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Date:

October 5, 2007

Subject:

Evolution Transforms "Junk" DNA; Super Heroes & GM Foods; GM crops may be good for insects

 

* Fungus Genome Yielding Answers
* Plant Processes Shed Light On Antioxidants
* Evolution Transforms "Junk" DNA
* New Insights On 'Jumping Genes'
* GM crops may be good for insects
* Mexico Agricultural Situation
* Syngenta upheld in patent dispute
* Super Heroes & GM Foods

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Fungus Genome Yielding Answers To Protect Grains, People And Animals

- Purdue University via Science Daily, Oct. 5, 2007

http://www.sciencedaily.com/releases/2007/10/071004221809.htm

Why a pathogen is a pathogen may be answered as scientists study the recently mapped genetic makeup of a fungus that spawns the worst cereal grains disease known and also can produce toxins potentially fatal to people and livestock.

The fungus, which is especially destructive to wheat and barley, has resulted in an estimated $10 billion in damage to U.S. crops over the past 10 years. The scientists who sequenced the fungus' genes said that the genome will help them discover what makes this particular pathogen so harmful, what triggers the process that spreads the fungus and why various fungi attack specific plants.

These investigations also may lead to producing plants that are completely resistant to the fungus Fusarium graminearum, something that hasn't been possible previously, said Jin-Rong Xu, a Purdue University molecular biologist. He is pinpointing which genes enable the fungus to cause the disease Fusarium head blight, or scab.

In a recent issue of the journal Science, Xu and an international scientific team reported that certain chromosomal regions in Fusarium graminearum appear to dictate plant and fungus molecular interactions that allow the fungus to contaminate crops and cause disease.

The researchers located all of the genes on the fungus' chromosomes and then determined the genes' chemical makeup, or sequence.

"The Fusarium graminearum genome was easy to assemble because, unlike other fungal genomes, there aren't too many repetitive DNA sequences," Xu said. "It seems that this Fusarium can efficiently detect and remove duplicated sequences or transposable elements, which kept the genome clean and well-organized."

This basic information on the Fusarium graminearum genome will aid in further research and also provide information on other fungi and their interaction with plants, he said.

"Because we now have the genome sequence and a microarray containing the whole genome, it will help us determine what genes allow this fungus to behave as it does," Xu said. "It also will make it easier to identify and determine the function of similar genes in other pathogens and their plant interactions."

Fusarium graminearum, which exists worldwide, cuts crop yield, damages grain quality and produces mycotoxins. The fungus caused a widespread head blight epidemic during the 1990s in wheat- and barley-growing regions around the world. Experts estimate that from 1998 to 2000 the central and northern Great Plains of the United States suffered economic losses of $2.7 billion due to the disease. In Indiana alone in 1996, the fungus caused at least $38 million in crop loss, according to the USDA.

The mycotoxins caused by the fungus can affect people and livestock that ingest infected grain. Pigs, cattle, horses, poultry and people can develop vomiting, loss of appetite, diarrhea, staggering, skin irritation and immunosuppression. The most severe cases can be fatal.

Some scientific evidence suggests that these toxins cause cancer. People in developing countries are at the greatest risk of eating grain contaminated with Fusarium mycotoxins. Although not all types of Fusarium cause disease and produce toxins, those types that do infect other crops, including corn and hay.

Currently, fungicides aren't effective because the fungus only attacks during the beginning of the plants' flowering stage. It's difficult to gauge the precise time to spray, and it's expensive to try to protect the crops over a long period. The fungus can survive through the winter in crop remnants left in fields as natural mulch.

The pathogen is most likely to appear and cause infection in early spring when the weather is warm and humid or rainy. By the time Fusarium contamination is noticeable on plants, head blight has already damaged the grain.

Xu is searching for the genes involved in the infection process.

"We are using the whole-genome microarray of Fusarium graminearum to identify the genes that are functional during plant infection," Xu said. "We are looking at the biochemical signaling pathways that influence whether a gene is turned on or off. This will help us find ways to develop new, stable and environmentally safe ways to prevent these infections."

Xu was one of the co-applicants for a $1.9 million grant from a U.S. Department of Agriculture/National Science Foundation partnership that funded the genome project. The endeavor was headed by Corby Kistler, a USDA-Agricultural Research Service geneticist based at the University of Minnesota.

