Tag Archives: dna

A Startup That Builds Biological Parts

 In a warehouse building in Boston, wedged between a cruise-ship drydock and Au Bon Pain’s corporate headquarters, sits Ginkgo BioWorks, a new synthetic-biology startup that aims to make biological engineering easier than baking bread. Founded by five MIT scientists, the company offers to assemble biological parts–such as strings of specific genes–for industry and academic scientists.

“Think of it as rapid prototyping in biology–we make the part, test it, and then expand on it,” says Reshma Shetty, one of the company’s cofounders. “You can spend more time thinking about the design, rather than doing the grunt work of making DNA.” A very simple project, such as assembling two pieces of DNA, might cost $100, with prices increasing from there.

Synthetic biology is the quest to systematically design and build novel organisms that perform useful functions, such as producing chemicals, using genetic-engineering tools. The field is often considered the next step beyond metabolic engineering because it aims to completely overhaul existing systems to create new functionality rather than improve an existing process with a number of genetic tweaks.

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This is the stuff we need.

Why bother repairing our failing tissues for decades on end when you can just replace them with new ones?

From an engineering standpoint, this is just a plain and simple practical solution!

Medicine goes digital

The convergence of biology and engineering is turning health care into an information industry. That will be disruptive, says Vijay Vaitheeswaran (interviewed here), but also hugely beneficial to patients.

Innovation and medicine go together. The ancient Egyptians are thought to have performed surgery back in 2750BC, and the Romans developed medical tools such as forceps and surgical needles. In modern times medicine has been transformed by waves of discovery that have brought marvels like antibiotics, vaccines and heart stents.

Given its history of innovation, the health-care sector has been surprisingly reluctant to embrace information technology (IT). Whereas every other big industry has computerised with gusto since the 1980s, doctors in most parts of the world still work mainly with pen and paper.

But now, in fits and starts, medicine is at long last catching up. As this special report will explain, it is likely to be transformed by the introduction of electronic health records that can be turned into searchable medical databases, providing a “smart grid” for medicine that will not only improve clinical practice but also help to revive drugs research. Developing countries are already using mobile phones to put a doctor into patients’ pockets. Devices and diagnostics are also going digital, advancing such long-heralded ideas as telemedicine, personal medical devices for the home and smart pills.

The first technological revolution in modern biology started when James Watson and Francis Crick described the structure of DNA half a century ago. That established the fields of molecular and cell biology, the basis of the biotechnology industry. The sequencing of the human genome nearly a decade ago set off a second revolution which has started to illuminate the origins of diseases.

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Scientists’ stem cell breakthrough ends ethical dilemma

Scientists have found a way to make an almost limitless supply of stem cells that could safely be used in patients while avoiding the ethical dilemma of destroying embryos.

In a breakthrough that could have huge implications, British and Canadian scientists have found a way of reprogramming skin cells taken from adults, effectively winding the clock back on the cells until they were in an embryonic form.

The work has been hailed as a major step forward by scientists and welcomed by pro-life organisations, who called on researchers to halt other experiments which use stem cells collected from embryos made at IVF clinics.

Sir Ian Wilmut, who led the team that cloned Dolly the Sheep and heads the MRC Centre for Regenerative Medicine at Edinburgh University where the work was done, said: “This is a significant step in the right direction. The team has made great progress and combining this work with that of other scientists working on stem cell differentiation, there is hope that the promise of regenerative medicine could soon be met.”

Stem cells have the potential to be turned into any tissue in the body, an ability that has led researchers to believe they could be used to make “spare parts” to replace diseased and damaged organs and treat conditions as diverse as Parkinson’s disease, diabetes and spinal cord injury.

Because the cells can be made from a patient’s own skin, they carry the same DNA and so could be used without a risk of being rejected by the immune system.

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Synthetic life form grows in Florida lab

When NASA began thinking about missions to look for life beyond Earth, it realized it had a problem: how to recognize life if it were found.

Scientists came up with a definition for life — a self-sustaining chemical system capable of Darwinian evolution — but remained understandably fuzzy on the details.

It is still not known how life on Earth took hold, what happened to a bunch of chemicals that made them capable of supporting a metabolism, replicating and evolution. But a new field of science, called synthetic biology, is aiming to find out.

One of the most promising developments lies in a beaker of water inside a Florida laboratory. It’s an experiment called AEGIS — an acronym for Artificially Expanded Genetic Information System. Its creator, Steve Benner, says it is the first synthetic genetic system capable of Darwinian evolution.

