New Method Helps Separation of DNA Fragments in Hydrogels

A Texas A&M University chemical engineer has provided an important advancement to DNA analysis by revealing a new method of separating DNA fragments more effectively, which has the potential to benefit the fields of genetic engineering, biomedical research and forensics.

Victor M. Ugaz, an associate professor in the university's Artie McFerrin Department of Chemical Engineering, along with Nan Shi, a graduate student, have been working with a gelatin called hydrogel in order to develop and observe the certain types of conditions that "result in the optimum gel pore structure for separation of a wide range of DNA fragment sizes." The way DNA fragments moved through the hydrogel was key to their findings.

Ugaz and Shi's research consisted of using a process called electrophoresis, where negatively charged DNA is inserted into a porous hydrogel. Then, an electric field is applied in order to make DNA fragments move though the hydrogel's pores. Smaller chains are able to move through pores easier and faster, where longer chains have to "unthread" and separate in order to pass through pores that are either the same size or smaller than the coiled DNA fragment. This separation process is called entropic trapping. Longer DNA chains separate and squeeze quickly through smaller pores and return to its coiled shape in larger pores.

"It changes the way you think about the entire process because these findings demonstrate a rational way to connect the pore structure of the gel quantitatively to the mechanism by which the DNA moves through the gel," said Ugaz. "Researchers can now actually design gels to specifically harness certain effects, and they will need this information we have found to do that."

What makes Ugaz and Shi's work an important advancement is the use of entropic trapping for separation within a hydrogel because up until this point, scientists were unsure as to how the DNA fragment's transport system was linked to the hydrogel's structure of pores. Choosing the correct hydrogel for these types of processes was difficult because hydrogels have specific properties, and there was no way of knowing which hydrogel possessed the right properties for this type of research. But entropic trapping within the gel has proved to be an efficient way for DNA fragments to travel through the pores.

"You want to be able to detect the smallest possible difference in size between DNA fragments," said Ugaz. "The size of the fragments may be very close, and you may need to detect a difference of one unit in size. To do this, you would want to be able to specifically construct a hydrogel with the necessary pore structure to achieve this.

"We have a better picture of how to do this than what has existed. We know what the gel needs to look like and how it needs to be prepared. We're able to understand how to construct a gel that would allow DNA to move via an entropic trapping method that enhances separation performance and in turn leads to more effective analysis. This finding could have enormous implications by helping remove current barriers to separation efficiency."

Via : dailytech.com

Gene Copies to Be Studied

New research institution of Russian academy of sciences will study gene copies among other things.

Recently established Institute of Cell and Molecular Biology of Siberian branch of Russian academy of sciences lists genetic engineering among other research topics. Some laboratories deal with animal genomes, because this work is interesting and promising for the mankind. Some mammals. For instance, have so-called accessory chromosomes, also known as B-chromosomes, and no one knew why. Now researchers known, that these B-chromosomes carry copies of very important genes, which can be damaged on main chromosomes.

The Institute also deals with genetic therapy, which is replacing incorrectly working genes with their correctly working artificial copies. Scientists will try to introduce correctly working genes into B-chromosomes, because trying to insert a gene directly into genome often results in misplacements, which, in their turn, may lead to additional problems with health.

Via : russia-ic.com

Scientists develop fast method to pinpoint genes behind TB virulence

Scientists from Europe and Asia have identified 10 virulence genes of the tubercle bacillus, which causes tuberculosis or TB. This discovery offers the medical world an opportunity to develop new treatments and test novel vaccine candidates against one of the world's most common yet deadliest diseases. The findings of the study, funded in part by the EU, are presented in the PLoS (Public Library of Science) Pathogens journal.

Despite the complex task at hand, the scientists successfully obtained their results in just two weeks thanks to a new screening technique they developed. This method could be transposed to other intracellular pathogens without any problem, according to them.

While physicians do their best to quash this disease, tuberculosis continues to kill almost 2 million people worldwide each year. TB is caused by bacteria of the mycobacterium family, which includes Mycobacterium tuberculosis, the agent of TB in people. How it propagates within the host cell determines its pathogenicity (virulence).

What researchers have known until now is that this pathogenic agent can actually break free from the defence hold of the host. So it infects through parasitism of the macrophages, which play a vital role in the body's immune response by destroying any microbes.

M. tuberculosis enters the lungs, is ingested by the alveolar macrophages and positions itself in a phagosome, an intracellular compartment. Phagosomes usually kill off the bodies ingested by the macrophage via acidification, but TB blocks the acidification and proliferates fruitfully.

Thanks to the new screening method developed by the scientists, which involves a robot, cellular phenotype samples can be identified both visually and automatically. The upshot is that researchers have more time to identify the microbial bodies involved in the parasitism of cells.

