I think I’m having some fun with transitions. Hey, at least I didn’t do any star fades! (You aren’t safe from them, though)

Potentially promiscuous pollen from corn tassels by circulating via Flickr.

Many people, including me, are concerned about potential harm to crop biodiversity from gene flow. Most people’s concern focuses on transgenics. There is a certain probability, albeit small, that transgenes will end up in the progeny of non-transgenic plants, weedy relatives of the crop, or wild relatives that grow nearby due to pollen flow. Transgenes can also be moved from place to place by accidental or purposeful movement of seeds.

How much transgene flow is actually happening is a subject of some controversy, but what about gene flow between non-transgenic plants?

There is potential for problems whenever plants that aren’t supposed to cross stray from their intended mates. Some things to think about include how gene flow happens at the field and genetic levels and what characteristics of the genes themselves can affect permanence of contaminating genes once they get into a variety they shouldn’t be in.

Gene flow with transgenes can help us to think about gene flow of “regular” genes

In the 2004 paper Gene Flow from Cultivated Rice (Oryza sativa) to its Weedy and Wild Relatives, Li Juan Chen showed that a marker gene “flowed” in their test field from transgenic cultivated rice  to weedy rice at rates between 0.011 and 0.046 % and to wild rice at rates between 1.21 and 2.19 %. The marker gene Chen used is called bar, which is easy to screen for because it makes plants resistant to the antibiotic and herbicide biaphalos. Just spray the progeny and you’ll know if they’ve got the gene. Chen confirmed presence of the bar gene with PCR. These rates seem pretty low, but rice is mostly a self-pollinator, and the pollen is very short lived. If out-cross rates in rice reach 2.19 % we could expect to see rates even higher in other species. This tells us that transgenes can be passed to weeds, but also, more broadly, tells us that any gene can be passed from cultivated rice to weed rice.

Gene flow could be a problem in the opposite direction as well. In the 2009 paper Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids, Vinod Shivrain showed that progeny of a cross between weedy red rice and cultivated rice were more successful if their mother was the cultivated plant. These hybrid grains can fall back to the field on accident or be collected and planted the following year with the regular seed. Either way, the rice farmer now has rice plants that don’t have all of the desired characteristics of the cultivated rice. The plants will have at least some genes from the weedy rice that could help it out compete the desired rice plants but produce less grain. This paper shows that gene flow from weeds to crops can happen, and that it can be a problem.

Maize, unlike rice, is a promiscuous out-crosser. The pollen is heavy and still fairly short lived, so mostly pollinates plants that are nearby, but wind-carried pollen and stray seed can carry transgenes away from their intended fields. The story of transgenes in landraces of maize is summed up beautifully in the 2007 paper Gene flow from transgenic maize to landraces in Mexico: An analysis (pdf). Kristin Mercer tells us that research on the subject has had mixed results. Transgenes likely do exist in landraces in Mexico, but the extent of the “contamination” is not as wide as some researchers have proposed. Some of Kristen’s other research focuses on how crop alleles move in wild sunflower populations. The sum of her research is that we can expect gene flow back and forth between any compatible plants: wild, weedy, cultivated, transgenic, landrace.

Gene flow’s effect on biodiversity

Image of corn plant by University of Nebraska Lincoln, adapted by Anastasia Bodnar. All other images in this post by Anastasia Bodnar.

Understanding the impact of gene flow on biodiversity (or more appropriately, crop diversity) requires some understanding of what happens at the genetic level. I like to sit down and draw pictures to help me think about genetics. I hope it helps some Biofortified readers as well!

The image to the right shows two hypothetical varieties of corn. On the left is a modern inbred variety. All the plants are identical. There is no or low genetic variability within the inbred, because there is only one version of each gene present in the variety. On the right is a landrace or heirloom variety. All the plants are different from each other to some degree. There is high genetic variability within the landrace because there can be many versions of each gene present in the variety.

Below  is a (very) simplified view of what happens at the chromosomal level when an inbred is crossed with a landrace (in a hypothetical crop with one chromosome). Note: a hybrid or even an open pollinated variety could be substituted for inbred here, it was just easier to use an inbred. Similarly, a wild variety could contaminate a landrace. One landrace can contaminate another. One inbred could contaminate another. Weedy relatives can contaminate crops. Crops can contaminate wild varieties… you get the idea.

In the inbred (red), the two sister chromatids for each chromosome are identical to each other. There is only one version of each gene in the inbred, also known as two copies of the same allele. In the landrace (blue), the two sister chromatids are different from each other. For each gene in the landrace, there can be two different alleles. The different shades of blue indicate different alleles for some genes on the sister chromatids.

Imagine a situation where a field with the inbred is right next to a field with the landrace. Pollen will flow between the fields (to some degree – depending on weather conditions, pollen size, and tons of other factors). If the inbred and the landrace are crossed (whether pollen from the inbred fertilizes the landrace or vice versa), each of the offspring will have about half of the genetic information from the inbred and half from the landrace. Since the two chromatids are the same for the inbred, none of the information from the inbred is lost in any individual. Since the two chromatids in the landrace individual are different, each of the offspring only receive half of the genetic information from the landrace.

