Tuesday, February 28, 2006

Claimed damage to soil bacteria - DOESN'T HAPPEN!

Damage to soil bacteria non existent!


"Damage to soil bacteria, notably through horizontal transfer: Heinemann J.A, Traavik T. (2004) Problems in monitoring horizontal gene transfer in field trials of transgenic plants. Nat. Biotechnol. 22, pp 1105-1109."

GMO Pundit has carefully read this HT 2004 citation and it is grossly misleading: The JIGMOD claim is a clear missuse of science.

The "damage" doesn't exist. There is actually no explicit description of detected damage to soil bacteria in this paper.
The "problems" of its title refer to "analytical problems" in detection of extremely rare events. Eg difficuties in detection of trace genetic materials.

There is one necessary correction to a seriously misleading statement in the Heinemann Traavik 2004 paper (leading to a published corrigenda)

Quotes from the abstract of Heinemann and Traavik 2004:

(There is a Corrigenda (April 2005) associated with this Perspective.)
Problems in monitoring horizontal gene transfer in field trials of transgenic plants Jack A Heinemann & Terje Traavik

Summary: Transgenic crops are approved for release in some countries, while many more countries are wrestling with the issue of how to conduct risk assessments. Controls on field trials often include monitoring of horizontal gene transfer (HGT) from crops to surrounding soil microorganisms. Our analysis of antibiotic-resistant bacteria and of the sensitivity of current techniques for monitoring HGT from transgenic plants to soil microorganisms has two major implications for field trial assessments of transgenic crops: first, HGT from transgenic plants to microbes could still have an environmental impact at a frequency approximately a trillion times lower than the current risk assessment literature estimates the frequency to be; and second, current methods of environmental sampling to capture genes or traits in a recombinant are too insensitive for monitoring evolution by HGT. A model for HGT involving iterative short-patch events explains how HGT can occur at high frequencies but be detected at extremely low frequencies.

Corrigenda Nature Biotechnology 23, 488 (2005)
Corrigendum: Problems in monitoring horizontal gene transfer in field trials of transgenic plants Jack A. Heinemann & Terje Traavik Nat. Biotechnol. 22, 1105−1109 (2004)

On page 1108, paragraph 1, line 7, reference 49 in the statement "B. thuringiensis has 'a significant history of mammalian pathogenicity'46 and is thus not irrelevant to food safety or other environmental issues" was inappropriately cited (reference 46 states: "Bt does not have a significant history of mammalian pathogenecity".) The text should have read that "B. thuringiensis belongs to a closely related clade of bacteria, which includes Bacillus cereus and Bacillus anthracis, and which has a significant history of mammalian pathogenicity1, 2 and is thus not irrelevant to food safety or other environmental issues. Members of this group are so closely related that they may be considered members of the same species, often differing only by the presence or absence of certain plasmids3, 4".

1. Helgason, E., Caugant, D.A., Olsen, I. & Kolsto, A.-B. Genetic structure of population of Bacillus cereus and B. thuringiensis isolates associated with periodontitis and other human infections. J. Clin. Microbiol. 38, 1615−1622 (2000).
2. Økstad, O.A., Hegna, I., Lindbäck, T., Rishovd, A.-L. & Kolstø, A.-B. Genome organization is not conserved between Bacillus cereus and Bacillus subtilis. Microbiol. 145, 621−631 (1999).
3. Helgason, E. et al. Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis—one species on the basis of genetic evidence. Appl. Environ. Microbiol. 66, 2627−2630 (2000).
4. Hoffmaster, A.R. et al. Identification of anthrax toxin genes in a Bacillus cereus associated with an illness resembling inhalation anthrax. Proc. Natl. Acad. Sci. USA 101, 8449−8454 (2004).

Note also there was another related Perspective, taking a different theme, on gene movement published jointly with the HT 2004 paper.

Monitoring and modeling horizontal gene transfer
Kaare M Nielsen & Jeffrey P Townsend

Monitoring efforts have failed to identify horizontal gene transfer (HGT) events occurring from transgenic plants into bacterial communities in soil or intestinal environments. The lack of such observations is frequently cited in biosafety literature and by regulatory risk assessment. Our analysis of the sensitivity of current monitoring efforts shows that studies to date have examined potential HGT events occurring in less than 2 g of sample material, when combined. Moreover, a population genetic model predicts that rare bacterial transformants acquiring transgenes require years of growth to out-compete wild-type bacteria. Time of sampling is there-fore crucial to the useful implementation of monitoring. A population genetic approach is advocated for elucidating the necessary sample sizes and times of sampling for monitoring HGT into large bacterial populations. Major changes in current monitoring approaches are needed, including explicit consideration of the population size of exposed bacteria, the bacterial generation time, the strength of selection acting on the transgene-carrying bacteria, and the sample size necessary to verify or falsify the HGT hypotheses tested.

Nature Biotechnology 22, 1110 - 1114 (2004)
Published online: 31 August 2004; | doi:10.1038/nbt1006

Sunday, February 26, 2006

Analysis of Pusztai Study on GM Potatoes and their effect on Rats

Analysis of Pusztai Study on GM Potatoes and their effect on Rats

By Dr. Nina V. Fedoroff
Willaman Professor of Life Sciences and Evan Pugh Professor
Huck Institutes of the Life Sciences (http://www.lsc.psu.edu/)
201 Life Sciences Building
Pennsylvania State University
University Park, PA 16802

Website: http://hils.psu.edu/lsc/fedoroff.html

On August 10th, 1998, Arpad Pusztai of the Rowett Research Institute in Aberdeen, Scotland appeared on the British TV show "World in Action." In the course of the interview, he announced that his experiments showed that rats fed a diet of potatoes expressing a gene coding for a snowdrop sugar-binding protein showed stunted growth and reduced immune function (Enserink, Science 281.1184). He is further quoted as saying that he would not eat GM food and that he found it "very, very unfair to use our fellow citizens as guinea pigs" (Lee and Tyler, 1999).

The study made headlines around the world. According to Science’s Martin Enserink, the Rowett Institute was flooded with calls from reporters even before the show aired. He quotes Rowett director Philip James saying that the Institute was faced with “a megacrisis we didn't remotely anticipate.” James is said to have examined the experiments and found them a total “muddle.” Pusztai’s laboratory was sealed, his notebooks were turned over to an audit committee and Pusztai was put on indefinite leave – he was out of a job. The audit committee’s report, released in October of 1998, concluded that Pusztai’s data did not support the conclusion that the transgenic plants had a deleterious effect on growth, organ development, or immune function in rats.

Pusztai, whom Rowett had been forbidden to talk to the press, got in touch with a number of scientists and asked them to review the audit report and his rebuttal to it, as well as a transcript from the World in Action show (Enserink, Science 283:1094-5). On February 12 1999, Professors Edilbert van Driessche and Thorkild C. Bøg-Hansen, colleagues who had collected the responses, issued a memorandum supported by more that 20 other scientists who had studied Dr. Pusztai's findings (Lee and Taylor, 1999).

Their memorandum stated (the following is largely verbatim from the WSWS website): "Those of us who have known Dr. Pusztai's work or have collaborated with him, were shocked by the harshness of his treatment by the Rowett and even more by the impenetrable secrecy surrounding these events. It is an unacceptable code of practice by the Rowett and its Director, Professor James, to set themselves up as arbiters or judges of the validity of the data which could have such a profound importance not only for scientists, but also for the public and its health." The memorandum concludes, "There is no doubt in our minds that the reviews will remove the stigma of alleged fraud and will restore Dr. Pusztai's scientific credibility."

One of the scientists who reviewed Pustzai's work, Dr. Vyvyan Howard, foetal and infant toxico-pathologist at the University of Liverpool, told the World Socialist Web Site, "I am working on some features of lectin toxicity and that is how I came to know Arpad Pusztai, who is certainly one of the world's experts in this field." Dr. Howard said that he believed Dr. Pusztai's data was (sic) sound. "We think it would pass peer review and be published and we are at a loss to really explain why the Rowett Institute came to the conclusion it did." Dr. Howard added that Pusztai's findings "are of considerable importance in the current debate on the safety and hazard assessment of genetically modified foods".

