Fuel for Poverty

It was in back in 2007 when President Bush and the left-of-center Brazilian President Luis Inacio Lula da Silva, proclaimed a partnership between their countries in order to promote the use of biofuel as a source of alternative energy.

That was an amazing turn of events, considering the fact that the American administration never had the best of relationships with governments that come from the left side of the political spectrum. Even more amazing was the fact, that George W. Bush, a person whose political career revolves around petroleum, would support partnerships involving alternative sources of energy.

It seems that President Bush was a strong supporter of the “development and production of fuels and automobiles that would decrease the use of oil” way before his visit to Brazil. 1

The consequences of this sudden interest on the future of the environment were extremely worrying. The prices of agricultural products rocketed, violent riots erupted in many of the underdeveloped countries and a climate of insecurity struck masses of people that already lived in abhorrent conditions.

There are unconfirmed rumors that the increasing production of biofuel was responsible for 75% of the total increase in food prices. The correlation between biofuel production was described in the best way possible in the articles that follow, both by C. Ford Runge and Benjamin Senauer.

1 Bush Urges Cuts in Gasoline Use, More Biofuel Production

How Biofuels Could Starve the PoorC. Ford Runge and Benjamin Senauer

From Foreign Affairs, May/June 2007

Summary: Thanks to high oil prices and hefty subsidies, corn-based ethanol is now all the rage in the United States. But it takes so much supply to keep ethanol production going that the price of corn -- and those of other food staples -- is shooting up around the world. To stop this trend, and prevent even more people from going hungry, Washington must conserve more and diversify ethanol's production inputs.

C. Ford Runge is Distinguished McKnight University Professor of Applied Economics and Law and Director of the Center for International Food and Agricultural Policy at the University of Minnesota. Benjamin Senauer is Professor of Applied Economics and Co-director of the Food Industry Center at the University of Minnesota.....

Link to the article

How Ethanol Fuels the Food Crisis

C. Ford Runge and Benjamin Senauer

From foreignaffairs.org - author update, May 28, 2008

Summary: Runge and Senauer's update to their May/June 2007 essay ''How Biofuels Could Starve the Poor.''

In the year since the publication of our article, "How Biofuels Could Starve the Poor" (May/June 2007), the average price of corn has increased by some 60 percent, soybeans by 76 percent, wheat by 54 percent, and rice by 104 percent. What at first seemed alarmist has turned out to be an underestimate of the effects of biofuels on both commodity prices and the natural environment. These price increases are substantial threats to the welfare of consumers, especially in poor developing countries facing food deficits. They are especially burdensome to the rural landless and the urban poor, who produce no food at all. Josette Sheeran, the Executive Director of the World Food Program, calls this a global "tsunami of hunger." Robert Zoellick, President of the World Bank, estimates that there are 100 million newly poor and hungry people as a result of rising food prices.....

Link to the article

C. Ford Runge is Distinguished McKnight University Professor of Applied Economics and Law at the University of Minnesota. Benjamin Senauer is Professor of Applied Economics at the University of Minnesota.

Candidates weigh in on biomedicine

By Janet Raloff

Web edition : Friday, August 29th, 2008

As people wait expectantly for answers from John McCain and Barack Obama to the Science Debate ’08 questions, some clues of what might be coming can be gleaned from the senators’ answers to a written questionnaire sent the candidates by Research! America. This group bills itself as the nation's largest not-for-profit public education and advocacy alliance. It should be noted, however, that the Alexandria, Va.-based group has a definite bias. It’s stated mission: “making research to improve health a higher national priority.”

Earlier this week, I spoke with Stacie M. Propst, the organization’s vice president for science policy and outreach about McCain and Obama. “There are some commonalities between the candidates that come through loud and clear,” she said. “Both would shift to a health-care system that addresses and preempts disease.” Both also value research as the foundation of innovation, back stem-cell research (though McCain with caveats), want to reform the H-1B visa program to allow in more non-immigrant foreign workers with specialty skills (that include but are not limited to engineering, mathematics, physical sciences and medicine), and favor digitizing medical records to streamline costs and limit medical errors.

“We do a lot of opinion research,” Propst says, “and we started to see a trend emerge from the public — that although Americans say they would back a candidate who supports greater funding for research, they don’t actually know that much about the positions on this by their elected officials and candidates.”

Obama sent in his responses to Research! America’s 17 questions late last year. McCain’s answers arrived much later — this summer. The group also has responses from Chuck O. Baldwin (the Constitution party candidate from Palmyra, N.Y.), Rep. Bob Barr (the Libertarian party candidate from Atlanta), Rep. Cynthia McKinney (the Green party candidate from Atlanta), and Ralph Nader (the Independent candidate from Washington, D.C.).

You can view the whole list of responses on the group’s website. Below, I’ve digested what seemed the salient elements of responses from Obama and McCain for people who are more generally interested in the research.

Research America’s Questions to Presidential Candidates (link to the questions)

The stem cell question...

Do you support or oppose expanded federal funding for research using embryonic stem cells?

Obama: Stem cells hold the promise of treatments and cures for more than 70 major diseases — conditions affecting more than 100 million Americans. “As president, I would: promote embryonic stem cell research" (as he did when he introduced legislation as a member of the Illinois Senate "that specifically permitted embryonic stem cell research in Illinois”). He would also expand the number of stem cell lines available for research. He cosponsored the current Stem Cell Research Enhancement Act. "My plan would reverse the president’s policy that has allowed hundreds of thousands of frozen embryos, left over from in vitro fertilization, to simply be discarded.”

McCain: ““While I do support federal funding for embryonic stem cell research, I also believe that clear lines should be drawn to reflect a refusal to sacrifice moral values and ethical principles for the sake of scientific progress. Moreover, I believe that recent scientific breakthroughs raise the hope that one day this debate will be rendered academic. I also support funding for other research programs, including amniotic fluid and adult stem cell research which hold much scientific promise and do not involve the use of embryos. I strongly oppose the intentional creation of human embryos for research purposes. I voted to ban the practice of 'fetal farming,' making it a federal crime for researchers to use cells or fetal tissue from an embryo created for research purposes."

Comment: clearly Mr. Obama will turn a new leaf in the way that the U.S. federal government handles the issue of stem cell research. Hopefully, the medieval frame of mind of the Bush administration on this matter will be left behind. That would be great news for the global scientific community; undoubtedly the pharmaceutical multinational companies have to change their views and policies about many issues concerning biotechnology under the new probable Obama administration.

Scientific information largely ignored when forming opinions about stem cell research

When forming attitudes about embryonic stem cell research, people are influenced by a number of things. But understanding science plays a negligible role for many people.

That's the surprising finding from a team of University of Wisconsin-Madison communications researchers who have spent the past two years studying public attitudes toward embryonic stem cell research. Reporting in the most recent issue of the International Journal of Public Opinion, the researchers say that scientific knowledge - for many citizens - has an almost negligible effect on how favorably people regard the field.

"More knowledge is good - everybody is on the same page about that. But will that knowledge necessarily help build support for the science?" says Dietram Scheufele, a UW-Madison professor of life sciences communication and one of the paper's three authors. "The data show that no, it doesn't. It does for some groups, but definitely not for others."

Along with Dominique Brossard, a UW-Madison professor of journalism and mass communication, and graduate student Shirley Ho, Scheufele used national public opinion research to analyze how public attitudes are formed about controversial scientific issues such as nanotechnology and stem cells. What they have found again and again is that knowledge is much less important than other factors, such as religious values or deference to scientific authority.

In the case of stem cells, values turn out to be key, says Scheufele. For respondents who reported that religion played a strong role in their lives, scientific knowledge had no effect on their attitudes toward stem cell research. But for those who claimed to be less religious, understanding the science was linked to more positive views of the research.

"Highly religious audiences are different from less religious audiences. They are looking for different things, bringing different things to the table," explains Scheufele. "It is not about providing religious audiences with more scientific information. In fact, many of them are already highly informed about stem cell research, so more information makes little difference in terms of influencing public support. And that's not good or bad. That's just what the data show."

On the other hand, a value system held by a much smaller portion of the American public works in just the opposite direction. The attitudes of individuals who are deferential to science - who tend to trust scientists and their work - are influenced by their level of scientific understanding.