When those offspring make gametes, recombination often occurs which results in chromatids that contain some alleles from each grandparent. Crossing over, shown here, is one type of recombination. If those gametes then combine with the inbred, their progeny will only have about 1/4 of its genes from the landrace grandparent.

Genetic diversity can be lost in certain situations. For example, if a farmer growing a landrace finds plants in the field that have positive traits, the farmer will choose to plant those seeds for the next year. If those beneficial traits are due to genes from the inbred, the farmer could effectively select for plants with one or more genes with the inbred and against plants that don’t contain any genes from the inbred. If pollen from the inbred is reintroduced year after year, the farmer could plant seeds from those plants that contain more and more alleles from the inbred variety, and alleles from the landrace could be lost over time.

On the other hand, if the farmer chooses seeds from plants that look more like the landrace, then alleles from the inbred could be lost fairly quickly. If pollen or seeds from the inbred are introduced infrequently, the landrace would maintain a low level of alleles from the inbred, with those alleles eventually disapearing.

Of course there are many situations in between, and those depend greatly on what effect each gene or allele has on the plants they have contaminated.

Once it’s in there, how long will it stay?

Transgene or not, wild or cultivated, all of the genetic material goes into a big mixing pot to be stirred by random mating and natural selection in the case of wild plants or by breeding and artificial selection in the case of cultivated plants. One of Kristen’s points in Gene flow from transgenic maize to landraces in Mexico: An analysis (pdf) is that the permanence of transgenes in a non-transgenic population depends a lot on what the transgene is exactly, and the same idea applies to non-transgenic alleles.

To break it down: Any given transgene or any allele of a gene can have one of three effects on the plant: positive, neutral, and negative. The effect depends on what plant the allele is contaminating and what trait is conferred by the allele. Finally, how long a contaminating allele stays in a population depends on all of these factors.

Positive

Some alleles would be beneficial in almost any situation. Herbivore resistance, including genetically engineered Bt toxin and increased expression of non-transgenic chemical defenses, would help both cultivated and non-cultivated plants escape damage from susceptible herbivores. These types of transgenes and alleles would be likely to persist in any population they contaminated. These would definitely be bad traits to have in weeds. They could be desirable in a landrace from a farmer’s point of view.

Neutral

A gene that increases the size and number of fruits produced by a plant is desirable from an agricultural perspective, but could have a negative effect a wild plant, because the plant would have less resources to devote to other needs like herbivore defense and drought tolerance. These types of alleles will not persist in a wild population, but could persist in a landrace if it is seen as desirable to farmers.

Negative

Alleles or genes that are specific for certain farming systems won’t persist in wild populations, weeds, or landraces unless they are exposed to those farming conditions. These include genetically engineered genes like glyphosate tolerance and the non-transgenic allele for Clearfield tolerance. If these alleles or genes contaminate a population but that population is never sprayed with the chemical, there is no selection pressure to keep the trait.

Of course these are just three examples of different traits and there are thousands if not millions of traits out there that might have different effects, but you get the idea.

Every day, pollen blows and seed is moved. Every day, genes and alleles are transferred from one plant population to another, no matter if they are transgenes or not. Those naughty plants just won’t keep to themselves! If we are truly concerned about gene flow, we really should be considering gene flow from all sources, not just transgenic crops.

Chen LJ, Lee DS, Song ZP, Suh HS, & Lu BR (2004). Gene flow from cultivated rice (Oryza sativa) to its weedy and wild relatives. Annals of botany, 93 (1), 67-73 PMID: 14602665

Shivrain VK, Burgos NR, Gealy DR, Sales MA, & Smith KL (2009). Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids. Pest management science, 65 (10), 1124-9 PMID: 19530257

Mercer, K., & Wainright, J. (2008). Gene flow from transgenic maize to landraces in Mexico: An analysis Agriculture, Ecosystems & Environment, 123 (1-3), 109-115 DOI: 10.1016/j.agee.2007.05.007

Here’s to hoping that I win a prize again! Here are the other submissions, check them out!

Viral DNA in food? How nefarious! Well, not really.

The most common piece of viral DNA in GE crops is the 35S promoter from the Cauliflower Mosaic Virus. Promoters are like “on switches” that tell the cell when and how strongly to express or “turn on” a gene. The 35S CaMV promoter is a very well-described one that tells the cell to always leave the light on. Though part of those inserted genes came from a virus, it doesn’t make viruses of any kind.

Another way you might find viral DNA involved in genetic engineering is in developing virus resistance. A protein that coats the Papaya Ringspot Virus was engineered into Papayas to block where the virus attaches to the cell and prevent infection. Later on, as we started to understand more about some really cool aspects of genetics, it was discovered that the viral gene that was inserted also does a little gene silencing.

Susceptible papayas on the left, resistant on the right

Termed RNA Interference, or RNAi, you can stick a piece of viral DNA that the cell uses to recognize infecting viruses so it can destroy them – kind of like a vaccination for plants. In the case of inserting a viral coat protein, a virus-infected papaya will also have this harmless protein everywhere in the fruit, and in the case of the latter, RNAi doesn’t even produce proteins and carries very few safety concerns.

