In addition to designing single template and multiplex experiments version 4 includes support for designing species identification and taxa discrimination assays for popular real time PCR chemistries such as SYBR® Green, TaqMan® and TaqMan® MGB (Minor Groove Binding).

"AlleleID can be effectively used in developing assays for biodefense, environmental monitoring, prevention/control of infectious diseases, development of surveillance tests and biodiversity studies." says Kay Brown, V.P. Business Development and Marketing. "We are pleased with how well AlleleID has been received by researcher all over the world. We are proud to have organizations such as FDA, CDC, and USDA as our customers."

To design species identification assays, AlleleID aligns sequences using ClustalW and analyzes conserved and species specific regions to design molecular probes for microarrays and TaqMan®/molecular beacon real time PCR assays. The assays are designed to detect only the strain or species of interest from the mix. For cross species assays, AlleleID identifies conserved regions of related organisms that can be used with samples from any of the organisms. This powerful functionality can also be used for detection, identification, quantification of contaminants.

"Minimal Set", one of the most innovative features in AlleleID, helps design the fewest number of primers and probes that uniquely identify each of the desired species/strain/taxa from the mix, lowering assay costs. For taxa or cross species assays, this feature is especially useful when the group or taxa is highly dissimilar. For a partial set of pre-designed or published set of primers, AlleleID can design compatible primers and probes for the rest of sequences for species or taxa specific assays.

AlleleID employs a sophisticated algorithm to assure assay success. Highly specific oligos are designed by avoiding regions of significant homology found by automatically interpreting BLAST search results. The oligos designed can be BLAST searched, to verify their specificity. Primer efficiency is enhanced by automatically avoiding template secondary structures.

The P2-billion project is planned to include construction of two other plants, namely, a yeast plant and an alcohol-free carbon dioxide plant.

Mr. Ledesma explained that 100,000 liters of ethanol will require some Pl billion in investment for a plant. If an ethanol-fuel project also seeks to add a cogeneration plant, he added, then the investment may reach about P1 .5 billion.

Mr. Ledesma said there may be other foreign investors, apart from the four, which are exploring sugar-based fuel-ethanol investments in other areas of the country. "There may still be others who may not have gone through the SRA," he said.

SRA, as a regulatory agency, said Mr. Ledesma, is also still ascertaining the planned projects' impact on food security, since the resources eyed are also food commodities like sugar, corn and cassava.

"As a department, we have to ensure that sugar [for food] is sufficient and will not be compromised by these projects," Mr. Ledesma said. "We don't want a problem between fuel and food; we can't sacrifice one for the other."

Copyright ABP Pvt Ltd Publications

Currently, the black cottonwood is still considered “wild,” even though its grown for lumber and pulp. Fifteen years from now, fully domesticated varieties of the tree, optimally tuned to grow faster and longer, better resist insects and disease and require less water and nutrients, could be growing like any other crop on tree farmer spread across large regions of the united states, researchers, said.

To create such poplars, researchers first must hunt among the trees more than 45,500 genes to understand how they control its growth doing so can allow later tinkering, including selective breeding and genetic manipulation to bring out desirable traits. Already, they have found 93 genes associated with the production of cellulose and hinging, which form the walls of plant cells.

One goals is to create a poplar variety that can be ethanol, which can be burned a fuel. Currently ethanol is more expensive and difficult to produce from wood than it is from crops like corn.

Researchers also would like to create poplar varieties to soak up even more carbon dioxide from the atmosphere and lessen the impact of the gas on global warming.

The black cottonwood is the third plant, after rice and a weed called Arabidopsis thalami, to have its genome sequence published. Comparing their respective genomes is expected to shed light on their separate evolutionary paths, researchers, said.

The team isolated the sequenced DNA from a poplar tree growing along the Nisqually River in Washington state. Move than three dozen researchers from the US, Australia, Belgium, Canada, Finland, France, Germany and Sweden were led by Gerald Tuskin of Oak Ridge National Laboratory in Tennessee

Copyright The Tide Online

Biotechnology-altered foods are the focus of a World Trade Organization ruling scheduled for release this month, a landmark event expected to have a major impact on trade in agricultural products, one of the largest sectors governed by the WTO.

