Agnet Dec. 18/03 -- II
GMO gaffe
OSU
researchers make plants disease-resistant
Scientists
discover way to streamline analysis of maize genome
Traditional
Christmas snack under threat
Overharvesting
of Brazil nuts leading to fewer trees
Examining
the many faces of Xylella
Pine cones
recalled because of pest infestation
Groups clash
over soybean boom in Brazil
Filbert
blight threatens historic Springfield, Ore., farm
how to subscribe
GMO
gaffe
Dec. 18/03
AP
By PAUL ELIAS
AP Biotechnology Writer
SAN FRANCISCO -- Researchers at the University of California, Davis, were cited
as saying Thursday they shipped a small number of genetically engineered tomato
seeds they thought were naturally grown to fellow scientists during the last
seven years, adding that all the seeds were shipped exclusively for research
purposes, and that there is no evidence the mistake ended up in food.
The story adds that the Food and Drug Administration approved the genetic
modification for human consumption in 1994 and a tomato paste containing the
engineered crops was sold in Great Britain until 1999.
Some scientists were cited as saying the mistake ruined years-long experiments
and biotechnology critics said the gaffe underscored their concerns that
government regulations and laboratory security are too lax.
Neal Van Alfen, dean of UC Davis' College of Agricultural and Environmental
Sciences, was cited as saying that school officials have notified the 12 U.S.
institutions, 14 foreign research facilities and two demonstration gardens that
each received 25-seed shipments of the mislabeled seeds, adding, "You're
never going to be able to account for all the seeds. But we're talking about a
very small amount."
Van Alfen was further cited as saying the mistake occurred when Davis
researchers asked the Petoseed Co. to help the school replenish its dwindling
seed stock of the tomato strain and the business shipped the wrong seeds in
1996.
Greg Jaffe of the Center for Science in the Public Interest was quoted as
saying, "Although there's no food safety risk because of this accident, it
still shows that the regulatory system in the United States is not
adequate."
OSU
researchers make plants disease-resistant
December 17, 2003
Bend.com
http://www.bend.com/news/ar_view%5E3Far_id%5E3D12855.htm
CORVALLIS -- Researchers at Oregon State University have developed a way to
genetically engineer plants that have total resistance to crown gall disease, a
pervasive, multi-million dollar problem that for decades has plagued the nursery
and horticultural industries around the world.
The system has been tested with tobacco plants and apple trees and appears to
provide virtually complete protection from this plant disease, which can cause
unsightly tumors on plants, usually on their roots, and diminish plant
productivity, affect their structural integrity and often force their
replacement.
OSU scientists believe this genetic technology could be applicable to a wide
variety of other fruit, nut, and ornamental trees and plants – everything from
grapes to roses, apple trees and chrysanthemum – which can suffer impacts from
crown gall disease.
The findings were just published in two professional journals, Plant Physiology
and Molecular Breeding.
"Crown gall can be a disaster for nursery owners, and people have been
trying to develop ways to address this problem for decades," said Walter
Ream, a professor of microbiology at OSU. "The problem is serious enough
that it's illegal to sell a plant that has been infected. But this technique
should work on a wide variety of plants and it's reasonable to believe it will
find at least some applications in agriculture."
The commercial use of this technology, Ream said, may be slowed somewhat by the
cost of field trials and the significant regulatory hurdles that face any use of
a genetically engineered plant. Some of the crops that it could be applied to,
he said, are also niche markets, such as ornamental rhododendrons, roses, or nut
trees.
Crown gall disease is caused by Agrobacterium tumefaciens, bacteria found in
soils around the world that can genetically transform plant cells to grow as
tumors. The bacteria are widespread. It's not unusual for a single gram of soil
to harbor a million or more bacterial cells, and it's been found in native
grasslands that have never been cultivated.
The bacteria usually infect a plant when it is wounded by some type of cut. The
benign tumors produced by an infected plant are usually, but not always, found
on the plant roots, and some of the unsightly "galls," or tumors, have
grown to several feet in diameter in the branches of trees.
In Oregon and Washington, it's known that crown gall disease causes the
destruction of at least $400,000 of nursery stock in an average year, but the
losses may be far higher than that. That figure does not include losses in
established orchards and vineyards.
In California, a typical walnut orchard loses 1-2 percent of its trees every
year to crown gall, costing the walnut growers of the state at least $1 million
a year. In one especially severe outbreak in an Oregon nursery, 14,000 fruit
trees had to be destroyed in a single season.