Nevertheless, the prospect of eating viruses still sounds scary. Well guess what, you are yourself made partly from viruses, and are eating things made from viruses. The complete sequence of the B73 Maize Genome has just been published, and at final count*, it seems that corn itself is mostly virus, if you look at its DNA sequence. Upon reading this, Abbie Smith at ERV says that she has fallen in love with corn all over again. She noticed that corn has a lot of viruses in its genome:

The human genome is made up of about 45% of this stuff.

Corn genome?

84.2%

WHOAAA!

A full 75.6% is Class I retrotransposons! Thats so cool!**

Yes that’s right, the corn genome is made up of mostly viral DNA, and the same is probably true for most of the plants you eat. Heck, we ourselves are almost half virus on the DNA level!

This really puts into perspective focusing on the source of the DNA (virus, plant, animal…) when talking about genetic engineering. If you think that “viral DNA” is unsafe in and of itself, then you might not want to eat anything at all, because it is everywhere and in everything.

For complete coverage of the Corn Genome and its discoveries, take a trip to James and the Giant Corn.

I always find discussions of “plant genes” vs “animal genes” and “viral genes” interesting, because what about the genes that are shared by different organisms? Plants and animals are all eukaryotic cells with nuclei and mitochondria, which share a common ancestor as well as a whole slough of common genes. Can you call a gene shared by both plants and animals a gene that ‘belongs’ to either one? Both? Neither?

Forgive me, but I’m a bit of a nominalist on this topic when it comes down to the nitty gritty philosophical details: my position is that there is no such thing as a plant gene. Or an animal gene, viral gene, etc. There are, instead, genes found in plants, genes found in animals, and genes found in viruses. Genes shared by Eukaryotes are just that – genes in common. Apart from the syntactical preferences of different organisms in how they like their DNA to read, there is nothing about a gene that makes it belong to one lineage or another.

Previous philosophers would think about these things in terms of ‘essence,’ and the term still has its uses. Like essential oils, the essence of something is what is left after you have ‘boiled down’ that something to its most ultimate and fundamental parts. There seems to be a pervasive notion that all genes carry the “essence” of the organism they are found in. When people talk about “fish genes in my tomato” they are expressing a worry that their familiar tomato will have some of its essential characteristics mixed up with those of a fish and that it will cease to be a tomato anymore.

The fish-tomato example is rather ironic, as this meme began when scientists were experimenting with using the “antifreeze protein” from a species of fish to see if they could keep tomatoes from freezing (They were never commercialized). But as it turns out, a similar antifreeze protein in cod evolved out of noncoding DNA – going from useless sequences (sometimes haphazardly referred to as ‘junk DNA’) into a functional and essential gene. If you put this antifreeze gene in a tomato, is it even a fish gene? Or a junk gene? What if it once was a viral gene that got into fish, and eventually became what it was before a genetic engineer stuck it in a fruit, is it still a viral gene?

It’s an antifreeze gene… that evolved in fish. And you would essentially still be eating a tomato.

What should be the final nail in the coffin of the genic essentialism going around in these discussions is the fact that the foods we eat are made up of so much DNA from other species. Corn is 84% virus yet it still manages to be Corn. I also just found references to these issues in a book called Acceptable Genes: Religious Traditions and Genetically Modified Foods. Does a plant with a ‘pig gene’ carry the essence of a pig and present a problem for Jews and Muslims?

We’re entering an age where genetics are going to play a much bigger role in our lives, and in our food, so we need to wrap our collective heads around how our gathered knowledge compels us to change our perspectives. We may be 45% virus ourselves, but at least we could stop acting like them and propogate ideas that help us understand this stuff rather than add to the confusion!

*Nothing in science is truly final, but this is about as close as it gets.

**It is really cool, Abbie. Except when you are searching for a gene and you keep running into broken bits of retrotransposons all over the place! Can’t your people clean up after themselves?

(By law, any discussion of chloroplast origins compels me to mention the similar origin of the mitochondrion. With those requirements now met, let us now continue.)

The focus of this post will be more technological than biological, but there are a few basic facts we need to get out of the way before we can proceed. Briefly:

• Chloroplasts, along with leucoplasts, proteinoplasts, elaioplasts, amyloplasts, statoliths, and chromoplasts, belong to a class of organelles known as plastids. The names of these other plastids aren’t important so long as you realize the chloroplast isn’t the only game in town. That’s why the title of this post is “Plastid Engineering” and not “Chloroplast Engineering.”

• Plastids replicate separately from their host cell, and in any given cell there can be 100 to 1,000 plastids. Moreover, plastids contain multiple copies of their genome (plastome) to the point where a single plant cell may contain 10,000 plastomes.  By contrast, the nuclear genome has only one copy (this is manifestly untrue, but we’re talking orders of magnitude here).

• Plastids behave a lot like prokaryotes. Their genome is circular, their proteins aren’t glycosylated (i.e., have sugars attached to them), and they can process polycistronic mRNA (i.e., more than one protein produced from a single mRNA; most eukaryotic genes are monocistronic).

• Over history, most plastid genes have migrated into the nucleus, even though the protein produced might still accumulate in the plastid. Those proteins are instead brought back to the plastid by a specific targeting sequence. Quite a few genes have been lost from the original cyanbacterial ancestor, leaving only 50 to 200 of the original ~3,000 genes in most plastids today. In scientifically and agriculturally important species, these genes have all been sequenced and characterized.