The final report of the WTO Panel in European Communities – Measures Affecting the Approval and Marketing of Biotechnology Products – rules on a dispute founded on differing perceptions about what constitutes legitimate precaution when regulating biotechnology.

Should a country have the unfettered right to refuse trade in such products as genetically-modified grain or hormone-injected beef based on doubts about their safety? Or is such "precautionary" action trumped by World Trade Organization membership obligations?

In other words: when can a nation's interpretation and invocation of "the precautionary principle" be ruled trade protectionism in disguise? And which party should shoulder the burden of scientific proof when the safety of a product is disagreed?

These concerns are prompting a growing number of international trade clashes over the perceived safety of products derived from cutting edge biotechnology and other sciences. Most recently, Japan banned imports of US long-grain rice in August amid reports that traces of a genetically-modified variety had been found in American crops; European Union officials likewise imposed a temporary import ban pending more information. In earlier clashes, Zambia refused a US-AID offer of GM corn over concerns that acceptance would imperil the GM-free status of their exports to the EU. The collapse of the Doha Round means that more of these types of clashes are likely to end up in the WTO.

Averting such conflicts requires a better, common definition and understanding of the "precautionary principle," among other measures, according to the Japan-based Institute for Advanced Studies of the United Nations University. In a report, it calls for international agreement on common approaches to risk assessment and suggests the WTO dispute settlement system is not the "best way in which to resolve disputes in these important areas of policy making."

Prepared by Sabrina Shaw and Risa Schwartz, both professional alumnae of the WTO Secretariat in Geneva, the report warns that disputes over biotechnology products, founded in part on cultural differences, are creating a "trans-Atlantic divide." It highlights similarities and differences between agreements and organizations with respect to precaution – and the consequences of those differences.

According to Gary Sampson, Professor of International Economic Governance at UNU-IAS and author of the recent book, The WTO and Global Governance: "Precaution – not science – lies at the heart of much of the public concern about the regulation of biotechnology products. In the absence of scientific justification for trade restrictive measures, the WTO will increasingly find itself passing judgment on which regulations are 'legitimate' and which are 'unnecessary barriers to trade.' This will put the WTO increasingly between a rock and a hard place to say the least.

"The relative weight assigned to science and societal choice in the determination of standards – or how 'precautionary' regulations should be – underpins much of the possible future disagreement over the legitimacy of standards relating to genetically modified products within the context of dispute settlement in the WTO," he adds.

"The seriousness of these disputes and the importance of the technology threaten great damage to international cooperation and law," says UNU-IAS Director A.H. Zakri. "More and more commentators are beginning to openly wonder whether the World Trade Organization will be able to survive the full effects of the European Commission -Biotechnology panel, for example."

"How a society chooses to manage the risks of biotechnology will be affected by such factors as confidence in the regulators, acceptance of new technologies, the need for the new benefits and general levels of awareness," says Dr. Zakri.

He notes that several international organizations, often pursuing different objectives, are rushing to regulate biotech, creating "a complex policy and regulatory environment."

The precautionary principle is a central element of several multilateral environmental agreements, a reflection of past instances of underestimated and unanticipated impacts of new technologies – perhaps most famously the industrial release of POPs, a family of organic pollutants subsequently shown to persist stubbornly in the environment – and the use for refrigeration of chemicals later found to destroy atmospheric ozone.

So far, however, the precautionary principle has not been adopted authoritatively beyond international environmental law.

The UNU-IAS report notes differences between Europe and North America are highly pronounced with respect to genetically modified organisms and labeling of GM products, with European concerns about the risks manifested in trade restrictions on biotech goods deemed "acceptable or even desirable in the United States."

Differing perceptions about appropriate levels of precaution for biotechnology was the underlying cause of the WTO dispute where the US and EU disagreed about the safety of beef produced from cattle injected with hormones to bolster their growth. This fundamental difference will drive the US and the EU to the WTO Dispute Settlement mechanism again. US industry has already started lobbying the US Government for a WTO challenge to the EU GM labeling and traceability requirements.

Other earlier disagreements have prevented foods such as unpasteurized European cheeses from entering US markets and past WTO decisions have established that the lack of "absolute certainly" with respect to science cannot be used to justify trade restrictions.