Professor S. Pierzynowski, from the Department of Animal Physiology, Lund University, Sweden, said, " I must stress that there is enough strong evidence that the work of the audit group was not objective and per se dangerous, not only for Dr. Pusztai, but generally for free and objective science." Joe Cummins, Emeritus Professor of Genetics at the University of Western Ontario, Canada described the Rowett Institute's treatment of Pusztai as "a great injustice", adding that the "Institute continues to look inward to cover up its mistakes".
These eminent scientists have not only raised serious concerns about the way research into GM food is being conducted, but that those who have dissenting voices are being suppressed and have had their careers ruined, and sometimes their health. Dr. Pusztai has suffered a mild heart attack brought on by the stress caused by trying to restore his scientific reputation and the credibility of his research. These concerns were echoed by Dr. Kenneth Lough, FRSE, a former principal scientific officer at the Rowett Institute between 1956 and 1987. He said, "In my view the evidence presented in the audit report must be considered as unsafe and is without justification for use against the scientific reputation of Dr. Pusztai. The Institute is at risk in sending the wrong signals to scientists in this field of research that any sign of apparent default will be treated with the utmost severity. The awareness will of course act as strong deterrent to those who wish to conduct research in this vitally important field." (end of stuff from WSWS).

But a committee of six eminent members of the British Royal Society, set up in April of 1999 to review the Pusztai data, reached the opposite conclusion. The committee sent out the material they received from Pusztai, the Rowett and other sources to scientists with expertise in statistics, clinical trials, physiology, nutrition, quantitative genetics, growth and development, and immunology. The committee reviewed the opinions it received and issued a summary statement in June of 1999. The consensus of these experts was that the experiments were poorly designed, the statistical inappropriate, and the results inconsistent. Their recommendation was that the experiments be repeated and the results published.

Pusztai jumped to his own defense with a detailed response (http://www.freenetpages.co.uk/hp/a.pusztai/). He and a colleague with whom he had worked for some years published their study in medical journal Lancet (Ewen and Pusztai, 1999). Lancet, in turn, came under sharp criticism from a number of quarters, including U.K.'s Biotechnology and Biological Sciences Research Council, which called the journal "irresponsible." But Lancet’s editor, Richard Horton, stood by the publication. Five of 6 reviewers had favored publication and he believed that it was appropriate for the information to be available in the public domain (Enserink, Science 286:656).

So what’s this all about? Why this titanic battle of experts? Why is Pusztai, until this incident considered an authority on the plant proteins called lectins, under such fierce attack? He’s written three books on lectins and published 270 research papers. Moreover, he’d worked at the Rowett Institute for 35 years. On the surface of it, his now-controversial research was perfectly straightforward: he fed genetically modified potatoes expressing a snowdrop lectin to rats and looked to see whether this food affected their physiology, particularly the gut, metabolic process and immune system. What are lectins? Should we worry about them? Should we share Pusztai’s concern and conclusion that genetic engineering itself results in "……possible gene silencing, suppression and/or somaclonal variation"?

The protein in question is called the Galanthus nivalis agglutinin after the Latin name of the snowdrop and it is abbreviated GNA. It was originally isolated from snowdrop bulbs and is a kind of protein that recognizes and bind to sugars on proteins. Such proteins are called ‘lectins’ as a group. Although lectins were first discovered in plants, they are now known to exist in animals in great profusion (Rudiger 2000). Many proteins – in all kinds of organisms – are decorated with sugar molecules – sometimes with long strings or branches of several sugar molecules. Such derivatized proteins are called glycoproteins.

Each glycoprotein has a different complement of sugar molecules, depending on what it does and where it does it. The sugar signature works like a zip code in the cell, determining where the protein is delivered by the machinery that produces it. When such decorations are on the surface – be it of a virus, a bacterium, or a cell – they serve as a recognition molecules. Lectins recognize the sugar molecules with such exquisite correctness and specificity that they have long been used to identify what sugars are present on a protein. Today it is increasingly recognized that the sugar ‘codes’ serve a large variety of internal functions. One of these is recognizing disease organisms.

So, for example, it has been known for a number of years that the AIDS virus HIV (human immunodeficiency virus) has mannose sugars on its surface and the ability of cells to recognize these surface sugars with their own lectins is part of the infectious process (Hammar 1995). Plant lectins like GNA, which recognizes mannose, bind to the virus and inactivate it. They also interfere with its ability to infect cells (Hammar 1995). Because of its ability to bind to these surface sugars, GNA has been used to purify the HIV surface glycoproteins, which were in turn used to produce an immune response, albeit not much of one (Gilljam, 1993). Similarly, Chlamydia trachomatis has surface mannose-containing glycoproteins that allows the organism to infect cells by binding to a surface lectin (Siridewa 1993).

Plants – no less than animals – have mechanisms for defending themselves from microorganisms and insects. Plant produce lectins as one of their defense strategies against insects (Carlini 2002). Indeed, a good deal of evidence has accumulated that GNA, which binds specifically to a sugar called mannose, is rather toxic to certain kinds of insects pests of important crop plants, including rice (Du et al. 2000; Fitches et al., 2001). GNA does not seem to affect ladybird beetles, considered to be a beneficial insect (Down et al., 2000), although it does affect parasitic wasps, also considered to be beneficial insects (Romeis 2003). Some lectins, including ricin, are quite toxic because they’re taken up by cells and block protein synthesis (Olsnes 2001). These are called ribosome-inactivating proteins or RIPs. But GNA doesn’t have this activity (Batelli 1997).

Better yet, Pusztai’s own studies showed that purified GNA wasn’t toxic to rats (Pusztai 1990). In fact, he and his colleagues had shown that GNA had a protective effect against bacterial infection with Salmonella, a nasty intestinal bug (Naughton et al., 2000). All of this made the gene coding for GNA an attractive choice for increasing the insect resistance of crop plants. To test this possibility, the gene was introduced into a number of different crop plants, including potatoes and rice. And it does, indeed, increase their resistance to some important insect pests (Rao 1998; Foissac 2000). Because GNA binds to the surface cells of insects guts and enters their blood stream, it is also thought to have potential as a vehicle for delivering more toxic peptides to insects (Fitches 2002).

Sugar signatures are ubiquitous in biology – and as yet, we know rather little about what they do. It is known, for example, that there are two critical kinds of cells – the T and B cells – that must interact for the body’s immune response to be activated. It has been reported that these interactions occur through a mannose-containing glycoprotein and that this interaction can be blocked by GNA (Savage 1993). Thus some of the same signature sugars central to important cellular functions. Pathogens take advantage of essential intercellular recognition mechanisms to gain a foothold, both by binding to the cell’s own lectins and by evading the immune response because they resemble the cell’s own molecules. So, for example, a lectin called DC-SIGN (dendritic dell-specific intercellular adhesion molecule-3 grabbing nonintegrin) binds sugars on the HIV envelope and facilitates infection of its target CD4 T cells (Geijtenbeek 2003).
The DC-SIGN lectin is referred to as an HIV ‘receptor’ because of this specific recognition of HIV, but it is actually a universal pathogen receptor (Geijtenbeek 2003). It normally captures viruses and other pathogens through their sugar-containing protein molecules and pulls them into the cell, where they are broken down and displayed on the cell surface to trigger a protective immune response (Kooyk 2003). HIV hijacks this system. It stays intact when it binds to DC-SIGN and rides along to be presented to its target T4 cells in an infectious form. This is a rather effective evasion system. It makes it quite unlikely that the body will successfully fight back by making antibodies, the body’s proteins that recognize and destroy pathogens. This is because the immune system learns early in life to discriminate between its own proteins and foreign proteins. But one particular HIV glycoprotein, gp120, has a dense cluster of mannose residues that has not been seen in any mammalian glycoprotein (Calarese 2003) and a few HIV patients make good antibodies to this protein. Recent work on one such antibody showed that it binds to the gp120 – the same protein to which DC-SIGN binds to promote viral infection – in a very unusual way. Antibodies generally recognize and bind to just one sugar residue, but this unusual antibody has an extended structure that permits it to recognize more than one mannose residue at a time. This is actually similar to the way that certain lectins recognize sugars because lectins consist of two or more identical proteins, each of which has a sugar-binding site (Hester 1996; Calarese 2003). The discovery of this unusual antibody raises new hope for stimulating the immune system to produce anti-HIV antibodies, immunizing people against AIDS.