• Plastids are inherited uniparentally, that is, from one parent and not the other. In most flowering plants, only maternal plastids are passed on. In some species, such as pine trees, paternal transmission in the pollen is the norm.

Ideally as you pored over those facts your brain started piecing together the reasons why we would want to tinker with plastid – rather than nuclear — DNA. Uniparental inheritance is a big one: even people who know next to nothing about GM crops know there’s concern about, say, GM corn in one farmer’s field contaminating non-GM corn in their neighbor’s field. Crops with genetically engineered plastids (known by the awesomely retro-sounding name transplastomics) don’t have this problem since plastids aren’t usually found in pollen. Of course plant biology is, technically, a biological science, so there are exceptions that will to be need to be addressed.

Extreme polyploidy is another attractive feature: inserting a gene of interest (GOI) into the chloroplast genome means having up to 10,000 or more copies of that gene per cell. That translates (hah!) into very high levels of protein production indeed. And since most plastid genomes are already well characterized, we can know in advance where our inserted DNA will wind up.

Non-glycosylation differs in usefulness depending on the source of the foreign gene. Plants, mammals, fungi, and insects all have different patterns of glycosylation, with plastids and prokaryotes not participating in the ritual at all. So, proteins normally present in prokaryotes are produced identically in plastids, whereas proteins of eukaryotic origin might be missing structural elements crucial to their function (or the protein might find it does just fine without those extra sugars, you never know).

So what are some limitations and problems with plastid engineering? To answer that question, we must first learn how transplastomic plants are created.

Today, only a few species have had their plastids successfully transformed. The first transplastomic organism was created in 1988 using the unicellular alga Chlamydomonas reinhardtii, notable for having only one large chloroplast. Two years later, stable tobacco transplastomics were created. Since then, varying levels of success have been achieved with potato, tomato, rapeseed, cauliflower, poplar, rice, soybean, and a few others, but only in tobacco is plastid transformation routine.

The first step in plastid transformation is introducing the new genes to the old. Typically this is done by particle bombardment (“biolistics” or the “gene gun”) or polyethylene glycol (PEG) treatment. In the latter, you remove the cell wall of a plant cell to create a protoplast and then subject it to a solution of DNA in PEG, whereas in the former you basically shoot the plant with DNA. Since particle bombardment is the more commonly used of the two, I’ll explain its mechanism.

First you need your gene of interest in a plasmid (a small circle of DNA that contains of a few genes and can be grown in and purified from bacteria). The plasmid will also contain a selectable marker (a gene that confers resistance to antibiotics like spectinomycin, streptomycin, or kanamycin) and a visual marker (green fluorescent protein or a derivative thereof). The GOI, selectable marker, and visual marker will be flanked by sequences taken from the plastid genome, carefully chosen so that the site of homologous recombination (see further reading) does not disrupt the function of normal plastid genes.

Next, the plasmids are expressed to high quantities in bacteria and purified, then adhered to small particles of tungsten or gold, often to less than a millionth of a meter in diameter. A small section of leaf tissue is placed into a low-pressure vacuum chamber and bombarded with a volley of DNA-coated particles, obliterating most of it.

A very small percentage of the remaining tissue will contain transformed plastids at this point. Worse yet, a surviving cell with a transformed plastid will still overwhelmingly contain untransformed plastids. The next steps are the lengthiest and most tedious part of the process, for now the bombarded tissue must be coaxed into regenerating into a wholly new plant while at the same time eliminating any untransformed plastids it may still harbor. Stringent antibiotic regimens are applied to emerging plantlets, and visual inspection of GFP expression reveals areas of transformed plastids. Those areas are then sliced away and grown on their own regenerative media. This process is repeated for about 20 cell divisions before a state of exclusively transformed plastids (homoplasmy) is achieved. Once reached, the plantlets are allowed to grow in the absence of antibiotic selection and set seed at maturity. If the progeny are shown to be homoplasmic, then the line is considered stably transformed.

So you’ve created a transplastomic plant. Now what? Obviously that antibiotic resistance gene is no longer doing you any good, so you’ll have to find a way to get rid of it lest it sap precious metabolic resources and stunt your plant’s growth. And just how certain are we that plastid inheritance is uniparental? What if life, as renowned chaos theorist Ian Malcolm once gravely intoned, finds a way? Shouldn’t we run a few tests to determine the likelihood of plastid-transference via pollen? And what about those really important plants, the cereals? Why are their plastids so difficult to transform?

All important questions, yes, but we’ve already reached 1,200+ words in this primer, so you’ll have to wait for subsequent posts to quench your curiosity!

Further reading:

Web

Plastid Transformation

Dead tree

Daniell, H., Khan, M.S., & Allison, L. (2002). Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology. Trends in Plant Science, 7(2), 84-91. PMID: 11832280

Maliga, P. (2004). Plastid transformation in higher plants. Annual Review of Plant Biology, 55, 289-313. PMID: 15377222

Cody Cobb is a first year Ph.D. student in plant biology & pathology at Rutgers, the State University of New Jersey. He has lived his entire life previous to this point in Texas and is currently enjoying his first autumn. He feels he should mention that his earliest desktop PC was an Acer.  So is his ‘mustache.’