Christina Cuomo of the Broad Institute at the Massachusetts Institute of Technology led the sequencing. Other members of the research team included scientists from Michigan State University; Cornell University; Pacific Northwest National Laboratory; University of Arizona; St. Louis University; University of Tennessee; and institutions in Germany, Canada, Austria, England, France, Ukraine and the Netherlands.

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Processes That Give Plants Color Shed Light On Antioxidants

- Biotechnology and Biological Sciences Research Council via Science Daily, Oct. 5, 2007

http://www.sciencedaily.com/releases/2007/10/071002213456.htm

Scientists have made an important advance in understanding the genetic processes that give flowers, leaves and plants their bright colours. The knowledge could lead to a range of benefits, including better understanding of the cancer-fighting properties of plant pigments and new, natural food colourings.

The scientists, at the John Innes Centre and Institute of Food Research in Norwich, have pinpointed a key group of enzymes involved in the production of plant pigments. The pigments, called anthocyanins, are what give some plants the vivid colours that they use to attract insects and foraging animals. They also give plants protection against environmental stresses and disease.

Hundreds of different anthocyanins exist in nature, all with slightly different chemical compositions. The international research team identified the genes responsible for the enzymes which chemically modify anthocyanins to alter their properties.

Prof Cathie Martin at the John Innes Centre who co-led the project explains: "Using a new strategy, we conducted biochemical studies on the brassica plant Arabidopsis. We found that a small number of genes responsible for the enzymes that chemically modify anthocyanins were 'switched on' when the plants were making anthocyanins in response to stress.

"When we transferred these genes to a tobacco plant, the colour of the tobacco flowers changed slightly, confirming that these genes, and the enzymes that they produce, were indeed responsible for modifying anthocyanins.

"What's more, these anthocyanins that had been modified by the enzymes were more stable than those that hadn't. This is significant because stabilised anthocyanins could be used as natural food colourants to replace many artificial colours used in various foods. This improved understanding of the genetics of anthocyanins also provides a better platform for studying their antioxidant properties, important in the fight against cancer, cardiovascular disease and age-related degeneration."

The research is highlighted in the new issue of Business from the Biotechnology and Biological Sciences Research Council (BBSRC). BBSRC provided funding for the research.

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Evolution Transforms "Junk" DNA into Genetic Machinery

- Howard Hughes Medical Institute, Oct. 5, 2007

http://www.hhmi.org/news/rubinstein20071004.html

Evolution has mastered the art of turning trash to treasure - though, for scientists, witnessing the transformation can require a bit of patience. In new genetic research, scientists have traced the 170 million-year evolution of a piece of "junk" DNA to its modern incarnation as an important regulator of energy balance in mammals.

The discovery, they said, suggests that regions of the genome formerly presumed to be a genetic junkyard may actually be a hardware superstore, providing components that can be used to evolve new genes or new species.

The discoveries were reported by Howard Hughes Medical Institute international research scholar Marcelo Rubinstein and his colleagues October 5, 2007, in the online PLoS Genetics. Rubinstein is at the Institute for Research on Genetic Engineering and Molecular Biology of the National Council for Science and Technology in Argentina, and the University of Buenos Aires.

Researchers have long known that all genomes are prodigiously sprinkled with DNA fragments derived from mobile elements that have jumped to apparently random points in the genome. For example, the Human Genome Project revealed that about 45 percent of our genome consists of mobile element-derived sequences.

"The classical view has considered genomic sequences derived from mobile elements as "junk" DNA - a large accumulation of useless sequences," said Rubinstein. "However, more recent work, including the findings in this paper, is producing convincing evidence that these sequences provided raw material for the evolution of novel gene functions."

Rubinstein and his colleagues had been studying one such piece of DNA, called nPE2, which enhances the activity of a gene called POMC (proopiomelanocortin). The POMC gene is expressed in cells in the brain and produces peptides that regulate a variety of behaviors, including food intake and stress-induced analgesia.

"Our studies showed that nPE2 is highly conserved in mammals but absent in other vertebrates, so we became interested in studying its evolutionary origins," said Rubinstein. "We then found nPE2 to be highly similar to sequences present in the genomes of the marsupials opossum and wallaby. So we thought we had found the tip of the iceberg of an evolutionary process that started around 200 million years ago, and we got really fascinated by the idea of pulling up the entire iceberg from the depths." In fact, Rubinstein and his colleagues realized that all similar sequences originated from a superfamily of mobile elements called CORE-short interspersed elements (CORE-SINES). CORE-SINES are retroposons, meaning the genetic sequence has been copied before being inserted into new sites in the genome.