The UNU-IAS report says nations need to determine a common threshold of risk "or, at a minimum, a common practice of risk assessment".

"What is lacking is a uniform description of the precautionary principle in these agreements, leading some critics to argue that the principle is overused without a clear understanding of its meaning and consideration of its implementation," the paper says.

"The flexible definition of the precautionary principle may be its strength, but also one of its greatest weaknesses. Several WTO Members have noted in the Committee on Trade and Environment (CTE) that the difficulty of further integrating precaution in the WTO lies in the lack of an internationally-agreed definition of the precautionary principle."

Says Dr. Zakri: "A clearer understanding of the various uses of the precautionary principle or approach will contribute to a more cohesive and harmonious approach to the regulation of biotechnology at the international level and mitigate some of the damage that is threatened by the current state of affairs."

Says UN Under Secretary-General Hans van Ginkel, Rector of UNU: "There is an important need now to take stock, reassess basic positions, principles and areas of agreement about the precautionary approach before countries initiate a new wave of disputes about biotechnology and the precautionary approach.

"Such a discussion could not be more timely given the recent controversy about genetically-modified contamination of US rice exports, the suspension of the Doha round and the prospect of countries re-examining disputes and grievances in the wake of the upcoming WTO ruling."

Four research projects in the Ontario Agricultural College have been awarded more than $100,000 from U of G's Hannam Soybean Utilization Fund to investigate new ways of using soy.

The utilization fund is a $1-million, 10-year initiative created in 2000 by the co-founder of First Line Seeds, Peter Hannam, and his family. Funding is awarded each year to researchers who are tapping into the many beneficial properties of soybeans, one of Canada's most popular commodities.

Prof. Peter Pauls, Plant Agriculture, is receiving support for a new project delving into the potential of soybean protein as a raw material for biofibre production. Some proteins can be fashioned into thread, with extremely high strength and flexibility. As a result, they can be used in a variety of applications such as clothing, car seats and plastics. Introducing soybeans into the biofibre industry could help increase market opportunities for soybean growers and decrease dependency on fossil fuel-derived materials, such as synthetic fibres.

The other three projects  all based in the Department of Food Science  are building on previous support from the fund.

Two of the projects are focused on ensuring that the nutritional benefits of soybeans, particularly the links to reduced risk of cardiovascular disease, are maintained when soy is used as a food additive.

Prof. Milena Corredig is continuing her research on the processing performance of soy protein in soy-based drinks. This has the potential to ensure that soy proteins maintain their nutritional edge when added to a product, so their health benefits are passed on to the consumer.

Prof. Shai Barbut is building on research to increase the use of soy protein isolates in meat products. Alternative ingredients such as soy are being added to improve the texture and binding of low-fat meat products.

Prof. Art Hill is looking at developing new soy products by gelling soy proteins. His end goal is a totally soy-based product with the consistency of cheese rather than tofu.

Monsanto buys equipment, such as the type of magnetic resonance imaging, or MRI, machine used in hospitals. Its engineers create gizmos, including one that uses air to suck kernels into a tube where it is weighed. Runts are automatically rejected and the remainder are dropped into tiny wells in trays fed into the MRI for scanning, 2,595 at a time.

The goal is to measure the components — starch, protein, fiber, oil and moisture — that make up corn. Those with the most starch that can be broken down by enzymes yield the most ethanol.

High lysine leads to more nutritious distiller's grains, an ethanol co-product sold as animal feed. Lysine also may improve the performance of yeast in fermenting fuel, Das said.

The best corn is used by Monsanto's breeding group to produce seed. It is genetically modified with additional traits, such as insect resistance and herbicide tolerance, that will improve overall yield for farmers, Das said.

The seed is sold as "Processor Preferred," in competition with corn similarly developed by companies including DuPont's Pioneer Hi-Bred International Inc. of Johnston, Iowa. Monsanto equips ethanol producers with near-infrared scanners and computer software to analyze the grain and verify its high-starch composition; they pay a premium to growers.

"The results are real time. The seeds are already on the market," Das said.

His group performs basic ethanol production at the lab bench to test theories. At the Corn-to-Ethanol center in Edwardsville, agriculture and ethanol companies contract to have the process scaled up and make sure their improvements carry to a commercial level.

