Sunday, August 05, 2012

Steps Toward the Mastery of DNA Based Life

Synthetic biologists are hard at work designing ways for microbes to produce new drugs, fuels, high value chemicals, and other important products to facilitate an abundant human future. Much of this work is being held back by the difficulty of moving beyond the primitive prokaryote bottleneck of bacterial cell signaling and transcription factors -- toward the mastery of more complex eukaryotic cells and gene expression found in yeast and higher organisms.

MIT's Timothy Lu and his collaborators at Boston University, have created 19 new transcription factor which work in (eukaryotic) yeast. They are hoping that some of them will also work in algae and other higher eukaryotic organisms.
So far, most researchers have designed their synthetic circuits using transcription factors found in bacteria. However, these don’t always translate well to nonbacterial cells and can be a challenge to scale, making it harder to create complex circuits, says Timothy Lu, assistant professor of electrical engineering and computer science and a member of MIT’s Research Laboratory of Electronics.

...“If you look at a parts registry, a lot of these parts come from a hodgepodge of different organisms. You put them together into your organism of choice and hope that it works,” says Lu, corresponding author of a paper describing the new transcription factor design technique in the Aug. 3 issue of the journal Cell. _MITNews_via_NBF

The project is part of a larger, ongoing effort to develop genetic “parts” that can be assembled into circuits to achieve specific functions. Through this endeavor, Dr. Lu and his colleagues hope to make it easier to develop circuits that do exactly what a researcher wants.

...Recent advances in designing proteins that bind to DNA gave the researchers the boost they needed to start building a new library of transcription factors. In many transcription factors, the DNA-binding section consists of zinc finger proteins, which target different DNA sequences depending on their structure. The researchers based their new zinc finger designs on the structure of a naturally occurring zinc finger protein. “By modifying specific amino acids within that zinc finger, you can get them to bind with new target sequences,” Dr. Lu says.

The researchers attached the new zinc fingers to existing activator segments, allowing them to create many combinations of varying strength and specificity. They also designed transcription factors that work together, so that a gene can only be turned on if the factors bind each other.

Such transcription factors should make it easier for synthetic biologists to design circuits to perform tasks such as sensing a cell’s environmental conditions. The researchers built some simple circuits in yeast, but they plan to develop more complex circuits in future studies. “We didn’t build a massive 10- or 15-transcription factor circuit, but that’s something that we’re definitely planning to do down the road,” Dr. Lu says. “We want to see how far we can scale the type of circuits we can build out of this framework.”

The researchers are also planning to try their new transcription factors in other species of yeast, and eventually in mammalian cells including human cells. “What we’re really hoping at the end of the day is that yeast are a good launching pad for designing those circuits,” Dr. Lu says. “Working on mammalian cells is slower and more tedious, so if we can build verified circuits and parts in yeast and then import them over, that would be the ideal situation. But we haven’t proven that we can do that yet.” _Genetic Engineering News

Cell article abstract

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Wednesday, August 01, 2012

Breakthroughs in Stroke, Brain Cancer, and Tissue Engineering

We may dream of discovering a "fountain of youth," a magic bullet treatment to achieve immortality with just a single elixir, fruit, capsule, or injection. But the modern reality of the anti-aging effort is that, for now, we must attack each killer disease individually.

An impressive new treatment for cerebrovascular accidents -- brain strokes -- was developed at the University of Manchester.
Researchers induced a stroke in the rats and the drug IL-1Ra, or a placebo for comparison, was injected under the skin. The researchers did not know which animals had been given which drug. This is a similar process to what happens in clinical trials of medicines.

The results were startling. MRI scans revealed that the rats that were given IL-1Ra up to three hours after the stroke had only about half the brain damage of the placebo group.

Professor Rothwell said: “This is the first time that we are aware of a potential new treatment for stroke being tested in animals with the same sort of diseases and risk factors that most patients have. The results are very promising and we hope to undertake further clinical studies in stroke patients soon.”