Overall, says Brossard, "more understanding doesn't always change attitudes. A lot depends on people's values. And those values need to be considered carefully when we communicate with the public about these issues." Source : University of Wisconsin-Madison

Monkeys genetically modified to have Huntington's

Sun May 18, 2008 4:10pm EDT

By Will Dunham

WASHINGTON (Reuters) - Scientists have created monkeys genetically modified to have Huntington's disease in an effort to gain a deeper understanding of the fatal ailment and uncover clues to possible new treatments.

In the journal Nature on Sunday, the researchers said one of two surviving rhesus macaque monkeys engineered to have the defective gene that causes Huntington's in humans already is showing tell-tale symptoms at age 10 months.

Huntington's -- incurable and hereditary -- is caused by a single abnormal gene in which certain nerve cells in the brain waste away. People are born with the gene but symptoms typically do not appear until middle age.

Researchers often study laboratory animals such as mice to get insights into the underlying biology of diseases. But monkeys and other primates are more similar to people than rodents in physiological, neurological and genetic features.

The scientists at Emory University's Yerkes National Primate Research Center in Atlanta said the monkeys are the first primates genetically modified to have a human disease.
They hope studying the monkeys will allow for greater knowledge of Huntington's and ideas for new drugs.

"Rodent species can capture some of the characteristics of the disease, but they have not been satisfactory in being able to really capture the essence of the disease," Stuart Zola, head of the Yerkes center, said in a telephone interview.

"Now we have a genetically modified nonhuman primate that really has captured the clinical signs that we see in patients with Huntington's disease."

Those with the progressive, degenerative disease experience uncontrolled movements, emotional disturbances and mental deterioration.

Drugs can help manage symptoms but do not stop the physical and mental decline. People typically die within 10 to 15 years after symptoms arise.

The researchers said they chose Huntington's as the disease for creating the genetically modified monkeys with an eye toward simplicity -- because it is linked to mutations in a single gene rather than multiple genes.

Zola said the achievement could pave the way for creating genetically modified primates with other neurodegenerative ailments such as Parkinson's disease and Alzheimer's disease.

"This research allows scientists to advance beyond mouse models, which do not replicate all of the changes in the brain and behavior that humans with Huntington's disease experience," said John Harding, a primate resources official at the National Institutes of Health, which funded the study.

Using so-called viral vector technology, the researchers transferred the Huntington's gene into a monkey egg cell. After using in vitro fertilization, the egg grew into a four-cell embryo and was then placed in the womb of a female monkey acting as a surrogate mother.

Of the five baby monkeys born using this process, two died within about a day, another one died in about a month and two are still living at age 10 months, according to Anthony Chan of the Yerkes center and Emory University School of Medicine.

One of the two surviving monkeys has developed symptoms including involuntary movements of the hands and face, Chan said. The other has no symptoms of the disease yet but may develop them later, he added.

(Editing by John O'Callaghan)

Article

MPs back hybrid embyro research

BBC Page last updated at 21:57 GMT, Monday, 19 May 2008 22:57 UK

The government has survived two big challenges to its controversial plans to change the law on embryo research for the first time in 20 years.

A cross-party attempt to ban hybrid human animal embryos was defeated on a free vote, by 336 to 176.

Catholic cabinet ministers Ruth Kelly, Des Browne and Paul Murphy voted for a ban. PM Gordon Brown and Tory leader David Cameron both opposed it.

A bid to ban "saviour siblings" was voted down by 342 votes to 163.

The votes followed two impassioned debates in the committee stage of the Human Fertilisation and Embryology Bill, aimed at updating laws from 1990 in line with scientific advances.

'Ethically wrong'

On Tuesday, MPs have a further free vote on the emotive issue of cutting the abortion time limit.

Mr Cameron, along with Mr Brown, has backed the use of hybrid embryos as a means to develop treatments for cancer and conditions such as Parkinson's and Alzheimer's disease. They also both support the creation of "saviour siblings".

However, the majority of the Tory shadow cabinet, including shadow foreign secretary William Hague and shadow home secretary David Davis, backed the unsuccessful attempt to ban hybrids.

Critics say tinkering with human embryos is 'immoral'

Ex-minister Edward Leigh, who led the fight against the creation of hybrid "admixed" embryos, said they were "ethically wrong and almost certainly medically useless".

He said there was "no evidence yet to substantiate" claims the work could lead to treatment for degenerative diseases like Parkinson's and Alzheimer's.

The bill would allow regulated research using hybrid or "admix" embryos, where the nuclei of human cells are inserted into animal eggs. The resulting embryos would be kept for up to 14 days to harvest stem cells.

Health Minister Dawn Primarolo says any research done using human embryos "must satisfy the Human Fertilisation and Embryology Authority that it was necessary or desirable".

No human "admix" embryo would be implanted into a woman or animal, she says.

'Too human'?

But Mr Leigh said: "We do not believe that regulation is enough. We believe this is a step too far and therefore should be banned.

"In embryos, we do have the genetic make up of a complete human being and we could not and should not be spliced together with the animal kingdom."

How hybrid embryos might be created

And ex-Labour minister Sir Gerald Kaufman, agreed, adding: "How far do you go? Where do you stop? What are the limits and what are the boundaries?

"If you permit the creation of hybrid embryos now, what will you seek to permit next time, even if you have no idea where it will lead?"

Labour's Chris Bryant, a former Anglican curate, said Mr Leigh's arguments were like those used by church leaders against the smallpox vaccine.

"They were wrong and I think you are wrong today," he said.

Liberal Democrat Evan Harris criticised those who argued hybrid embryos were too human.

"If it's ethically acceptable to use up and destroy fully human embryos with all the potential they have, how is it right to provide for hybrid embryos, with less potential of viability, greater protection?" he said.

A separate attempt to ban "pure" hybrid embryos, that would mix a human egg with animal sperm or vice versa, was also defeated in the Commons by 286 votes to 223, a government majority of 63.

Tory David Burrowes' attempt to stop parents having so-called "saviour siblings" - babies selected to provide genetic material for seriously ill relatives - also suffered defeat.

The Bill would allow the selection of embryos that are a tissue match for a sick older brother or sister.

But Mr Burrowes said it was wrong to create a child for the benefit of another, regardless of "the need".

MPs are being given a free vote on four controversial parts of the bill. The other two areas are:
Role of fathers in fertility treatment: Would end the requirement for IVF clinics to consider the "welfare" of any child created in terms of need for a father. Debate from 1530 BST Tuesday, with vote at about 1830 BST.

The upper limit for abortion: Amendments have been put down to the bill to cut from 24 weeks the time limit for abortions. Debate on Tuesday from 1830 BST, with votes at about 2200 BST.
The Roman Catholic Church has branded the use of hybrid embryos as "monstrous" and says tinkering with life in this way is immoral.

Catholic bishops in Britain and the Irish Republic have given £25,000 to scientists using adult stem cells, which is less controversial than using immature ones.

Such cells can be used to create brain, skin, heart and other tissue for treating diseases.
But Sir Leszek Borysiewicz, chief executive of the Medical Research Council, said the result would keep the UK at the forefront of embryo research.

Conservative leader David Cameron, along with Mr Brown, has backed the use of hybrid embryos as a means to develop treatments for cancer and conditions such as Parkinson's and Alzheimer's disease. They also both support the creation of "saviour siblings".

Scientists at Newcastle University announced last month that they had created the first part-human, part-animal hybrid embryos in the UK.

They were created by injecting DNA derived from human skin cells into eggs taken from cows' ovaries which had had virtually all their genetic material removed.

Researchers say these human-animal "admixed" embryos could help solve the current problem of the lack of human eggs from which to generate embryos.

Article

Dr. Craig Venter to create fuel out of CO2!

B.Sameer Mar 1 2008

Genetic engineering along with nanotechnology are two branches of science that hold a future for human race that is so spectacular in magnitude that is hard to fathom the future anymore. They have progressed beyond our imagination to create reality that more likely appear to be more the contrived creative juices of a writer of science fiction. While one dream of science fiction named ‘time travel’ is still many miles away if not impossible (and we will leave that idea with the quantum physicists to realize) many more things that we once dreamed of are becoming a reality.

Dr. Craig Venter is no ordinary person. Listed by the Time magazine as among the 100 most influential men on the planet; he is the one who mapped the genome and the genetic diversity of the oceans. Just a couple of days ago he made the amazing revelation that he is creating a life-form that is going to feed on Carbon dioxide to produce fuel! Yes, that is right. He is going to make an organism that will produce fuel from exhaust! Now if that indeed comes to be a reality (and knowing this man’s credentials and ability, there is no need to doubt his claims), then we are looking at possibly the greatest piece of invention in the history of mankind.