AEGIS is not self-sustaining, at least not yet, and with 12 DNA building blocks — as opposed to the usual four — there’s little chance it will be confused with natural life. Still, Benner is encouraged by the results.

“It’s evolving. It’s doing what we designed it to do,” said Benner, a biochemist with the Gainesville, Fla.-based Foundation for Applied Molecular Evolution.

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Scientists expect to create life in next 10 years

Around the world, a handful of scientists are trying to create life from scratch and they’re getting closer.

Experts expect an announcement within three to 10 years from someone in the now little-known field of “wet artificial life.”

“It’s going to be a big deal and everybody’s going to know about it,” said Mark Bedau, chief operating officer of ProtoLife of Venice, Italy, one of those in the race. “We’re talking about a technology that could change our world in pretty fundamental ways — in fact, in ways that are impossible to predict.”

That first cell of synthetic life — made from the basic chemicals in DNA — may not seem like much to non-scientists. For one thing, you’ll have to look in a microscope to see it.

“Creating protocells has the potential to shed new life on our place in the universe,” Bedau said. “This will remove one of the few fundamental mysteries about creation in the universe and our role.”

And several scientists believe man-made life forms will one day offer the potential for solving a variety of problems, from fighting diseases to locking up greenhouse gases to eating toxic waste.

Bedau figures there are three major hurdles to creating synthetic life:

  • A container, or membrane, for the cell to keep bad molecules out, allow good ones, and the ability to multiply.
  • A genetic system that controls the functions of the cell, enabling it to reproduce and mutate in response to environmental changes.
  • A metabolism that extracts raw materials from the environment as food and then changes it into energy.

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Extinct animals could be brought back to life thanks to advances in DNA technology

The idea of resurrecting extinct animals moved a step closer to reality last year when scientists announced that they had decoded almost all of the genome of the woolly mammoth, from 60,000-year-old remains found frozen in Siberia.

Now New Scientist magazine has named the 10 other beasts most likely to rise again, including the Irish elk deer whose antlers measured 12 feet across, the dodo and Neanderthal man.

Animals that died out thousands of years ago could be recreated using genetic information retrieved from well-preserved specimens recovered from permafrost, dark caves or dry desserts.

There is no chance of bringing back the dinosaurs because genetic information is unlikely to survive more than a million years in any environment.

But scientists have just announced they had “resurrected” a gene from the Tasmanian tiger by implanting it in a mouse and examined its function – the first time such a feat had been achieved.

The genomes of several extinct species besides the mammoth are already being sequenced.

To revive a long-dead species scientists would have to recover enough DNA from a well-preserved specimen and find a suitable surrogate species similar to that of the extinct animal in which to grow the new baby from an embryo.

“It’s hard to say that something will never ever be possible,”said Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who is sequencing the Neanderthal genome.

“But it would require technologies so far removed from what we currently have that I cannot imagine how it would be done.”

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Harvard Scientists Unravel The Secret Of Aging

As we get older, our health becomes our worst enemy. What’s the secret of living a longer healthy life, is a question still unanswered. At least until today, when Harvard researchers sustain that they might know the secret of aging.

Their paper published in this week issue of the journal Cell is the latest to draw attention to sirtuins, proteins involved in the aging process. Sirtuins become increasingly important as people age, according to lead author David A. Sinclair, a Harvard Medical School professor and co-founder of the Cambridge biotechnology company Sirtris Pharmaceuticals, Inc. The proteins help maintain a youthful pattern of gene expression by ensuring that the genes that should be “off” remain silent.

The same proteins appear to also repair DNA damage as we age, Harvard researchers found.

“The critical protein controls both which genes are off and on as well as DNA repair; it’s used for both processes, and that’s the catch,” said Sinclair.

As we get older, more and more chromosomes get damaged and the SIR1 proteins can’t handle both jobs as well. This causes gene activity to go “haywire” leading to symptoms associated with the process of aging.

Bu the good part is just starting. The scientists have found evidence that the aging process can be slowed. They discovered that mice with more SIRT1 proteins have an improved ability to repair the DNA and to prevent the unwanted changes in the gene expressions.

Previous studies have shown that resveratrol, a chemical found primarily in red wine, helps activate the SIRT1 protein, which aids in the repair of broken chromosome. It’s true that the studies have been conducted on mice, but it’s an important step forward and a reason to believe that the possibility of improving our life is closer than we think.