To reveal more of nPE2's evolutionary history, the researchers compared nPE2 sequences from 16 mammalian species, including human, dog, mouse, and rabbit. They found the nPE2 enhancer sequence to be highly conserved. By creating altered versions of the nPE2 sequence and testing their ability to enhance gene expression in transgenic mice, they showed that the regions that were critical to nPE2's function were most rigorously conserved over evolution. The findings, Rubinstein said, indicated that nPE2's function "contributed to the fitness of all mammals, probably by better tuning the central regulation of energy balance."

"This paper shows, for the first time, that a retroposon of this superfamily got inserted near the POMC gene sometime before 170 million years ago; and after suffering a limited number of random mutations, it acquired a novel and useful function and became fixed in the genome of an ancestor to all mammals," said Rubinstein.

The findings provide clear evidence that genes use a collection of functional sequences incorporated at different times during a very long-lasting evolutionary process, said Rubinstein. "Novel sequences that improved fitness got fixed into the genomes and continued to travel to the future together with more ancient functional sequences," he said.

The researchers found a large number of other CORE-SINE superfamily members that had changed very little over evolutionary time, suggesting that nPE2's evolution from junk to regulatory DNA was not a unique event. In fact, Rubinstein suspects that thousands of currently functional elements are derived from ancient retroposon insertions - but their evolutionary history still needs to be untangled. "We are starting to understand how insertional elements, instead of being useless or harmful for the genomes, may be beneficial."

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KGI Professor Contributes New Insights On 'Jumping Genes'

- Keck Graduate Institute (press release), Oct. 4, 2007

http://www.prnewswire.com/cgi-bin/stories.pl?ACCT=104&STORY=/www/story/10-04-2007/0004676356&EDATE=

CLAREMONT, Calif. -- Keck Graduate Institute (KGI) today announced that Dr. Animesh Ray, KGI professor and director of KGI's PhD program, has published a paper in the international online journal PLoS ONE that sheds new light on the evolution of moveable genetic elements, or "jumping genes."

"We have known for some time that some genes can move from one place to another within the genome," said President Sheldon Schuster, PhD, KGI's president. "Dr. Ray's research provides evidence that this movement of genes does not cause instability at the point from which the gene moves. This discovery has important implications for our understanding of molecular evolution and genetic research involving plants, including genetically modified crops. These findings take us closer, for example, to more precisely predicting the changes a drought-resistant jumping gene from one plant put into another may cause to the DNA."

Using the plant Arabidopsis thaliana, Ray and his students studied the "footprint" that is left behind when a jumping gene moves to another locus. They devised a test for examining these footprints that revealed a mechanism for the broken DNA at the launching pad region (the original location of the jumping gene) to join together to repair the vacant area. The results indicated that the DNA repaired itself in a manner that did not produce drastic abnormalities.

Ray characterized the genomic DNA as "smart" for repairing itself in a manner that doesn't produce drastic abnormalities. He also said that the process of repairing is "ancient" because the mechanism appears similar to that used by the immune system of mammals. Ancestors of plants and mammals diverged early in evolution, at least 1.5 billion years ago.

The findings of Ray, his students Marybeth Langer and Lynn Sniderhan from the University of Rochester and co-author Ueli Grossniklaus, professor at the University of Zurich, were reported in the paper "Transposon Excision from an Atypical Site: A Mechanism of Evolution of Novel Transposable Elements." The work extends theories of the renowned cytogeneticist Barbara McClintock, who originally discovered moveable genetic elements. Ray's research also follows on the work of molecular geneticist Enrico Coen who has examined implications of moveable genes in plants and first proposed a similar mechanism of chromosome healing.

Ray's laboratory conducts research in systems biology, and he teaches courses that include the logic and methods of gene function discovery and their applications to human therapeutics. He is a pioneer in computing with molecules and designed the first artificial logic circuits with DNA. He previously conducted research at the Institute of Molecular Biology, University of Oregon, and at the Department of Biology, Massachusetts Institute of Technology.

Ray earned his PhD in microbial genetics from Monash University in Melbourne, Australia. Previously he was a faculty member at the University of Rochester and at the University of California, San Diego.