But there are many kinds of lectins and they can have quite different effects. For example, Pusztai and his colleagues had reported 10 years earlier that a kidney bean lectin, phytohemagglutinin or PHA, caused the surface cells of rats’ intestines to turn over more quickly (Pusztai 1993). The younger replacement cells on the tiny surface projections – called villi – of the intestinal cells had a high proportion of proteins with mannose sugars at the ends of their sugar signatures. This made the cells more susceptible to bacterial overgrowth with Escherichia coli, a common gut bacterium, because the bacterium has projections – called fimbrae – that recognize and bind to mannose. Including GNA in the diet reduced the extent of bacterial overgrowth because the GNA binds to the mannose on the intestinal cells.
PHA is a normal component of red kidney beans – and people get sick from eating too much of it. Allergist David Freed recounts an incident that occurred in 1988 when a hospital had a “healthy eating day” in its staff canteen at lunchtime (Freed 1999). He recounts that 31 portions of a dish containing red kidney beans were served that day and over the next several hours, 11 customers were experienced profuse vomiting, some with diarrhea – typical food-poisoning symptoms. All recovered by the next day, but no pathogen was found in the food. It turned out that the beans contained an abnormally high concentration of PHA.
There are many different kinds of plant lectins and they are present in most plants, especially abundant in seeds, including cereals and beans, and in tubers, including potatoes. They tend to survive cooking and digestive enzymes. Pusztai and many other investigators have shown that they affect intestinal cells. It isn’t surprising that they occasionally cause symptoms of food poisoning (Freed 1999). As in insects, some can get into and through cells and into the blood stream. Some lectins are also potent allergens. So even through GNA appears to be a relatively benign lectin as evidenced by rat feeding studies, there is absolutely no doubt that a food expressing such a protein needs careful testing, first in animals.

Sensibly, the Scottish Office Agriculture, Environment and Fisheries Department (SOAEFD) commissioned a 3-year study in 1995 titled “Genetic engineering of crop plants for resistance to insect and nematode pests: effects of transgene expression on animal nutrition and the environment.” Its objective was "to identify genes encoding antinutritional factors which will be suitable for transfer into plants to enhance their resistance towards insect and nematode pests, but will have minimum impact on non-target, beneficial organisms, the environment, livestock fed on these plants, and which will present no health risks for humans either directly or indirectly through the food chain." The University of Durham and the Scottish Crop Research Institute were to provide the transgenic plants and the Rowett Research Institute was to do a chemical analysis of the transgenic plant materials. They were also to do both short-term (10 day) and long-term (3 months) rat feeding trials to determine whether the effect of the transgenic plant materials was similar to that of the parent lines.

The chemical analysis of the transgenic plants showed them to be quite different from the parent lines (http://www.rowett.ac.uk/gmo/ajp.htm) – although the audit report curiously concludes that they weren’t (http://www.rowett.ac.uk/gmoarchive/gmaudit.pdf). The researchers measured total protein concentration, as well as the content of several relevant proteins, including GNA, potato lectin and several others. All of these differed between transgenic lines and in comparison with the parental lines. Rats in Pusztai’s study were fed either raw or cooked potatoes. Non-transgenic potatoes were supplemented with GNA. The results showed that rats fed the transgenic potatoes had significantly lower organ weights. They found that GNA added to the potatoes made the animal’s lymphocytes, which are cells in the immune system, more responsive to stimulation by other lectins. By contrast, lymphocyte responsiveness was depressed in the animals fed the transgenic potatoes expressing GNA.
What these studies basically showed was that the transgenic potato lines were different from each other, as well as from the parental potatoes. A later study on transgenic potatoes came to the same conclusion (Down 2001). Here Pusztai jumped to the conclusion that these differences must be attributable to the fact that the plants were transgenic – and he went public with his conclusion. What he probably didn’t know – because he was neither a plant breeder nor a plant biologist – was that the very process through which the plants are put during the introduction of the transgene – culturing through a callus stage and then regeneration of the plant – can cause marked changes in both the structure and expression of genes.

The variation that arises as a result of passage through tissue culture is called “somaclonal variation” and is both a nuisance and a potent source of new materials for plant breeding. The variation is both genetic (single base changes, deletions, insertions, transpositions) and epigenetic – this means modifications that can affect expression of genes, but not their structure. For plant breeders, this means that new materials and new varieties derived using culturing techniques must be evaluated for both their growth and their food properties. This is particularly important for potato breeding, because potatoes produce toxic substances called glycoalkaloids (Kozukue 1999). Glycoalkaloids are normally present in potatoes, can contribute to inflammatory bowel disease, and are concentrated by frying potatoes (Patel 2002). So potato breeders must carefully monitor these compounds, irrespective of the means by which new potato varieties are generated.

Unfortunately, Pusztai’s analyses of the chemical composition of the transgenic lines were rather superficial. And his quick leap to the conclusion that the variation he observed was attributable to the fact that they were transgenic was simply unwarranted. This mistake has proved costly to Pusztai himself. And unfortunately, the expertise battle that sprang up around the experiments has obscured the importance of carrying out well-designed experiments to evaluate the food qualities of transgenic crop plants expressing proteins that have the potential of affecting human health. Lectins are clearly in this category.

Pusztai has been criticized severely for the quality of his experiments. His experiments have been attacked for their small sample sizes, the use of inappropriate statistical procedures, and the fact that a diet of raw – or even cooked – potatoes is a bad diet for rats (people too), even when supplemented with a bit of extra protein. But oddly enough, in all that has been written about these experiments, no one seems to have seen their central flaw, which was that he did not use appropriate controls. A “control” is the part of an experiment that allows the researcher to examine the consequences of just the change (in this case) or the treatment (in the case of a drug) under study. In Pusztai’s experiments, the control potatoes had a different history than the transgenic potatoes and, in particular, that history included a culture procedure that induces somaclonal variation. The likeliest source of the variation he detected – and of the differences he attributed to the fact that they contained foreign DNA – was the culture procedure itself. In order to be able to attribute the deleterious effects of the transgenic potatoes to the newly introduced gene or to some other part of the introduced DNA, he would have had to make a comparison between potatoes that had the very same history, but either had or lacked the transgenic construct. This can be done, but the study that Pusztai participated in was simply not designed for such a test.

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GMO Pundit on this topic:

For a collection of comments and references on this first see

Rats fed bad diets have lots of changes in their guts, which is the best the Pundit can collect from the web and from his advisers.

but also here and here, Potatoes not perfect food, Genetic Roulette.

Academics Review on this topic

1.1—Pusztai’s Flawed Claims

Some examples of Nina V Fedoroff' s Scientific leadership.

Prehistoric GM Corn
Nina V. Fedoroff
Corn (maize) is arguably man's first, and perhaps his greatest, feat of genetic engineering. Its huge ears--each packed with firmly attached kernels filled with starch, protein, and oil--make it a food staple. Contemporary corn, unlike its wild grassy ancestor teosinte, can't survive without people because it can't disperse its own seeds. The origins of maize have long intrigued geneticists, but only recently have new molecular methods enabled evolutionary sleuths to pinpoint its origins and identify the genetic modifications (GMs) that enabled the radical transformation of teosinte into contemporary maize. On page 1206 of this issue, Jaenicke-Després, Doebley, and their colleagues (1) provide the latest chapter in this detective story and suggest that prehistoric people were quick to adopt GM corn.

Teosinte and corn (Zea mays) don't look much alike, but they are interfertile. Teosinte-corn hybrids arise in the wild but look so different from either parent that they were originally classified as a different species (Zea canina). In the 1920s, Beadle examined chromosomes in teosinte-corn hybrids and concluded that the two plants belonged to the same species, and even shared the same chromosomal order of genes...

So how, when, and where was teosinte transformed into maize? Beadle gave his mentor, Emerson, credit for the idea that just a few mutations changed teosinte into maize (4). Analyzing backcrossed maize-teosinte hybrids with molecular probes, Doebley's group came to a startlingly similar conclusion: The differences between maize and teosinte could be traced to just five genomic regions (5). In two of these regions, the differences were attributable to alternative alleles of just one gene: teosinte glume architecture (tga1) and teosinte branched (tb1), which affect kernel structure and plant architecture.

The tga1 gene controls glume hardness, size, and curvature (6). Teosinte kernels are surrounded by a stone-like fruitcase, assuring their unscathed passage through an animal's digestive tract, which is required for seed dispersal. But the plant's reproductive success is the consumer's nutritional failure. Not surprisingly, one of the major differences between maize and teosinte kernels lies in the structures (cupule and outer glume) enclosing the kernel. Maize kernels don't develop a fruitcase because the glume is thinner and shorter and the cupule is collapsed. The hardness of teosinte kernels comes from silica deposits in the glume's epidermal cells and from impregnation of glume cells with the polymer lignin. The maize tga1 allele supports slower glume growth and less silica deposition and lignification than does the teosinte tga1allele.