When I first heard about the contest, the grand prize was a ‘social media training’ session and a conversation with Michael Pollan. As I noted on my personal blog, I have been waiting to do an interview with him for almost three years. Back in 2006, I participated in a panel discussion (available here on UCTV) with him and others on Food, Farming, and Genetics, as part of the Community Book Project at UC Davis, which focused on The Omnivore’s Dilemma. Pam Ronald was also the moderator of the discussion. Our group conversation left more questions than answer in my head, so I asked him if I could interview him sometime on my radio show and he agreed. A combination of timidity, lack of radio show after moving to Madison for grad school, and the sheer amount of demand on Pollan’s time, it hasn’t yet happened.

In the interim, more questions have piled up. Not just about genetics, but even about the philosophy of science, the future of agriculture, and whether he thinks that health food stores like Whole Foods have the highest concentration of contradictory food philosophies or if he didn’t notice the food supplement aisles. I could write several pages of questions, always thinking that I will have to jettison most of them to make for a radio/podcast interview someday that will will have continuity and make sense. Over time, questions related to The Omnivore’s Dilemma slid away to be replaced by questions related to In Defense of Food. A few questions about plant genetics held steady in the heirarchy of importance.

I initially entered the contest so that I could win the conversation with him and see if he wouldn’t mind adding a microphone to it as a podcast interview. I assumed that it would be a conversation over the phone as well. The other part of the prize, the social media training, didn’t have much appeal considering I’ve been doing social media for years! You could pretty much say I entered us in the changemakers contest to talk to Pollan. But then after I entered, the contest deadline was extended and a $1,500 grant was added to the grand prize. This was going to change the dynamics of the contest dramatically, and it did.

We haven’t yet mentioned what happened in the background since the contest extension. Anastasia and I collaborated on perfecting our entry, given the amount of space allowed, and we also set to upgrading and improving the site, and mapping out a future for Biofortified. Frank started twittering (there were requests for it from readers, too), and I installed the new forum. Lists of resources are being put together, along with more information about the site. There are more improvements being planned that all of us are working on in the background to turn the idea of Biofortified into a reality.

Consequently, it was not my entry of this site I started anymore, it is our entry of the site we’re building. If we win this contest and thus the conversation with Pollan, it will be our conversation, and according to an email I got last week the winner gets to meet him, which implies a round-trip airplane ticket for someone. Without going into too many details, it is quite possible that several of us may be able to meet him in Berkeley later this year. And my guess is that collectively, the conversation would be about the topics we discuss on this site, about genetic engineering, food, sustainability, intellectual property, and journalism. A few people on PZ Myers’ blog wondered why we would want to talk to Pollan about genetic engineering?

I can certainly speak for myself, for instance in 2001 he called Golden Rice, the humanitarian project about biofortifying rice with pro-vitamin A to combat malnutrition and blindness, “The world’s first purely rhetorical technology.” Only five years ago, he said in an interview that “I don’t think in ten years we’ll be talking about GMOs. I can easily see the industry withering away.”

That doesn’t sound like someone who doesn’t think much of genetic engineering.

But then, look at this:

That’s right, Michael Pollan is expressing his opinion that he would be open to “Open-Source” genetic engineering. This is something that I have been meaning to bring to this blog but I have not yet been able to enlist the help of a particular proponent of open source genetics to be a guest author. But imagine Linux and Creative Commons applied to plant genetics. This is a dramatic turnaround from predicting that the industry will wither away. As you can see, there’s a lot more than meets the eye when it comes to Michael Pollan’s views on genetic engineering in agriculture, but he still has not said much in recent years. Perhaps we can get a good dialogue going.

Frank 'n' Pollan

But if you paid attention to the interview above, did you notice that he said that genetic engineering has not increased yields, that only plant breeding has? He may be referring to the Union of Concerned Scientists’ report, Failure to Yield, which actually found that genetic engineering has increased yields, although the report de-emphasized it.

Moreover, Pollan said “A lot of GE is being sold to us based on a future promise, that I don’t even think they’re working on it.” Is this another gut opinion that will it take its place alongside the ten year prediction?

The most important thing that he said in the above video is that he is open to learning about it. There are probably a great many things that we could talk about with Michael Pollan, places where we agree, disagree, and perhaps don’t yet know where we stand. A conversation with him would promise to be very interesting in the least, and we will ask him if we could tape our discussion and put it on the net. Naturally, we have to win the contest first!

How interesting of a conversation would the Non-GMO Project have about GE crops? Or how about any of the other anti-GE entries? Would you hear an exploration of ideas that you haven’t yet encountered, or a rehash of the usual topics in this debate? Perhaps this may be a worthy appeal to those who are not keen on genetic engineering – if you vote for us, as a result you may get to see or hear an interesting, dynamic, and focused conversation with Michael Pollan on GMOs. We can’t promise it because a lot of it depends upon him (and the specific details of the prize that are not quite clear to us at this point), but this is what we would like to do. Can any other entrant say they’ve thought this far ahead?

Although the changemakers site had a countdown this evening that suggested the voting would be over at midnight, in a bizarre fashion it was counting down the minutes to the last day to vote. Weird. But this means that you still have a chance to pitch in and be a part of this voting effort. The polls close at 6 pm EST on Wednesday, so please take a few minutes to pump up our numbers just a little more. Let’s get to 1,000 votes before this ends!

