VentureBeat: $3 million raised for experience-sharing site

Experience Project: The San Francisco company has raised $3 million in a first round of funding to expand its anonymous social experience site.

Experience Project has quietly drawn a big community of people who share life experiences with one another anonymously. Since it started a little more than a year ago, users have created a million distinct experiences on intimate subjects, such as "I live in a sexless marriage."

D.E. Shaw Group led the round. Other investors include Maples Investments and Baseline Ventures. Despite the tough economic environment, founder Armen Berjikly said he got to know the investors over several months, but once he decided to do it, the deal was done in a matter of weeks.

Sprout: The San Francisco- and Honolulu-based start-up behind an easy-to-use tool for creating Flash applications has been having a very good year. It launched in January at DEMO (where it snagged a "DEMO god" award), made its app builder publicly available in March, then released a bunch of new features in April. Now it has raised $5 million in a second round of venture funding.

Through Sprout, you can use a "what you see is what you get" interface reminiscent of Photoshop to build applications that the company calls "sprouts." The apps are basically widgets, but with the interactivity of a Flash Web site. The process is made especially accessible through Sprout's templates, which can be customized with just a few clicks.

The release of Sprout version 2.0 is imminent, says Chief Executive
Carnet Williams, and the new funding will be used expand the
engineering, business development, marketing and support teams. The
round was led by Polaris Venture Partners, with participation from existing investor Global Venture Capital and Lotus founder Mitch Kapor. The start-up had previously raised $3.3 million.

Viator:
The San Francisco-based travel Web site, which specializes in daytime
tours, has raised $6.7 million in a third round of funding, according
to VentureWire.

Founded in 1995, the company makes money
by purchasing tours at bulk rates than selling them to individuals. It
offers 5,500 tours to more than 400 destinations.

The funding was led by Carlyle Venture Partners and Technology Venture Partners,
and it follows $10 million raised in 2005 and 2006. The new money will
be used to expand into the international and cruise markets.

Gevo: The Pasadena developer of synthetic biofuels just wrapped up a $17 million third round of funding. New investors Burrill & Co. and Malaysian Life Sciences Capital Fund joined clean-tech regulars Khosla Ventures and Virgin Green Fund. The biofuel start-up has already raised more than $30 million since the beginning of last year.

Like competitors LS9, OPX Biotechnologies and Amyris,
Gevo is trying to change the face of the biofuel industry by using
synthetic biology to engineer enzymes and microorganisms to convert
cellulosic crops and waste into advanced biofuels like isobutanol and
butanol. Butanol, the company claims, is superior to first-generation
biofuels like corn ethanol. It has higher energy content, does not
absorb water and can easily be transported through the existing gas
infrastructure. Perhaps most important, it can be directly pumped into
current vehicles.

The company is working on an alternative jet fuel for Richard Branson's Virgin Airways and is otherwise focusing on optimizing the conversion efficiencies of its proprietary microorganism strains and enzymes.

Biofuel Innovators with Alternatives to Oil

Oil soars to $125 per barrel and economies around the world sputter or fall into recession. Enough is enough. Many biofuels can be blended with gasoline and diesel refined from oil, then pumped into our existing vehicles. Even making our fuels with ten percent biofuel and ninety percent refined oil is enough to drop demand for oil and send the price south.

At the moment, this approach has major drawbacks. Food prices are soaring as more ethanol is made from corn, and biodiesel from soy and palm oil. Rain forests are being slashed and burned to increase production of soy and palm oil. Next generation biofuels, however, promise to minimize these downsides while ending our dependency on oil.

“Once viewed as an environmentally-friendly, silver bullet alternative to fossil fuels, biofuels have recently become "public enemy number one” in regard to rising food prices. But what role does the growing biofuels market really play in the current food crisis?” Asks James Greenwood, President and CEO, Biotechnology Industry Organization, who goes on to answer the question.

“There are a number of factors contributing to rising food costs. Poor harvests over the past year in Australia, Canada, South America and Eastern Europe. Protectionist tariff policies affecting the rice-producing nations of South Asia. A weak dollar is driving up the demand for U.S. exports of grains, a dynamic exacerbated by hedge fund and pension fund managers who are pouring unprecedented levels of investment in grain commodities. Growing incomes and meat-eating preferences of an emerging middle class in countries like India and China are increasing global demand for animal feed and the fuel required for production and transport. But the most significant factors driving up food prices are ever-rising energy and transportation costs.

“In coming years, biotechnology will allow us to create biofuels from non-food crops, crops that yield more per acre, require less fertilizer and are more tolerant of drought and other adverse conditions. These scientific breakthroughs will only enhance the world's ability to feed and fuel itself in a responsible and sustainable way. As biofuels production transitions to these second and third generation biofuels, biotechnology will play an essential role in providing the world with cleaner fuel and more affordable food.”

The U.S. Agriculture Department projects that the combination of a shrinking corn crop and the swelling appetite for corn ethanol will keep the price of the nation's largest crop in record territory into 2009. USDA economists expect U.S. farmers to produce 12.1 billion bushels of corn, down 7.3% from the record 13.1 billion bushels they harvested in 2007, as farmers grow more soy.

In the U.S., ethanol is currently in far greater demand than biodiesel. By law, 36 billion gallons of ethanol must be in use by 2020 in the USA. This ethanol will primarily be blended with gasoline. E10, a blend of ten percent ethanol and ninety percent petroleum refined gasoline will be common. By contrast, in the U.S. most diesel fuel is consumed by heavy vehicles with expensive engines that must run for years. Warranties can be voided and maintenance cost increase unless the diesel fuel meets exacting standards.

Biofuel innovators were discussed and presented at the Platts Advanced Biofuels Conference, which I attended. With improved biofuels we will achieve increased energy security while reducing greenhouse gas emissions. This article examines short-term and longer-term biofuel solutions.

In the heart of Silicon Valley, Khosla Ventures is funding innovative solutions for clean transportation and other major global problems. Brilliant innovators such as Vinod Khosla and Samir Kaul are involved in a number of companies creating cleaner fuels with cellulosic ethanol, biomass gasification, and synthetic biology.
Platt conference keynote speaker Vinod Khosla predicts that within five years fuel from food will no longer be competitive with cellulosic ethanol. He also predicts, “In five years, oil will be uncompetitive with biofuel, even at $50 per barrel, though oil will take longer to decline in price.”

Khosla Ventures identifies several sources of cellulosic ethanol. “There are four principal sources of biomass and biofuels we consider (1) energy crops on agricultural land and timberlands using crop rotation schemes that improve traditional row crop agriculture AND recover previously degraded lands (2) winter cover crops grown on current annual crop lands using the land during the winter season (or summer, in the case of winter wheat) when it is generally dormant (while improving land ecology) (3) excess non-merchantable forest material that is currently unused (about 226 million tons according to the US Department of Energy), and (4) organic municipal waste, industrial waste and municipal sewage.” Khosla Papers and Presentations

Sugarcane is the currently the most efficient feedstock for larger scale ethanol production. While corn ethanol delivers little more energy output than the total energy necessary to grow, process, and transport it; sugarcane ethanol delivers eight times the energy output as lifecycle energy input. Also, sugarcane typically produces twice as much fuel per acre as corn.

Brazil produces almost as much sugarcane ethanol as the United States produces corn ethanol, but at a fraction of the energy cost. Sugarcane is also grown in the southern U.S., from Florida to Louisiana to California.

Brazil is free from needing foreign oil. Flex-fuel vehicles there get much better mileage than in the U.S. If you drive into any of Brazil’s 31,000 fueling stations looking for gasoline, you will find that the gasoline has a blend of at least 20% ethanol, as required by law. 29,000 of the fueling stations also offer 100% ethanol. Ethanol in the U.S. is normally delivered on trucks, increasing its cost and lifecycle emissions. Brazil's largest sugar and ethanol group, Cosan SA announced the creation of a company to construct and operate an ethanol pipeline.

Most sugarcane is grown in the southern state of Sao Paulo. Economics do not favor its growth in rain forests, although those who favor blocking its import make that claim. It is cattle, soy, palm oil, logging, and climate change that most threaten the rain forests. Some environmentalists are concerned that a significant percentage of Brazil’s sugarcane is grown in the cerrado, which is one of the world’s most biodiverse areas. The cerrado is rich with birds, butterflies, and thousands of unique plant species. Others argue that without sugarcane ethanol, more oil will come from strip mining Canadian tar sands and from a new “gold rush” for oil in the melting artic.



Sugarcane growers are planning the development of varieties that can produce a larger quantity of biomass per hectare per year. These varieties are being called “energy cane” and may produce 1,200 to 3,000 gallons of ethanol per acre, contrasting with 300 to potentially 500 gallons of ethanol from an acre of corn.
Although sugarcane ethanol is currently the low-cost winner, long-term economics are likely to favor cellulosic sources.

In his keynote speech, Vinod Khosla sited promising sources such as paper waste, wood waste, forest waste, miscanthus, sorghum, hybrid poplar trees, winter cover crops, and perennial crops have deep roots and sequester carbon. Cellulosic ethanol could potentially yield 2,500 gallons per acre.