IL-1Ra works by blocking the naturally occurring protein interleukin 1. Researchers at The University of Manchester have identified that it is a key cause of brain injury following a stroke.

Interleukin 1 encourages inflammation in the area of the brain affected by stroke. This sends out signals to attract white blood cells and to switch on microglia cells in the brain. Because the barrier surrounding the brain has been weakened by the stroke the white blood cells find it easier to enter the brain. But instead of helping the inflamed area they actually kill nerve cells and worsen the injury. The increasing presence of these cells also explains why the damage in the brain gets worse over time following a stroke.

IL-1Ra also reduces the amount of damage to the blood-brain barrier following a stroke so the harmful cells can’t enter the brain. In the recent experiments IL-1Ra reduced the damage to the blood-brain barrier by 55% in healthy rats and 45% in rats with underlying health conditions. In all types of rats the drug reduced the amount of activated microglia cells by 40% compared to the placebo group. _Manchester
A similar type of anti-inflammatory therapy is also being developed to combat Alzheimer's, multiple sclerosis, traumatic brain injury, and other forms of neurodegenerative and inflammatory brain disease.

The fight against brain cancer and other solid tumours was advanced recently by the University of Tennessee Space Institute. The technique utilises a femtosecond laser to both precisely target and destroy tumours.
“Using ultra-short light pulses gives us the ability to focus in a well confined region and the ability for intense radiation,” said Parigger. “This allows us to come in and leave a specific area quickly so we can diagnose and attack tumorous cells fast.”

Once the cancerous area is precisely targeted, only the intensity of the laser radiation needs to be turned up in order to irradiate, or burn off, the tumor. This method has the potential to be more exact than current methods and to be done as an outpatient procedure replacing intensive surgery.

“Because the femtosecond laser radiation can be precisely focused both spatially and temporally, one can avoid heating up too many other things that you do not want heated,” said Parigger. “Using longer laser-light pulses is similar to leaving a light bulb on, which gets warm and can damage healthy tissue.”

The technology can be especially helpful to brain cancer victims. The imaging mechanism can non-invasively permeate thin layers of bone, such as the skull, and can help define a targeted treatment strategy for persistent cancer. The method also overcomes limitations posed by current treatments in which radiation may damage portions of healthy brain tissue. It also may overcome limitations of photodynamic therapy that has restricted acceptance and surgery that may not be an option if not all carcinogenic tissue can be removed. _UTSI

Combining the targeting function with the therapeutic heating function saves time and improves therapeutic precision, and the improved precision of targeting saves surrounding normal tissue.

Research engineers at the University of Toronto have developed a new, rapid method of tissue engineering, capable of creating 3-D layered tissues in an advanced hydrogel.
Scientists manipulate biomaterials into the micro-device through several channels. The biomaterials are then mixed, causing a chemical reaction that forms a "mosaic hydrogel"—a sheet-like substance compatible with the growth of cells into living tissues, into which different types of cells can be seeded in very precise and controlled placements.

Unique to this new approach to tissue engineering, however, and unlike more typical methods for tissue engineering (for instance, scaffolding, the seeding of cells onto an artificial structure capable of supporting three-dimensional tissue formation) cells planted onto the mosaic hydrogel sheets are precisely incorporated into the mosaic hydrogel sheet just at the time it's being created—generating the perfect conditions for cells to grow. _UToronto
This approach is likely to evolve rapidly to provide quick replacement tissues of a simpler nature, such as skin grafts. More complex tissues and organs will require sophisticated scaffolds, to allow the tissue to maintain shape and resist a variety of physical forces likely to come to bear in a variety of implant locations.

The fight against deadly diseases and ageing itself, must necessarily take on multiple forms. Humans have not, after all, conquered even the most rudimentary of enemies -- the virus. Despite our best efforts, we are still vulnerable to new outbreaks of emerging infectious diseases. And we will always be vulnerable to chance events such as accidents -- both terrestrial and cosmic.

But it is in the nature of our slightly advanced monkey selves to pursue our continued existence, as long as we can. h/t Brian Wang

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