Thanks for your support, and keep an eye here in the next week as we watch the end of the final day of voting, and await the official announcement from changemakers!

It was his state of Georgia, however where those infamous stickers disparaging evolution could be found – Cobb County to be precise. In 2004, his statement for a “balanced” approach to teaching evolution – where it is not taught as “fact.” Apparently he wants the benefits of a thriving biotechnology industry in his state without supporting the bedrock of modern biology in his state’s high school science classrooms. It seems that Florida is not the only state where the living is contradictory!

The star of the lunchtime diversion from our food, however, was Elton John. With music awards too numerous to list, and a prominent role in the fight against HIV and AIDS, he delivered an impassioned speech in which he said that we are losing. Not only have we not been able to completely stop the spread of the disease on a biological level, but the primary ground that we are losing on is the social level. Although his speech was not about plants, it was excellent and I would like to share a portion of it:

I recorded the last ten minutes of his speech, which I will post later on my blog. Elton John’s speech was emphatic, moving, and a real treat to witness.

The first panel discussion that I attended was called Saving Harvests, Lives & Livelihoods: Breakthroughs in Plant Stress Tolerance Technologies. This was certainly the most science-heavy talk that I went to during the convention. Luckily, I had just completed my plant physiology course one week ago, so when the speakers talked about sodium transport proteins and Abscisic Acid sensitivity and how manipulating them may help modify plants to endure environmental stresses, it was very digestible. The research content of the panel was partly due to the fact that two of the four panelists were university professors.

They talked about drought tolerance, salt tolerance, adaptations to a world with more carbon dioxide in the atmosphere, which was all good. But more than just describing possibilities, one panelist had pictures of corn and tomatoes modified with the same gene, demonstrating drought tolerance with adding a single gene. (I’ll see if I can get those pictures.) The most surprising thing I learned was that it is estimated that we get less than a quarter of the full genetic potential of the crop that we grow – and with 70% of the losses due to abiotic stress, you can easily see the potential to increase crop yields by preventing those losses. Losses which might get worse as our climate continues to change.

I wrote the whole thing up, which you can read on the AgBiotech@Bio blog: Saving Plants from Stress.

Then finally, I hurried out to sit in the audience of a “Think & Drink.” Although I didn’t get a drink myself, there was a pretty good crowd of people listening in on a conversation between several members of academia and industry, relaxing with various forms of ethanol delivery mechanisms. The discussion was titled, Industry Is from Mars, Academia Is from Venus, and it was moderated by the Editor of Nature Biotechnology, Andrew Marshall. When I got there they seemed to be wrapping up a discussion about how the two kinds of researchers differ in their approaches and interactions. The rest of the discussion mainly focused on the hairy issues of public-private partnerships, and there were some good points made about conflicts of interest. (And a brief discussion about patents)

I particularly liked some of the comments made by Christopher Scott, from the Stanford Center for Biomedical Ethics. He drew some important distinctions between the kinds of conflicts of interest that arise in public-private partnerships in basic research, versus clinical trials. The latter, of course, is extremely problematic because it involves testing things on people. While also discussing the degree to which researchers can get vested in these arrangements, he also joked about how many deals stem cell researcher Irving Weissman has coming his direction all the time.

When it came to the discussion about these partnerships, I noticed that none of the panelists were particularly critical of the concept itself – I think the discussion would have been improved if there was someone who was a little more wary of such interactions. (Part of why I thought Chris’s contributions to the discussion were so valuable.) Not that I’m particularly wary of such interactions myself, but discussions are better if the viewpoints are a little more widely distributed.

After the panel discussion, I also had a good conversation with Chris about stem cell research, a little politics, and the need to continue to study embryonic stem cells. We discussed the methods that some researchers are using to try to generate ES cells from adult cells, which often comes up in political discussions as an ‘alternative’ to ES cell research – ignoring the fact that in order to know if you have reverted an adult cell to an embryonic state, you need to be studying ES cells in the first place!

I snagged Andrew Marshall for a moment to say hi and tell him about Biofortified. Hey, how often do you get to meet the editor of a scientific journal? (Ok twice so far, that I have been aware of – they’re nondescript.) Although I was tired from getting up at 4 am that morning for my flight, I did my best to cogently explain what I hope to accomplish with the blog. Wouldn’t it be great to have us profiled in a journal article? It is not a new thing for science blogs. Let that be a prod to my fellow bloggers.

Tuesday was a fairly light day, and as I wound down the evening I didn’t realize how busy I was going to be on Wednesday… to be continued.

Full Disclosure: My trip to the BIO convention is courtesy of the Council for Biotechnology Information. I am also not getting paid for anything I write about the convention.

P.S. If you see any pictures from the BIO convention with someone wearing a bright orange pumpkin-print shirt, let me know because I know I was in the line-of-sight of some snapping cameras Tuesday!