Large-scale reliance on ethanol fuel will require new conversion technologies and new feedstock. Much attention has been focused on enzymes that convert plant cellulose into ethanol. Because cellulose derived ethanol is made from the non-food portions of plants, it greatly expands the potential fuel supply without cutting our precious food supplies.

Pilot plants are now convert wood waste into ethanol. Over the next few years, much larger plants are likely to come online and start becoming a meaningful part of the energy mix. In Japan, Osaka Project, Verenium utilizes demolition wood waste as a feedstock in producing up to 1.3 million liters of cellulosic ethanol annually. A second phase, planned for completion in 2008, will increase production to 4 million liters per year. Verenium Ethanol Projects

Norampac is the largest manufacturer of containerboard in Canada. Next generation ethanol producer TRI is not only producing fuel, its processes allow the plant to produce 20% more paper. Prior to installing the TRI spent-liquor gasification system the mill had no chemical and energy recovery process. With the TRI system, the plant is a zero effluent operation, and more profitable.

The spent-liquor gasifier is designed to processes 115 Metric tons per day of black liquor solids. The chemicals are recovered and sent to the mill for pulping; the energy is recovered as steam which offsets the production of steam using purchased natural gas. All thermal energy in the plant is now renewable.
Producing cellulosic ethanol over the next few years is unlikely to be cost competitive with oil refining, unless other benefits accrue such as Norampac’s improved plant efficiency, savings in energy, heat, steam, reduction of plant waste, and/or production of multiple products from the plant. In the longer term, 100 million gallon per year cellulosic plants may be profitable without byproduct benefits.

Another Khosla Ventures portfolio company is Range Fuels which sees fuel potential from timber harvesting residues, corn stover (stalks that remain after the corn has been harvested), sawdust, paper pulp, hog manure, and municipal garbage that can be converted into cellulosic ethanol. In the labs, Range Fuels has successfully converted almost 30 types of biomass into ethanol. While competitors are focused on developing new enzymes to convert cellulose to sugar, Range Fuels' technology eliminates enzymes which have been an expensive component of cellulosic ethanol production. Range Fuels' thermo-chemical conversion process uses a two step process to convert the biomass to synthesis gas, and then converts the gas to ethanol.

The U.S. Department of Energy is negotiating with Range Fuels research funding of up to $76 million.
Range Fuels was awarded a construction permit from the state of Georgia to build the first commercial-scale cellulosic ethanol plant in the United States. Ground breaking will take place this summer for a 100-million-gallon-per-year cellulosic ethanol plant that will use wood waste from Georgia's forests as its feedstock. Phase 1 of the plant is scheduled to complete construction in 2009 with a production capacity of 20 million gallons a year.

Abengoa Bioenergy, also announced the finalization of a $38-million collaboration agreement signed with the DOE for the design and development of the Hugoton, Kansas cellulosic ethanol plant which will process over 11 million gallons of ethanol per year with renewable energy as a byproduct. The biomass plant will be situated next to a conventional grain-to-ethanol plant with combined capacity of 100 million gallons, using scale to make cellulosic ethanol more cost-competitive. Abengoa Bioenergy will invest more than $500 million in the next five years in their production of biomass into ethanol in the U.S., Brazil, and Europe.
Poet, the nation’s largest ethanol maker with 22 plants now turning out 1.2 billion gallons a year, plans to open a 25-million-gallon cellulosic facility in 2009 alongside its expanded grain ethanol plant in Emmetsburg, Iowa. Corn cobs from local fields will supply it. Ethanol 2.0

Ethanol is not the only bio-game in town. Many European cars and most U.S. heavy vehicles use diesel not gasoline. New generations of biodiesel, biobutanol, and synthetic fuels are being developed that could be blended with diesel or replace it. Some of these fuels could also be blended with gasoline and jet fuel. BP and DuPont have teamed to produce biobutanol which has a higher energy density than ethanol, can be delivered in existing pipelines, and can be blended with a wider range of fuels.

Amyris will use synthetic biology to develop microorganisms that produce biofuels. LS9 Inc. is in the early stage of using synthetic biology to engineer bacteria that can make hydrocarbons for gasoline, diesel, and jet fuel.

Algae have the potential to be an efficient producer of oil for biodiesel with byproducts of including hydrogen and carbohydrates which could be converted into ethanol. Biodiesel from algae can be done today. The challenge is to make production large scale and cost effective. Ideal forms of algae need to be developed. Oil must be “brewed” with the right solution, light, mixing and stirring. Cost-effective photobioreactors must be developed.

“If we were to replace all of the diesel that we use in the United States" with an algae derivative, says Solix CEO Douglas Henston, "we could do it on an area of land that’s about one-half of 1 percent of the current farm land that we use now."

Mike Janes, Sandia National Labs, is even more optimistic, "Recent studies using a species of algae show that only 0.3 percent of the land area of the U.S. could be utilized to produce enough biodiesel to replace all transportation fuel the country currently utilizes….In addition, barren desert land, which receives high solar radiation, could effectively grow the algae, and the algae could utilize farm waste….With an oil-per-acre production rate 250 times the amount of soybeans, algae offers the highest yield feedstock for biodiesel."

At the Platts Advanced Biofuels Conference, most algae experts, from scientists to CEOs of algael fuel companies, see challenging years ahead before cost-effective commercial scale production of biofuel from algae will be possible. As one expert quipped, “The greatest progress to scale is being done by Photoshop.”
A number of companies are actively exploring the potential for fuel from algae. "Algae have great potential as a sustainable feedstock for production of diesel-type fuels with a very small CO2 footprint," said Graeme Sweeney, Shell Executive Vice President Future Fuels and CO2. Shell is investing in using algae to produce fuel.

These innovators will only make a difference if they receive funding and distribution. Some of the energy giants are helping. Shell is recognized as the largest biofuel distributor among the “oil majors.” Shell has invested heavily in Choren biomass-to-liquids (BTL) in Europe. Shell has invested in Iogen, a maker of cellulosic ethanol catalysts and technology.

Biofuels have the potential to provide solutions for energy security and transportation with a much smaller carbon footprint. Other solutions include reduction in solo driving due to urban density and corporate programs, public transit, more fuel efficient vehicles, and the shift to electric vehicles that require no fossil fuel or biofuel. The new biofuels have the potential to encourage sustainable reforesting and soil enrichment. Biofuel 2.0 provides a path to fuel from wood and waste, not food and haste.
John Addison publishes the Clean Fleet Report. He owns a modest number of shares of Abengoa.

Labels: ABG.MC, biobutanol, biodiesel, biofuels, BP, cellulosic ethanol, clean fleet, cleantech, DD, RDSA, SU, VRNM

Cancer Prevention Drug Being Developed By NCI

While researching new ways to stop the progression of cancer, researchers at the University of Oklahoma Health Sciences Center, have discovered a compound that has been shown to prevent cancer in the laboratory. The research appears in the journal Gene Regulation and Systems Biology.

The compound, which still faces several rounds of clinical trials, successfully stopped normal cells from turning into cancer cells and inhibited the ability of tumors to grow and form blood vessels. If successful tests continue, researchers plan to create a daily pill that would be taken as a cancer preventive.

"This compound was effective against the 12 types of cancers that it was tested on," said Doris Benbrook, Ph.D., principal investigator and researcher at the OU Cancer Institute. "Even more promising for health care is that it prevents the transformation of normal cells into cancer cells and is therefore now being developed by the National Cancer Institute as a cancer prevention drug."

The synthetic compound, SHetA2, a Flex-Het drug, directly targets abnormalities in cancer cell components without damaging normal cells. The disruption causes cancer cells to die and keeps tumors from forming.

Flex-Hets or flexible heteroarotinoids are synthetic compounds that can change certain parts of a cell and affect its growth. Among the diseases and conditions being studied for treatment with Flex-Hets are polycystic kidney disease, kidney cancer and ovarian cancer.

Benbrook and her research team have patented the Flex-Het discovery and hope to start clinical trials for the compound within 5 years. If the compound is found to be safe, it would be developed into a pill to be taken daily like a multi-vitamin to prevent cancer.

The compound also could be used to prevent cancer from returning after traditional radiation and chemotherapy treatments, especially in cancers that are caught in later stages such as ovarian cancer where life expectancy can be as short as 6 months after treatment.

"It would be a significant advancement in health care if this pill is effective in preventing cancer, and we could avoid the severe toxicity and suffering that late stage cancer patients have to experience," Benbrook said. test

Amyris unveils bio-diesel fuel deal, joins forces with Brazilian company

An Emeryville biotech company that gained fame creating a less-costly anti-malaria drug has turned to its next challenge: making clean fuel for the world's cars, trucks, jets and generators.

Today, Amyris said it has signed a deal with a large Brazilian ethanol maker to create renewable diesel using its synthetic biology technology.

The feedstock will be Brazil's plentiful sugarcane, already being used to make ethanol in that country. Santelisa Vale, the nation's second-largest ethanol and sugar producer, will devote 2 million tons of crushing capacity to the project.