Crown gall is a bacterial infection in plants that causes them to convert the
amino acid tryptophan into an auxin, which is a hormone that can promote rooting
and growth. Plants routinely make some auxins in normal development, but a crown
gall infection causes the process to get out of control.
The "gene silencing" technique developed by OSU researchers to deal
with this problem essentially tricks plants into sensing that they are being
attacked by a virus, which they then destroy with their own defense systems.
According to Ream, this approach allows crown gall bacteria to infect a plant,
inject tumor-inducing genes into the plant's DNA, and then begin to express RNA
as the plant begins a biochemical process that would eventually lead to
uncontrolled growth of a tumor. But the genetically engineered plants make
double-stranded RNA, instead of the single-stranded RNA ordinarily produced.
The plant recognizes the double-stranded RNA as a virus, which it has the
capacity to destroy with its own natural defense systems. So even though the
plant has been infected by crown gall bacteria, the process of tumor formation
is interrupted before any damaging effects can occur.
"We've already demonstrated the efficacy of this approach with tobacco and
apples, and other scientists have used it effectively on walnuts," Ream
said. "It appears we can make this system work with most plants, and create
varieties that are genetically resistant to the damaging effects of crown gall
disease."
The commercial use of this technology may be facilitated, Ream said, by its use
just on the root stocks of plants, which are often grafted with fruiting wood of
various types above the root structure.
This would prevent concerns about genetic drift of newly engineered plant
characteristics, since the genetically changed part of the plant would play no
role in its seed production, pollination or other reproductive systems.
This research was supported by the U.S. Department of Agriculture and the OSU
Agricultural Research Foundation.
Scientists
discover way to streamline analysis of maize genome
December 18, 2003
The Institute for Genomic Research (TIGR)
Like tiny islands in a vast sea, the gene clusters in maize are separated by
wide – and extremely difficult to decipher – expanses of highly-repetitive
DNA. This complex structure has greatly complicated efforts to sequence the
genome of maize, which is one of the world’s most important crops.
In an effort to streamline the way that researchers identify and sequence the
DNA in those gene-rich islands, scientists at The Institute for Genomic Research
and collaborators have discovered that two different approaches to identifying
the non-repetitive regions of the genome together provide a complementary and
cost-effective alternative to sequencing the entire genomes of complex plants.
In a paper published in the December 19th issue of the journal Science, the
researchers found that two independent gene-enrichment techniques –
methylation filtering and High-C0t selection – target somewhat distinct but
overlapping regions of the genome and therefore could be used together to help
identify nearly all of the genes in maize as well as their genomic structures.
This finding is significant because the maize genome, which includes about 2.5
billion base pairs of DNA, is about 20 times larger than the first plant genome
to be deciphered, Arabidopsis thaliana, and nearly six times larger than the
rice genome. The reason that the maize genome is so large is that approximately
80% consists of families of nearly identical repetitive sequences. The
gene-containing sequences are concentrated in the remaining 20% of the genome.
The challenge for genomic researchers is to explore the gene-rich islands
without having to negotiate through the sea of highly-repetitive DNA surrounding
them. In the Science study, researchers reported on two “filtration”
techniques that separate the gene-rich regions from the gene-poor ones,
providing about a four-fold reduction in the amount of sequencing necessary to
find all of the maize genes.
“A combination of these techniques may be an excellent method for sequencing
maize as well as other large and complex plant genomes at a cost far lower than
current approaches,” says Cathy A.Whitelaw, the TIGR researcher who led the
maize analysis project and is the first author of the Science paper.
The major collaborators for the study were the Donald Danforth Plant Science
Center in St. Louis, MO.; the University of Georgia’s genetics department in
Athens, GA; and Orion Genomics, in St. Louis. The project was sponsored by the
National Science Foundation’s Plant Genome Research Program.
“The success of this project highlights the importance of virtual center
projects in bringing together the expertise required to tackle large complex
problems in genomics,” says Jane Silverthorne, who leads the NSF’s plant
genome program.
TIGR Investigator John Quackenbush, the paper’s senior author, says, “Maize
is the single largest food crop in the United States, so developing strategies
to decode its complex genome is a high priority. More importantly, the
techniques that we have developed will be useful in the analysis of many other
crops such as soybean whose genomes are also highly repetitive.”
The two filtration techniques – methylation filtering and High-C0t selection
– are not new, but this was the first time that they were tested together on a
major scale, in this case with a combined total of about 93 million DNA base
pairs from the maize genome.
The methylation filtering technique excludes hyper-methylated DNA sequences (a
characteristic of highly-repetitive DNA) by means of bacterial restriction
systems that cleave those areas of the genome. The technique was first developed
by scientists at Cold Spring Harbor Laboratory.