Pam Keck, acting director, said she couldn't reveal the center's partners or discuss their proprietary projects.

Pioneer has said it worked with the center to improve the nutrition of distiller's grain.

Renessen LLC, a joint venture of Monsanto and Wayzata, Minn.-based Cargill Inc., with headquarters near Chicago, sells high-lysene corn. It also is developing an ethanol production method that could further improve animal feed co-products and make ethanol plants more profitable.

Critics who say increasing national ethanol production will drive up prices of food and animal feed by creating competing uses for limited acres are off track, Tolman said. Despite having fewer acres than in the recent past under corn production, the 2003 through 2005 corn harvests were the largest on record, with a high of 11.8 million bushels in 2004. This is because of the use of biotech seeds and breeding technology, he said.

As the nutrition of distillers' grain improves, it will displace the use of whole corn in animal feed — making even more kernels available for ethanol production, said the NCGA.

"We in the industry really don't see a trade-off between food and fuel," Tolman said.

The association believes that with technology improvements, American growers could harvest 14 billion to 15 billion bushels by 2015 or 2016, with about 5.5 billion of that available for ethanol production after other demands have been satisfied. That would yield nearly 16 billion gallons of ethanol, enough to meet about 10 percent of U.S. gasoline demand.

© 2006 Times Argus

And Ceres, a plant genetics company in California, is at work on turning switch grass, a Prairie States native, into an energy crop.

“You could turn Oklahoma into an OPEC member by converting all its farmland to switch grass,” said Richard W. Hamilton, the Ceres chief executive.

Developing energy crops could mean new applications of genetic engineering, which for years has been aimed at making plants resistant to insects and herbicides, but would now include altering their fundamental structure. One goal, for example, is to reduce the amount of lignin, a substance that gives plants the stiffness to stand upright but interferes with turning a plant’s cellulose into ethanol.

Such prospects are starting to alarm some environmentalists, who worry that altered plants will cross-pollinate in the wild, resulting in forests that practically droop for want of lignin. And some oppose the notion of altering corn to feed the nation’s addiction to automobiles.

“I don’t think people want extra enzymes in the food supply put there to better fit the crops for energy production,” said Margaret Mellon, director of the food and environment program at the Union of Concerned Scientists.

But proponents of designer fuel crops argue that the risks are small compared with the threat of dependence on foreign oil. Some studies also suggest that ethanol use could help fight global warming because the crops that help produce ethanol absorb carbon dioxide.

So far, much of the attention on bioenergy has focused on improving the chemical processes for turning crops into ethanol. But experts say that if biofuels are to make a significant dent in the nation’s petroleum consumption, the crops themselves must be improved to provide more energy from an acre.

And new agricultural sources beyond corn must be developed, they say. Even if the nation’s entire corn crop were converted to ethanol production, it would replace only about 15 percent of petroleum use, according to an Energy Department report.

“Half the improvement we make over the next 10 to 15 years will come from improving the feedstocks,” said Gerald A. Tuskan, a biofuel expert in the department, referring to the crops fed into the ethanol factories.

Some of the work will not necessarily involve genetic engineering. Notably, Monsanto, the leader by far in crop biotechnology, says that its biofuel development will focus on conventional breeding, which it says is quicker.

Monsanto has tested its existing corn varieties to determine which ones are better for ethanol production. Pioneer Hi-Bred International, the DuPont subsidiary that is Monsanto’s rival in the corn-seed business, is doing the same.

The companies say that the designated varieties, which have higher fermentable starch content, can increase ethanol production 2 to 5 percent over other corn. And some factories are starting to request certain types of corn or to pay a premium for more desirable corn, said Pradip Das, head of crop analytics at Monsanto.

Still, some ethanol factory operators say they do not really care which corn they get. The factories are so hungry that they take “pretty much all the commercial corn you can get your hands on,” said David Nelson, chairman of Midwest Grain Processors, which runs an ethanol plant in Lakota, Iowa.

William S. Niebur, vice president for crop genetics research and development at DuPont, said the demands of ethanol production would require extremely hardy corn.