A joint venture between Amyris and Crystalsev, majority-owned by Santelisa, will make the fuel. A pilot plant is expected to go into operation in early 2009 and commercial production could commence in 2010, according to Amyris.

The US National Cancer Institute Extends its Contract with GENEART - Order Volume USD 1.9M

GENEART, the global leader in gene
synthesis and specialist in the field of Synthetic Biology, today
announces the continuation of the collaboration with the US National
Cancer Institute, which is part of the NIH. The contract was awarded
and extended by SAIC Frederick, Inc. on behalf of the NCI. Within the
scope of the ongoing contract, GENEART has already produced more than
3,500 genes with an order volume of about USD 3.5M. The follow-up
order comprises a volume of USD 1.9M for the synthesis of another 200
highly complex genes. With the genes synthesized by GENEART, the NCI
complements the NIH "Mammalian Gene Collection (MGC) Program". This
comprehensive collection of human and mouse genes represents a
significant resource for basic research as well as for clinical
research and development.

The 3,500 genes so far synthesized by GENEART include a large number
of highly complex sequences, which could not be isolated with
classical methods of biotechnology in the course of the MGC project
between 2002 and 2006. A major fraction of genes in this group showed
a high number of repetitive DNA sequence elements, or were toxic for
the production host E. coli. To efficiently synthesize this large
number of genes in a high-throughput manner, GENEART had to further
advance its existing technologies and establish new production
techniques.

Professor Dr. Ralf Wagner, CSO of the GENEART AG, adds: "The
advancements in technology have elevated our gene synthesis platform
to a new level, and further strengthen our leadership role in this
market. We therefore expect to profit far more than average from the
increasing demand for complex genes, gene clusters and entire genomes
in pharmaceutical research and in the synthetic biology field."

Christian Ehl, CFO of the GENEART AG, elaborates: "This order has
been the greatest challenge in our company history so far, and we
have mastered it with great success. Our performance demonstrates the
capability of our team, and it proves the power of the GENEART
Technology Platform. We are especially delighted about the extended
collaboration with NCI because it confirms our ability to perform.
Additionally, the NCI/NIH project provides us with a singular
reference in the field. This will certainly help us to acquire more
major projects in the global market."

One Step Closer To Elusive Cancer Vaccine

When cells become cancerous, the sugars on their surfaces undergo distinct changes that set them apart from healthy cells. For decades, scientists have tried to exploit these differences by training the immune system to attack cancerous cells before they can spread and ravage the body.

Now, researchers at the University of Georgia Cancer Center have synthesized a carbohydrate-based vaccine that – in mice – has successfully triggered a strong immune response to cancer cells. The finding, published in the October issue of the journal Nature Chemical Biology, brings the scientists one step closer to a much-sought-after “cancer vaccine.”

“In mice we can illicit very strong antibody responses and we have shown that the antibody responses are functional – that they can kill cancer cells,” said lead author Geert-Jan Boons, Franklin professor of chemistry.

Vaccines are currently used to prevent diseases by priming the immune system to recognize and attack a virus or bacteria. The vaccine that Boons and his team have developed, on the other hand, is a therapeutic vaccine that trains the body’s immune system to fight an existing disease.

The discovery in the 1970s of unique sugars on cancer cells set scientists in search of a way to get the immune system to recognize and attack cells that express these cancer-associated sugars. Until now, however, the results have been less than spectacular.

Cancer cells originate in the body, and the immune system leaves them alone because it distinguishes between the body’s own cells and foreign invaders such as viruses and bacteria.

Boons explained that early cancer vaccines were created by linking the tumor-associated carbohydrate with a foreign protein. The immune system, perhaps not surprisingly, attacked the protein and the linker molecules, but generally left the carbohydrate alone.

“We needed to come up with a vaccine that does not give our immune system a chance to go after anything else but the tumor-associated carbohydrate,” Boons said. “In other words, there should no junk that can induce an immune response to something other than the tumor-associated carbohydrate.”

Rather than using naturally derived and purified proteins and linkers, Boons and his team created a vaccine synthetically from scratch by stacking molecules together and arranging them in the appropriate configuration. In 2005, they created a fully synthetic vaccine that stimulated an immune response to the tumor-associated carbohydrate alone. The vaccine stimulated only low antibody levels, however, so the researchers began optimizing the components of the vaccine to illicit a stronger immune response.

Their optimized vaccine includes a tumor-associated carbohydrate that triggers the immune system’s B cells, a part of a protein that triggers the immune system’s T cells and a linker molecule that stimulates the production of generalized immune components known as cytokines.

The results of their three-pronged approach were astounding, particularly with respect to a critical component of the immune system known as IgG.

“When we tested our best vaccine we got really, really fabulous antibody levels that have never been seen before,” Boons said. “The levels of IgG antibody production were 100 times better than with conventional approaches.”

The vaccine has been successful in creating an antibody response that can kill cultured epithelial cells – those commonly involved in most solid tumors, such as breast and colorectal cancer – derived from mice and in stimulating an immune response in healthy mice. The researchers are currently testing the vaccine in mice with cancer, and Boons hopes to start phase I clinical trials in humans within a year.

Despite his enthusiasm for his work, Boons cautions that it’s too early to predict how the vaccine will perform in humans.

“There’s a very big step going from mice to humans,” he said. “Other cancer vaccines have worked in mice but not in humans.”

In addition to testing the new vaccine, Boon’s team is exploring the specific components of the immune response as they relate to cancer, determining the exact cytokines and antibodies that are most effective against cancer cells.

“We’re looking at which molecules are being upregulated at each level of immune response,” Boons said. “That gives us a road map to further optimize each component of the vaccine.”

The research is supported by the National Cancer Institute.

Source

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What is the Chiari Malformation?

The Chiari I Malformation is considered a congenital malformation, although there have been some reported cases of an acquired form. It is characterized by a small or misshapen posterior fossa (the compartment in the back of the skull), a reduction in cerebrospinal fluid pathways and a protrusion of the cerebellar tonsils through the bottom of the skull (foramen magnum) into the spinal canal. The tonsils would normally be round but often become elongated as they protrude down the spinal canal. Diagnosis can be difficult because not all patients will have the classical sign of deeply herniated tonsils.

Since the advent of MRI, the incidence of the Chiari I Malformation has risen
dramatically. MRI is safe and painless and currently the most reliable means available for diagnosing Chiari Malformations. Chiari Malformations are also known as herniation of the cerebellar tonsils, cerebellar ectopia, hindbrain herniation and Arnold-Chiari malformations.
A German pathologist, Professor Hans Chiari, first described abnormalities of the brain at the junction of the skull with the spine in the 1890's. He categorized them in order of severity, types I, II, III, and IV.

The Chiari type II Malformation is usually found in children with spina bifida or myelomeningocele. Not only is part of cerebellum unusually low and lying below the bottom of the skull, but the brain stem can be malformed in several ways. Types III and IV represent gross herniations of the cerebellum and are very rare.

What are the symptoms?
Many people with the Chiari I Malformation experience no symptoms. When symptoms are present, they usually do not appear until adolescence or early adulthood, but can occasionally be seen in young children. The majority of patients complain of severe head and neck pain. Headaches are often accentuated by coughing, sneezing or straining. Patients may complain of dizziness, vertigo, disequilibrium, muscle weakness or balance problems. Often fine motor skills and hand coordination will be affected.

Vision problems can also occur. Some patients experience blurred or double vision, difficulty in tracking objects or a hypersensitivity to bright lights. Physical examination may reveal nystagmus (involuntary eye movements). Other symptoms include tinnitus (buzzing or ringing in the ear), hearing loss or vocal cord paralysis. Patients may have difficulty swallowing, frequent gagging and choking and, in some cases, sleep apnea may be present.

The Chiari I Malformations may also be associated with other disorders such as hydrocephalus (build up of fluid in the ventricles of the brain) or Syringomyelia. Syringomyelia is a disorder in which cerebrospinal fluid enters the spinal cord, forming a cavity known as a syrinx. It is recommended that patients diagnosed with a Chiari Malformation have the entire spine imaged to rule out the presence of a syrinx, since it may be a consideration in treatment and prognosis.

Is there a treatment?
Surgical procedures to enlarge the posterior fossa are considered a treatment option for patients with the Chiari I Malformation. Techniques are quite diversified amongst neurosurgeons, and patient responses vary greatly. A successful surgery will alleviate pressure on the neural elements and may result in an improvement of symptoms.

The decision to treat a Chiari Malformation surgically requires careful consultation between patient and physician. Factors to be considered are the patient's current neurological condition and progression of symptoms over a period of time.

Is this condition hereditary?
Research into the risk of inheritance for the Chiari I Malformation is still in its early stages. In some families, more than one member has been documented to have the Chiari I Malformation. Familial recurrences are suggestive of a possible genetic component of the condition, but unfortunately there is no conclusive answer to the question of inheritance at this time. It is currently recommended that only those relatives experiencing symptoms commonly associated with the Chiari I Malformation need undergo investigational procedures.

