,” promising mandatory labels for GMOs. Their source, however, is Jeffrey Smith again, at his website, responsibletechnology.org. This is where it gets a little weird. The link (above) provided by the OCA was a link to a petition for Obama to support the mandatory labeling of GE foods. Wait, if Obama has already promised to support mandatory labeling of GE foods, why the petition?

It gets better. NJ Jaeger, Smith’s communication representative, wrote a story a year ago claiming a bit more.

In late November, after reviewing the latest data about genetically modified organisms (GMOs), also known as “biotech foods”, all leading democratic presidential candidates agreed to fast track the mandatory labeling of genetically engineered foods.

Apparently, they, including Obama, all agreed not only to mandatory GE food labeling, but also to “fast-track” it – like you could expect them to get it done in their first 100 days or something.

But if you read Obama’s stated agenda at Change.gov, you will find no reference to GE food labeling, mandatory or not, nor for fast-tracking it either. There are quite a few other things in his Rural Agenda like tightening down on CAFOs and rebuilding rural infrastructure. No GE labeling promise there. (I have also not found anything from the Clinton or Edwards campaigns that use this language either.)

All references lead to Smith, so I contacted his organization. NJ Jaeger responded, saying that written support for mandatory labeling of GE foods was secured the previous fall by Craig Winters at TheCampaign.org – a site devoted to labeling foods derived through genetic engineering.

Not in the Agenda

After searching the site, I found only two references to the claim that Obama would push these labels. The first is a page on the campaign that just states that Obama, along with a few others, “supports mandatory labeling.”

The second is an article from early on in the primaries. The Democratic Candidates were asked about various rural issues, and genetic engineering was mentioned. According to the article, published on November 10, 2007 in the Des Moines Register,

He said he will stand up against conglomeration in the farm industry, and that he’s already working to support the packer ban, which would limit ownership of livestock by meatpacking companies.

Obama said he wants food labeled for its country of origin, and marked if it’s genetically modified. And he would push for renewable energy, by investing in biofuels, solar and wind.

Notice the difference between what is attributed to Obama in the article, and some of the items on his Rural Agenda:

• Regulate CAFOs: Strictly regulate pollution from large factory livestock farms, with fines for those that violate tough standards. Support meaningful local control.
• Establish Country of Origin Labeling: Implement Country of Origin Labeling so that American producers can distinguish their products from imported ones.
• Encourage Organic and Local Agriculture: Help organic farmers afford to certify their crops and reform crop insurance to not penalize organic farmers. Promote regional food systems.
• Promote Leadership in Renewable Energy: Ensure that our rural areas continue their leadership in the renewable fuels movement.

Meat, check. Country of Origin, check. Local Agriculture, check. Biofuels, check. GE food labeling, absent. I tried to get in touch with the author of the article to see if they had more details in the form of notes, audio or video clips, but I have not received a response at all.

I did manage to get in contact with Craig Winters, and he confirmed that the Des Moines Register article was the source for the claim that Barack Obama ‘promised’ to label GE foods. Unless I hear back from the author of the Register article, the only evidence we have is a sentence that states that he “wants” GE crops labeled, which is not a promise for mandatory labeling.

According to this YouTube video, he also thinks we should decriminalize marijuana. As much as I might hope that he would make some effort in this area during his presidency, he has not made it a part of his platform or agenda, and I do not expect that he will do it.

Craig was not aware of the positive statements Obama has made about genetic engineering, and he was doubtful about Obama’s true position, hoping that Obama could be convinced to oppose genetically engineered crops. He also told me that he has not received any written statements from, nor had any contact with Barack Obama’s election campaign on the issue. It’s beginning to unravel.

From the text of the TheCampaign.org site, however, it implies that they have gotten a response from Obama’s campaign, so I can understand where Smith et al may have misunderstood it. The site does not state that Obama promised anything, although from talking to Craig it appears he took the sentence in the Des Moines Register article as a promise.

So I contacted NJ Jaeger again. Now that NJ had the article to look at, the response was:

In the article [Obama said he wants food labeled for its country of origin, and marked if it's genetically modified.] He also said [ “We’ll take action on a rural agenda in my first 100 days in office,” } That is a pretty powerful fast track statement.

President Obama is a smart cookie, and his oratory skills and communication abilities are virtually unmatched. I believe that if Obama made a campaign promise to label GE crops, it would indeed be a clear, unambiguous pledge. And it would be in more places than a single article, it would be on his agenda, and there would be consistent campaign statements. NJ seems convinced that this article still supports their claims. Take a second look.

Obama told the farmers that as soon as he takes office, he would hold a summit on rural issues in Iowa, bringing Democrats and Republicans together.

“We’ll take action on a rural agenda in my first 100 days in office,” he said.

He pledged to put the people’s interests ahead of the special interests.

“That’s why Washington insiders matter when they’re in Washington County, Iowa, not Washington, D.C.” said Obama, who was flanked by four Secret Service agents.