The tb1 locus is largely responsible for the different architecture of the two plants. Teosinte produces many long side branches, each topped by a male flower (tassel), and its female flowers (ears) are produced by secondary branches growing off the main branches. Modern corn has one main stalk with a tassel at the top. Its lateral branches are short and bear its large ears. Much of the difference is attributable to the tb1 gene, originally identified in a teosinte-like maize mutant. Mutations generally abrogate gene function, indicating that the maize allele acts by suppressing lateral shoot development, converting grassy teosinte into slim, single-stalked modern corn and male into female reproductive structures (7).

Knowing that this cluster of traits is controlled by just two genes makes it less surprising that genetic differences in these genes could render teosinte a much better food plant. Yet however useful to people, a tga1 mutation would have been detrimental to teosinte, making it more vulnerable to destruction in the digestive tract of the consumer and so less able to disperse its seeds. Thus, the only way this mutation could have persisted is if our ancestors propagated the seeds themselves. This implies that people were not only harvesting--and likely grinding and cooking--teosinte seeds before these mutations came along, but also were selecting for favorable features such as kernel quality and cob size. In turn, this suggests a "bottleneck" in corn evolution: Several useful GMs were brought together in a single plant and then the seeds from this plant were propagated, giving rise to all contemporary maize varieties. Such a prediction can be tested by calculating the number of generations and individuals it would take to account for the molecular variability present in contemporary maize. The results of such a test suggest a bottleneck for maize domestication of just 10 generations and a founding population of only 20 individuals (8). Did this happen once or many times? Because genetic differences arise at a fairly constant rate, this question can be answered by constructing family trees using similar sequences from different varieties of teosinte and contemporary maize. The results are unequivocal: All contemporary maize varieties belong to a single family, pointing to a single domestication event.

Knowing how quickly differences arise, how many there are today, and where the family of origin survives, it is possible to determine when--and where--it all started. The answer is that maize most probably arose from teosinte of the subspecies parviglumis in the Balsas River basin of southern Mexico roughly 9000 years ago (9). Recent redating of cobs from the Guilá Naquitz cave (about 500 km from the Balsas River basin) demonstrated that they were more than 6200 years old, providing archaeological support for the molecular findings (10, 11). These earliest corn cobs don't look much like those of modern corn, but they look even less like teosinte cobs (see the figure). They are tough and have several rows of tightly attached kernels, implying that the plants wouldn't have survived without people to detach and plant the seeds. By contrast, teosinte's reproductive structure, the rachis, falls apart when mature to release its hard seeds. Thus, even 6000 years ago, ancient maize cobs were already corn-like.

The GM corn spread far--and fast. Maize appears in the archaeological record of the southwestern United States more than 3000 years ago (12), and it is evident that cob size had already increased under selection. The Jaenicke-Després et al. study (1) examines the selection of traits that can't be observed in fossilized cobs...They report that alleles of these genes typical of modern corn were already present more than 4000 years ago, implying that plant architecture and kernel nutritive properties were selected early, long before corn reached North America.

The authors conclude that "... by 4400 years ago, early farmers had already had a substantial homogenizing effect on allelic diversity at three genes associated with maize morphology and biochemical properties of the corn cob." This suggests that once this special combination of GMs was assembled, the plants proved so superior as a food crop that they were carefully propagated and widely adopted, perhaps causing something of a prehistoric Green Revolution. It also implies that the apparent loss of genetic diversity following the introduction of high-yielding Green Revolution wheat and rice varieties in the 1960s and 1970s, and attending the rapid adoption of superior GM crops today, is far from a new phenomenon.

Science. 2003 Nov 14;302(5648):1158-9.

Transposable Elements As a Molecular Evolutionary Force
So voluminous is the recent literature on transposable elements that it is difficult to imagine making an original observation; it seems that virtually anything that can be said about them, has been. My modest goal is to reexamine what we already know, viewing transposable elements as central players in a dynamic system of complex chromosome structure. McClintock often expressed the intuition that the genome responds to perturbation as an integrated system and acknowledged that we did not know how to think about such a higher level of integration. Although we still lack the analytic tools, there is a growing appreciation that organisms constitute complex, self-organizing systems whose properties can be understood through the study of interactions within and between networks of mutually interacting components, be they DNA sequences, proteins, or cells. Organisms must also be appreciated as historic entities. Today's genome reveals its evolution, which in turn is shaped and limited by the tools and materials available.

In an endeavor to see the familiar with new eyes, I begin by examining a property of eukaryotic genomes so familiar today that it is largely taken for granted: the presence of repetitive DNA. Whereas a high level of internal redundancy is appreciated as one of the most distinctive features of the complex genomes of higher eukaryotes, the theoretic and practical difficulties associated with the origin and maintenance of redundancy, in my view, have gone largely unrecognized and may be central to understanding contemporary genome structure. Redundant sequences can be either adjacent in the genome or dispersed. Different, albeit related, replication mechanisms give rise to each and pose different challenges to the stability and flexibility of the genome as a system. I will address the evidence that eukaryotes have special mechanisms to process duplications.

A rapidly growing body of data from genome characterization, cloning, and sequencing in a variety of organisms is making it increasingly evident that transposable elements have been instrumental in sculpting the contemporary genomes of all organisms. 1-7 The conversation has shifted from conjecture to fact. An understanding of genome evolution must necessarily include consideration of the role of transposable elements in the derivation of today's genomes. Transposable elements comprise a special category of reduplicated sequence whose inherent propensity for dispersal may be its most important property. I will review some of the mechanisms, both genetic and epigenetic, that regulate the movement of transposons and minimize their impact. Finally, the discussion must address the limits of the epigenetic regulatory systems, asking questions about the short- and long-term stability of eukaryotic genome structure.

My central theses are three: (1) that the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy, (2) that the special contribution of transposable elements is to modularize the genome, maintaining it in a structurally dynamic state despite increasing size and complexity, and (3) that the labilizing forces of recombination and transposition are just barely contained, giving a dynamic system of ever increasing complexity, verging on the chaotic.

Ann N Y Acad Sci. 1999 May 18;870:251-64.
Annals of the New York Academy of Sciences 870:251-264 (1999)

Nina Fedoroff
Huck Institute of Life Sciences, Pennsylvania State University
Evan Pugh Professor of Biology
Willaman Professor of Life Sciences, Biology Department
External Faculty, Santa Fe Institute
B.S., Syracuse University, Biology and Chemistry, summa cum laude (1966)
Ph.D., The Rockefeller University, Molecular Biology (1972)

Research Interests:
• Plant stress response
• Hormone signaling
• Transposable elements
• Epigenetic mechanisms

Plant stress response: A major project in the laboratory is investigating the responses of plants to biotic (pathogens) and abiotic (ozone, temperature, chemicals) stresses using DNA microarray gene expression profiling and reverse genetics. We have identified more than 1200 stress-modulated Arabidopsis genes and studying their expression under various conditions. The illustration shows the change in gene expression of 366 genes that are induced (red) or repressed (green) by ozone. Among the genes induced by various stresses are signaling genes, transcription factors, and effector genes that include enzymes that alter the cells structure and properties in response to stress. The signaling molecules include MAP kinases and receptor-like kinases. We are suppressing and overexpressing potential regulatory genes to identify the genes under their control. We want to understand the structure of the stress-response gene networks and to explores molecular genetic approaches to modifying the stress response (see Holter et al, 2000, 2001).

Hormone responses: The hyl1 Arabidopsis mutant (right) has a transposon insertion mutation in a gene that is involved in several hormonal signaling pathways, including those for abscisic acid, auxin and cytokinin. The mutant is affected in many growth parameters, including graviperception. It is not as sensitive to exogenous auxins and cytokinins as the wiltype, but it is hypersensitive to abscisic acid. The HYL1 protein binds to double-stranded RNA and localizes to the nucleus. The mutant is described in Lu and Fedoroff (2000). We are investigating how this protein affects hormone signaling.

Transposable elements: transposable elements or transposons were discovered in corn (maize) plants by the famous geneticist Barbara McClintock through classical genetic analysis of unstable mutations (for a brief history, see http://www.ergito.com or Fedoroff 2001). Maize transposons were cloned in our laboratory almost 20 years ago and are now widely used for insertional mutagenesis. We have created a database of several hundred Arabidopsis transposon insertion lines using a transposon tagging system developed in the laboratory (Smith et al., 1996; Raina et al., 2001). A map of the insertions is shown and the database can be searched at: http://sgio2.biotec.psu.edu/sr.