Now the science buffs will pardon me if I get this wrong, but since no such organism inherently exists in nature and Dr. Venter is going about creating one, I suppose I can take the liberty of calling it an invention. I mean, this is his creation. Geneticist Craig Venter disclosed his potentially world-changing “fourth-generation fuel” project at an elite Technology, Entertainment and Design conference in Monterey, California. He went on to claim that he had a ‘modest goal’ of ‘replacing the whole petrochemical industry and becoming a major source of energy’! Talk about modesty and having a damn good sense of humor too.

But I suppose for a man of his potential such a goal might indeed look modest and maybe he meant what he said. His team is using synthetic chromosomes to modify organisms that already exist, not making new life, he said. Organisms already exist that produce octane, but not in amounts needed to be a fuel supply. Dr. Venter has apparently 20 million genes at his disposal to set about at work and I suppose that is pretty much everyday job for this man.

The limiting part of the equation isn’t designing an organism, it’s the difficulty of extracting high concentrations of CO2 from the air to feed the organisms, the scientist said in answer to a question from Page. To top it all off he said that they also put suicide genes in the organisms in case they escape his lab. So basically there is no life out of the lab for them and no need for all the crazy guys to go trying to find a doomsday scenario in this. The heartening aspect is that the claim comes from a man who knows what it takes to get there. It is not some lunatic working in his garage just to get cheap publicity. Al gore was there listening and if you ask me, it would do well for us to keep a close eye on this too!

Making Gas Out Of Crude Oil: Discovery Could Lead To Dramatic Improvement In Fossil Fuel Processing

ScienceDaily (Dec. 18, 2007)

An international team that includes University of Calgary scientists has shown how crude oil in oil deposits around the world -- including in Alberta's oil sands -- are naturally broken down by microbes in the reservoir.

Their discovery could revolutionize heavy oil and oil sands production by leading to more energy-efficient, environmentally friendly ways to produce this valuable resource.

Understanding how crude oil biodegrades into methane, or natural gas, opens the door to being able to recover the clean-burning methane directly from deeply buried, or in situ, oil sands deposits, says Steve Larter, U of C petroleum geologist in the Department of Geoscience who headed the Calgary contingent of the research team.

The oil sands industry would no longer have to use costly and polluting thermal, or heat-based, processes (such as injecting steam into reservoirs) to loosen the tar-like bitumen so it flows into wells and can be pumped to the surface.

"The main thing is you'd be recovering a much cleaner fuel," says Larter, Canada Research Chair in Petroleum Geology. "Methane is, per energy unit, a much lower carbon dioxide emitter than bitumen. Also, you wouldn't need all the upgrading facilities and piping on the surface."

Biodegradation of crude oil into heavy oil in petroleum reservoirs is a problem worldwide for the petroleum industry. The natural process, caused by bacteria that consume the oil, makes the oil viscous, or thick, and contaminates it with pollutants such as sulphur. This makes recovering and refining heavy oil difficult and costly.

Some studies have suggested that biodegradation could by caused by aerobic bacteria, which use oxygen. But Larter and colleagues from the U of C, University of Newcastle in the U.K., and Norsk Hydro Oil & Energy in Norway, report in the journal Nature that the dominant process is, in fact, fermentation. It is caused by anaerobic bacteria that live in oil reservoirs and don't use oxygen.

"This is the main process that's occurring all over the Earth, in any oil reservoir where you've got biodegradation," Larter says.

Using a combination of microbiological studies, laboratory experiments and oilfield case studies, the team demonstrated the anaerobic degradation of hydrocarbons to produce methane. The findings offer the potential of 'feeding' the microbes and rapidly accelerating the breaking down of the oil into methane.

"Instead of 10 million years, we want to do it 10 years," Larter says. "We think it's possible. We can do it in the laboratory. The question is: can we do it in a reservoir?"

Doing so would revolutionize the heavy oil/oil sands industry, which now manages to recover only about 17 per cent of a resource that consists of six trillion barrels worldwide. Oil sands companies would be able to recover only the clean-burning natural gas, leaving the hard-to-handle bitumen and contaminants deep underground.

Understanding biodegradation also provides an immediate tool for predicting where the less-biodegraded oil is located in reservoirs, enabling companies to increase recovery by targeting higher-quality oil. "It gives us a better understanding of why the fluid properties are varying within the reservoir," Larter says. "That will help us with thermal recovery processes such as SAGD (steam-assisted gravity drainage)."

The research team also discovered an intermediate step in the biodegradation process. It involves a separate family of microbes that produce carbon dioxide and hydrogen from partly degraded oil, prior to it being turned into methane. This paves the way for using the microbes to capture this CO2 as methane, which could then be recycled as fuel in a closed-loop energy system. This would keep the CO2, a greenhouse gas blamed for global warming and climate change, out of the atmosphere.

The petroleum industry already has expressed interest in trying to accelerate biodegradation in a reservoir, Larter says. "It is likely there will be field tests by 2009."

Link

Detecting Human-to-Human Transmission of Avian Influenza A (H5N1)

Abstract

Highly pathogenic avian influenza A (HPAI) subtype H5N1 has caused family case clusters, mostly in Southeast Asia, that could be due to human-to-human transmission. Should this virus, or another zoonotic influenza virus, gain the ability of sustained human-to-human transmission, an influenza pandemic could result. We used statistical methods to test whether observed clusters of HPAI (H5N1) illnesses in families in northern Sumatra, Indonesia, and eastern Turkey were due to human-to-human transmission. Given that human-to-human transmission occurs, we estimate the infection secondary attack rates (SARs) and the local basic reproductive number, R0. We find statistical evidence of human-to-human transmission (p = 0.009) in Sumatra but not in Turkey (p = 0.114). For Sumatra, the estimated household SAR was 29% (95% confidence interval [CI] 15%–51%). The estimated lower limit on the local R0 was 1.14 (95% CI 0.61–2.14). Effective HPAI (H5N1) surveillance, containment response, and field evaluation are essential to monitor and contain potential pandemic strains.

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Molecular Map Helps Illuminate Why Mice Only Live For Two Years

ScienceDaily (Dec. 3, 2007)

Researchers at the National Institute of Aging and Stanford University have used gene arrays to identify genes whose activity changes with age in 16 different mouse tissues. The study uses a newly available database called AGEMAP to document the process of aging in mice at the molecular level. The work describes how aging affects different tissues in mice, and ultimately could help explain why lifespan is limited to just two years in mice.

As an organism ages, most tissues change their structure (for example, muscle tissues become weaker and have slow twitch rather than fast twitch fibers), and all tissues are subject to cellular damage that accumulates with age. Both changes in tissues and cellular damage lead to changes in gene expression, and thus probing which genes change expression in old age can lead to insights about the process of aging itself.

Previous studies have studied gene expression changes during aging in just one tissue. The new work stands out because it is much larger and more complete, including aging data for 16 different tissues and containing over 5.5 million expression measurements.

One noteworthy result is that some tissues (such as the thymus, eyes and lung) show large changes in which genes are active in old age whereas other tissues (such as liver and cerebrum) show little or none, suggesting that different tissues may degenerate to different degrees in old mice.

Another insight is that there are three distinct patterns of aging, and that tissues can be grouped according to which aging pathway they take. This result indicates that there are three different clocks for aging that may or may not change synchronously, and that an old animal may be a mixture of tissues affected by each of the different aging clocks.

Finally, the report compares aging in mice to aging in humans. Several aging pathways were found to be the same, and these could be interesting because they are relevant to human aging and can also be scientifically studied in mice.

Journal citation: Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, et al. (2007) AGEMAP: A gene expression database for aging in mice. PLoS Genet 3(11): e201. doi:10.1371/journal.pgen.0030201

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Researchers make chromosomes to order

Breakthrough may ease development of foods, medicines

Source: Chicago Tribune
Date: October 19, 2007

By Jon Van Tribune staff reporter


It's been a brave new world for genetic crops for some time now but Chicago-based researchers say they have developed a method to take crop manipulation to a higher level: the chromosome.


Creating an artificial chromosome, into which several manipulated genes can be inserted, may speed efforts to produce fuels and medicines from plants as well as boosting crop nutrition and yield.