The team, led by Dr Olivier Neyrolles from the Institut de Pharmacologie et de Biologie Structurale (CNRS, Centre national de la recherche scientifique/Université de Toulouse) and Dr Priscille Brodin from INSERM (Institut national de la santé et de la recherche médicale) and Institut Pasteur, used the method on a virulent strain of M. tuberculosis and screened over 11,000 mutants of TB rather quickly. The robot was programmed to find out if the 'acidification function' was enabled or not. So the scientists isolated the mutants that failed to block acidification of the phagosome. Genetic engineering helped the team identify the mutations, and they later succeeded in characterising 10 genes involved in the parasitism of the macrophage.

The team pointed out that most of the genes code for the synthesis of products secreted by the bacteria: proteins and lipids. They also noted how the isolated mutants could be used when new vaccines are to be developed.

Scientists involved in the study were from France, South Korea, Spain and the UK.

The findings are an outcome of three EU-funded projects: TB-MACS; TB-VIR; and NEWTBVAC. TB-MACS ('Identification and characterisation of mycobacterium tuberculosis virulence genes involved in macrophage parasitism') received more than EUR 734,000 under the 'Life sciences, genomics and biotechnology for health' Thematic area of the Sixth Framework Programme (FP6) to improve human health by defining bacterial products and processes that are essential to infection.

TB-VIR ('Mycobacterium tuberculosis W-Beijing genetic diversity and differential virulence and host immune responses'), backed with almost EUR 3.9 million, and NEWTBVAC ('Discovery and preclinical development of new generation tuberculosis vaccines'), which received EUR 12 million, are supported under the Health Theme of the Seventh Framework Programme (FP7).

Via : cordis.europa.eu

Amryis Files with SEC to Raise $121 Million in IPO

Amyris, a developer of microbial technologies for producing biofuels and medicines, has filed an amendment to its registration with the Securities and Exchange Commission for an initial public offering of stock, indicating that it intends to sell about 5.3 million shares and raise an estimated $121 million in the deal.

In April, the company indicated in an SEC filing that it intended to raise an estimated $100 million.

Founded in 2003 and based in Emeryville, Calif., Amyris initially developed its technology under a non-profit initiative to provide a reliable and affordable source of artemisinin, which is an anti-malarial drug.

The company has developed genetic engineering and screening technologies that modify the way microbes process sugar, turning them into “living factories, or biorefineries.” It is now applying its industrial synthetic biology platform to provide alternatives to a range of petroleum-sourced products.

Amyris is focusing on Brazilian sugarcane as its primary biofuel feedstock. Its subsidiaries include Amyris Brasil, a majority-owned Brasilian company through which it conducts Brasilian operations for the manufacture and trade of products, and Amyris Fuels, a wholly-owned subsidiary through which it is building U.S. fuels distribution capabilities.

Amyris has raised a total of around $244 million in venture capital and employs about 200 people.

Via : smartenergynews.net

Synthetic Life Now A Fact

EVERYONE grumbles from time to time about doctors “playing God,” but now scientists have finally managed to create a cell that has fully synthetic DNA. In the most literal sense, we are now in the business of creating life.

It used to be the stuff of science fiction (what isn’t these days?), but it’s true, and it’s happening today.

Combining advanced computer modeling techniques with genetic engineering, researchers have managed to recode the DNA of a bacterium, more or less at will. Keep in mind, the bacteria hasn’t been created “from scratch,” rather, the individual DNA sequences were synthesized from a “blueprint” on a computer.

At present, the implementation of the technique is more of a “micro-transplant” than anything else. A DNA synthesizer generates the customized sequences, which are then added to specialized yeast cultures. The yeast’s built-in genetic mechanisms tie together the new sequences in their proper order. After this has been done, the completed genomes are extracted, and then planted into donor cells. The donor cells will then reproduce according to the instructions printed on the synthetic DNA.

So what’s the upshot of all of this technical mumbo-jumbo? Initially, not much. They can encode some junk strands with strings of letters, or inject genes that will cause the cells to produce a specific protein. In the near term, applications are broad, ranging from new types of oil-eating bacteria to improved antibiotics.

In the long term, the implications are staggering. If we can recode the genomes of individual bacterial cells, we’ll soon be able to do the same for more complex creatures, like tardigrades (small animals that can survive in extreme weather), capybaras, or humans. With this technique, we’re a big leap closer to being able to correct genetic conditions, for example. But of course, there’s a catch (in bioscience, there’s always a catch to any new advancement).

If we can inject DNA into bacteria that makes it produce an antibiotic or other useful compound, the same techniques could be used to make an engineered organism more resistant to antibiotics, or better suited to biological warfare.

So, while scientists will herald this and other advancements as a great leap forward, whistleblowers, doomsday theorists and other naysayers will see this as yet another skid down a steep slippery slope. Religious groups will no doubt take offense to humans tinkering with our own genetic blueprints.

My perspective on it – the real breakthrough here is the ability to easily model and design genes. The rest of the technology, as described, is simply a refinement of pre-existing techniques. Ethical concerns aside, these techniques are here to stay, and they’ll only improve with time.