Volker Brendel, professor of bioinformatics at Iowa State, spoke at the Maize Genetics Conference about the need for a better system of community annotation of the maize genome. The genome of the popular maize inbred line B73 is sequenced, but we don’t actually know what a lot of the code stands for. It’s going to take a lot of collaborative effort to discover and annotate (explain) the function of each gene and to put all of that information in one place so it will be useful.
Volker reminds us that the Arabidopsis 2010 funding is running out, so we need to assess the plant genetics situation. How many genes do we know the function of? There is still much to learn.
Maize is uniquely positioned to replace Arabidopis as a focus for basic plant research due to the many resources that are already established, the most important of which is the extensive maize genetics community (he didn’t say it, but there is another reason why maize is a better choice than Arabidopsis right now – all of our major grains are very closely related, so work on maize applies to rice, wheat, sorghum, and more). The community needs to work together in the annotation process, assigning functions to the genes that have been sequenced, putting the data from a variety of sources together to make a bigger picture. Each researchers has a favorite gene (pathway, organelle, etc) – how can each of the researchers contribute to the annotation process?
PlantGDB is a comparative genomics site funded by NSF has information on 14 species, including maize, which is very useful. However, no matter how clever the computer programs are, the human touch is still needed. Filling in information on any of these species helps us to better understand all of them. On the site, community members can flag genes for which the models don’t seem to fit, and can contribute alternative explanations. The final goal is to have every gene model approved by the relevant community member(s). When a person annotates a gene, the PlantGDB committee reviews it, approves it, and the information is shortly available on the site. Annotating the genes you are working on is your civil duty, something you owe due to public funding you receive.
After Volker’s talk, the attendees discussed what is the public’s role in the attenuation process should be. There are a lot of cases where the the gene model can be checked without any lab work, simply by looking at the sequences. Some members of the community think we should harness the brainpower of thousands of biology undergraduate students by assigning annotations for class. I like the idea of getting students involved, and hope they follow through.Diversity of people to represent the maize genetics community.
A panel discussion followed, where a lot of great new ideas for annotation were brought up (unfortunately I don’t have the names of some of the people that spoke).
One panel member said we need “Zeazomics” – a collection of information including genomics, metabolimics, proteomics, and whatever else we can come up with – to fill in gaps in our knowledge. being able to link all of this information together will lead to stronger explanations of the phenotypes we see. He said this process will not be definitive, it will create a series of hypothesis that will lead to more hypotheses. The hypothesis testing will lead to functional biolgoy, from physiology to biochemistry to cell biology and more. Additional genome sequencing is necessary to capture the entire diversity of maize. Maize is the model for grasses, for crops, for future applications like biofuels. Now is the time to push maize research to a much higher level.
To accomplish all this, we’ll need to take care of a few things, as the other panel members and members of the community brought up:

• Need to have reciprocal links from genes from MaizeGDB to NCBI Entrez Gene. Currently, about 20,000 NCBI Entrez Genes need links back to MaizeGDB.
• To help with annotation, Lisa Harper, curator of MaizeGDB, will do a movie that shows the common problems of using the databases, including how the genome changes over time as the contigs are reordered, etc. This is needed because people are often working off of older copies of the information for a given gene, as it might not be updated frequently enough.
• There is also a need to integrate microarray data into the databases. Particularly complicated are those microarrays that are specific to a particular tissue and/or developmental stage. Volker says that this problem is common and new technologies with new ways to visualize data are necessary.
• MaizeGDB needs a forum such that people working on the same genes can coordinate their work.
• iPlant is organizing a workshop in St. Louis in June to help coordinate the various genome annotation groups.

• There is a plan to create outreach information that any member of the maize community will be able to download and use to communicate the needs and accomplishments to the public and to government officials.

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!

Welcome to the 29th edition of Mendel’s Garden, the monthly one-stop-shop for the best the blogosphere has on Genetics. I have hosted the Garden a couple times before on my personal blog, but this month we find ourselves on Biofortified. This is a group blog on plant genetics and genetic engineering, to try to sprinkle a little fertilizer on the discussion of the majority of the eukaryotic biomass on this planet – plants! And we’ve got some plant genetics-based blog posts to talk about, but the theme for this edition is FRANKENPEOPLE!

Yes, human genetics has been up in the news lately, and there is no shortage of blog posts discussing it.

We begin with Josh Witten at the Rugbyologist, who discusses the uncanny genetics of the X-Men. Wrestling with mutation rates and variable mutant powers, Josh settles on the weirdness of the claim that the mutant gene is inherited from the father – wait, if it is on the Y-Chromosome, how come there are female mutants? Perhaps the X-gene is not a mutant gene per se, but an epimutant that is the result of a change in paternal gene imprinting?

Changes in gene expression are becoming more and more important these days, as our tools to study them are improving. Eliza Strickland at the 80beats Discover Blog talks about the long-lasting effects of child abuse on the genome. We must learn from the rats and lick our offspring more… no wait, maybe treat them well in our own human fashion to prevent epigenetic changes that could make them depressed down the road!

Speaking of tools improving, the cost of whole-genome sequencing is coming down. FuturePundit Randall Parker wonders whether we will see $100 personal genome sequencing by 2014? I don’t know about you, but I’d rather pay the extra 50 bucks to get both halves of my genome sequenced when I do. Screw this haploid genome stuff – I’m a heterozygote!