In a scientific paper set for publication Friday researchers from Chicago-based Chromatin Inc. and the Universities of Chicago and North Carolina reported success in creating an artificial chromosome for corn plants. Through four generations, the corn treated the man-made chromosomes as if they were natural and passed them along to offspring intact at a rate nearly as high as for chromosomes native to the plants.


"This appears to be the tool that agricultural scientists and farmers have long dreamed of," said Daphne Preuss, a University of Chicago professor of molecular genetics and Chromatin's president.


Preuss said that adding a chromosome to a plant's genetic makeup is more useful to scientists than adding individual genes one at a time, as is the way most genetic engineering is done now.


When a single gene is added to a plant its placement tends to be random, so many plants must be used to get a few that use the new gene to acquire a trait, such as better tolerance for drought. Often, a plant needs two or three new genes to acquire drought resistance, Preuss said, which is difficult to achieve using today's technology.


An artificial chromosome can carry several desired genes and be inserted in a targeted location in a plant, she said, giving scientists the power to imbue plants with desired traits much more quickly and reliably than has been possible before.


Earlier this year Monsanto Co. signed a non-exclusive agreement to use Chromatin's technology and Chromatin has been in discussions with several other agribusiness firms, expecting to conclude similar agreements.


The corn results "will make Monsanto very pleased, I'm sure," said Michael Hogg, a Chicago attorney who specializes in biotech matters.


"This is a very big deal," said Ron Meeusen, a biotech veteran who heads an Indianapolis biotech venture capital fund."


We have a ceiling in what we can do with crops. If you want to insert one, two or three genes, that is doable. But if you need more genes than that to make the next improvement, it starts to get much tougher," said Meeusen, who does not have a financial interest in Chromatin.


"Many traits in crops might need seven, 12 or 15 genes, and we cannot do that today. Putting them in individually is like trying to put Humpty Dumpty together again. Chromatin has opened the ceiling on what we can do.


"They've demonstrated this isn't just a lab curiosity. It can actually be used," he said.


Technique started with weeds


Preuss developed the artificial chromosome technique when doing academic studies of weeds but much development work was needed to adapt the technology to corn. Chromatin researchers are working to adapt their techniques to other plants, including switch grass and sugar cane, seeking to help researchers make those crops more productive when they are converted to ethanol fuels.


Chromatin's techniques may also be adapted for creating plants that yield therapeutic products. Making drugs from plants is a young field, but some commercial biotech operations have products in development.


A Canadian firm, SemBioSys Genetics Inc., seeks to use safflower plants to produce insulin, and Biolex Inc. in North Carolina is working to produce monoclonal antibodies from aquatic plants.


Many varieties of soybeans, corn and other cash crops have resulted from genetic manipulation that has been under way for a generation.


Food crops in particular have stirred some opposition from people who believe that such manipulation is dangerous. European activists opposed to "Frankenfoods" have successfully retarded embrace of genetically modified crops in much of the world.


Chromatin's technology is intended to give scientists tools to make their work more targeted and efficient, said Preuss, who is on leave from her university post to oversee the technology's commercialization.


Safety called vital


"It is subject to the same regulation as any genetic manipulation," she said. "No matter how you put a gene into a plant, it is all regulated. Government agencies look at varieties produced by our partners and investigate the safety. This isn't a way to avoid that. We insist that the plants are properly examined.


"Successful implantation of the artificial chromosomes, which researchers call "mini-chromosomes," will be published in the journal PLoS-Genetics.

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Inovio Biomedical to Present DNA Vaccine Overview at Scientific Meeting

Source: via Business Wire
Date: November 15, 2007

SAN DIEGO--(BUSINESS WIRE)--Inovio Biomedical Corporation (AMEX:INO), a leader in enabling the development of DNA vaccines using electroporation-based DNA delivery, announced that Dr. Michael Fons, Vice President, Corporate Development, has been invited to present an overview of the company’s technology and products at the 2007 Annual Meeting of the American Association of Pharmaceutical Scientists being held at the San Diego Convention Center in San Diego, California. The presentation, scheduled for 2 p.m. PST on Wednesday, November 14th, is entitled “Devices Used for Nucleic Acid Delivery.”

“Delivery of DNA vaccines and plasmid-based immunotherapy products has been one of the biggest challenges in the race to create new vaccines for cancers and chronic infectious diseases,” stated Avtar Dhillon, MD, Inovio’s CEO. “We are pleased to present our technology solution to this problem to the pharmaceutical scientist community and look forward to developing a number of vaccine products.”

About Inovio’s DNA Vaccine Technology

DNA vaccines have the potential to by-pass inherent scientific obstacles of conventional vaccines that prevent their development for cancer and chronic infectious diseases such as HIV and hepatitis C. Pre-clinical data has indicated the ability of Inovio’s technologies to effectively deliver and significantly enhance the potency of such immunotherapies without the potential safety concerns of viral delivery systems.

Inovio’s DNA-based immunotherapy products consist of DNA plasmids and electroporation-based DNA delivery systems. DNA plasmids are designed to express (produce) antigens that can induce an immune response specific to a cancer or infectious disease-causing organism. These plasmids are created synthetically and readily manufactured using well-established bacterial fermentation and purification technology. After a plasmid is delivered into muscle or tumor cells, production of the desired antigens may induce a preventive or therapeutic immune response against the intended disease. Inovio’s advanced electroporation devices facilitate delivery and expression of DNA vaccines to produce the desired antigens. Primate and/or interim Phase I data have shown significantly enhanced antibody and T-cell immune responses relative to plasmid DNA delivered by other methods, suggesting the potential to provide better preventive or therapeutic effects against complex infectious diseases and cancers.

Inovio is poised to deliver advanced DNA-based vaccines and immunotherapies, devices and know-how in this rapidly advancing field. The company is actively licensing its technology to pharmaceutical and biotechnology companies and supporting early stage clinical studies arising from its own research efforts or through academic collaborations.

About Inovio Biomedical Corporation

Inovio Biomedical (AMEX:INO) is focused on developing multiple DNA-based vaccines and immunotherapies. Inovio is a leader in developing human applications of electroporation, using brief, controlled electrical pulses to increase cellular uptake of a useful biological material. Interim human data has shown that Inovio’s DNA delivery technology can significantly increase gene expression and immune responses from DNA vaccines. Immunotherapy partners include Merck, Wyeth, Vical, University of Southampton, Moffitt Cancer Center, the U.S. Army, National Cancer Institute, and International Aids Vaccine Initiative. Inovio’s technology is protected by an extensive patent portfolio covering in vivo electroporation. More information is available at www.inovio.com.

This press release contains certain forward-looking statements relating to our plans to develop our electroporation drug and gene delivery technology. Actual events or results may differ from our expectations as a result of a number of factors, including the uncertainties inherent in clinical trials and product development programs (including, but not limited to, the fact that pre-clinical results referenced in this release may not be indicative of results achievable from testing in humans and that results from one study may necessarily not be reflected or supported by the results of other similar studies), the availability of funding to support continuing research and studies in an effort to prove safety and efficacy of Inovio’s technology as a delivery mechanism, the availability or potential availability of alternative therapies or treatments for the conditions targeted by Inovio or its collaborators, including alternatives that may be more efficacious or cost-effective than any therapy or treatment that Inovio and its collaborators hope to develop, evaluation of potential opportunities, issues involving patents and whether they or licenses to them will provide Inovio with meaningful protection from others using the covered technologies, whether such proprietary rights are enforceable or defensible or infringe or allegedly infringe on rights of others or can withstand claims of invalidity and whether Inovio can finance or devote other significant resources that may be necessary to prosecute, protect or defend them, the level of corporate expenditures, assessments of our technology by potential corporate or other partners or collaborators, capital market conditions, and other factors set forth in our Annual Report on Form 10-K for the year ended December 31, 2006, our 10-Q for the nine months ended September 30, 2007, and other regulatory filings. There can be no assurance that any product in our product pipeline will be successfully developed or manufactured, or that final results of clinical studies will be supportive of regulatory approvals required to market licensed products.

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Cloning: a giant step

Source: The Independent - Online Edition
Date: November 13, 2007

For the first time, scientists have created dozens of cloned embryos from adult primates. But what are the implications of this technical breakthrough for the future of mankind?

By Steve Connor, Science Editor
Published: 12 November 2007


A technical breakthrough has enabled scientists to create for the first time dozens of cloned embryos from adult monkeys, raising the prospect of the same procedure being used to make cloned human embryos.