Epigenetic mechanisms: The maize Suppressor-mutator (Spm) transposon is epigenetically inactivated by methylation and encodes a protein, TnpA, which is capable of reversing the inactivation (Schläppi et al., 1994; Fedoroff et al., 1995). Using an inducible promoter to express TnpA, current experiments seek to understand how it demethylates the Spm promoter. Some ideas about plant transposon evolution are explored in Fedoroff (2000).

MENDEL IN THE KITCHEN: A Scientist's View of Genetically Modified Foods
Nina Fedoroff and Nancy Marie Brown.
Joseph Henry, (352p) ISBN 0-309-09505-1

Wall Street Journal Review
The Miracles of Modifying
November 11, 2004; Page D9
In the distant past, ruddy husbandmen tilled the earth, yielding the pure bounty of nature. Then scientists came along, and nature gave way to artifice with the use of unnatural hybrids and chemicals, and, inevitably, despoliation of the environment. Or so the story goes.
As it happens, agricultural practices have been "unnatural" for 10,000 years. With the exception of wild berries and wild mushrooms, virtually all the grains, fruits and vegetables in our diets (including "organic" ones) are, strictly speaking, genetically modified. Potatoes, tomatoes, oats, rice and corn, for instance, come from plants created -- during the past half-century -- by "wide cross" hybridizations that transcend "natural breeding boundaries."
This is only one of the many surprises in store for readers of "Mendel in the Kitchen" (John
Henry, 370 pages, $24.95) (Gregor Mendel, a 19th-century Austrian monk, first described the
basic laws of heredity that became the foundation for modern genetics.) Nina V. Fedoroff, a plant biologist, and her co-writer Nancy Marie Brown meticulously depict the past, present and future of genetics in agriculture. They mix didactic science (including diagrams reminiscent of a highschool biology textbook) with accounts of what farmers, naturalists, plant breeders and biologists have wrought over time. The saga brings rationality to the controversy now haunting the newest, most precise and most predictable manifestation of genetic modification -- gene-splicing.


Nina V Fedoroff

Evan Pugh professor of biology and Willaman professor of life science at Pennsylvania State University
Scientific ideas can and must be tested and verified in the real world, in order for people to believe in them

What I wish everyone understood about science is that scientific ideas are like philosophical, political or religious ideas, in the sense that they are the products of people's minds and imaginations. But at the same time, scientific ideas are profoundly different from philosophical, political and religious ideas, because they can - and must - be tested and verified in the real world, in order for people to believe in them.

This means that scientific ideas are constantly changing, self-correcting and useful, as evidenced by the way they have allowed humans to grow food, build buildings and cities, travel, cure diseases, communicate and understand the universe. But I wish people understood that science as a way of living provides us with a viable social organising principle, that does not demand the kinds of rigid loyalty that is at the heart of much of the cultural and religious strife in the world. Science may therefore be the only way that human cultures can get beyond the social, cultural, economic and religious differences that underlie wars.

Wednesday, February 22, 2006

Survey of Recent studies on Mutator like elements (Mules) , mobile DNA that moves and different species and scrambles and mutates the genome.

Mutator mobile genes (Mules) that move around between species such as maize, millet, rice diverse angiosperms, yeast Yarrowia lipolytica, Petunia, flatworm Caenorhabditis, sugarcane, fungus Fusarium oxysporum, fruitfly Drosophila, and grasses, which scramble and delete genes, are genetically unstable, and which are common in nature - and completely NATURAL:

Diao X, Freeling M, Lisch D.
Horizontal Transfer of a Plant Transposon.
PLoS Biol. 2005 Dec 20;4(1):e5 [Epub ahead of print]

McCarty DR, Settles AM, Suzuki M, Tan BC, Latshaw S, Porch T, Robin K, Baier
J, Avigne W, Lai J, Messing J, Koch KE, Hannah LC.
Steady-state transposon mutagenesis in inbred maize.
Plant J. 2005 Oct;44(1):52-61.

Cowan RK, Hoen DR, Schoen DJ, Bureau TE.
MUSTANG is a novel family of domesticated transposase genes found in diverse
Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.
6: Mol Biol Evol. 2005 Oct;22(10):2084-9. Epub 2005 Jun 29.

While transposons have traditionally been viewed as genomic parasites or "junk DNA," the discovery of transposon-derived host genes has fueled an ongoing debate over the evolutionary role of transposons. In particular, while mobility-related open reading frames have been known to acquire host functions, the contribution of these types of events to the evolution of genes is not well understood. Here we report that genome-wide searches for Mutator transposase-derived host genes in Arabidopsis thaliana (Columbia-0) and Oryza
sativa ssp. japonica (cv. Nipponbare) (domesticated rice) identified 121 sequences, including the taxonomically conserved MUSTANG1. Syntenic MUSTANG1 orthologs in such varied plant species as rice, poplar, Arabidopsis, and Medicago truncatula appear to be under purifying selection. However, despite the evidence of this pathway of gene evolution, MUSTANG1 belongs to one of only two Mutator-like gene families with members in both monocotyledonous and
dicotyledonous plants, suggesting that Mutator-like elements seldom evolve into taxonomically widespread host genes.

Neuveglise C, Chalvet F, Wincker P, Gaillardin C, Casaregola S.
Mutator-like element in the yeast Yarrowia lipolytica displays multiple
alternative splicings.
Eukaryot Cell. 2005 Mar;4(3):615-24.

Stuurman J, Kuhlemeier C.
Stable two-element control of dTph1 transposition in mutator strains of Petunia
by an inactive ACT1 introgression from a wild species.
Plant J. 2005 Mar;41(6):945-55.

Brownlie JC, Johnson NM, Whyard S.
The Caenorhabditis briggsae genome contains active CbmaT1 and Tcb1 transposons.
Mol Genet Genomics. 2005 Mar;273(1):92-101. Epub 2005 Feb 9.

Rossi M, Araujo PG, de Jesus EM, Varani AM, Van Sluys MA.
Comparative analysis of Mutator -like transposases in sugarcane.
Mol Genet Genomics. 2004 Sep;272(2):194-203. Epub 2004 Aug 24.

The maize Mutator ( Mu) system has been described as the most active and mutagenic plant transposon so far discovered. Mu -like elements (MULEs) are widespread among plants, and many and diverse variants can coexist in a particular genome. The autonomous regulatory element MuDR contains two genes:
mudrA encodes the transposase, while the function of the mudrB gene product remains unknown. Although mudrA -like sequences are ubiquitous in plants, mudrB seems to be restricted to the genus Zea. In the SUCEST (the Brazilian Sugarcane EST Sequencing Project) database, several mudrA -like cDNAs have been identified, suggesting the presence of a transcriptionally active Mu system in sugarcane. Phylogenetic studies have revealed the presence in plants of four classes of mudrA -like sequences, which arose prior to the monocot/eudicot split. At least three of the four classes are also found in the progenitors of
the sugarcane hybrid (Saccharum spp.), Saccharum officinarum and S. spontaneum.
The frequency of putatively functional transposase ORFs varies among the classes, as revealed at both cDNA and genomic levels. The predicted products of some sugarcane mudrA -like transcripts contain both a DNA-binding domain and a transposase catalytic-site motif, supporting the idea that an active Mu system exists in this hybrid genome.

Xu Z, Yan X, Maurais S, Fu H, O'Brien DG, Mottinger J, Dooner HK.
Jittery, a Mutator distant relative with a paradoxical mobile behavior:
excision without reinsertion.
Plant Cell. 2004 May;16(5):1105-14. Epub 2004 Apr 9.

The unstable mutation bz-m039 arose in a maize (Zea mays) stock that originated from a plant infected with barley stripe mosaic virus. The instability of the mutation is caused by a 3.9-kb mobile element that has been named Jittery (Jit).
Jit has terminal inverted repeats (TIRs) of 181 bp, causes a 9-bp direct duplication of the target site, and appears to excise autonomously. It is predicted to encode a single 709-amino acid protein, JITA, which is distantly related to the MURA transposase protein of the Mutator system but is more closely related to the MURA protein of Mutator-like elements (MULEs) from Arabidopsis thaliana and rice (Oryza sativa). Like MULEs, Jit resembles Mutator in the length of the element's TIRs, the size of the target site duplication, and in the makeup of its transposase but differs from the autonomous element Mutator-Don Robertson in that it encodes a single protein. Jit also differs from Mutator elements in the high frequency with which it excises to produce germinal revertants and in its copy number in the maize genome: Jit-like TIRs are present at low copy number in all maize lines and teosinte accessions examined, and JITA sequences occur in only a few maize inbreds. However, Jit cannot be considered a bona fide transposon in its present host line because it does not leave footprints upon excision and does not reinsert in the genome. These unusual mobile element properties are discussed in light of the structure and gene organization of Jit and related elements.