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Codon Devices Awarded $1.5 Million Grant by National Institute of Standards and Technology

Codon Devices, Inc., the Constructive Biology Company™, today announced that it has been awarded a $1.5 million grant from the U.S. Commerce Department’s National Institute of Standards and Technology (NIST).

With the support of the grant, Codon Devices will develop an integrated microfluidics platform to significantly reduce the cost and complexity of building complex DNA fragments. This platform will advance the state of the art in gene synthesis to improve the utility of synthetic biology approaches for biotechnology research.

"We are thrilled that NIST has recognized Codon Devices with this ATP award,” said Brian M. Baynes, Founder and President of Codon Devices. “Funding from this initiative will enable us to develop a new generation of rapid, automated systems for construction of longer, more complex DNA sequences. By integrating this technology with our BioFAB™ Production Platform, we will make these new tools available to our customers and partners and accelerate critical applications such as drug discovery and development of renewable energy systems.”

The NIST award was granted under the Agency’s Advanced Technology Program (ATP). Awarded projects were selected for funding by a competitive, peer-reviewed process that evaluated the scientific and technical merit of each proposal and the potential for broad-based benefits to the nation. NIST promotes U.S. innovation and industrial competitiveness by advancing measurement science, standards and technology in ways that enhance economic security and improve our quality of life.

About Codon Devices

Codon Devices, Inc., based in Cambridge, MA, is a privately-held biotechnology company focused on enabling commercial applications of synthetic biology. Codon Devices' proprietary synthesis and design technologies improve the productivity of its industrial, pharmaceutical and academic customers in a paradigm shift to what the Company calls Constructive Biology™. The Company's focus is on developing and delivering high-value products and design services in a variety of application areas, including engineered gene libraries, engineered cells that produce novel pharmaceuticals, improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy. Codon Devices' BioFAB™ Production Platform uses sophisticated informatics, robotics and sequencing technologies to accurately synthesize genetic codes orders of magnitude more rapidly and cost-effectively than other currently available technology. More information about Codon Devices is available at www.codondevices.com.

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Guarding against the misuse of synthetic genomics

Synthetic genomics research involves using chemically created pieces of DNA known as oligonucleotides to design and assemble parts of, or complete chromosomes and genes.

In theory, these can then be used to generate new 'lifeforms' that can produce new biological drugs or biologically produced green fuels, which are impractical to engineer using more conventional biotechnology approaches.

However, as with any new technology that has the ability to be used for good comes the possibility that it can be subverted for evil means such as bioterrorism.

The 66 page report, entitled "Synthetic Genomics: Options for Governance", is a result of a 20 month examination of the field and has highlighted areas three key areas for policy intervention to ensure that this promising technology cannot be misused.

The need for such a review has accelerated over the last 5 years or so as the speed at which genetic constructs can be developed has increased dramatically, as has the number of companies that have the ability to develop them -this in turn has led to prices dropping rapidly.

"Designing ways to impede malicious uses of the technology while at the same time not impeding, or even promoting beneficial ones, poses a number of policy challenges for all who wish to use or benefit from synthetic genomics" said Michele Garfinkel, policy analyst at the J Craig Venter Institute and lead author of the report.

The first area involves those companies that supply synthetic DNA, oligonucleotides, genes or genomes and how they can ensure that they can trust that the researchers they are shipping their goods to are 'legitimate' users and not potential terrorists. In addition, the report recommends that these firms should collect customer details and information about their orders.

Some companies are already going beyond these recommendations of their own volition.

According to Dr Michael Dyson, Codon Devices' European managing director; every sequence they are asked to synthesise is checked against a database of high-risk sequences that could be used for nefarious means.

If a sequence is flagged up then the manufacture is stopped and discussions with the purchaser are initiated to find out exactly what the sequence is and what it will be used for.

The second area covers recommendations to control and/or monitor the use of DNA synthesisers, such that owners would have to be licensed and register the instruments as well as needing a license to buy reagents and services.

The third area involves the compilation of a manual for "biosafety in synthetic biology laboratories" as well establishing a recognised clearing house for best practice.

The review also calls for the broadening of the US Institutional Biosafety Committee's (IBC) review responsibilities to consider risky experiments as well as enhancing the enforcement of compliance with US National Institutes of Health (NIH) biosafety guidelines.

While these suggestions may appear to some to be somewhat draconian and could hinder honest research into beneficial systems, the committee was keen to stress that all the recommendations were designed to impose the minimum burden on researchers, industry and government.

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This 'new life form' is just reassembled car parts

Great scientific advances - unlike these latest claims - open up whole new areas of knowledge, says Nick Gay

Dr Nick Gay
Wednesday October 10, 2007
The Guardian

The Guardian's front-page story reported Craig Venter's claims that he is "poised to announce the creation of the first new artificial life form on Earth" (I am creating artificial life, declares US gene pioneer, October 6). On the face of it this seems to be a spectacular advance. Unfortunately the truth is rather different.

To provide an analogy, it is as if he had selected a set of car parts, assembled them into a car and then claimed to have invented the car. It will not "herald a giant leap forward in the development of designer genomes". It is merely the crudest and most facile kind of reductionism, an experimental approach that provides no insight whatever into the fundamental nature of cellular processes.

In fact the ability to carry out such a project relies on the work of thousands of scientists who have studied the molecular biology of the cell during the last 50 years and defined the function of basic cellular processes such as the replication of DNA and the conversion of RNA into proteins, and developed key methods such as the chemical synthesis of nucleic acids. Simply reassembling these cellular components into an "artificial" organism will not further our understanding of these life processes.

Your article also claims that his work "could unlock the door to new energy sources and techniques to combat global warming". It is certainly possible that the plant enzyme responsible for removing carbon dioxide from the atmosphere could be engineered to be more efficient, but this would not need Venter's artificial life - it could be achieved easily with the existing methods of genetic manipulation.

In another article on the same day you referred to the sequencing of Venter's own genome (Gene genie, October 6). This is an obvious, if somewhat egocentric, thing to do and a number of other single-genome sequences are in progress. But the idea alluded to, that you could predict the date of your death using this information, is absurd. Most human diseases are caused by the action of many genes in a complex interaction with the environment. The origin and progression of these polygenic diseases is poorly understood, and sequence information alone will not provide the answers.

It should also be noted that the ability to sequence whole genomes has little to do with Venter. It derives from the work of Fred Sanger at Cambridge in the 1970s. Venter, remember, was the man who tried to patent the human genome sequence and then exploit it for profit.

It is a feature of great scientific advances that they open up whole new areas of knowledge to view. This is well illustrated by the award this week of the Nobel prize for medicine to Martin Evans, Mario Capecchi and Oliver Smithies for the discovery and exploitation of stem cells.

These findings have led to a revolution in our understanding of cell and developmental biology and offer the prospect of new therapies for human diseases such as Alzheimer's. Venter's "artificial life" is not in the same league.

· Dr Nick Gay is a reader in cell signalling and development at the department of biochemistry, University of Cambridge

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Codon Devices expands gene scaffolding reach

Constructive Biology expert, Codon Devices, has opened a European subsidiary in the UK to support the rapid growth of the advanced gene synthesis and protein engineering markets.

The new subsidiary, Codon Devices UK, will focus in offering service and support help to its expanding synthetic biology customer base in Europe, Scandinavia and Israel.

The use of synthetic biology methods to construct engineered cell lines that increase the efficiency of biological drug and vaccine formation or speed-up the drug discovery process is ever increasing.

In addition, such systems can be used to generate enzymes that produce industrial chemicals or aid in the breakdown of plants for biofuel applications.

Traditionally, researchers have had to clone specific genes and splice them into an organism's DNA.

Codon Devices' fee-for-service offering allows researchers to specify a sequence that Codon will then synthesise and ship to the customer, enabling them to spend more time studying the effects of the sequences.

"There is a move away from cloning genes yourself in the laboratory as long as you can find a vendor such as Codon to supply you with gene constructs for expression libraries protein structure libraries," said Dr Michael Dyson, European Managing Director and head of Codon'd European subsidiary.

Such is the groundswell of demand that Dr Dyson estimates that the market will reach a size of around $2bn a year in the near future, compared with $40m a year before 2005.

This growth is helped by reduced costs associated with making these sequences enabled by high throughput parallel synthesis techniques that. Codon's facility can currently make up to 5 megabase pairs a month and is still scaling up production.

Historically, manufacturing of DNA was to stick together oligonucleotides but was only really useful in making oligomers up to 100 base pairs, and anything bigger was very difficult to QC.

Codon has developed a parallel synthesis platform dubbed BioFAB, which uses sophisticated informatics, robotics and sequencing technologies to accurately synthesize genetic codes.

The company claims that its BioFAB system can produce the gene constructs more rapidly and cost-effectively than other currently available technology

Indeed, last July, the company announced the successful construction and delivery of a sequence-verified, 35-kilobase genetic construct for Microbia's Precision Engineering business unit.

The construct was an 80 per cent synthetic gene cluster that codes for an optimised biosynthetic pathway used to produce an active pharmaceutical ingredient.

The company is also heavily involved in partnering companies to help them overcome especially challenging projects.