The High-C0t selection technique, developed by researchers at the University of
Georgia’s genetics department, excludes highly-repetitive DNA sequences by
using a different method that separates DNA segments into “low-copy” (High
C0t) and “high-copy” (Low C0t) sequences, which correspond roughly to
gene-rich and gene-poor sections of the genome, respectively.
When researchers analyzed the composition of Simple Sequence Repeats – short,
repetitive segments of two, three or four DNA bases – recovered from the two
techniques, they were able to show that the filtration methods targeted
different regions of the maize genome.
An analysis of “genetic markers” – sequences related to the maize genetic
map – reinforced that conclusion and further indicated that these methods do
not have significant biases, as newly-sequenced regions are evenly distributed
across the 10 maize chromosomes.
“While both of these methods increase the rate of gene identification from
maize genomic sequence, our analysis implies that they have biases; this
suggests that both methods are required to ensure comprehensive coverage of the
maize gene space,” says W. Brad Barbazuk, Ph.D., senior bioinformatics
specialist at the Danforth Center.
TIGR’s President, Claire M. Fraser, calls the maize study is an important step
in tackling the genomes of complex plants: “Not only has this project given us
a preview of the structure of the maize genome, it also has helped us find a
rapid and cost-effective alternative to sequencing the entire genome.”
The Institute for Genomic Research (TIGR) is a not-for-profit research institute
based in Rockville, Maryland. TIGR, which sequenced the first complete genome of
a free-living organism in 1995, has been at the forefront of the genomic
revolution since the institute was founded in 1992. TIGR conducts research
involving the structural, functional, and comparative analysis of genomes and
gene products in viruses, bacteria, archaea, and eukaryotes.
Traditional
Christmas snack under threat
December 18, 2003
University of East Anglia
An international group of scientists is warning that the traditional Christmas
snack of Brazil nuts could be under threat if intensive harvesting practices
continue in persistently exploited areas.
Writing in this week's edition of the international journal Science (19 December
2003) the main author of the report, Dr Carlos Peres of the University of East
Anglia, says: "The clear message is that current Brazil nut harvesting
practices at many Amazonian forest sites are not sustainable in the long
term."
Brazil nuts, the only internationally traded seed crop collected from the wild,
are traditionally harvested from trees that can reach 50 meters in height and
16.5 meters in circumference at breast height. The scientists surveyed 23
natural Brazil nut tree populations in the Brazilian, Bolivian and Peruvian
Amazon, and found that populations that have been extensively harvested over
several to many decades are dominated by older trees, with very few younger
trees present, suggesting that the normal regeneration cycle has been disrupted.
Having established the facts about Brazil nut tree populations at these sites,
the scientists then ran computer models to predict population trends for the
next 200 years. The patterns observed in the simulations were highly consistent
with those observed in real data.
Dr Peres says that both the data collected and the computer models point to a
dwindling number of increasingly older trees in persistently overexploited
areas, which have not been adequately replaced by young trees in recent decades.
Brazil nuts contribute significantly to the Amazonian economy with more than
45,000 tonnes collected annually from the Brazilian Amazon alone, worth more
than US$33 million. The reason that Brazil nuts are so easy to collect is that
the seeds fall to the ground encased in large woody fruits (about the size of a
large grapefruit), each of which may contain 10-25 seeds.
In order to avert an eventual collapse of the Brazil nut industry, the
researchers recommend close monitoring and careful management of exploited
populations to avoid future regeneration failure and encourage establishment of
younger trees.
Other suggestions include managing the annual quota of seeds that can be
harvested and implementing a rotation system with alternating areas where
harvesting would not take place. Planting of viable seeds or nursery-grown
seedlings could also increase the supply of young trees within natural
populations, and control of seed eaters and large herbivores could help maximise
the chance of seeds germinating and seedlings surviving to become established
juveniles.
Although continued intensive harvesting is a concern, the scientists conclude
that the trade itself is not a threat and that there are other, more immediate
worries for the Brazil nut extractive industry including deforestation and
forest degradation. "Both sound proactive management of natural Brazil nut
tree populations and protection of the larger primary forest areas where the
trees are found are required to avert the decline of Brazil nut populations and
the erosion of this cornerstone of the Amazonian economy."
Overharvesting
of Brazil nuts leading to fewer trees
December 18, 2003
University of Florida
Brazil nuts, those time-honored holiday stocking stuffers, will continue to help
save the rainforest -- as long as at least a few of the brown morsels are left
behind to grow into trees.