Genome sequencing will be very fascinating at least for what it will tell us about our geneology. Erin at The Spittoon describes how mitochondrial DNA was used to confirm the identity of two ‘missing’ Romanovs. Also up at The Spittoon is a discussion of how some tiny changes in a gene, FOXO3A have been associated with longevity. Now those are some SNiPs that I hope I have in my genome!

This edition of the Garden comes on the heels of Barack Obama’s momentous lifting of the embryonic stem cell research ban in the US. So to get ourselves ready for the influx of stem cell research coming our way, Chris Patil primes us with some research on the function of telomerases – we’ll reprogram our cells yet!

The Pope Wears Prada

Next, there’s a rising trend in discussion of so-called “Designer Babies,” which isn’t quite the GATTACA-storyline bioethics issue, but touches pretty close to it. Can prospective parents pre-screen embryos for genetic diseases prior to implantation? On one hand, you have the issue of choosing the genetics of your offpsring on a [possibly mistaken] whim, and on the other hand you have the possibility of prevent kids with inborn genetic diseases from being born. Well, Pope Benedict, seen here sporting his “Pagan” ruby slippers, chimed in against the very concept of screening embryos, calling it “Genetic Discrimination.”

As the American Freethought blog astutely points out, apparently genetic discrimination is wrong – except for priests. Genetic discrimination against the human XX karyotype is alive and well in the catholic church.

Finally in our human genetic section, Abbie Smith aka ERV says that a gene called ERV9 beat Jesus to the punch by resurrecting a dead gene long before humans split from our ape cousins. Read ERVs=Jesus: Bringing dead genes back to life.

To make the segue from humans to plants for us we no one else to thank than the FrankenSenator from Arizona, John McCain. Sidestepping email entirely, he’s taken to twittering what he sees as pork-barrel projects that he finds puzzling. That’s a low bar to start with, which is why many are pointing out the strange preponderance of scientific research in his list of “pork.” Well Grace Ibay at Genetics and Health has assembled a short list of his tweets on genetics and science, and reveals that he really doesn’t know what all of it is for.

Here’s the best one:

“$1,427,250 for genetic improvements of switchgrass – I thought switchgrass genes were pretty good already, guess I was wrong.”

Haha, yeah. You are. In case any of you are curious what kinds of genetic improvements are being worked in in switchgrass, I just happen to have a video I produced about switchgrass breeding. Why don’t you cool your mind for a moment on the effort to combine Upland and Lowland prarie grasses?

Does that make you feel like becoming a plant breeder? I hope so, that’s why I’m making them. To view a higher resolution version of this video, or to see the other ones I have produced in this series, visit the UW’s Plant Breeding and Plant Genetics website. I just showcased the newest video on How to Breed Cucurbits here on Biofortified.

I have a couple posts from the Agricultural Biodiversity Weblog. Luigi announces the start of a new plant breeding journal. Submit away, it’s also Open Access! And he also put up a post about a fascinating piece of news (which will get attention soon here on Biofortified): The Hawaii legislature is considering banning genetically engineered Hawaiian Taro because it “changes the basic structure” of the Taro plant. Well if that’s actually in the proposed legislation, then what will that do considering that plant breeding changes the structure of Hawaiian Taro? Read Making Breeding Illegal and join [us] in the discussion.

And Jeremy blogged about Darwin’s Birthday, on the subject of Beans and Selection. Check it out, and click through to Darwin Online, too!

Greg Laden also wrote about Chuck for his birthday, and wondered Why didn’t Darwin Discover Mendel’s laws? He also seems to have voted for Al Franken, by the look of his posts on politics. Another FrankenPerson!

Here on Biofortified, we have a few plant-related posts you might be interested in. First, I did some legwork and found out that some anti-GE activists have been promoting some false claims about Obama’s plans in the White House.

Pam Ronald writes about GE crops on the big island of Hawaii following her trip to the same place in Big Island Transgenics. On her own blog, she also posted a time-lapse video of her work with flood-tolerant rice in The Power of Genetics.

Pam’s husband and co-author Raoul Adamchak wrote a guest post about the necessity of allowing university scientists to do research on GE crops. Scroll to the bottom – Monsanto even reads this blog!

And my friend Melinda Markham enlightens us with a guest post on the first successful attempt to engineer a vaccine against tetanus into plants. I think it’s ironic that tobacco can now be used to make people healthier! Read Breeding Tetanus Vaccines into Plants.

Let’s end with something funny, and something pretty. Andrew at the Southern Fried Scientist talks about the need to give genes meaningful names. What’s wrong with Hedgehog and Sonic the Hedgehog? Okay maybe you’ve got a point about “I’m not Dead Yet.” Check out the End of the Cheap Date for a little laugh at crazy Drosophila names and a little realism about genic nomenclature.

Finally, the Myrmecos Blog posts a picture of bees in the shape of DNA that was unfortunately rejected by a journal publisher, but take heart! We don’t care that the picture was the wrong dimensions – you got the DNA coiling the right way so you deserve a little buzz.

Bumblebee DNA

That’s all for this edition of Mendel’s Garden, thanks everyone for taking the time to read. Do check back here soon, because both Anastasia and I will be attending the Maize Genetics Conference starting tomorrow and we’ll have some deliciously corny stuff for everyone!

And it appears that no one has claimed the next Mendel’s Garden – now’s your chance!