"It's very complex biology and what we do is a generation away from simply constructing oligomers using the Caruthers synthesis, we look at how to best construct the molecules, how you error check them and checking them for function," said Dr Dyson.

Indeed, the global demand for Codon's approach is such that the company has plans to expand operations in the Pacific Rim regions.

"Codon is investing heavily to address the global need for this technology and our expansion into Europe is being matched by an expansion into Japan and the Pacific Rim," said Dr Dyson.

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Gene Expression Profiling of Cuticular Proteins across the Moult Cycle of the Crab Portunus pelagicus

Background

Crustaceans represent an attractive model to study biomineralization and cuticle matrix formation as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers some of which become calcified and some which remain uncalcified. The cuticle matrix consists of many different proteins which confer the physical properties, such as pliability, of the exoskeleton.

Results

We have used a custom cDNA microarray chip, developed for the blue swimmer crab Portunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. Twenty-one distinct moult cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Thirteen contain copies of the cuticle_1 domain, previously isolated from calcified regions of the crustacean exoskeleton. Four transcripts contain a chitin_bind_4 domain (RR consensus sequence), associated with both the calcified and un-calcified cuticle of crustaceans. Four transcripts contain an unannotated domain (PfamB_109992) previously isolated from C. pagurus. Additionally cryptocyanin, a hemolymph protein, involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains.

Conclusions

The large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening which involve many components and require strict regulatory mechanisms. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.

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Grant winner scoffs at genius label

By Elise Kleeman Staff Writer

PASADENA - Paul Rothemund does not consider himself a genius.

"At Caltech and elsewhere, I am surrounded by real geniuses all the time, people much quicker than me in a variety of ways," said the tall, brown-haired Caltech scientist.

Some, it seems, would disagree.

Rothemund, 35, was one of 24 recipients of the prestigious MacArthur Fellowship, a $500,000 prize often known as the "genius grant."

The no-strings-attached award can be used by the recipients any way they please and is intended to "enable recipients to exercise their own creative instincts for the benefit of human society," according to the MacArthur Foundation.

When they call you, Rothemund said, "they say, `The only thing you have to do is cash the checks. We have no expectations of you, you don't need to report back what you're doing, you're never going to hear from us again. Bye."'

Among this year's other prize winners are a blues musician, a spider silk biologist, a medieval historian, two painters, an author of short stories and another Caltech scientist - Michael Elowitz, a 37-year-old molecular biologist.

Like all the other winners, Elowitz found out about the prize a week before the rest of the Advertisement world.

"I received a phone call, which, among other things, swore me to secrecy," he wrote by e-mail last week from Greece, where he was attending a conference. "The element of secrecy, however transient, really added to the fun. It was one of the best phone calls for me in recent memory."

Both Elowitz and Rothemund are in the forefront of a new interdisciplinary field that some call synthetic biology.

"There's a convergence between a number of fields - chemistry, biology and computer science, where people are thinking about how to create biological circuits or how to program biology," said Erik Winfree, the director of the lab in which Rothemund works and himself a 2000 MacArthur Fellow.

Elowitz's work involves studying chains of interactions between genes and proteins that allow cells to process information, make decisions and communicate.

"He does some of the most beautiful experiments I know of," Winfree said. "They're simultaneously aesthetically pleasing - you could put them on your wall - and scientifically elegant, rigorous."

(In fact, Elowitz does display some images from his experiments on the walls of his lab.)

He studies genetic pathways by linking different genes in bacteria to the production of a rainbow of fluorescent colors. By videotaping how the bacteria's colors change, he can watch as the microbes pass through the steps of the genetic circuit.

"You have something that sort of looks like Froot Loops, except it's growing organisms," said Winfree of the bacteria.

Winfree describes Elowitz as "a joy because he's an enthusiastic, funny guy" who is "so excited about the things he's doing."

Rothemund also works with genetic material, using a loop of virus DNA to create what he calls "DNA origami."

By adding smaller, synthetic strands of DNA that act as staples, he figured out how make the viral DNA fold itself into any shape he wants, each about one-one-thousandth the width of a human hair.

So far, those shapes have included smiley faces, maps of North America, and snowflake patterns. But his technique could one day be the basis for the construction of smaller and faster computer chips.

"It was an exciting development," said Ned Seeman, a New York University chemist who also uses DNA as tiny molecular building blocks. "A lot of the things that we're doing in my lab have been reoriented because of the things Paul did."

Unlike previous, less successful techniques for constructing with DNA, Rothemund's is surprisingly simple.

The virus DNA is easy to come by and the DNA staples can be made to order, Rothemund said.

"They come in a FedEx package, and you take the little tubes and dump them together, add a little saltwater, heat them up and cool them off," he said.

Then, voila - in a single drop of water are a hundred billion shapes.

One "enormous challenge," though, "is figuring out how to put them where you want them and get them in the right orientation," he said.

"I haven't even begun to think of what to do with the money, but one non-scientific fantasy involves tennis lessons," Elowitz wrote. "I plan to resist the temptation to take up an extreme sport."

Source : www.whittierdailynews.com


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Griffith UNiversity Brisbane Science seeks cures in exotic australia.

The country that produced such oddities as the planet’s only egg-laying, duck billed, mammal could also hold the secret to curing cancer, researchers believe. Home to the world’s weirdest, wildest plants and animals, Australia’s little-understood outback is now at the centre of an A$100 million project to reveal untapped sources of drug compounds from natural products.

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China, Australia to collaborate on genetic research

Australian and Chinese researchers have agreed to collaborate on a new genetic research project to find a link between genes and diseases.

They will use the information gathered to develop new medicines that can help people according to their specific genetic make-up.

Liver disease and obesity are just two conditions that can benefit from a better understanding of human genes and personally-targeted drug treatments.

The director of the China-Australia Centre for Phenomics Research, Dr Ed Bertram, has told Radio Australia's Connect Asia program, the project will be fast-tracking research by many years.

He says they are teaming up with the Beijing Genomics Institute, a world leader in genome sequencing technology for more than 10 years.

"One of the key projects that we will be working with is to build a large-scale library of some 10,000 unique fully-sequenced genetic mice with mutations of every gene in the genome," he said.

"Researchers can then access to study or validate genes from the human genome sequences for finding cause and mutations that are involved in disease."

Dr Bertram says the information will allow them to develop new therapies and drugs, as well as look at current drugs and treatments and their suitability for patients.

The China-Australia Centre, located at the Australian National University in Canberra, was one of four joint research centres set up with the support of the Australian and Chinese governments in 2008.

Dr Bertram says the new initiative is the start of a long-term partnership.

"It's really the latest technology development that will allow us to rapidly increase that output," he said.

"And we've found working with China to be a very good collaboration, particularly in this area."

 

source: Radio Australia News

Biocon arm partners Bristol-Myers

Syngene International Pvt. Ltd., a subsidiary of Biocon, has formed a research partnership with Bristol-Myers Squibb.

The initiative is to provide research and development services for discovery and early drug development, Biocon said here on Wednesday.

Bristol-Myers Squibb will significantly increase the scope of its existing relationship with Syngene to develop integrated capabilities in medicinal chemistry, biology, drug metabolism and pharmaceutical development.

The partnership will include a dedicated research facility at the Biocon Park here which will eventually house a team of 400 scientists.

Biocon Chairperson, Kiran Mazumdar-Shaw, said, "The new research facility will take us forward in our evolution as a vaulable partner to the global pharma industry. Syngene has advanced capabilities in high-end services in discovery research." This one-of-its kind alliance in the biotech sector will leverage the current global demand for `bio-partnering' and access to top scientific talent in India for the overseas partner.

Chief Scientific Officer and President, Pharmaceutical Research, Bristol-Myers Squibb, Elliott Sigal, said, "This broad expansion of R&D in India will allow us to grow competitively and provide access to world-class talent to deliver and grow our robust product pipeline."

Syngene International is a custom research company that does research for client companies across the world and has multi-disciplinary skills in synthetic chemistry and molecular biology. It also leverages the convergence of information technology and biotechnology to conduct early stage drug discovery and was started in 1994.

Microsoft Announces Synthetic Biology Grants

Microsoft Research (MSR) has announced the six winners of its inaugural grants in synthetic biology. The company issued a request for proposals a few months ago, seeking to identify outstanding research projects aimed at tackling the computational challenges in two areas of synthetic biology:

• The re-engineering of natural biological pathways to produce interoperable, composed, biological parts; and
• The development of tools and information repositories relating to the use of DNA in the fabrication of nanostructures and nanodevices

The company said that 49 proposals were submitted from 11 countries, including many leading researchers and labs in the field. Following external peer review, six proposals were chosen. They are as follows:

• Computational Interchange Standards for Synthetic Biology -- Herbert Sauro, University of Washington
• Design and Synthesis of Minimal and Persistent Protein Complexes -- David Green and Steven Skiena, Stony Brook University
• BioStudio: A Collaborative Editing and Revision Control Environment for Synthetic Genomes -- Joel Bader and Jef Boeke, Johns Hopkins University School of Medicine
• Identification of Standard Gene Regulatory Sequences for Synthetic Biology -- Robert Holt, University of British Columbia, Canada
• Using programmable stacking bonds to combine DNA origami into larger, more complex, reconfigurable structures -- Paul Rothemund and Erik Winfree, California Institute of Technology
• Noise Suppression and Next-Generation Cloning Vectors -- Johan Paulsson, Harvard University

Summaries of the six selected research abstracts can be found here.