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Has universal ageing mechanism been found?

An overworked protein that causes yeast to age when it neglects one of its functions may trigger ageing in mice too. If the same effect is found in people, it may suggest new ways to halt or reverse age-related disease.

As we get older, genes can start to be expressed in the wrong body tissues – a process that is thought to contribute to diseases like diabetes and Alzheimer’s. But while sunlight or chemicals are known to cause limited DNA damage, how more widespread changes in gene expression come about has been unclear.

To investigate, David Sinclair and colleagues at Harvard Medical School turned to yeast cells. These produce a dual-function protein called Sir2 that, while being involved in DNA repair, also helps keep certain genes switched off.

As yeast cells age, the protein can’t do both jobs and neglects its role as a gene suppressor.

Now Sinclair’s team has shown that SIRT1, the mammalian version of Sir2, also begins to neglect its gene-suppressor role in mice whose DNA is damaged, and that this may contribute to ageing.

This raises the hope that, if gene-suppressing proteins become similarly overworked in ageing people, they could become prime targets for drugs to keep us young.

This possibility is boosted by the team’s finding that mice engineered to over-express the gene for SIRT1 were better at repairing DNA, more resistant to cancer, and maintained a more youthful pattern of gene expression.

“The most exciting thing is that this work may unify in a single molecular pathway what we know about ageing in different organisms such as yeast and mammals,” says Maria Blasco of the Spanish National Cancer Research Centre in Madrid, who works on mechanisms of cellular ageing.

“It opens up the possibility of restoring youth in the elderly by re-establishing a useful pattern of gene expression,” adds Sinclair.

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Triple Helix: Designing a New Molecule of Life

For all the magnificent diversity of life on this planet, ranging from tiny bacteria to majestic blue whales, from sunshine-harv­­est­­ing plants to mineral-digesting endoliths miles underground, only one kind of “life as we know it” exists. All these organisms are based on nucleic acids—DNA and RNA—and proteins, working together more or less as described by the so-called central dogma of molecular biology: DNA stores information that is transcribed into RNA, which then serves as a template for producing a protein. The proteins, in turn, serve as important structural elements in tissues and, as enzymes, are the cell’s workhorses.

Yet scientists dream of synthesizing life that is utterly alien to this world—both to better understand the minimum components required for life (as part of the quest to uncover the essence of life and how life originated on earth) and, frankly, to see if they can do it. That is, they hope to put together a novel combination of molecules that can self-organize, metabolize (make use of an energy source), grow, reproduce and evolve.

A molecule that some researchers study in pursuit of this vision is peptide nucleic acid (PNA), which mimics the information-storing features of DNA and RNA but is built on a proteinlike backbone that is simpler and sturdier than their sugar-phosphate backbones. My group developed PNA more than 15 years ago in the course of a project with a rather more immediately useful goal than the creation of unprecedented life-forms. We sought to design drugs that would work by acting on the DNA composing specific genes, to either block or enhance the gene’s expression (the production of the protein it encodes). Such drugs would be conceptually similar to “antisense” compounds, such as short DNA or RNA strands that bind to a specific RNA sequence to interfere with the production of disease-related proteins [see “Hitting the Genetic Off Switch,” by Gary Stix; Scientific American, October 2004].

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Woolly mammoth task: Critter’s DNA mapped

WASHINGTON – Scientists for the first time have unraveled much of the genetic code of an extinct animal, the ice age’s woolly mammoth, and with it they are thawing Jurassic Park dreams.

Their groundbreaking achievement has them contemplating a once unimaginable future when certain prehistoric species might one day be resurrected.

“It could be done. The question is, just because we might be able to do it one day, should we do it?” asked Stephan Schuster, the Penn State University biochemistry professor and co-author of the new research. “I would be surprised to see if it would take more than 10 or 20 years to do it.”

The million-dollar project is a first rough draft, detailing the more than 3 billion DNA building blocks of the mammoth, according to the study published in Thursday’s journal Nature. It’s about 80 percent finished. But that’s enough to give scientists new clues on the timing of evolution and the deadly intricacies of extinction.

The project relied on mammoth hair found frozen in the Siberian permafrost, instead of bone, giving biologists a new method to dig into ancient DNA. Think of it as CSI Siberia, said Schuster. That different technique — along with soaring improvements in genome sequencing and the still embryonic field of synthetic biology — are inspiring scientists to envision a science-fiction-like future.

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