Attempts to clone human embryos for research have been dogged by technical problems and controversies over fraudulent research and questionable ethics. But the new technique promises to revolutionise the efficiency by which scientists can turn human eggs into cloned embryos.
It is the first time that scientists have been able to create viable cloned embryos from an adult primate – in this case a 10-year-old male rhesus macaque monkey – and they are scheduled to report their findings later this month.

The scientists will also demonstrate that they have been able to extract stem cells from some of the cloned embryos and that they have managed to encourage these embryonic cells to develop in the laboratory into mature heart cells and brain neurons.

Scientists who know of the research said it was the breakthrough that they had all been waiting for because, until now, there was a growing feeling that there might be some insuperable barrier to creating cloned embryos from adult primates – including humans.

The development will not be welcomed in all quarters. Opponents of cloning will argue that the new technique of manipulating primate eggs to improve cloning efficiency will lead to increased attempts at creating – and destroying – cloned human embryos for research purposes.
Although it is illegal in Britain to place any such cloned embryos into the womb of a woman, many people also fear that the relative ease of being able to perform cloning using the skin cells of an adult will increase the chances of its being applied to produce a cloned baby. Scientists in South Korea reported in 2004 that they had created the first cloned human embryo but in 2006 their study was retracted after it emerged that its main author, Hwang Woo-suk , had committed fraud.

There has only been one other documented example of a human embryonic clone, but it died after a few days and did not produce stem cells. The work has so far not been replicated.
The scientists who carried out the latest primate work are believed to have tried to implant about 100 cloned embryos into the wombs of around 50 surrogate rhesus macaque mothers but have not yet succeeded with the birth of any cloned offspring.

However, one senior scientist involved in the study said that this may simply be down to bad luck – it took 277 attempts, for instance, to create Dolly the sheep, the first clone of an adult mammal.

The work was led by Shoukhrat Mitalipov, a Russian-born scientist at the Oregon National Primate Research Centre in Beaverton. Dr Mitalipov helped to pioneer a new way of handling primate eggs during the cloning process, which involved fusing each egg with a nucleus taken from a skin cell of an adult primate.

Dr Mitalipov said he was unable to comment on the study until it was published in the journal Nature. But he told colleagues at a scientific meeting this year that he had made two batches of stem cells from 20 cloned embryos and tests had shown they were true clones.

Professor Alan Trounson of Monash University in Australia said Dr Mitalipov's findings represented the long-awaited breakthrough. Despite many attempts, no one had been able to produce cloned primate embryos from adult cells, yet this had been done on dozens of other non-primate species. " This is 'proof of concept' for the primate. It has been thought by some [to be too] difficult in monkeys – and humans – but those of us who work [with] animals such as sheep and cattle thought that success rates would be much like that achieved in these species," Professor Trounson said.

"Mitalipov's data confirms this. They have the skills necessary and we can now move on to consider what might be able to be achieved in humans."
Professor Don Wolf, who led the laboratory at the Oregon National Primate Research Centre before his recent retirement, said the new procedure was based on a microscopic technique that does not use ultraviolet light and dyes, which appear to damage primate eggs.
"In the early days we tried to use that technique in the monkey and unbeknownst to us at the time that was basically damaging the egg. So one of the keys was to remove that step from the process," Dr Wolf said.

"We could now produce cloned blastocysts [embryos] in the monkey at a reasonable frequency, at least a frequency that would allow us ...to study the cloned blastocyst ," Professor Wolf said.
The Oregon team, working with a group in China, has so far produced about 100 cloned embryos that have been transferred into around 50 female macaques, but none has resulted in a full-term pregnancy, he said.

"It's possible that we're still just having bad luck. We're producing may be one in 20 or one in 30 cloned blastocysts that are 'normal' and capable of producing a pregnancy and we just haven't got them into the animal recipient at the right time to allow implantation and pregnancy to occur," Professor Wolf said.

"The focus now is going to be on therapeutic cloning and using the non-human primate as a paradigm for therapeutic cloning for what you might be able to do clinically," he said.
"We're the first to do it, although it's a tainted subject because of the fraudulent research that came out of South Korea. One can never be sure but there may be some validity to what the South Koreans did. But this would now be the first documented therapeutic cloning in a primate," he added.

A brief history of cloning

The monkey-cloning technique is the same basic procedure that resulted in Dolly the sheep. The nucleus of a healthy, unfertilised egg is removed and another nucleus from the mature skin cell of an adult animal is placed inside the egg. With careful timing and the use of electrical pulses, an embryo can be created which is a genetic clone of the skin tissue donor. It is possible to implant embryos created in this way into the womb to produce cloned animals. This so-called 'reproductive cloning' of humans is illegal in Britain and many other countries. However it has been applied to a range of animal species, including:

* Cow: Many domestic cattle have been successfully cloned. First attempt to clone an endangered species was Noah, a rare gaur ox, which was cloned in the US in 2001 but died 48 hours after birth

* Mouse: Cumulina was a common brown house mouse, cloned from adult cells at the University of Hawaii in 1997. She survived to adulthood and produced two litters, before dying in May 2000

* Horse: Called Prometea, the first cloned horse, born in Italy in May 2003

* Cat: A kitten called CopyCat was born in 2002 in Texas, and gave birth to three kittens by a natural father in September 2006

* Dog: Snuppy, born in South Korea. Doubts about its authenticity were dispelled by DNA tests. The group has also cloned two wolf cubs, called Snuwolf and Snuwolffy using the same procedure. Cloned Afghan hounds named Bona, Peace and Hope have also been born

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A Faster, More Sensitive Method For Detecting Anthrax

ScienceDaily (Nov. 8, 2007)

Amid continuing concerns that anthrax might be used as a bioterrorism weapon, government researchers report development of a faster, more sensitive blood test for detecting the deadly toxins produced by the anthrax bacterium, Bacillus anthracis. The test produces results in only 4 hours and could save lives by allowing earlier detection of infection, they say.

Standard identification of anthrax (Bacillus anthracis) infection relies on a combination of time-consuming steps, including cell culture and gene amplification, which can take several days to provide a diagnosis and have limitations for detecting early stages of infection. Early diagnosis is critical for effective treatment of pulmonary or inhalation anthrax, the most deadly form.

Anthrax spores as photographed under an electron microscope.

John R. Barr and colleagues in a multi-center team effort used a form of mass spectrometry to detect the presence of 'lethal factor,' the key toxin produced by the anthrax bug, in the blood of monkeys with inhalation anthrax.

The method took only four hours to identify the toxin and detected it at very low levels, demonstrating its potential for early detection of infection, the researchers say. The new method also shows promise as a research tool for providing a better understanding of the anthrax infection cycle and for evaluating the effectiveness of different therapies and methods to fight infections.

The article "Detection and Quantification of Anthrax Lethal Factor in Serum by Mass Spectrometry" is scheduled for publication in the Nov. 22 issue of ACS' Analytical Chemistry.

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More about biological warfare and bioterrorism

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French Clay Can Kill MRSA And 'Flesh-Eating' Bacteria

ScienceDaily (Oct. 26, 2007)

French clay that kills several kinds of disease-causing bacteria is at the forefront of new research into age-old, nearly forgotten, but surprisingly potent cures. Among the malevolent bacteria that a French clay has been shown to fight is a "flesh-eating" bug (M. ulcerans) on the rise in Africa and the germ called MRSA, which was blamed for the recent deaths of two children in Virginia and Mississippi.

"There are very compelling reports of clay treating infections, but that's anecdotal evidence, not science," said Lynda Williams, an associate research professor in the School of Earth and Space Exploration at Arizona State University, Tempe. Williams is coordinating three teams of U.S. researchers (at ASU, USGS, and SUNY-Buffalo) studying healing clays under a two-year, $440,000 grant from the National Institutes of Health-National Center for Complementary and Alternative Medicine. Her ASU colleague Shelley Haydel is lending her expertise in clinical medicine to perform the microbiological research.

For thousands of years, people have used clay to heal wounds, soothe indigestion, and kill intestinal worms. Though the practice has declined in modern times, the recent rise of drug-resistant germs has scientists looking more closely at these ancient remedies to learn exactly what they can do and how they do it.

"We're beginning to generate the first scientific evidence of why some minerals might kill bacterial organisms and others might not," said Williams.