A group of researchers has discovered that overharvesting of Brazil nuts, the
only commercially available nut collected exclusively from wild trees, has
significantly reduced the number of seedling and young trees in the trees’
native Amazon. An article about the research, co-authored by a University of
Florida scientist, is scheduled to appear Friday in the journal Science.
Because Brazil nut trees can live 500 years or longer, their decline won’t
affect harvests anytime soon. On the contrary, the scientists say consumers
should buy more of the nuts, because they support an environmentally friendly
industry that depends on rainforest preservation rather than destruction.
The study reveals that even the seemingly innocuous activity of harvesting
wild-grown nuts can have a long-term impact, and that managers may need to take
steps to ensure that more Brazil nuts grow into young trees, the scientists say.
“It’s a very simple message: If you collect too many seeds, you’re not
going to have seedlings,” said Karen Kainer, who has a joint appointment as an
assistant professor with UF’s Center for Latin American Studies’ tropical
conservation and development program and the School of Forest Resources and
Conservation.
Avecita Chicchon, director of the Latin America and Caribbean Program for the
Wildlife Conservation Society, said the findings point up the need to begin
Brazil nut conservation programs.
“For the past two decades, Brazil nut extraction has been promoted as an
economic alternative to logging and other destructive economic activities
without words of caution,” she said. “These findings tell us that Brazil nut
economic systems are still much better than other extraction systems in the
Amazon, but it is crucial to establish annual harvesting quota today, even in
lightly used areas.”
The Brazil nut tree, known scientifically as Bertholletia excelsa, flourishes
throughout the Amazon’s lowland forests. Large and long-lived, mature Brazil
nut trees produce hundreds of extremely hard, softball-sized fruits containing
10 to 25 seeds or “nuts.” Local harvesters collect the fruit on the ground,
where they fall from heights of 150 feet or more, and open them with machetes.
In the sparsely populated Amazon, where barter is common and opportunities to
earn cash are few, Brazil nuts are a vital industry. In the Brazilian Amazon
alone, harvesters annually collect about 45,000 tons valued at about $43 million
worldwide, according to the Science paper. In parts of the Amazon forest where
traditional peoples still live in the forest, the nuts are their primary source
of income, Kainer said.
Wild trees are the exclusive source of Brazil nuts because plantations have not
been successful, Kainer said, a situation for which she said there are several
possible explanations. In the wild, large bees called euglossines are important
pollinators of Brazil nut trees, but these bees depend on orchids that grow
almost exclusively in the rainforest and may not thrive in plantations. The
nutritive content of the soil in plantations also may be a problem, she said.
Some scientists have argued that collection of the nuts doesn’t affect the
wild trees, which makes some intuitive sense. Even the best harvesters can’t
get 100 percent of the nuts. Rabbit-sized rodents called agoutis also target the
nuts, burying them like squirrels for later consumption. These agoutis don’t
retrieve all of their stashes, and their buried nuts are an important source of
new trees. As Kainer put it, “there are just leaks in the system, and you
don’t need that many to rejuvenate.”
The scientists examined the issue comprehensively, comparing surveys of young
and adult Brazil nut trees in nearly two dozen Amazonian forest stands with
current and historical data about nut harvests in each. The research was
conducted in parts of the Brazilian, Peruvian and Bolivian Amazon.
For the surveys, the scientists recorded every tree with a trunk diameter of at
least 10 centimeters, or about 4 inches. To learn how each stand was harvested,
they examined records, interviewed nut gatherers and, in some cases, counted the
number of opened or harvested Brazil fruits on the ground. The stands ranged in
size from about 22 acres to about 3,336 acres, and some of the historical
harvest data dated back to 1900.
The result of the research was unambiguous, the authors wrote.
New trees “were most common in unharvested and lightly harvested stands,
uncommon to rare in moderately harvested stands and virtually absent where seeds
had been persistently collected in the 20th century,” the paper says. “The
clear message from this study is that current Brazil nut harvesting practices at
many Amazonian forest sites are not sustainable in the long term.”
Kainer said Brazil nuts have long been considered a model “nontimber forest
product” because they enable local populations to earn cash without engaging
in more destructive practices, such as timbering or clearing the land for
farming. In fact, because Brazil nut trees flourish only in the wild, they
provide an economic incentive to preserve the rainforest. While the research
does not indicate any short-term threat to this ecologically sustainable
industry, it does suggest managers should plan for the future now, she said.
Options include limiting harvests, restricting harvest seasons, or nurturing and
planting more Brazil nut trees, she said.