Sijen T, Plasterk RH.
Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.
Nature. 2003 Nov 20;426(6964):310-4.

Slotkin RK, Freeling M, Lisch D.
Mu killer causes the heritable inactivation of the Mutator family of
transposable elements in Zea mays.
Genetics. 2003 Oct;165(2):781-97.

May BP, Liu H, Vollbrecht E, Senior L, Rabinowicz PD, Roh D, Pan X, Stein
L, Freeling M, Alexander D, Martienssen R.
Maize-targeted mutagenesis: A knockout resource for maize.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11541-6. Epub 2003 Sep 3.

Vastenhouw NL, Fischer SE, Robert VJ, Thijssen KL, Fraser AG, Kamath RS,
Ahringer J, Plasterk RH.
A genome-wide screen identifies 27 genes involved in transposon silencing in C.
Curr Biol. 2003 Aug 5;13(15):1311-6.

Chalvet F, Grimaldi C, Kaper F, Langin T, Daboussi MJ.
Hop, an active Mutator-like element in the genome of the fungus Fusarium
Mol Biol Evol. 2003 Aug;20(8):1362-75. Epub 2003 May 30.

Pooma W, Gersos C, Grotewold E.
Transposon insertions in the promoter of the Zea mays a1 gene differentially
affect transcription by the Myb factors P and C1.
Genetics. 2002 Jun;161(2):793-801.

Bessereau JL, Wright A, Williams DC, Schuske K, Davis MW, Jorgensen EM.
Mobilization of a Drosophila transposon in the Caenorhabditis elegans germ
Nature. 2001 Sep 6;413(6851):70-4.

Lisch DR, Freeling M, Langham RJ, Choy MY.
Mutator transposase is widespread in the grasses.
Plant Physiol. 2001 Mar;125(3):1293-303.

Singer T, Yordan C, Martienssen RA.
Robertson's Mutator transposons in A. thaliana are regulated by the
chromatin-remodeling gene Decrease in DNA Methylation (DDM1).
Genes Dev. 2001 Mar 1;15(5):591-602.

Fedoroff NV.
The suppressor-mutator element and the evolutionary riddle of transposons.
Genes Cells. 1999 Jan;4(1):11-9. Review.

Kloeckener-Gruissem B, Freeling M.
Transposon-induced promoter scrambling: a mechanism for the evolution of new
Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1836-40.

Eisen JA, Benito MI, Walbot V.
Sequence similarity of putative transposases links the maize Mutator autonomous
element and a group of bacterial insertion sequences.
Nucleic Acids Res. 1994 Jul 11;22(13):2634-6.

Pan and Peterson (1988) note that it would appear that the corn genome is highly volatile. That is, these transposons are now known to be quiescent in the genome. They appear also to be spontaneously activated. This is evident in almost any line one looks at with appropriate reporter alleles as indicated in the paper by Pan and Peterson (1988), where sectors were pervasive in these lines. It would appear, therefore, that the corn genome has a built-in system of activation and redeployment of genome segments and in a final result, leads to a great deal of variability.

Annual Review of Genetics
Vol. 23: 71-85 (Volume publication date December 1989)
Maize Transposable Elements
A Gierl, ­H Saedler, and ­P A Peterson­

Genetics, Vol 128, 823-830, Copyright © 1991
Spontaneous Germinal Activation of Quiescent Uq Transposable Elements in Zea mays L
Y. B. Pan and P. A. Peterson
Department of Agronomy and Department of Genetics, Iowa State University, Ames, Iowa 50011 Present address: Department of Immunology/Microbiology, Rush-Presbyterian-St. Luke's Medical Center, 1653 West Congress Parkway, Chicago, Illinois 60612-3864.

The spontaneous germinal activation of quiescent Uq transposable elements is reported. Thirty-nine spotted exceptions were observed at a rate of about 2 X 10(-4) from 687 otherwise colorless ears produced from the cross of a-ruq/a-ruq (colorless or occasionally sectored) X an a-ruq tester (colorless). All exceptions had spotting patterns distinct from the pattern of our original standard Uq (Uq1)-a-ruq spotting. From these spotted exceptions five new Uq elements (Uq2, Uq3, Uq4, Uq5 and Uq6) have been isolated. Genetic evidence for the Uq nature of the five germinal isolates is presented. First, each of the five spotted exceptions was homozygous for the a-ruq reporter allele. Second, four new Uq isolates (Uq2, Uq3, Uq4 and Uq5), after being reconstituted into a a{deg} sh2/a{deg} sh2 (no Uq) line, could transactivate the standard a-ruq allele and continue to produce their distinct spotting phenotypes. Third, these five new Uqs are also capable of transactivating the c-ruq65 and c-ruq67 alleles. However, the transactivation of c-ruq is generally weaker than that of a-ruq.

Tagging of a maize gene involved in kernel development by an activated Uq transposable element
Yong-Bao Pan1 and Peter A. Peterson1 Contact Information
(1) Department of Genetics and Department of Agronomy, Iowa State University, 50011 Ames, IA, USA
Received: 12 April 1989
Communicated by H. Saedler

Summary A quiescent Uq transposable element has been activated in a maize plant treated with 5-aza-2prime-deoxycyti-dine. This activated Uq cosegregates with a heritable dominant miniature (Mn) kernel phenotype, indicating its physical association with a maize miniature locus (Mn:: Uq). The Mn:: Uq mutant is dominant in producing a miniature seed phenotype of variable size and in reducing seedling vigor in the early growth stage. Genetic experiments indicate that the Mn:: Uq mutant also affects the activity of the male gametophyte, whereby pollen germination is inhibited, thus lacking pollen tube growth resulting in the male nontransmissibility of this mutant. Proof for the Uq element in this mutant is derived by its ability to transactivate the standard a-ruq reporter allele to yield spotted aleurone tissue. However, the Mn:: Uq mutant does not transactivate a normally Uq-responsive c-ruq allele, suggesting a structural difference between the two ruq receptors at the A1 and C1 loci. It is anticipated that cloning of the Uq transposable element would facilitate the molecular cloning and characterization of the maize miniature gene.

Key words Zea mays - Uq transposable element - miniature gene - Mn:: Uq - Activation
Journal Paper No. J-13425 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011, USA, Project No. 2850

Genetics, Vol 120, 587-596, Copyright © 1988
The Mutator-Related Cy Transposable Element of Zea mays L. Behaves as a Near-Mendelian Factor

P. S. Schnable and P. A. Peterson
Present address: Department of Genetics Iowa State University, Ames, Iowa 50011.

The bz-rcy allele arose in a single gamete of the TEL (transposable-element laden) population, when the rcy receptor element inserted into the Bronze1 locus. This newly arisen receptor allele conditions a stable bronze kernel phenotype in the absence of the independently segregating regulatory element, Cy. In the presence of Cy, bz-rcy conditions fully colored spots on a bronze background. The spots represent clonal sectors arising from mutations of bz-rcy to Bz'. Although Cy exhibits genetic interactions with the Mutator system it differs from Mu-homologous elements in its near-Mendelian behavior which is in contrast to the non-Mendelian inheritance of Mutator and Mu-homologous elements. Evidence is presented which suggests that the timing and mode of Cy transposition differ from those of Mu1.

Further reading at Academics Review

Friday, February 17, 2006

Submission to Agriculture and Food Policy Reference Group

By Dr David Tribe, Senior Lecturer, University of Melbourne and Dr Roger Kalla, Director Korn Technologies.

The issues paper on ‘Ensuring a profitable and sustainable agriculture and food sector in Australia’ presents a number of challenges facing Australian governments’ agricultural producers, marketers, scientists and consumers now and in the future.

We have focussed our submission on the benefits arising from the continued adoption of Biotechnology to Australian agriculture and food sector and a way forward for the testing of parallel GM and non- GM grains supply chains.

In a recent paper presented to the 9th Conference on Agricultural Biotechnology hosted by the International Consortium on Agricultural Biotechnology Research (www. economia.uniroma2.it/conferenze/icabr2005/papers/Tribe_Davi_Kalla_Roger.pdf) we described the results of an analysis of the economic and environmental impact of genetically modified insect resistant cotton in Australia.