In laboratory tests at ASU's Biodesign Institute, co-PI Haydel, an assistant professor in the School of Life Sciences, showed that one clay killed bacteria responsible for many human illnesses, including: Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), penicillin-resistant S. aureus (PRSA), and pathogenic Escherichia coli (E. coli).

It also killed Mycobacterium ulcerans, a germ related to leprosy and tuberculosis that causes the flesh-eating disease Buruli ulcer. This effect was first described in 2002, by Line Brunet de Courssou, a French humanitarian working in the Ivory Coast, Africa, who cured Buruli ulcers with daily applications of French clay she knew from childhood. Currently, advanced cases of Buruli ulcer can only be cured by surgical excision or amputation.

The new medicinal clay research will be presented on Monday, 29 October 2007, at the Geological Society of America Annual Meeting in Denver.

In the same session there will be a related presentation describing the work 100 years ago of Julius Stumpf, a German physician and scientist who used white clay from Germany to treat a deadly form of Asian cholera; diphtheria; gangrene; ulcers of the tibia (a bone between the knee and foot); and the skin disease eczema.

'Bionic' Nerve To Bring Damaged Limbs And Organs Back To Life

ScienceDaily

(Oct. 18, 2007)

University of Manchester researchers have transformed fat tissue stem cells into nerve cells - and now plan to develop an artificial nerve that will bring damaged limbs and organs back to life.
In a study published in October's Experimental Neurology, Dr Paul Kingham and his team at the UK Centre for Tissue Regeneration (UKCTR) isolated the stem cells from the fat tissue of adult animals and differentiated them into nerve cells to be used for repair and regeneration of injured nerves. They are now about to start a trial extracting stem cells from fat tissue of volunteer adult patients, in order to compare in the laboratory human and animal stem cells.

Following that, they will develop an artificial nerve constructed from a biodegradable polymer to transplant the differentiated stem cells. The biomaterial will be rolled up into a tube-like structure and inserted between the two ends of the cut nerve so that the regrowing nerve fibre can go through it from one end to the other.

This 'bionic' nerve could also be used in people who have suffered trauma injuries to their limbs or organs, cancer patients whose tumour surgery has affected a nearby nerve trunk and people who have had organ transplants.

With a clinical trial on the biomaterial about to be completed, the researchers hope the treatment could be ready for use in four or five years.

Dr Kingham said: "The differentiated stem cells have great potential for future clinical use, initially for treatment of patients with traumatic injuries of nerves in the arms and legs."This work will also help to develop a similar surgical approach for organ transplant, to give full functional recuperation to the transplanted tissue.

"Furthermore, the technique of artificial nerve grafting could also be applicable when tumour mass has involved a nearby nerve trunk, which consequently has to be excised together with the tumour, such as the removal of a prostate tumour where damage to the nerve leads to male impotence."

Director of the UKCTR, Professor Giorgio Terenghi said: "This new research is a very exciting development with many future clinical applications that will improve the lives of many different types of patients and therefore many, many people."The frequency of nerve injury is one in every 1,000 of the population - or 50,000 cases in the UK - every year.

"The current repair method - a patient donating their own nerve graft to span the gap at the injury site - is far from optimal because of the poor functional outcome, the extra damage and the possibility of forming scars and tumours at the donor site. Tissue engineering using a combination of biomaterials and cell-based therapies, while at an early stage, promises a great improvement on that. Artificial nerve guides provide mechanical support, protect the re-growing nerve and contain growth factor and molecules favourable to regeneration. The patient will not be able to tell that they had ever 'lost' their limb and will be able carry on exactly as they did before."

He added: "The facilities available at the UKCTR have been developed jointly by the University of Manchester and the North West Development Agency, with exactly this aim - to provide the transition from experimental research to new clinical treatment."

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Insight

There was a similar attempt back in 2002, again using adult stem cells taken from fat and then transformed them into nerve cells. The reprogramming of stem cells is a matter of research for several years and with great success. The most interesting of these attempts came from Portugal where adult stem cells found in the nose were just transplanted to spinal cord gaps that were the result of severe injuries. The same procedure is in practice in Russia since 2005 with supposedly “phenomenal success”. In the same way neuroscientist Geoffrey Raisman of U.C.L. developed a similar procedure again in 2005. The uniqueness of the above story is about the microtube used in order to enclose the stem cells, would be very interesting to see how that will work.

D.G.T.

Genetically Engineered Poplar Plants Disarm Toxic Pollutants 100 Times Better Than Controls

Source: University of Washington
Date: October 16, 2007

Science Daily — Scientists since the early '90s have seen the potential for cleaning up contaminated sites by growing plants able to take up nasty groundwater pollutants through their roots. Then the plants break certain kinds of pollutants into harmless byproducts that the plants either incorporate into their roots, stems and leaves or release into the air.

The problem with plants that are capable of doing this is that the process is slow and halts completely when growth stops in winter. Using plants in this way, a process called phytoremediation, often hasn't made sense given the timetables required by regulatory agencies at remediation sites.

Scientists led by the University of Washington's Sharon Doty, reporting in the Proceedings of the National Academy of Sciences, say that genetically engineered poplar plants being grown in a laboratory were able to take as much as 91 percent of trichloroethylene, the most common groundwater contaminant at U.S. Superfund sites, out of a liquid solution. Unaltered plants removed 3 percent. The poplar plants -- all cuttings just several inches tall growing in vials -- also were able to break down, or metabolize, the pollutant into harmless byproducts at rates 100 times that of the control plants.

While federal regulations allow the growing of transgenic trees in greenhouses and controlled field trials for research purposes, they do not allow the commercial growing of transgenic trees. A transgenic plant is one in which its genetic material is manipulated. Sometimes only its own genetic material is altered and sometimes genetic material is added from other plants, bacteria or animals.

The work now being published raises the interesting question of the potential for using transgenic trees on sites where toxic plumes of pollutants are on the move in groundwater.
"Small, volatile hydrocarbons, including trichloroethylene, vinyl chloride, carbon tetrachloride, benzene, and chloroform, are common environmental pollutants that pose serious health effects. Some of these are known carcinogens," Doty, an assistant professor of forest resources, said.

Trichloroethylene is a heavily used industrial degreaser that's made its way into groundwater because of improper disposal. Both unaltered poplars and the transgenic poplar plants produce the enzymes to break down trichloroethylene, C2HCl3, into chloride ions -- harmless salt that the plant sheds -- and recombines the carbon and hydrogen with oxygen to produce water and carbon dioxide.

The transgenic poplar plants just do it a lot faster. The enzymes used to metabolize the contaminants are from a group called cytochrome P450 found in both plants and animals. Poplars have a lot of P450s and Doty said scientists hope to eventually sort them to find ways to manipulate the plant's own genes to ramp up pollution degradation. In the meantime they are conducting experiments inserting a gene that produces cytochrome P450 in mammalian livers, in this case the livers of rabbits. Poplar genes producing cytochrome P450 is expressed in all their cells, but not at the rates achieved by the transgenics.

"We overcame the rate-limiting step by causing the poplar plants to overexpress the first enzyme in the degradative pathway," Doty said. "Using the mammalian gene is just a step toward the day when we understand the poplar P450 genes well enough to use promoters to enhance production of their own enzymes that degrade contaminants. With the plant's own genes, the results should be even better."

Mammalian cytochrome P450 has already been used in transgenic plants that can detoxify herbicides applied to fields to kill weeds. Japanese researchers, for example, published findings in 2005 about using a human gene to make rice plants degrade a suite of herbicides, something they said could help reduce the load of herbicides in paddy fields and streams.

Along with the trichloroethylene tests, the new results also found improved rates of uptake from solutions of chloroform, the byproduct of disinfecting drinking water; carbon tetrachloride, a solvent; and vinyl chloride, a substance used to make plastics. In air pollution experiments using 6-inch plants in closed containers, the transgenic plants had increased absorption of gaseous trichloroethylene and benzene, a pollutant associated with petroleum.

Work on phytoremediation at the UW has been funded by the National Institute of Environmental Health Sciences, National Science Foundation, Environmental Protection Agency and Department of Energy.

Doty and her colleagues plan to do additional experiments to determine the detoxification rates when poplars are grown in soils, and to ensure that plant tissues do not harm non-target organisms, such as bugs that might chew on them.