In announcing the program in December, MSR Bioinformatics Program Manager Simon Mercer said the challenges faced by scientists today will be faced by business tomorrow and eventually by everyone. “Encouraging and participating in basic research helps us to better understand these problems and their potential solutions.” Synthetic biology is a particularly interesting field, Mercer said, because it has “the potential to provide insights into living systems, transform biotechnology and perhaps generate entirely new industries.”

Gene therapy for blindness clears hurdle in mice

researchers have used an experimental therapy in mice to shut down a gene that plays a crucial role in a leading cause of inherited blindness.

The technique, detailed in an upcoming issue of Vision Research, involves injecting the eye with a bit of genetic material called interfering RNA, which helps disable the gene.

Normally the gene is essential for healthy eyesight, but mutated versions of it are passed from generation to generation in some families and can lead to blindness.

Disabling the gene is a step toward developing a gene therapy to treat people with retinitis pigmentosa, an inherited disease that attacks the light-sensing cells in the eye. It affects about one in 60,000 people, with an estimated 1.5 million people afflicted worldwide.

Read the complete article here

Systems and Synthetic Biology

Editors-in-Chief: P.K. Dhar; R. Weiss

Systems and Synthetic Biology is a new biomedical journal publishing original papers and articles on all aspects of Systems and Synthetic Biology.

Systems Biology is an integrated approach to study collective behaviour of biological interactions. The grand challenge in Systems Biology is to connect molecular topography with physiological responses. Systems Biology field will realize its fullest potential once individual contributions are tied to variations in the system level behavior.

The emerging field of synthetic biology combines knowledge from various disciplines including molecular biology, engineering, mathematics, and physics to design and implement new cellular behaviors. The goal of synthetic biology is both to improve our quantitative understanding of natural phenomenon as well as to foster an engineering discipline for obtaining new complex cell behaviors in a predictable and reliable fashion. Systems and Synthetic Biology will publish research articles that either advance this field as an engineering discipline or use synthetic biology to improve our scientific knowledge of existing phenomena.

Synthetic biology: new engineering rules for an emerging discipline

I came across this very informative article...it's really long, but very good..

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

Read the rest of the article here

Synthetic Biology is 'Extreme Genetic Engineering' and Far More Dangerous

A new report by the ETC Group concludes that the social,
environmental and bio-weapons threats of synthetic biology surpass
the possible dangers and abuses of biotech. The full text of the 70-
page report, Extreme Genetic Engineering: An Introduction to
Synthetic Biology, is available for downloading free-of-charge on the
ETC Group website: www.etcgroup.org

"Genetic engineering is passe," said Pat Mooney, Executive Director
of ETC Group. "Today, scientists aren't just mapping genomes and
manipulating genes, they're building life from scratch - and they're
doing it in the absence of societal debate and regulatory oversight,"
said Mooney.

Synbio - dubbed "genetic engineering on steroids" - is inspired by
the convergence of nano-scale biology, computing and engineering.
Using a laptop computer, published gene sequence information and mail-
order synthetic DNA, just about anyone has the potential to construct
genes or entire genomes from scratch (including those of lethal
pathogens). Scientists predict that within 2-5 years it will be
possible to synthesise any virus; the first de novo bacterium will
likely make its debut in 2007; in 5-10 years simple bacterial genomes
will be synthesised routinely and it will become no big deal to
cobble together a designer genome, insert it into an empty bacterial
cell and - voila - give birth to a living, self-replicating organism.
Other synthetic biologists hope to reconfigure the genetic pathways
of existing organisms to perform new functions - such as
manufacturing high-value drugs or chemicals.

A clutch of entrepreneurial scientists, including the gene maverick
J. Craig Venter, is setting up synthetic biology companies backed by
government funding and venture capital. They aim to commercialise new
biological parts, devices and systems that don't exist in the natural
world - some of which are designed for environmental release.
Advocates insist that synthetic biology is the key to cheap biofuels,
a cure for malaria, and climate change remediation - media-friendly
goals that aim to mollify public concerns about a dangerous and
controversial technology. Ultimately synthetic biology means cheaper
and widely accessible tools to build bioweapons, virulent pathogens
and artificial organisms that could pose grave threats to people and
the planet. The danger is not just bio-terror, but "bio-error," warns
ETC Group.

Despite calls for open source biology, corporate and academic
scientists are winning exclusive monopoly patents on the products and
processes of synthetic genetics. Like biotech, the power to make
synthetic life could be concentrated in the hands of major
multinational firms. As gene synthesis becomes cheaper and faster, it
will become easier to synthesise a microbe than to find it in nature
or retrieve it from a gene bank. Biological samples, sequenced and
stored in digital form, will move instantaneously across the globe
and be resurrected in corporate labs thousands of miles away - a
practice that could erode future support for genetic conservation and
create new challenges for international negotiations on biodiversity.

"Last year, 38 civil society organizations rejected proposals for
self-regulation of synthetic biology put forth by a small group of
synthetic biologists," said Kathy Jo Wetter of ETC Group. "Widespread
debate on the social, economic and ethical implications of synbio
must come first - and it must not be limited to biosecurity and
biosafety issues," said Wetter.

The tools for synthesising genes and genomes are widely accessible
and advancing at break-neck pace. ETC Group's new report concludes
that it is not enough to regulate synthetic biology on the national
level. Decisions must be considered in a global context, with broad
participation from civil society and social movements. In keeping
with the Precautionary Principle, ETC Group asserts that - at a
minimum - there must be an immediate ban on environmental release of
de novo synthetic organisms until wide societal debate and strong
governance are in place.

The Dangers of Synthetic Biology

Nobel Prize winner David Baltimore explains why building smallpox from scratch is a key safety concern in synthetic biology.

The emerging field of synthetic biology -- the quest to design and build new life forms that can perform useful functions -- brings exciting promise and potentially dangerous capabilities. Scientists have the ability to synthesize entire strings of DNA and put together complicated molecular machinery. But that power has raised some troubling questions. Could terrorists recreate viruses such as smallpox? Or engineer a virus even more deadly than avian flu? (see "The Knowledge").

In the 1970s, scientists faced a similar dilemma. The advent of recombinant DNA technology meant biologists could manipulate DNA as they never could before. Concerned about the potential perils of this new tool, a prominent group of scientists held the now-famous Asilomar Conference in 1975 (formally titled the "International Congress on Recombinant DNA Molecules") to determine how to proceed safely.

Thirty years later, at the Synthetic Biology 2.0 meeting at the University of California, Berkeley this month, scientists met to discuss not only new developments in the field, but also how the community should deal with the growing safety concerns surrounding synthetic biology.

David Baltimore, a winner of the 1975 Nobel Prize in physiology or medicine, and president of the California Institute of Technology, was one of the organizers of the Asilomar Conference. At the Synthetic Biology conference last week, he reflected on changes in the field over the last 30 years. Baltimore talks here with Technology Review about what scientists have learned since 1975 and the specific dangers we should be most worried about.

Technology Review: What were you were most concerned about 30 years ago?

David Baltimore: The Asilomar Conference was convened in a very different context than we have today. We were marveling at a wholly new world of experimentation -- we literally had no experience with moving DNA around. But people were also concerned, and rightly so, about issues of intrinsic safety. They were worried, for example, that we could create organisms that we didn't know how to control.

At the conference, we decided to focus purely on safety, rather than ethics or biowarfare. We believed, somewhat naively, that there was a treaty that everyone held to prohibiting use of technology to make biological weapons. In retrospect, the U.S.S.R. had a huge clandestine program. We also didn't have the situation we have today, where terrorist organizations cross boundaries and are not held by treaties. So we clearly have an unfinished agenda from Asilomar on biowarfare.

TR: What issues are you most worried about today?

DB: The real danger today is from organisms that already exist. The idea of synthesizing something worse than that, of taking bits of Ebola and other viruses to create something more deadly, underestimates how hard it is to survive in the natural world.

Adapting to the human lifestyle is very complicated, so I would guess that we would fail if we tried to engineer a dangerous organism. Ebola, for example, is very pathogenic. It infects families and health workers, but it never spreads widely because it is too lethal -- it isn't in the community long enough to spread. Bird flu is not likely to spread widely until it mutates to become less pathogenic.

Read the full interview here

Next-Generation Retinal Implant

On Thursday, scientists at the University of Southern California (USC) announced their plans to test an improved retinal implant in blind patients. The new implant, which scientists hope will better improve patients' vision, has four times the resolution of the previous version.

"My expectation, without really knowing what is going to happen, is that this will be useful for people in allowing them to find a lit doorway or the edge of an object when going into a room," says James Weiland, a scientist at USC involved in the project.