He said he will stand up against conglomeration in the farm industry, and that he’s already working to support the packer ban, which would limit ownership of livestock by meatpacking companies.

Obama said he wants food labeled for its country of origin, and marked if it’s genetically modified. And he would push for renewable energy, by investing in biofuels, solar and wind.

Notice that the statement that he ‘wants’ GE foods labeled does not indicate a promise. Notice that the “rural agenda” statement in reference to 100 days was separate. In fact, Obama did make a fast-track promise on a rural agenda, but his published agenda does not include GE food labels. You cannot honestly twist this article to reach the conclusion that Jaeger and Smith have.

At the time that he wrote his article, Jaeger was not aware of the Des Moines Register article, which was the de facto source of the claim. When I asked what the “fast-tracking” part of her article was based on when he wrote it, she said:

The information I had at that time was that all leading democratic presidential candidates had been approached and it was a priority for them.

You can easily see that not exercising a degree of skepticism, or doing the necessary fact-checking that comes with responsible journalism, combined with incomplete communication and wishful thinking is the basis for this claim. In light of this, Jeffrey Smith and all others who have repeated the claim that Barack Obama promised to label GE crops should retract their statements. But I won’t hold my breath.

Reconciling statements

How can we reconcile his statement regarding GE crop labeling early in the primaries with his agenda? He could certainly have changed his mind. Think about this: when focusing on an issue that ties together climate change, national security, energy policy, and agriculture, he settled on plant-based biofuels as a major issue. Some advances in genetic engineering may make biofuel production more efficient and environmentally friendly. Another development that is nearing the market are crops that use half the fertilizer, which could drastically cut the energy requirements of farming.

As I remember from the presidential debate that focused on the economy, he may need to choose a few plans from his stated agenda to cut for revenue reasons. He would be even less likely to add an extra cost that is not even on his agenda.

Added cost in a troubled economy, no tangible consumer benefit, and the fact that if there’s an added cost consumer support for labeling evaporates – may have persuaded Obama that it was not an important enough issue for him to take up. Additionally, the general desire to prevent a “Brain Drain” of experts to other countries, and to stay ahead of technological developments worldwide may also contribute to his decision. Even if it these points weren’t mind-changers during the election, they may dissuade him from pursuing GE food labels while in office.

And on that note, his generally favorable disposition toward GE crops may be an indicator that he may not want to pursue mandatory GE food labels. The two correlate, but I would like to note that being pro-GE does not necessarily translate to being anti-label. But that’s a post for another day.

Politicking?

On the other hand, the issue may not have been important to him from the start. According to this article, Obama was the only Democratic candidate to not respond to a request for a position on GE food labeling, less than a month before the Des Moines article was written. He may have wanted to avoid setting himself apart from his colleagues on this issue, and so tried adding it to his prepared speech, to try it on for size, but it has not been seen since.

What if Barack Obama did indicate that he did want to label GE crops during the primaries to try not to let his opponents get an edge over him in a close race, but did not plan to make it part of his platform? In that case he was being a politician. But the reverse, which anti-GE activists are counting on, is that he fully intends to fast-track GE food labeling, but didn’t want to make it a stated position on his platform, which instead makes him… a politician. But one version of this politician has the weight of evidence, and the other, wishful thinking.

Conclusion:

I realize that this wild goose chase has become a long post, so here’s a bullet-point summary of my findings:

• If anything, President Barack Obama appears to be warmly in favor of genetic engineering, although there is some wiggle room with his campaign statements.
• President Obama’s picks for Ag Secretary, campaign advisers, and other cabinet positions further suggest that he is positively disposed to GE crops. Given his emphasis on plant-based biofuels, he may also see it as a means to achieve his domestic renewable fuel goals.
• Obama did not make a written campaign statement promising to require mandatory labeling of genetically engineered foods.
• Obama did not respond to mailings from The Campaign to Label Genetically Engineered Foods, nor did his presidential campaign contact them.
• Obama’s declared agenda, now housed at the White House website, indicates that these labels are not on his agenda.
• The claim that he will “fast track” GE food labeling appears to be an invention or the result of miscommunication.
• President Obama only once expressed a desire for GE food labeling, but has not made a campaign promise or pledge that he will “require mandatory labeling” for GE food.

Maybe he will push for labeling. Maybe when he comes out of his Rural Agenda summit, the Obama Administration will announce that mandatory labeling for GE foods will be enforced within one year. That is still possible, which is why I say that Obama probably will not label GE foods. However one thing is clear and unambiguous: There is no evidence that Barack Obama ever made a statement strong enough to be considered as a campaign promise to label GE foods. He’s got a lot to work on cleaning up the mess that this country is in, and the last thing that President Obama needs are false claims of campaign promises that he never made.

It is important that the political discussions surrounding this historic presidency be honest and accurate. As Martin Luther King Jr. once said,

A lie cannot live.