“The demand for this corn grain could be so dramatic,” he said, “that it would change farming practices.” Instead of rotating corn with other crops, he said, farmers would be pressed to grow corn year after year, which could strain the soil and allow the buildup of insects and disease.

Many of the traits needed for energy corn — high yield as well as tolerance to disease, insects and drought — would also be desirable in corn used for human and animal food. That is not the case, though, with Syngenta’s enzyme corn, which would be specifically for energy production.

Generally, the enzyme, known as amylase, is made in vats of bacteria. Ethanol manufacturers add the enzyme to corn to break down starch into sugar, which can be fermented into ethanol.

To get corn to produce its own amylase, Syngenta inserted a gene borrowed from a type of microbe called archaea that live near hot-water vents on the floor of the ocean.

The gene — actually a composite of three amylase genes — was developed with the help of Diversa, a San Diego company that specializes in finding chemicals in organisms that inhabit extreme environments.

Diversa says that because its enzyme is derived from a heat-loving microbe, ethanol factories can operate at higher temperatures and under more acidic conditions, improving efficiency.

Some people in the biofuel industry question what the advantage is of having the enzyme in the corn rather than just buying the very similar amylase that Diversa is already selling.

While Syngenta’s corn is meant for industrial use in the United States, it is almost inevitable that some of it will get into human and animal food supplies, including exports, because of cross-pollination or seed intermingling. That is what happened in 2000 with Aventis CropScience’s StarLink corn, which was approved only for animal use, yet ended up in human food, forcing recalls and disrupting exports.

To prevent such liability, Syngenta is seeking approval of the corn for human and animal food use, not only in the United States but in Europe, South Africa and elsewhere. Syngenta says the amylase enzyme is safe, noting that these enzymes are found in saliva.

But Bill Freese of the Center for Food Safety, an advocacy group in Washington opposed to biotechnology crops, said that this particular amylase is from a little-studied exotic microbe and that some amylase induces allergy.

The Agriculture Department has asked Syngenta for more information on its application.

Regardless of what is done to corn, some experts say that starch alone will not provide enough ethanol. The new frontier is to produce ethanol from cellulose, the fibrous material in all plants. Cellulose is made of complex carbohydrates that can be broken down by enzymes into simpler sugars for fermenting into ethanol.

While some of the cellulose for biofuels could come from agricultural residue like corn stalks, there will probably be a need for other crops grown specifically for energy production — in particular, perennial plants like grasses that require far less energy-consuming irrigation and fertilization than crops like corn that have to be replanted each year.

That is why Ceres, a privately owned supplier of genetics technology to Monsanto, sees a future in switch grass. The company’s greenhouses are filled with versions of tall, gangly grass plants, some developed by conventional breeding and some by genetic engineering.

The grasses are meant to have higher yields, to withstand drought or to break down easily in the ethanol factory — “the energy crop that melts in your mouth, if you will,” Mr. Hamilton said.

Ceres, based in Thousand Oaks, Calif., is not working with Monsanto on switch grass but is collaborating with the Samuel Roberts Noble Foundation in Ardmore, Okla., a leading research institute on forage grasses. Mr. Hamilton said the partners were already testing conventionally bred switch grass varieties that yield eight or nine tons of biomass an acre, compared with about five tons for typical switch grass.

Mendel Biotechnology, based in Hayward, Calif., is looking more at miscanthus, a perennial grass native to China, where Mendel has set up an operation.

The company said miscanthus could produce well over 20 tons an acre each year. “No planting, no fertilizing, no irrigation,” said its chief executive, Chris Somerville, who is also the director of plant biology at the Carnegie Institution and a Stanford University professor. “You can just cut it every year for 10 years.”

Another cellulose candidate is poplar, which recently became the first tree to have its entire genome sequenced, an effort led by the Energy Department.

At first, significantly higher-yielding cellulose sources can come from conventional breeding, experts say. But later, genetic engineering may be needed. That could raise concerns because trees and grasses live longer and spread more easily than currently engineered crops like corn and soybeans.

And yet, energy crops may also be an opportunity for the industry to burnish its public image.

“After all,” the journal Nature Biotechnology said in a recent editorial, “it’s difficult to oppose a technology that’s helping to save the planet.”

Copyright 2006 The New York Times Company