Sites with contaminated groundwater are treated in a variety of chemical, physical and microbial ways, says Stuart Strand, UW professor of forest resources and a co-author of the paper. In some places the groundwater is pumped out of the ground and the contaminants allowed to evaporate into the air. In other places sugars pumped into the ground can clean contaminants but make the water anaerobic -- oxygen starved -- and can produce other toxic byproducts, he says. "It's destructive, disruptive and expensive," Strand says.

Some people see transgenic trees as risky. "As researchers we want to make sure such concerns are addressed and risks minimized. In the case of contaminated sites, we're already facing bad situations where the use of transgenic plants may reduce the known risks from carcinogens and other hazardous pollutants in the environment. Our ultimate goal is to provide a more rapid way to reduce the amount of carcinogens, one that is affordable so many sites can be treated," Doty said.

Because there is concern that transgenic trees might get into regular forests, Doty and her colleagues believe poplars may be a good choice, she said. Poplars are fast growing and can grow for several years without flowering, at which time they could be harvested to prevent seeds from generating. And unlike some other kinds of trees, branches of the hybrid poplar being studied do not take root in soils when branches fall to the ground.

Even though these things are true, Doty and her co-authors imagine that transgenic trees planted at contaminated sites would involve high levels of containment around where they are being grown.

"Commercial use of these trees requires federal regulatory approval and monitoring, and regulations are becoming increasingly strict for transgenic plants intended for biopharmaceutical or industrial purposes, including phytoremediation," the co-authors write in their paper.

Other co-authors are from the UW, Oregon State University and Purdue University.

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Blog Action Day

On October 15th, bloggers around the web will unite to put a single important issue on everyone’s mind - the environment. Every blogger will post about the environment in their own way and relating to their own topic. Our aim is to get everyone talking towards a better future

I would like to thank the people at http://blogactionday.org/ for taking such initiative.

Biotechnology could prove to be one of the most efficient tools our societies possess against the impending environmental disaster humankind is about to face. Over the years this science has developed solutions that actually have adapted very well in our everyday lives. Nevertheless, in the global scale biotech solutions are only a small fraction of what can be actually utilized in our fight against environmental destruction.

These new technologies can be used to eradicate problems that create environmental threats. Genetically modified organisms like bacteria will be used in the future in order to dispose of waste products, create new forms of usable energy of waste products and at the same time create oxygen. This could seem like a science fiction scenario but such technology is not only possible but it actually exists at a small scale.

The environmental revolution will begin with the practices developed by Environmental Biotechnology research and will bring solutions such as:

• Water treatment and purification
• Sewage treatment
• Industrial water treatment
• Abolition of chemical pesticides which will have a positive effect on the soil and on the ecosystem in general
• Agrofuel (biofuel) which is already in use in many countries
• Bioenergy from waste
• Creation of biodegradable plastics
• Elimination of oil slicks

Research centers like Center for Environmental Biotechnology are the pioneers of thought concerning such new technologies. To learn more visit:

http://www.biodesign.asu.edu/centers/eb/

Biotechnology will provide solutions for the environmental problems we face; this does not mean that we must get lethargic and confident that the scientific community will solve the problems of the world. The environment is a global issue that concerns us all, it is up to us to make a difference and change our mentalities towards the way we so willingly abuse the natural resources of our planet.

D.G.T.

Grid Computing Offers New Hope In Race Against Bird Flu

Source: Enabling Grids for E-science
Date: October 9, 2007

Science Daily — Last month a collaboration of European and Asian researchers launched a new attack against the deadly bird flu virus, harnessing the combined power of more than 40,000 computers across 45 countries to boost the pace of anti-viral drug discovery

Called Enabling Grids for E-sciencE, the computing grid connects ordinary PCs to form a super-sized supercomputer that is being used during this challenge to analyse the potential of more than 500,000 drug-like molecules over the next few weeks.

This effort comes as new data released last week by Peking University in Beijing, China, shows that the H5N1 bird flu virus can pass through the placenta of pregnant women to the unborn fetus, and can infect organs other than the lungs in adults. A rapid response to any pandemic outbreak of the virus would be essential to its control.

Dr Ying-Ta Wu, biologist at the Genomics Research Center of the Academia Sinica, says computing grids like EGEE are the fastest and cheapest way to discover new drug leads.

“We are using EGEE to find new molecules that can inhibit the activities of the influenza virus,” Dr Ying-Ta Wu explains “During previous challenges using the EGEE grid we discovered about 200 molecules with the potential to become drugs against bird flu.”

The EGEE computing grid powers drug discovery software that allows researchers to compute the probability that a drug-like molecule will dock with active sites on the virus and thus inhibit its action. Using the results of such in silico screening, researchers can predict which compounds are most effective at blocking the virus. This accelerates the discovery of novel potent inhibitors by minimising the non-productive trial-and-error approach in a laboratory.

“Asian flu remains a threat to world health and we are well aware that any pandemic could quickly spread throughout Europe" said Viviane Reding, European Commissioner for Information Society and Media. "I am pleased that the European project EGEE has found such an important application for computer grid technology as speeding-up drug discovery against neglected and emerging diseases. Collaboration between Europe and Asia is essential if we are to address world wide threats to public health”.

At the EGEE’07 conference in Budapest, Ulf Dahlsten, Director of “Emerging Technologies and Infrastructures” in the Information Society and Media Directorate-General of the European Commission, used the example of EGEE’s success with bird flu to illustrate the potential contributions of e-Infrastructures to science. "Computer Grids have achieved a productivity increase of more than 6000% in the identification of potential new drugs" he said. "300,000 molecules have already been screened using the EGEE grid. Of these, 123 potential inhibitors were identified, of which seven have now been shown to act as inhibitors in in-vitro laboratory tests. This is a six percent success rate compared to typical values of around 0.1 percent using classical drug discovery methods."

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Genetics' Super Summer

Source: Forbes.com
Date: October 02, 2007

The hunt for new genes has suddenly gone into overdrive.
Between the end of May and the beginning of September, scientists discovered telltale genetic markers that help predict the risk of nine major diseases, including breast cancer, multiple sclerosis, rheumatoid arthritis and heart disease. Some of these newly discovered markers will be used soon in diagnostic tests; others will help researchers better understand the diseases in order to invent new treatments.

"There is a new paper out every week. The pace of discovery continues to increase," says Dietrich Stephan of TGEN in Phoenix, Ariz. "It is just amazing."

Until now genetic "discoveries" often turned out to be just plain wrong upon further examination, mostly because they haven't been done in enough people to make sure the result is correct. Samples from thousands of patients are needed to make sure that a finding is not the play of chance; getting that much data used to be impossible.

Now DNA chips, tiny devices made by biotech companies Affymetrix and Illumina, allow scientists to sample the DNA blueprint for a person at 500,000 different places where differences are likely to occur, and to do so cheaply enough that tens of thousands of people can be tested. When they find a genetic variant that occurs in people with, say, multiple sclerosis, but not in those who don't, it is likely that that difference is linked to the disease.

A genetic difference is occasionally so predictive of disease risk that it can immediately be packaged as part of a diagnostic test to tell people whether they are going to get sick. Decode Genetics, a biotech company in Iceland that is running its own gene-finding experiments, sells tests for heart disease and diabetes, and hopes to market a glaucoma test too. The other use for the data is to invent drugs. Stephan, the TGEN researcher, founded a company called Amnestix in Burlingame, Calif., to develop medicines based on his discoveries of genes involved in memory disorders.

Eric Topol, the chief academic officer of Scripps Health, says the string of results this summer is "unprecedented," but warns, "we've just started this whole process. There's so much more work to be done to understand cause and effect."
It is not clear that society is ready for a flood of new genetic tests for common ailments. Myriad Genetics Salt Lake City recently started an ad campaign in major cities in the Northeast for its genetic test for flaws in a gene called BRCA. Most women with a bad version will get breast or ovarian cancer, and many take the radical step of having their breasts and ovaries removed before the disease occurs. But even with this test, which has been around a decade, commentators questioned whether people were ready to deal with being bombarded by TV advertisements.

There are going to be a lot more genetic tests, and they are going to give much muddier forecasts than BRCA. “I am very skeptical that genome-wide association studies will give us much of anything at all that will be useful for patients,” Leroy Hood, one of the pioneers of studying DNA and head of the Institute for Systems Biology in Seattle. He argues that knowing about the risks conferred by one gene are not very useful until you know what other genes play a role in causing the disease. Only then could patients know if they are really at risk.

