Tomorrow is Today

MIT Engineers Use Bacteria to Compute Logarithms

MIT engineers have transformed bacterial cells into living calculators that can compute logarithms, divide and take square roots, using three or fewer genetic parts.

Inspired by how analog electronic circuits function, the researchers created synthetic computation circuits by combining existing genetic “parts,” or engineered genes, in novel ways.

Read more: http://www.laboratoryequipment.com/news/2013/05/cells-can-be-living-calculators

(via laboratoryequipment, ht cyborgorgy)

Biochemists Create Enzyme-Based Memory Capable of Learning

Electronic processors are highly efficient at certain types of computation. For example, a standard PC can vastly outperform any human at arithmetic. However, computer scientists have long been fascinated by the ability of biological systems to do tasks, such as face recognition, at speeds and a power efficiency that put the most powerful supercomputers to shame.

Clearly, biology is able of computing in ways that traditional processors have failed to capture, which is why there is a significant interest in unconventional methods of computing that explore new ways of processing information.

One form of unconventional computing is biochemical and involves using molecules to encode information and using chemical reactions to process it. Nature has developed highly complex machinery for doing this so much of the focus has been on exploiting biological molecules for this task, using proteins, DNA and the like.

Today, Vera Bocharova and a few pals at Clarkson University in Potsdam, New York, say they ‘ve used a set of enzymes to create a memory system that can “learn” to produce a specific output given a certain input. They says this system can even “unlearn” again later. “We report the first realization of a simple variant of associative memory in an enzymatic biochemical process,” they say.

(via First Enzyme-Based Memory Created in the Lab | MIT Technology Review)

British Researchers Get Earthworms to Secrete Quantum Dots

The discovery came as the result of an educated guess. Green knew that placing thiols - sulphur-containing groups of atoms - on water-soluble cadmium telluride dots made them more luminescent.

When he learned that earthworms produce thiols that bind to metal atoms, he wondered whether worm-made quantum dots were a possibility.

Green [and colleagues] exposed the worms to cadmium chloride and sodium tellurite, and found that they moved the metals to their chloragogen cells - their equivalent of the liver.

After 11 days, the researchers removed the chloragogen cells, put them in water and exposed the mixture to a UV lamp. They found that it glowed green. …that characteristic behaviour meant only one thing: “…it was cadmium telluride quantum dots,” he says. …What’s more, the dots were able to light up cancer cells in an imaging experiment.

(via Earthworms roped into making quantum dots - physics-math - 02 January 2013 - New Scientist)

Temporary Tattoo Doubles as Medical Monitor

“We wanted a design that could conceal the electrodes,” Vinci Hung, the Ph.D. candidate in the Department of Physical and Environmental Sciences who helped create the new sensor, said in a university news release. “We also wanted to showcase the variety of designs that can be accomplished with this fabrication technique.”

As they report in Analyst, the Royal Society of Chemistry journal, Hung and her team laid down different sensing materials, including silver and carbon fiber-modified carbon and insulator inks, to detect various components of sweat, such as sodium, potassium, and magnesium.

The eyes on the smiley face serve as the electrodes, while the ears are the contact points for a measuring device to connect to. The sensor was applied to the skin much like other temporary tattoos, including using a paper towel soaked in warm water to remove the base.

(via This smiley face tattoo is monitoring you | Cutting Edge - CNET News)

In The Worlds First Actual Photo of DNA You Can See the Helixes

The image was taken by Enzo di Fabrizio from the University of Genoa, Italy. He choreographed the scene by pulling a small strand of DNA from a diluted solution and then propping it up like a clothesline between two nanoscopic silicon pillars.

The trick to the technique was in acquiring a discrete strand of DNA that could be stretched out and ready to view with an electron microscope. Di Fabrizio managed this by creating a pattern of pillars that repelled water — which resulted in quick moisture evaporation and a residual strand of DNA all ready to go.

Then, in order to create a high-resolution image, di Fabrizio drilled tiny holes in the base of the nanopillar bed and shone beams of electrons.

Aside from creating a cool image, the technique will allow the researchers to investigate DNA in greater detail, as well as seeing how it interacts with proteins and RNA.

(via Scientists snap a picture of DNA’s double helix for the very first time)

Mice Genetically Engineered to be Super-Sensitive to the Smell of TNT, Will Be Used to Clear Landmines

A Belgian organization called APOPO already uses giant African pouched rats as a cheaper way to sniff out landmines. The rats are not genetically modified, but their sense of smell is sharp enough to detect TNT.

…While the furry minesweepers are effective (with two handlers, they can cover a field in one hour that would take two full days for metal detectors), they need nine months of training to become reliable, a process that costs around 6,000 euros per rat.