Examining
the many faces of Xylella
December 18, 2003
ARS News Service
Agricultural Research Service, USDA
Thousands of southern California grapevines were wiped out several years ago by
a devastating affliction known as Pierce's disease. The disease is the work of a
microbe called Xylella fastidiosa (pronounced ZYE-lell-uh FAS-tid-ee-oh-suh).
Harmless to humans, X. fastidiosa is carried from one grapevine to the next by
insects such as the glassy-winged sharpshooter.
But it's not just grapevines that are beleaguered by X. fastidiosa and
sharpshooters. The microbe occurs in many forms, or strains, that sicken other
plants, including almond, citrus, peach, plum and oleander.
Agricultural Research Service experts at the agency's San Joaquin Valley
Agricultural Sciences Center at Parlier, Calif., are sorting out who's who in
the world of Xylella. They're doing that by comparing the microbes' genetic
material, or DNA.
Molecular biologist Jianchi Chen is developing a DNA-based test that would
determine which strain of Xylella--if any--certain plants are harboring or
specific insect pests are carrying.
Results of the DNA test could give growers of vulnerable plants a valuable
heads-up. In addition, the assay would give agricultural inspectors a fast,
accurate way to make sure that shipments of plants for commercial orchards or
backyard gardens are free of Xylella. Currently, plants sometimes have to be
monitored for weeks or even months to be certain they're disease-free.
Chen and his colleagues in the ARS Exotic and Invasive Diseases and Pests
Research Unit at Parlier--plant physiologists Hong Lin and Fred Ryan and
entomologists Elaine Backus and Russell Groves--are each pursuing unique
investigations of Xylella, the sharpshooters that spread it, and the diseases it
causes.
ARS is the U.S. Department of Agriculture's chief scientific research agency.
Pine
cones recalled because of pest infestation
December 18, 2003
Knight-Ridder Tribune
Michael Hawthorne, The Columbus Dispatch, Ohio
Scented pine cones from India are, according to this story, being recalled in
the U.S. after federal authorities discovered some were infested with
wood-boring beetles.
The story says that packaged individually or mixed with potpourri, the pine
cones were sold at several national chain stores, including Dollar Tree, Frank's
Nursery, JoAnn Fabrics, Kmart, Lowe's, Target and Wal-Mart.
The pests escaped detection when boxes and bags of the pine cones arrived in the
United States. A federal inspector this month noticed beetle dung on a pine cone
while shopping at a Target store in North Carolina.
No infested products have been found in Ohio. But the U.S. Department of
Agriculture ordered a nationwide recall after two types of beetles were found in
pine cones sold in California, Connecticut, Florida, Massachusetts, Michigan,
New Jersey, New York, North Carolina and West Virginia.
Groups
clash over soybean boom in Brazil
December 18, 2003
Associated Press
QUERENCIA, Brazil -- A new variety of soybean developed by Brazilian scientists
to flourish in this punishing equatorial climate is, according to this story,
good for farmers, putting South America's biggest country on the verge of
supplanting the United States as the world's leading exporter.
But, the story adds, to the horror of environmental activists, soybeans are
claiming increasingly bigger swaths of rainforest to make way for plantations,
adding to the inroads by ranching. The Amazon lost some 10,000 square miles of
forest cover last year alone -- 40 percent more than the year before.
In Querencia, cowboy-hatted ranchers recently transplanted from Brazil's
prosperous south rub shoulders with Amazon Indians as streams of
tractor-trailers kick up dust hauling fertilizer in and huge tree trunks out.
Nowhere is the doubled-edge thrust of soybeans more apparent than in this dusty
boom town on the rainforest's southern edge.
Filbert
blight threatens historic Springfield, Ore., farm
December 18, 2003
Knight-Ridder Tribune
Scott Maben, The Register-Guard, Eugene, Ore.
SPRINGFIELD, Ore.--Eastern filbert blight has, according to this story, infected
a tree near the historic Dorris Ranch, threatening to devastate the nation's
oldest commercial filbert orchard and one of the largest parks in the
Eugene-Springfield area.
The disease is continuing its march through the southern Willamette Valley,
until recently the last refuge from the fungus in the Pacific Northwest. It may
already have a toehold in most local orchards, including the 100-year-old Dorris
orchard just south of Springfield.
John Kraft, park operations manager, was quoted as saying,"It's an
incredible public asset. What's Dorris Ranch without hazelnuts?"
Even with the best management practices available, Kraft said, "the
prospect is dire."
The 250-acre ranch is on the National Register of Historic Places, and the trees
planted by George and Lulu Dorris as early as 1903 became the main source of
filbert trees in the Northwest.
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