Despite their power, the DNA chips only give scientists a limited view of the genome. They only allow researchers to look at 500,000 individual signposts scattered across 3 billion letters of DNA. Sometimes this locates a bad gene; other times, they find a marker that isn't part of the gene but is near it, allowing them to sleuth out what DNA difference is causing the disease.
A far more complete approach would be to sequence all 1 billion DNA letters and compare them. Until now, that's been impossible, but now scientists are starting to try. The Personal Genome Project at Harvard Medical School aims to sequence 1% of the genes of 100,000 people. The National Institutes of Health is funding a study that aims to sequence the genomes of up to 100 people to find genes involved in heart disease.

One use for new gene tests that is likely to come fast is in predicting which patients will be helped or harmed by a particular drug. This summer, a Pfizer AIDS drug, Selzentry, is approved only for patients who carry a particular version of an immune system gene, CCR5. The Food and Drug Administration is expected to approve more drugs only for use with people with particular genes, and is drafting guidelines for companies. Clinical Data, the latest effort from billionaire biotech investor R.J. Kirk, is being built around the idea of pairing drugs for depression and schizophrenia with gene tests.

An iffier area is predicting who will benefit or be hurt by a long-existing drug. The FDA added guidance suggesting the use of a gene test in picking the right dose of the blood-thinner warfarin, which is life-saving at the right dose but causes dangerous bleeding if a patient gets too much. Another promising area is the use of a gene test to keep from giving antidepressants to patients who might get suicidal thoughts from the medicines. But often these new findings aren't tested as rigorously. Janet Woodcock, the FDA's chief medical officer, predicts "a lot of scientific uncertainty."

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DNA Extracted From Woolly Mammoth Hair

Source: Penn State University
Date: September 27, 2007

Science Daily — Stephan C. Schuster and Webb Miller of Penn State, working with Thomas Gilbert from Copenhagen and a large international consortium, discovered that hair shafts provide an ideal source of ancient DNA -- a better source than bones and muscle for studying the genome sequences of extinct animals. Their research achievement, described in a paper to be published in the journal Science on Sept. 28, includes the sequencing of entire mitochondrial genomes from 10 individual woolly mammoths.

Schuster and Miller, working at Penn State's Center for Comparative Genomics and Bioinformatics, and Gilbert, from the Center for Ancient Genetics at the University of Copenhagen, led a team of collaborators that includes a large group of researchers and museum curators from the United States, Russia, Belgium, Denmark, France, Italy, Sweden and the United Kingdom.

The research team obtained hair from 10 woolly mammoths collected from a wide swathe of northern Siberia and with dates of death spanning approximately 38,000 years -- from 50,000 years to 12,000 years ago. Before this study, only seven mitochondrial genomes from extinct animals had been published: four from ancient birds, two from mammoths and one from a mastodon.

"DNA in bones and muscle usually degrades and becomes contaminated with genetic material from other sources such as bacteria, limiting its usefulness in scientific studies," Schuster explained. Because only a tiny proportion of ancient bones and muscle are preserved in such a way that uncontaminated DNA can be recovered, research with such materials has involved laborious efforts, sometimes spanning as long as six years for a single study. In contrast, Miller said, "Once I get the data from the genome sequencer, it takes only five minutes to assemble the entire mitochondrial genome."

The discovery to be published in Science demonstrates that hair clippings can give researchers enormous power and efficiency for divining the genetic makeup of ancient species.

The methods the team members developed for efficiently generating and analyzing large amounts of ancient mitochondrial-genome sequences now position them to generate such data for other extinct species, as well as to sequence the huge nuclear genome of an extinct species. "The data already generated from this study set the stage for the sequencing of a complete mammoth genome," said Schuster.

"We realized that the keratin in hair could protect the DNA it contains from outside influences and hence from the sorts of degradation that affect DNA in other parts of the body, such as bone," Gilbert said. Hair also can more easily be cleaned of environmental contaminants, such as bacteria. The researchers discovered that, even if the hair is washed in a solution that kills and washes off external DNA, the genetic material within the hair is unaffected.

"When people thought of sequencing DNA from hair, the usual assumption was that the material must come from the hair root, which contains recognizable cells, because the hair shaft appears to be dead," Miller explained; "however, we now know that a hair shaft consists essentially of DNA encased in a kind of biological plastic." Protected in this way, the DNA resists damage and readily can be separated from any bacteria that may contaminate the sample. "We discovered, moreover, that the DNA in hair shafts is remarkably enriched for mitochondrial DNA, the special type of DNA frequently used to measure the genetic diversity of a population," Gilbert added.

Several of the hair samples investigated were up to 50,000 years old. One of the samples came from the first specimen ever recorded: the so-called Adams mammoth, found in 1799 and dug out of the permafrost between1804 and 1806 by the botanist Michael Adams and members of the Tungus tribe. This mammoth died around 36,000 years ago. "Hair samples from this find were stored in a Russian museum for 200 years at room temperature, but still allowed for a complete analysis of its mitochondrial genome using only 0.2 grams of hair," Schuster said. As a result, he uses the term "museumomics" for his dream of deriving molecular-genomic-analysis data from the specimens stored in the collections of Charles Darwin, Alexander von Humboldt and Carl von Linne.

The new route to the genetic material of extinct animals also will enable researchers to study the relatedness of individual animals from different populations at a much higher resolution than previously thought possible. "We plan to use hair and other keratin-containing body parts, such as nail and horn, to untangle the secrets of populations that lived long ago, so these populations can send a message from the past about what it might have taken for them to survive," Schuster said. "This discovery is good news for anyone interested in learning more about how species of large mammals can go extinct."

Note: This story has been adapted from a news release issued by Penn State University.

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Mammoth hair produces DNA bounty

Last Updated: Friday, 28 September 2007, 03:32 GMT 04:32 UK

A rapid technique for isolating DNA in hair has yielded a mass of new information about woolly mammoths. An international research team says the process should work on other extinct animals, allowing their genetics to be studied in detail for the first time.

The mammoth DNA was taken from the hair shaft which was long thought to be a poor source for the "life molecule".

But the group tells Science magazine that the shaft's keratin material slows degradation and limits contamination.

"The idea has been that all the DNA is in the root and that the shaft is DNA-void, or of much lower quality," explained co-worker Dr Tom Gilbert from the University of Copenhagen, Denmark.

"This is why when we screened a whole load of mammoths, we thought we might be lucky if we took enough hair from one of them. Basically, for every mammoth we tried, it worked. That blew us away," he told the BBC.

Hair and hooves

The traditional route to DNA in ancient samples is through bones and preserved muscle, but any genetic material usually falls apart very soon after death and is prone to contamination from bacteria.

Having a new route to large quantities of well-preserved DNA should be a real boon to scientific research, Gilbert and colleagues say.

The team read the DNA using an established technology known as "sequencing-by-synthesis" - but its application to hair in the context of ancient samples is novel.

"The reason we think hair is so great comes down to the fact that as a structure, hair is made out of this material called keratin," explained Dr Gilbert, who works out of Copenhagen's Center for Ancient Genetics.

"It's a kind of protein that in a very simplistic sense can be viewed as a plastic that the DNA gets embedded in and surrounded by and protected by."

The scientists think the approach will also work for other items built from the durable protein, such as horns, nails, antlers, hooves and even feathers.

They say museum collections must hold countless specimens of recently extinct creatures from which researchers would love to get genetic information but had never bothered because they believed their DNA to be corrupted and beyond analysis.

Ice mummies

Gilbert and colleagues targeted the mammoths' mitochondrial DNA, a special type of DNA frequently used to measure the genetic diversity of populations - how closely different groups of organisms are related to each other.

Where previously only two mitochondrial genomes had been published, the Science paper reports the production of 10 new genomes, including one from the very first mammoth that was studied - the so-called Adams mammoth, which was found in 1799 and has been stored at room temperature for the last 200 years.

"From our experience working with old samples, the colder a sample has been preserved the better the quality of DNA. So, we're looking at permafrost animals -woolly rhino, for example.

"There are also a lot of old bison and horse mummies turning up in the permafrost. It's not just animals, there are humans [too]; there are a lot of mummies around the world with hair, ranging from Egypt, South America to the more cold, better-preserved ones in Greenland."

Asked the classic question about whether it would be possible to clone any extinct creatures back into existence, Dr Gilbert said that even if the full genetic sequence of a mammoth could be retrieved, the technology did not currently exist to turn that biochemical information into a live animal.

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