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Research finds GM crops may be good for insects

- ABC Rural (Australia), Oct. 1, 2007

http://www.abc.net.au/rural/news/content/2007/s2047898.htm

Genetically modified crops could be good for the health of insects if they lead to a reduced use of chemicals.

An international bee conference has heard pesticides and herbicides are the biggest threat to insects like bees and more research should be done on the benefits and risks of GMOs.

New South Wales Department of Primary Industries' Doug Sommerville says while European trials show GMOs are bad for bees, there are contradicting results in Australia.

"We're actually looking at increasing the window of opportunity of putting bees on cotton crops in northern NSW because of GMOs," he said.

"Because of the reduced amount of insecticidal use in the crop, it may offer the opportunity for bees to be moved into that crop and increase the seed yield, or the crop yield, with the honeybee pollination aspect and bees may actually get a box of honey out of it."

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Mexico Agricultural Situation

- Gabriel Hernández, Dulce Flores, and Mark Ford, USDA Foreign Agricultural Service, GAIN Report No. MX7068, Sept. 28, 2007

http://www.fas.usda.gov/gainfiles/200710/146292598.pdf

[excerpted]

If Bio-technology is Constrained, Mexican Agriculture Will Be Negatively Affected

More than 25 million people related to the agricultural sector in Mexico will be negatively affected if bio-technology is "banned" from Mexico, according to Manuel Molano, consultant of the Mexican Institute for Competitiveness (IMCO). "Bio-technology is not evil and will not stop with just the indigenous varieties of corn," Molano stated. If restricted, however, Mexico will miss the opportunity to increase crop yields that would allow Mexican farmers to compete in global markets. Other countries currently fostering and using bio-technology have reached yields of up to 14 MT per hectare, while Mexico's average yield is only 3 MT per hectare. Molano explained that if not enough corn is produced and imports are banned, it is "ludicrous" not to expect corn, meat, tortilla and egg prices to go up. He stated that biotechnology will provide the necessary tools to enhance competitiveness, improve production, and increase welfare in the agricultural sector. (Source: El Financiero; 09/17/07)

Mexico's National University Will Supervise Transgenic Trade

Through its Food Program (PUAL), the Mexican National Autonomous University (UNAM) will be in charge of supervising the flow of transgenic products into Mexico after winning the bid launched by the Mexican Commission for Protection against Sanitary Risks (COFEPRIS). The project will concentrate on corn, and the PUAL staff will analyze samples of imported corn in order to catalogue and track products coming into Mexico. Currently, 17 varieties of transgenic corn have been approved for import. The project also includes training COFEPRIS staff to carry on the analysis in the near future. (Source: La Jornada; 09/18/07)

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Syngenta win upheld in Monsanto patent dispute

- Diane Bartz and Tim Dobbyn, Reuters, Oct. 4, 2007

http://www.reuters.com/article/companyNewsAndPR/idUSN0434101720071004

WASHINGTON - A U.S. appeals court on Thursday upheld findings that Syngenta AG (SYNN.VX: Quote, Profile, Research) did not infringe Monsanto Co (MON.N: Quote, Profile, Research) patents on genetic changes that make corn tolerant of the herbicide glyphosate.

The U.S. Court of Appeals for the Federal Circuit affirmed a ruling last year by the U.S. District Court in Delaware that two of the Monsanto patents were not infringed and claims on a third patent were invalid.

Monsanto had accused Syngenta of using seed sold by Monsanto licensees to create seeds that could thrive even if the herbicide is used to kill weeds in the same field.

Syngenta had bought the Garst Seed Co and Golden Harvest Seeds Inc, both of which were licensed to sell the resistant corn seed to farmers. The lower court said Syngenta lawfully obtained the seeds.

"Upon obtaining the seeds, Syngenta also acquired the right to further produce GA21 progenies containing the glyphosate resistance trait," the appeals court said in its 16-page ruling. (Reporting by Diane Bartz, editing by Tim Dobbyn)

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Super Heroes & Genetically Modified Foods

- microphonejones, YouTube, Oct. 4, 2007

Mic Solo Explains the importance of GM foods power to produce super heroes

http://www.youtube.com/watch?v=AshFpsGkpZU

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*by Andrew Apel, guest editor, andrewapel+at+wildblue.net