The paper outlines the factors that have contributed to the rapid adoption of GM cotton in the well integrated cotton supply chain. The conversion to insect resistant GM cotton in Australia has provided direct economic benefits while at the same time reduced use of pesticide with concomitant reduction in yield losses in yield. Put in another way the land sown to cotton in Australia is now more productive giving a raised output while requiring less input. The adoption of GM cotton has also ensured the competitiveness of Australian cotton growers against GM cotton producers in India, China, Mexico and USA as evidenced in a recent report from ABARE on Market issues for GM crops where Australia’s share of cotton exports over the five years from 1999 to 2003 represented 37 % of world export while Australia produced less than 3% of world cotton seed (Market Access Issues for Genetically Modified Products: Implications for Australia, abareonlineshop.com/product.asp?prodid=12559).

Innovation in Australia’s first fibre, food and feed crop continues unabated and in addition to input traits now output traits with direct health benefits to the consumer are being evaluated in small scale field trials (DIR 039/2003 - Field Evaluation of Genetically Modified High Oleic (HO) Cotton, www.ogtr.gov.au).

The main concern raised by participants in the canola and cereal grains supply chain against full scale commercial production of GM canola the second GM food and feed crop that has received federal regulatory approval (DIR 021/2002 - Commercial release of InVigor® hybrid canola (Brassica napus) for use in the Australian cropping system and DIR 020/2002 - General release of Roundup Ready® canola in Australia, www.ogtr.gov.au) has been the perceived threat against the international marketing advantage of the projected default ‘GM free’ status for Australian grain producers.

The notion that Australia could protect the image of its agriculture and food export sector as being 100 % GM free (in spite of rapidly having converted to GM cotton which constituted 80% of last year cotton harvest) by delaying the introduction of GM canola has been challenged by the recent finding of minuscule amounts of a strain of GM canola mixed up in an export consignment of conventional canola and detected by sensitive forensic DNA analysis technology. The origin of this approved, but obsolete, GM strain is under investigation by the Victorian Department of Primary Industries.

The most likely explanation is that this particular strain of GM canola got mixed up in a batch of conventional canola seed imported into Australia from North America.

The modern breeding of novel types of canola and cereal grains is a global pursuit with novel genes ( derived using GM or non GM technologies in molecular breeding research centres all over the world ) being crossed into plants that are well adapted to the local growth conditions in collaborative research programs between private and publicly funded agricultural R & D organisations. Often these programs take advantage of the counter seasons with seeds being multiplicated and evaluated on both sides of the globe and frequently exchanged before commercialisation in any one country.

There are previous examples of human error creeping into this interconnected system. A GM canola strain, mislabelled as of non-GM origin, was delivered by an overseas private seed company for evaluation in the field to the Victorian Department of Primary Industries in 2003. However, this case of mistaken identity was detected before the GM canola plants had flowered and the plants were destroyed. The incident was investigated by OGTR without any action and reported on its web site (www.ogtr.gov.au/rtf/public/sept2003qrpt.rtf).

We would argue that the benefits to Australian agriculture and food industries and the consumers of Australian research organisation continuing to take part in global technology diffusion far outweighs the perceived risks to our export markets by the tarnishing of a projected ‘GM free’ image due to such mix ups.

It is in the interest of private and public research organisations to carefully manage these risks due to real issues with IP management. Such incidences, if carefully monitored, certainly doesn’t warrant that we pull out of all work with overseas research organisations nor that Australia unilaterally ban all imports of any grains from North America due to the perceived risk of ‘contamination’ of the Australian ‘GM free’ image as has been suggested by some groups ideologically opposed to GM crops.

Likewise it is unreasonable to expect that parallel GM and non- GM canola and cereal grains supply chains could guarantee 100 % purity of any type of canola in our export grain.

We see a role for the Australian Government in partnership with companies involved in the providing services in the grains supply chain and State Governments to determine what are tolerable levels of admixture of GM canola in any type of exported grain. The Australian position needs to be underpinned by scientific and economic analysis of cost vs. benefit of the testing regimes that are required to adequately address the cut –off criteria.

It is worth noting that forensic DNA testing is technically challenging and costly (in the order of $ 100 -250 per sample analysed). There are also issues with standardisation of sampling protocols of bulk consignments seed for presence of GM canola seed along the supply chain.

If it was decided that Australia required to DNA test some or all of its export grains to meet internal or external market requirements there would be a potential role for Government in advising and accrediting research organisations involved in such analysis.

The EC Directorate General Joint Research Centre, within the Institute for Health and Consumer Protection, has got a dedicated Community Reference Laboratory (CRL) for GM food and Feed. The CRL develops tests for GM crops and evaluates their efficacy. A recent example is the standardised test it developed for the Bt 10 maize strain (http://gmo-crl.jrc.it/detectionmethods/Bt10%20Detection%20Protocol.pdf).

We believe that a thorough test of the capability of the grains supply chain to keep GM canola apart from non-GM canola is required. An approach to a trial of coexistence using the GM canola strains that had received regulatory approval was originally suggested by the Australian Oilseeds Federation in submissions to a number of State Governments in the beginning of 2003. We would suggest that the original proposal could be augmented by the establishment of independent testing authority modelled on the EC Community reference laboratory for GM food and feed.

There are companies involved in DNA testing of food and feed in Australia (www.agriquality.co.nz/horticulture/agriquality_gmo_services.cfm). Other major grain marketing organisation, including AWB, has decided to join groupings such as the Global Laboratory Alliance (GLA) which is supported by large US DNA testing companies such as Genetic ID. Genetic ID has recently also developed a test to Bt10 maize that is legally recognized by the EU (www.genetic-id.com/pr/bt10_test.pdf) and aligned with the CRL protocol.

Incidences such as the discovery of the non-approved Bt10 maize mixed in shipments of approved GM maize from US to Europe and the recent minor incidence with the approved GM canola strain being detected in Australian non-GM canola destined for export to Japan provides ample proof that the moratoria on GM canola and other GM novel crops are only a holding pattern and that proactive leadership from the Federal Government is required in order for Australia to continue to benefit from the world leading research being undertaken in agricultural biotechnology by Australian public and private research organizations. Australia’s agriculture and food sector and the Australian Government needs to take a pro active role in the development and ordered conversion of these technologies into solutions for the agricultural and food sectors.

Best wishes,

Yours sincerely,

Roger Kalla

PhD, Director Korn Technologies

David Tribe

Reader, University Of Melbourne, Department of Immunology and Microbiology



§ Our paper outlines the large economic and environmental benefits that insect resistant BT cotton, the first Australian GM fibre, food and feed crop, has provided until know.

§ The direct benefits to end consumers of GM cottonseed with modified oil content will be realised with High Oleic GM cotton strains being evaluated in the field.


§ The present blockage to the commercialization of GM canola, the second Australian GM food and feed crop is unsustainable.

§ The projected ‘GM free’ image of Australian agriculture and food export sector based on the State moratoria on GM canola is misleading and doesn’t acknowledge the realities of the globally integrated efforts in the development of novel strains of major food and feed crops such as cotton and canola.


§ Revamped Coexistence trials to evaluate the capacity for segregation along the grains supply chain needs to be undertaken by agriculture and food industry sector organizations and facilitated by Federal Government.

§ Standardized DNA testing protocols based on scientific and economically sound cut-off levels for admixture of GM crops in non-GM canola and grain bulk consignments overseen by independent national authority like the EU Community Reference Laboratory (CRL) for GM food and Feed.

§ In order for Australian agriculture and food sector to continue to be competitive in overseas markets Federal government needs to take a more proactive role in ensuring that Australian world class research and development efforts in these sectors converts good ideas and smart work to solutions that will benefit Australian rural communities, economy and end consumers.

Attached: Abstract to paper by Tribe and Kalla submitted and published by ICABR July 2005.

Collected scare stories about GM crops.

(This is a draft work in progress.)

Please go instead here

Thursday, February 09, 2006

Green water efficiencies help salinity on Australian drylands.