Via : timesleader.com

GM salmon faces widespread opposition

Food & Water Watch and other groups have sent a letter to the US Food and Drug Administration (FDA) demanding that it discontinue its mostly secretive approval process for genetically engineered (GE) salmon. The fish could be sold as food by 2012 if it wins approval once a 60 day consultation period begins on 19 September.

“Consumers have a right to know that the FDA lacks the means to assess this fish as a genetically engineered animal intended for human consumption. If this product was approved, the resulting consumer health impact could be disastrous,” Food & Water Watch said.

Consumer, environmental, fishing, and animal welfare groups are all asking the FDA to reject the transgenic fish.

“Furthermore, consumers should be aware that the FDA has purposefully scheduled public hearings to limit public participation, beginning them on a Sunday in a remote location (Rockville, Maryland) and creating a complicated registration process for the largely unpublicized events,” Food & Water Watch continued. “In addition, the agency, which has been studying this fish for nearly a decade, released an insufficient amount of information on the matter (in the form of studies performed by AquaBounty, the company with a vested interest in selling its own product), barely two weeks before the public hearings are set to begin on 19 September.”

AquaBounty Technologies Inc developed the GM salmon, which involved adding genetic material from King salmon to Atlantic salmon. This allows the GM fish to reach maturity in half as long as normal farmed Atlantic salmon take to mature.

AquaBounty says the GM fish is designed to grow in contained, land-based facilities and that the fish are all sterile females, so that if they escape into the wild they will not be able to cross-breed with wild salmon and harm fisheries.

Another problem facing genetically modified salmon farmers is that they might have trouble finding restaurants that will carry their fish even if the FDA approves it.

Numerous restaurant chefs stated that they would not work with GM fish. Some voiced moral concerns about private companies patenting organisms, about the potential health effects of GM food and concern for environmental impacts.

“The eventual damage to the environment would be catastrophic. Scientists say they have sterilized the GMO fish, but eventually one will adapt and destroy the natural process,” said Chris Carriker, executive chef of The Gilt Club Restaurant in Portland, Oregon.

In a poll conducted recently on the NRN blog Food Writer’s Diary, 26 out of 32 respondents, or 81 per cent, stated they would not eat GM salmon or serve it in their restaurant, with two respondents saying they would try the fish and four saying they would consider it.

“It goes against my principles,” affirmed Andy Arndt, executive chef of Aquariva Restaurant in Portland, Oregon.

Genetically engineering fish would not be necessary if fisheries were managed properly, he said.

“I’m not interested in seeing ‘genetically altered’ anything in my restaurant,” asserted Antonio Bettencourt, chef-owner of 62 Restaurant & Wine Bar in Salem, Massachusetts.

Via : fis.com

FDA set to approve genetically engineered salmon

The Food and Drug Administration is poised to approve the nation’s first genetically engineered animal designed to be eaten by people.

Next weekend the FDA will kick off a three-day meeting in which an agency-appointed panel of scientists and experts will discuss and listen to public opinion about food safety and environmental impacts of genetically engineered salmon.

The panel will also determine labeling requirements for the salmon, should it be approved.

The genetically engineered fish is an Atlantic salmon with a growth hormone gene from a Chinook salmon and a genetic on-switch from a fish known as the ocean pout. The company that created the fish is called AquaBounty Technologies, based in Waltham, Mass.

The added genes will allow the salmon to continue growing during the winter, a time when the fish usually do not grow. The result: a salmon that can grow to market size in 16 to 18 months instead of the usual three years.

Many environmental and food safety organizations are opposed to the approval.

They say the salmon company and the FDA have done nothing to alleviate their concerns about the safety of the salmon as food, nor have they properly considered the environmental consequences of farming genetically modified fish.

One paper, cited often by environmental groups opposed to AquaBounty’s salmon, showed that that a release of 60 genetically modified salmon into a wild population of 60,000 would lead to extinction of the wild population in less than 40 generations.

AquaBounty has said it will require producers to use their eggs only at inland facilities.

Charles Margulis, communications director for the Center for Environmental Health, an organization opposed to FDA approval, said the risks are too great and the system too unwieldy to feel reassured by these safeguards.

“If the FDA can’t track chicken eggs, you think they’re going to be able to track fish eggs?” he said.

He said the FDA has so far been vague on what kinds of controls, enforcement or guidelines they will set up if they approve the salmon.

Margulis and others are also concerned about the approval route the FDA is taking with genetically modified animals.

Instead of treating the genetically engineered salmon as a food, they are treating it as a veterinary drug.

Because of that, the application for approval must be kept confidential by the government.

So, how is the FDA deciding whether to approve the salmon or not?

“Basically, the FDA is saying if it looks like a salmon, sounds like a salmon and smells like a salmon, it must be a salmon,” Margulis said.

Via : californiawatch.org