People with retinal-degeneration diseases, such as retinitis pigmentosa and macular degeneration, lose their sight as the cells in the eye that normally sense light deteriorate. Retinal implants can take over for these lost cells, converting light into neural signals that are then interpreted by the brain. Simpler versions of these devices, developed by researchers at USC and other institutions, have already been tested in humans, giving patients rudimentary vision, such as the ability to detect light and to occasionally distinguish between simple objects. One patient, for example, wears the device to her grandson's soccer games and reports that she perceives the sensation of the players' movement as they run by, says Weiland.

The device, developed by Mark Humayun and colleagues at USC, consists of a tiny chip dotted with hair-thin electrodes. When implanted in the retina, the electrodes transmit electrical signals from the chip to neural cells in the eye, which then send the message to the brain. A wireless camera mounted on glasses and a video processing unit worn on the belt capture and process visual information from the wearer's surroundings and wirelessly transmit those signals to the chip.

The new version of the implant, which the researchers have been working on for the past eight years, has nearly quadrupled the number of electrodes--from 16 to 60--and is about half the size of the previous model. The researchers recently received permission from the Food and Drug Administration to start human tests, which they plan to begin in the next few months.

Once the device is implanted, researchers will need to do extensive tests to figure out how to optimize it. "A camera gets at least tens of thousands of pixel information, and we need to transmit that to just 60 stimulating channels," says Weiland. "We have to figure out what is the most important information to keep."

Read the rest of the article here

New DNA test in Anna Nicole Smith case

i know.. i know... but it's still about what genetics can do!!

A judge ordered another DNA sample be taken fromAnna Nicole Smith's body Thursday as he heard often fiery arguments in the fight over the former Playboy Playmate's remains and custody of her infant daughter.

The swab of Smith's cheek was to be taken in the afternoon, despite the objections of attorneys for her longtime companion, Howard K. Stern, and her estranged mother, Vergie Arthur, and testimony from the medical examiner and DNA experts that such an additional sample was likely not necessary.

Circuit Judge Larry Seidlin said he wanted to make sure all samples were taken before Smith was buried, so her body wouldn't have to be exhumed.

"When we bury her, I want it to be forever," he said in the second day of an emergency hearing.

Smith, 39, died Feb. 8 after collapsing at a Florida hotel.

As the proceedings dragged on, investigators in the Bahamas went into a mansion that Stern and Smith shared, though the officers declined to say why they were there. Stern filed a burglary report claiming a computer, home videos and other items were taken from the house after Smith's death.

Stern claims he is executor of Smith's will and wants to have her buried next to her son in the Bahamas. Arthur wants her daughter buried in her home state of Texas.

"She sits here today to take her to Texas and put her in the ground all alone ... and it's sad and it's sick," Stern's lawyer, Krista Barth, told the judge in attacking Smith's mother.

Arthur's attorney, Stephen Tunstall, said his client "wants to take her home to Texas to bury her with the rest of her family." Arthur wiped tears away outside an elevator during a break in the proceedings.

Photographer Larry Birkhead hopes DNA taken from Smith will help prove he fathered the former centerfold's 5-month-old daughter, Dannielynn, who could inherit millions.

The judge has said the dispute could be lengthy. The hearing, which began Wednesday, stretched into the afternoon Thursday and was to continue Friday.

Debra Opri, an attorney for Birkhead, said earlier in a news release that she was satisfied DNA samples would be provided by Florida authorities. Opri has said Smith's DNA is needed to connect her with Dannielynn, and to help prove there was no baby switch.

Prince Frederic von Anhalt, the husband of the actress
Zsa Zsa Gabor, has said he had a decade-long affair with Smith and may also be the father. He filed legal documents Thursday in California seeking a DNA test to determine if he is the father of the baby.

Smith's body remained at the medical examiner's office, and Seidlin said it would stay there. "This body's not leaving Broward County till I make the ruling."

Smith was the widow of Texas oil tycoon J. Howard Marshall II, whom she married in 1994 when he was 89 and she was 26. She had been fighting his family over his fortune since his death in 1995.

A judge in the Bahamas issued an injunction Tuesday preventing the baby from being taken out of the country until the custody case is resolved.

Arthur wants to be named guardian of her granddaughter and sought the order because she feared Stern would take the child from the Bahamas, her lawyer said.

Your Genetic Destiny for Sale

I found this article while browsing around... it's a very old one.. almost 6 years old..2001 i think.. but totally fascinating. I'm not publishing the whole article here, it's about 6 pages long.

Large extended families have traditionally been the mother lode of genetic research. From them came a precious commodity: links between the presence of a disease and the errant genes responsible for it. When medical researcher Nancy Wexler, for instance, went looking for the genetic cause of Huntington's disease in 1979, it was a 9,000-member Venezuelan family that enabled her to trace the telltale patterns of disease inheritance.

Wayne Gulliver's family is not nearly so large, but it is impressive nonetheless. Until two years ago, when his great-great-aunt passed away, six generations of Gullivers were alive in Newfoundland. His grandmother, who died last October, had some hundred descendants, while his parents, only in their 60s, already have 26 grandchildren to go with their 10 children. All of this would be professionally irrelevant if Gulliver's family were not typical of Newfoundland, and if Gulliver himself, a dermatologist who studies the genetics of psoriasis, were not involved in a rapidly emerging discipline called population genomics, the goal of which is to identify the underlying genes responsible for common chronic diseases, such as cancer and heart disease.

Two years ago Gulliver met Paul Kelly, CEO of the British company Gemini Genomics, which had already assembled a huge international network of twins to use in searching for gene-disease associations. Gulliver pitched Kelly the idea of supplementing Gemini's database with population statistics from Newfoundland and Labrador. His selling points were simple: a population of 550,000, of which almost 90 percent are descended from the original Irish, Scottish and English immigrants who arrived before the mid-19th century. It is, Gulliver says, a population in which the locals often know their family lineages back to the original immigrants. "Not like the States," he says, "where you have three kids, send them off to college, and you might be lucky if you see each other every fifth Thanksgiving."

And many of those families, like Gulliver's own, are large. In such a tightly knit population consisting of large extended families, common diseases might run in recognizable patterns-shared by siblings, for instance, or passing through paternal or maternal lines, or linked to other distinctive physical characteristics. All it would take to mine this rich vein of medical history for valuable clues to disease-causing genes would be a sufficient effort, some very advanced biotechnology tools and some startup capital.

Gulliver's pitch prompted Gemini to launch Newfound Genomics in February 2000. In the near term, Newfound Genomics aims to concentrate on diseases endemic to the local population-psoriasis, diabetes, obesity, inflammatory bowel disease, osteoporosis and rheumatoid arthritis-with the hope, considering the Irish/English/Scottish ancestry, that any relevant genes or gene variants that might be uncovered would play significant roles in other populations. The expectations behind the company are anything but modest, at least judging by the inaugural press release. "We have the potential here to develop a major international powerhouse of clinical genetics," said Kelly, "that will provide benefit not only for the Newfoundland and Labrador community but also patients suffering from these diseases worldwide."

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Can RNA Turn Genes On?

Researchers at the University of Texas Southwestern Medical Center have found that RNA may be a potential tool in activating dormant genes.

RNA--a tiny cousin of DNA that may be the key to developing genetic therapies for a huge range of diseases, including cancer, neurological and respiratory diseases, and HIV. Nearly eight years ago, researchers Craig Mello, of the University of Massachusetts Medical School, and Andrew Fire, of Stanford University's School of Medicine, discovered that RNA plays a crucial role in regulating gene expression: the ability to turn genes off. They won a Nobel Prize for their work in 2006 identifying the mechanism for a process called RNA interference, or RNAi. They found that RNA blocks a gene from delivering its message to proteins, essentially shutting down that gene. Since then, scientists around the world have run with the idea, finding ways for RNAi to turn off a variety of genes--in particular, those that cause disease. It's RNA's role in switching off genes that dominates the talks at this week's conference, titled "RNAi for Target Validation and as a Therapeutic."

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Human Model Completed

Researchers at the University of California, San Diego, have constructed the first complete computer model of human metabolism. Available free on the Web, the model is a major step forward in the fledging field of systems biology, and it will help researchers uncover new drug pathways and understand the molecular basis of cancer and other diseases.

Metabolism is the sum of all chemical reactions involved in breaking down the nutrients in food into energy and using them as the raw materials for making everything the body needs, from hormones like insulin to the lipids that make up cell membranes. The computer model of metabolism, constructed by researchers in the lab of Bernhard Palsson, professor of bioengineering, connects all such known chemical reactions in the body to every human gene.

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Sea Urchin Genome Is Sequenced

When scientists sequenced the sea urchin genome, they found surprising similarities to that of human beings AND are putting it to good use...

Who would have guessed that the lowly sea urchin, that brain-less, limb-less porcupine of the sea, would be the star of a multi-million dollar, worldwide effort to map out every letter of its genetic code? Or that the information gathered in that effort may eventually lead to new treatments for cancer, infertility, blindness, and diseases like muscular dystrophy and Huntington's Disease?