Drainage and change in soil water storage below the root-zone under long fallow and continuous cropping sequences in the Victorian Mallee
Mark G. O'Connell, Garry J. O'Leary and David J. Connor

A field study investigated drainage and changes in soil water storage below the root-zone of annual crops on a sandy loam soil in the Victorian Mallee for 8 years. It was designed to compare the effects of the common long (18-month) fallow in a 3-year rotation (fallow–wheat–pea, FWP) with a rotation in which the fallow was replaced with mustard (Brassica juncea), viz. mustard–wheat–pea (MWP). Drainage was measured over 2 periods (1993–98 and 1998–2001) using 9 in situ drainage lysimeters in each rotation. The first period of ~5 years was drier than average (mean annual rainfall 298 cf. 339 mm) and drainage was low and variable. Drainage was greater under the fallow rotation (average 0.24 mm/year) than under the non-fallow rotation (average <0.01>
Australian Journal of Agricultural Research 54, 663–675 (2003)

Production and Environmental Aspects of Cropping Intensification in a Semiarid Environment of Southeastern Australia
Víctor O. Sadras* and David K. Roget

Low and highly variable rainfall are major sources of risk for farms in semiarid environments, including the Mallee region of Australia where risk management is largely based on a conservative, low-input approach. This approach has substantial opportunity costs (missing the benefits of wetter seasons) and low yield per unit rainfall. We combined field and modeling experiments to evaluate an intensive, flexible cropping approach based on (i) an opportunistic combination of crops, including wheat (Triticum aestivum L), canola (Brassica napus L.), and grain legumes, and (ii) a close matching of N input to soil and seasonal conditions. In a 4-yr field trial established on a coarse-textured soil, an intensive cropping approach doubled gross margin and halved its coefficient of variation in relation to current practice. Modeling experiments revealed the underlying mechanisms of this response and estimated the effect of cropping intensification on N leaching and deep drainage. Simulated yield improvement under intensive cropping was related to increased water use efficiency [biomass per unit evapotranspiration (ET)] at the expense of N use efficiency (biomass per unit of N uptake); this is consistent with the theoretical expectation that plant growth is maximized when all resources are equally limiting. Simulations indicated no substantial increase in N leaching and moderate decrease in drainage beyond the root zone with the more intensive approach. The approach to intensification in this research provides a platform to improve production and profit and to reduce its seasonal variation with neutral or positive effects on environmentally relevant processes.
Abbreviations: ET, evapotranspiration • MAP, monoammonium phosphate • PAW, plant available water • T, transpiration

Published in Agron. J. 96:236-246 (2004).

Water balance changes in a crop sequence with lucerne
F. X. Dunin, C. J. Smith, S. J. Zegelin and R. Leuning

In a detailed study of soil water storage and transport in a sequence of 1 year wheat and 4 years of lucerne, we evaluated drainage under the crop and lucerne as well as additional soil water uptake achieved by the subsequent lucerne phase. The study was performed at Wagga Wagga on a gradational clay soil between 1993 and 1998, during which there was both drought and high amounts of drainage (>10% of annual rainfall) from the rotation. Lucerne removed an additional 125 mm from soil water storage compared with wheat (root-zone of ~1 m), leading to an estimated reduction in drainage to 30–50% of that of rotations comprising solely annual crops and/or pasture.

This additional soil water uptake by lucerne was achieved through apparent root extension of 2–2.5 m beyond that of annual crops. It was effective in generating a sink for soil water retention that was about double that of annual crops in this soil. Successful establishment of lucerne at 30 plants/m2 in the first growing season of the pasture phase was a requirement for this root extension. Seasonal water use by lucerne tended to be similar to that of crops in the growing season between May and September, because plant water uptake was confined to the top 1 m of soil. Uptake of water from the subsoil was intermittent over a 2-year period following its successful winter establishment. In each of 2 annual periods, uptake below 1 m soil depth began late in the growing season and terminated in the following autumn.

Above-ground dry matter production of lucerne was lower than that by crops grown in the region despite an off-season growth component that was absent under fallow conditions following cropping. This apparent lower productivity of lucerne could be traced in part to greater allocation of assimilate to roots and also to late peak growth rates at high temperatures, which incurred a penalty in terms of lower transpiration efficiency. The shortfall in herbage production by lucerne was offset with the provision of timely, high quality fodder during summer and autumn. Lucerne conferred indirect benefits through nitrogen supply and weed control. Benefits and penalties to the agronomy and hydrology of phase farming systems with lucerne are discussed.

Keywords: crop rotation, evapotranspiration, deep drainage, water use efficiency.

Australian Journal of Agricultural Research 52(2) 247 - 261
Full text doi:10.1071/AR00089

Estimating episodic recharge under different crop/pasture rotations in the Mallee region. Part 2. Recharge control by agronomic practices
L. Zhanga, W. R. Dawesa, T. J. Hattonb, I. H. Humec, M. G. O'Connelld, D. C. Mitchellc, P. L. Milthorpe and M. Yeee

Much environmental degradation, including salinity in the Mallee region of southeastern Australia, is associated with the loss of native vegetation and increased recharge. As a result, various agronomic practices have been proposed to reduce groundwater recharge. This study was conducted to evaluate the impact of these practices on recharge, in particular episodic recharge. A biophysically based model (WAVES) was used to estimate recharge rates under some typical crop and pasture rotations in the region using long-term meteorological data. Results show that: (1) recharge just below the root zone was episodic and that just 10% of annual recharge events contributed over 85% of long-term totals. Management options such as incorporating lucerne and deep-rooted non-fallow rotations can reduce both, mean annual recharge, and the number of episodic events, but not eliminate recharge completely; (2) winter fallows increased soil-water storage and some of the additional water was stored in the lower portion of the root zone or below it. This can increase the risk of recharge to groundwater system; (3) changes in land management may take a considerable period of time (>10 years) to have any noticeable impacts on recharge; and (4) recharge under lucerne was ≈30% of that under medic pasture.
Author Keywords: Agronomic practices; Episodic recharge; Fallowing; Root zone.

Agricultural Water Management
Volume 42, Issue 2 , November 1999, Pages 237-249

Monday, February 06, 2006

Salinity Solutions: Working with Science and Society

(A supplement to GMO Pundit Salinity Solutions Webpage)

Full table of contents:
Australian Journal of Experimental Agriculture
Volume 45 Number 11 2005
Salinity Solutions: Working with Science and Society

Preface: Salinity Solutions — Working with Science and Society
M. Crawford and K. Goss

The role of plants and plant-based research and development in managing dryland salinity in Australia
A. M. Ridley and D. J. Pannell
pp. 1341-1355

Potential of current perennial plant-based farming systems to deliver salinity management outcomes and improve prospects for native biodiversity: a review
E. C. Lefroy, F. Flugge, A. Avery and I. Hume
pp. 1357-1367

Capture of agricultural surplus water determines the productivity and scale of new low-rainfall woody crop industries
D. Cooper, G. Olsen and J. Bartle
pp. 1369-1388

Using soil and climatic data to estimate the performance of trees, carbon sequestration and recharge potential at the catchment scale
R. J. Harper, K. R. J. Smettem and R. J. Tomlinson
pp. 1389-1401

The economics of managing tree–crop competition in windbreak and alley systems
R. Sudmeyer and F. Flugge
pp. 1403-1414

Multi-disciplinary approaches suggest profitable and sustainable farming systems for valley floors at risk of salinity
E. G. Barrett-Lennard, R. J. George, G. Hamilton, H. C. Norman and D. G. Masters
pp. 1415-1424

Improving salt tolerance of wheat and barley: future prospects
T. D. Colmer, R. Munns and T. J. Flowers
pp. 1425-1443

Genetic variation in five populations of strawberry clover (Trifolium fragiferum cv. Palestine) in Western Australia
K. S. McDonald, P. S. Cocks and M. A. Ewing
pp. 1445-1451

Predicted salinity impacts from land use change: comparison between rapid assessment approaches and a detailed modelling framework
C. Beverly, M. Bari, B. Christy, M. Hocking and K. Smettem
pp. 1453-1469

Farm, food and resource issues: politics and dryland salinity
D. J. Pannell
pp. 1471-1480

Lessons from agri-environmental policies in other countries for dealing with salinity in Australia
A. Weersink and A. Wossink
pp. 1481-1493

Social persistence of plant-based management of dryland salinity
N. Barr and R. Wilkinson
pp. 1495-1501

Epilogue: from propaganda to practicalities — the progressive evolution of the salinity debate
J. Passioura
pp. 1503-1506

Wednesday, February 01, 2006

Why tryptophan is bad for people who have chemical imbalances related to histamine and serotonin.

This post is a continuation, with all the fine print, and gory pathological detail, of a post that starts at GMO Pundit as follows:

By a strange twist of fate, GMO Pundit is ideally placed to alert readers to a real hazard - excessive tryptophan intake in the wrong circumstances - that is widely misunderstood in the community, and is a previously falsely diagnosed risk.

The main point of this posting is to help people avoid ill health - that is avoid generalised muscular pains (myalgia, called EMS) - that might be caused by ill-advised self-medication with tryptophan, or excessive intake of foods rich in tryptophan. Such intake is commonly taken because it is perceived to help overcome mental depression caused by chemical imbalances in the brain.