The genetically engineered mice, however, are so sensitive to TNT that encountering the molecule is likely to change their behavior involuntarily, so they would need little to no training.

[Molecular Neurobiologist} Charlotte D’Hulst… used genetic modification to ensure that the mice have 10,000 to 1,000,000 odor-sensing neurons with a TNT-detecting receptor compared with only 4,000 in a normal animal, “possibly amplifying the detection limit for this odor 500-fold,” she says.

Each odor-sensing neuron in a mouse’s nose is spotted with one kind of odor receptor. Usually, each specific receptor is found in one out of every thousand odor-sensing neurons, but about half the scent-detecting neurons in D’Hulst’s mice have the TNT-detecting receptor.

(via Genetically Modified Mice Could Be Tiny Landmine-Sniffing Heroes | MIT Technology Review)

Researchers Developing 3D Printer for DNA, Will Print Viruses For Use In Vaccines

What could possibly go wrong?

Craig Venter imagines a future where you can download software, print a vaccine, inject it, and presto! Contagion averted.

“It’s a 3-D printer for DNA, a 3-D printer for life,” Venter said at the inaugural Wired Health Conference in New York City, Wired Science reports. The geneticist and his team of scientists are already testing out a version of his digital biological converter, or “teleporter.”

(via Craig Venter imagines a world with printable life forms | KurzweilAI)

Researchers Manipulate Shape of Nanoparticles to Deliver Gene Therapy Without Viruses

Researchers from Johns Hopkins and Northwestern universities have discovered how to control the shape of nanoparticles that move DNA through the body and have shown that the shapes of these carriers may make a big difference in how well they work in treating cancer and other diseases.

This study is also noteworthy because this gene therapy technique does not use a virus to carry DNA into cells. Some gene therapy efforts that rely on viruses have posed health risks.

“These nanoparticles could become a safer and more effective delivery vehicle for gene therapy, targeting genetic diseases, cancer and other illnesses that can be treated with gene medicine,” said Hai-Quan Mao, an associate professor… in Johns Hopkins’ Whiting School of Engineering.

(via Shape coding replaces risky viruses in DNA nanoparticle therapy | KurzweilAI)

Brainless Slime Molds Shed Light On The Evolution of Memory

“We have shown for the first time that a single-celled organism with no brain uses an external spatial memory to navigate through a complex environment,” said Christopher Reid from the University’s School of Biological Sciences.

…“Results from insect studies, for example ants leaving pheromone trails, have already challenged the assumption that navigation requires learning or a sophisticated spatial awareness. We’ve now gone one better and shown that even an organism without a nervous system can navigate a complex environment, with the help of externalized memory.”

The research method was inspired by robots designed to respond only to feedback from their immediate environment to navigate obstacles and avoid becoming trapped. This “reactive navigation” method allows robots to navigate without a programmed map or the ability to build one and slime molds use the same process.

When it is foraging, the slime mold avoids areas that it has already “slimed,” suggesting it can sense extracellular slime upon contact and will recognize and avoid areas it has already explored.

…“We then upped the ante for the slime molds by challenging them with the U-shaped trap problem to test their navigational ability in a more complex situation than foraging. We found that, as we had predicted, its success was greatly dependent on being able to apply its external spatial memory to navigate its way out of the trap.”

(via Brainless slime mold uses external spatial ‘memory’ to navigate complex environments | KurzweilAI)

Proteins Could “Remember” The Past to Prepare For the Future

The most efficient machines remember what has happened to them, and use that memory to predict what the future holds. That is the conclusion of a theoretical study by Susanne Still, a computer scientist at the University of Hawaii at Manoa and her colleagues, and it should apply equally to “machines” ranging from molecular enzymes to computers, Nature News reports.

The finding could help to improve scientific models such as those used to study climate change. Information that provides clues about the future state of the environment is useful, because it enables the machine to ‘prepare’ — to adapt to future circumstances, and thus to work as efficiently as possible.

…think of a vehicle fitted with a smart driver-assistance system that uses sensors to anticipate its imminent environment and react accordingly — for example, by recording whether the terrain is wet or dry, and thus predicting how best to brake for safety and fuel efficiency. That sort of predictive function costs only a tiny amount of processing energy compared with the total energy consumption of a car.

But for a biomolecule it can be very costly to store information, so its memory needs to be highly selective. 

…Because biochemical motors and pumps have indeed evolved to be efficient, says Still, “they must therefore be doing something clever — something tied to the cognitive ability we pride ourselves with: the capacity to construct concise representations of the world we have encountered, which allow us to say something about things yet to come”.

To be honest, I’m not sure I fully understand theoretical Biology well enough to know how “real” this is outside of simulation; but it sounds as if this research is helping to improve how biological processes get modeled.

(via Proteins remember the past to predict the future | KurzweilAI)