James Coffman, Ph.D., of the Mount Desert Island Biological Laboratory in Bar Harbor was one of the scientists who helped decode the 814 million pairs of nucleotide bases in the sea urchin's chromosomes. The Human Genome Sequencing Center at Baylor College of Medicine in Texas led the project and announced the completion of the three-year project today. Having the complete genome, Coffman says, "makes doing research on urchins so much easier."

Why would anyone want to do biomedical research on sea urchins? According to Coffman, sea urchins are remarkably similar to humans in many ways, sharing most of the same gene families, and yet differ in a few critical areas besides the obvious physical ones. For one thing, sea urchins have a "extraordinarily complex innate immune system" which is not based on antibodies, like that of jawed vertebrates, but is effective enough to give sea urchins a surprisingly long life span of up to a hundred years or more.

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Regards

Genetic map offers new tool for malaria research

Did you know that the malaria Parasite's DNA has nearly 47,000 genetic variations worldwide; kills every 30 seconds??

An international research team has completed a map that charts the genetic variability of the human malaria parasite, Plasmodium falciparum. The work, published in the Dec. 10 advance online edition of Nature Genetics, has already unearthed novel genes that may underlie resistance to current drugs against the disease.

The study reveals striking variation within the pathogen's genome, including an initial catalog of nearly 47,000 specific genetic differences among parasites sampled worldwide. That's more than double the expected level of diversity in the parasite's DNA. These differences lay the foundation for dissecting the functions of important parasite genes and for tracing the global spread of malaria.

The scientists who created the map are from the Broad Institute of MIT and Harvard, the Harvard School of Public Health and Cheikh Anta Diop University in Senegal, where malaria is endemic.

"Malaria remains a significant threat to global public health, driven in part by the genetic changes in the parasite that causes the disease," said senior author Dyann Wirth, a professor at the Harvard School of Public Health and co-director of the Broad Institute's Infectious Disease Initiative. "This study gives us one of the first looks at genetic variation across the entire malaria parasite genome--a critical step toward a comprehensive genetic tool for the malaria research community."

Plasmodium falciparum--the deadliest of the four parasites that cause malaria in humans--kills one person every 30 seconds, mostly children living in Africa. Despite decades of research, the genetic changes that enable it to escape the body's natural defenses and to overcome malaria drugs remain largely unknown.

To gain a broad picture of genetic variability--worldwide and genome-wide--the scientists analyzed more than 50 different P. falciparum samples from diverse geographic locations. This includes the complete genome sequencing of two well-studied samples, as well as extensive DNA analyses of 16 additional isolates.

By comparing the DNA sequences to each other and to the P. falciparum genome sequenced in 2002, the researchers uncovered extensive differences, including 47,000 single-letter changes called single nucleotide polymorphisms (SNPs). Although there are probably many more SNPs to be found, this initial survey provides a launching point for future systematic efforts to identify parasite genes that are essential to malaria.

"The roles of most of the malaria parasite's genes are still not known," said Sarah Volkman, a research scientist at the Harvard School of Public Health. "An important application of this new tool will be in pinpointing the genes that are vital to the development and spread of malaria."

Volkman and Pardis Sabeti, a postdoctoral fellow at the Broad Institute, are first authors on the paper.

One of the map's strengths is its ability to reveal evolutionary differences among parasites. This information can shed light on the genes responsible for malaria drug resistance--a major obstacle to adequate control of the disease.

Using the map to compare parasites exposed to different anti-malarial drugs, the scientists identified a novel genome region that is strongly implicated in resistance to the drug pyrimethamine, and also confirmed a region of the genome known to be involved in chloroquine drug resistance.

"The same genetic principles used to study human evolution can provide important clues about malaria," said Sabeti. "This tool has already yielded insights into the genetic changes that correlate with different drug treatments, pointing us to genes that may contribute to drug resistance."

The map can also define the genetic landscapes of different parasite populations. Applying it to parasites from various continents, the scientists discovered greater DNA variability among P. falciparum samples from Africa relative to those from Asia and the Americas. This knowledge guides the selection of genetic markers to track the transmission of distinct parasites, particularly ones that are virulent or drug resistant. It also lays the groundwork for connecting parasite genes with traits that vary geographically and bolster malaria's foothold in many parts of the world.

"Genomic tools have largely been applied to First World diseases up to now. This project underscores the power and importance of applying them to the devastating diseases of the developing world," said Eric Lander, one of the study's authors and the director of the Broad Institute. "By joining forces among scientists in the U.S., Africa and elsewhere, it should be possible to rapidly reveal the genetic variation in malaria around the world.

"Knowing the enemy will be a crucial step in fighting it," said Lander, who is also a professor of biology at MIT and a member of the Whitehead Institute for Biomedical Research.

The work is one of three large-scale studies of the parasite's DNA that appear together in Nature Genetics. It was supported by the Bill and Melinda Gates Foundation, the Burroughs-Wellcome Fund, the Exxon Mobil Foundation, the National Institutes of Allergy and Infectious Disease Microbial Sequencing Center and the National Institutes of Health.

MIT improves protein sorting with a new microchip

A new MIT microchip system promises to speed up the separation and sorting of biomolecules such as proteins. The work is important because it could help scientists better detect certain molecules associated with diseases, potentially leading to earlier diagnoses or treatments.

The microchip system has an extremely tiny sieve structure built into it that can sort through continuous streams of biological fluids and separate proteins accurately by size. Conventional separation methods employ gels, which are slower and more labor-intensive to process. The new microchip system could sort proteins in minutes, as compared to the hours necessary for gel-based systems.

The MIT team's results appear in the Feb. 5 issue of Nature Nanotechnology.

The new technology is an advance from a one-dimensional sieve structure reported by the same MIT group last year. The key to this new advance, called an anisotropic nanofluidic sieving structure, is that the researchers have designed the anisotropic sieve in two orthogonal dimensions (at a right angle), which enables rapid continuous-flow separation of the biological sample. This allows continuous isolation and harvesting of subsets of biomolecules that researchers want to study. And that increases the probability of detecting even the smallest number of molecules in the sample.

"With this technology we can isolate interesting proteins faster and more efficiently. And because it can process such small biologically relevant entities, it has the potential to be used as a generic molecular sieving structure for a more complex, integrated biomolecule preparation and analysis system," said Jongyoon Han, the Karl Van Tassel Associate Professor of Electrical Engineering and associate professor of biological engineering at MIT and head of the MIT team.

Han's coauthors of the Nature Nanotechnology paper are co-lead authors Jianping Fu, a Ph.D. candidate in the Department of Mechanical Engineering, and Reto B. Schoch, a postdoctoral associate in the Research Laboratory of Electronics (RLE). Additional authors are Anna Stevens, a postdoctoral associate in the Harvard-MIT Division of Health Sciences and Technology, and Professor Steven Tannenbaum of MIT's Biological Engineering Division.

Han noted that until the late 1990s, most advances in biological laboratory equipment were aimed at the Human Genome Project and discoveries related to DNA, which are larger molecules compared to proteins. However, because of the vital role proteins play in almost all biological processes, researchers began to focus their attention on proteins. But one obstacle has been the lack of good laboratory tools with which to prepare biological samples to analyze proteins, said Han, who also has affiliations in MIT's RLE, Computational and Systems Biology Initiative, Center for Materials Science and Engineering and Microsystems Technology Laboratories.

"I shifted my attention from DNA into the area of protein separation around 2002 with the shift to proteomics (the study of proteins)," Han said. "But the field was using decades-old gel electrophoresis technology. There is a big gap in the need for technology in this area."

Han and Fu therefore devised the anisotropic sieve that is embedded into a silicon chip. A biological sample containing different proteins is placed in a sample reservoir above the chip. The sample is then run through the sieve of the chip continuously. The chip is designed with a network of microfluidic channels surrounding the sieve, and the anisotropy (directional property) in the sieve causes proteins of different sizes to follow distinct migration trajectories, leading to efficient continuous-flow separation. The current sieve has an array of nanofluidic filters of about 55 nanometers, or billionths of a meter, wide.

"The proteins to be sorted are forced to take two orthogonal paths. Each path is engineered with different sieving characters. When proteins of different sizes are injected into the sieve under applied electric fields, they will separate into different streams based on size," Han explained. At the bottom of the chip the separated proteins are collected in individual chambers. Scientists then can test the proteins.

While other scientists have used similar continuous flow techniques to separate large molecules like long DNA, the MIT team succeeded with the tinier proteins. "This is the first time physiologically relevant molecules like proteins have been separated in such a manner," said Han. "We can separate the molecules in about a minute with the current device versus hours for gels."

Another advantage of the microchip is that it can have so many different pore sizes, and unlike gels, it is possible to design an exact pore size to increase the separation accuracy. That in turn can help researchers look for so-called biomarkers, or proteins that can reveal that disease is present, and thus help researchers develop diagnostics and treatments for the disease. "Sample preparation is critical in detecting more biomarker signals," said Han.

Funding came from the National Science Foundation, the National Institutes of Health and the Singapore-MIT Alliance.