Cellular ‘computers’ gain a hard drive

A new DNA-based recorder allows bioengineers to create cell cultures that detect information in their environment and store it for later use. Such ‘designer’ cells might in the future be used to monitor water quality in a village, or measure the amount of sugar a person eats. The technique is described this week in Science.

Read more (via Nature)

How Genetically Engineered Gardens Could Replace Airport Security Checkpoints

Fascinating article by Jason Koebler on motherboard about genetically engineered plants that could replace security checkpoints. Dr. June Medford, a pioneering synthetic biologist, already engineered a plant that changes color when it detects TNT or certain pollutants. Her vision:

"The way we screen airports to get on a plane is, everyone goes through detector systems and it’s slow. What would make much more sense, my vision is that you would walk through a garden-like setting, with a webcam looking down on plants, seeing if they detected anything."

The plants could also be hooked up to internet-connected systems. Medford is certain, that a mass production is feasible within 5 years.

[read more] [picture by kvd via wikimedia]

Bio-Lab - Embryo Injector

High Quality version here: http://imgur.com/gallery/loYjQF2/

The other day, I was reading a press release titled “UEA researchers discover Achilles’ heel in antibiotic-resistant bacteria" - but before I could even read the words in the article, the Eye Candy at the top of the page leapt out and VIOLENTLY ATTACKED ME WITH INSPIRATION! I was like "OH NO! MY OTHER PLANS FOR TONIGHT! THEY HAVE JUST DIED BECAUSE NOW I HAVE TO MAKE A GIF!!!" and then the modeling and animation for this design happened in about 3 hours. So I set it up to render at 3AM before going to bed. It was still rendering the next morning, so I went in to work, knowing that it would be done when I got home. Then I got home from work and realized that the output had flaws. So I was like "NOOOOOOOO~!". Then I fixed those issues in about 2 hours and rendered it again last night starting at 1.75AM, and it finished this morning before I had to leave for work.

I don’t know who took that photograph, but I want to tell them: “Thank you for violently attacking TWO NIGHTS worth of my evening plans. They DIED. BECAUSE OF YOU AND YOUR BEAUTIFUL ART. But seriously. Your photography is Yes. How did you come up with the ideas for that lighting setup? It is beautiful.”

This GIF is one in a set named “Bio-Lab" - and I hope to find - not the time, but the right inspiration - to make a few more of these, because this one is hella shiny and I’m totally down for that.

Please fire me. I did several experiments for my boss (I work in a biomedical research lab) and she used my data in her publications but did not make me an author.  Meanwhile my coworker’s son, a high school student, has been made second author on several papers, a position usually reserved for experienced researchers with PhDs.  His contribution?  Counting data points on a graph prepared by his mother and handing her the numbers.  

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Bacteria become ‘genomic tape recorders’, recording chemical exposures in their DNA

MIT engineers have transformed the genome of the bacterium E. coli into a long-term storage device for memory. They envision that this stable, erasable, and easy-to-retrieve memory will be well suited for applications such as sensors for environmental and medical monitoring.

“You can store very long-term information,” says Timothy Lu, an associate professor of electrical engineering and computer science and biological engineering. “You could imagine having this system in a bacterium that lives in your gut, or environmental bacteria. You could put this out for days or months, and then come back later and see what happened at a quantitative level.”

The new strategy, described in the November issue of the journal Science, overcomes several limitations of existing methods for storing memory in bacterial genomes, says Lu, the paper’s senior author. Those methods require a large number of genetic regulatory elements, limiting the amount of information that can be stored.

The earlier efforts are also limited to digital memory, meaning that they can record only all-or-nothing memories, such as whether a particular event occurred. Lu and graduate student Fahim Farzadfard, the paper’s lead author, set out to create a system for storing analog memory, which can reveal how much exposure there was, or how long it lasted. To achieve that, they designed a “genomic tape recorder” that lets researchers write new information into any bacterial DNA sequence.

Stable memory

To program E. coli bacteria to store memory, the MIT researchers engineered the cells to produce a recombinase enzyme, which can insert DNA, or a specific sequence of single-stranded DNA, into a targeted site. However, this DNA is produced only when activated by the presence of a predetermined molecule or another type of input, such as light.

After the DNA is produced, the recombinase inserts the DNA into the cell’s genome at a preprogrammed site. “We can target it anywhere in the genome, which is why we’re viewing it as a tape recorder, because you can direct where that signal is written,” Lu says.

Once an exposure is recorded through this process, the memory is stored for the lifetime of the bacterial population and is passed on from generation to generation.

There are a couple of different ways to retrieve this stored information. If the DNA is inserted into a nonfunctional part of the genome, sequencing the genome will reveal whether the memory is stored in a particular cell. Or, researchers can target the sequences to alter a gene. For example, in this study, the new DNA sequence turned on an antibiotic resistance gene, allowing the researchers to determine how many cells had gotten the memory sequence by adding antibiotics to the cells and observing how many survived.

By measuring the proportion of cells in the population that have the new DNA sequence, researchers can determine how much exposure there was and how long it lasted. In this paper, the researchers used the system to detect light, a lactose metabolite called IPTG, and an antibiotic derivative called aTc, but it could be tailored to many other molecules or even signals produced by the cell, Lu says.

The information can also be erased by stimulating the cells to incorporate a different piece of DNA in the same spot. This process is currently not very efficient, but the researchers are working to improve it.

“This work is very exciting because it integrates many useful capabilities in a single system: long-lasting, analog, distributed genomic storage with a variety of readout options,” says Shawn Douglas, an assistant professor at the University of California at San Diego who was not involved in the study. “Rather than treating each individual cell as a digital storage device, Farzadfard and Lu treat an entire population of cells as an analog ‘hard drive,’ greatly increasing the total amount of information that can be stored and retrieved.”

Bacterial sensors

Environmental applications for this type of sensor include monitoring the ocean for carbon dioxide levels, acidity, or pollutants. In addition, the bacteria could potentially be designed to live in the human digestive tract to monitor someone’s dietary intake, such as how much sugar or fat is being consumed, or to detect inflammation from irritable bowel disease.

These engineered bacteria could also be used as biological computers, Lu says, adding that they would be particularly useful in types of computation that require a lot of parallel processing, such as picking patterns out of an image.

“Because there are billions and billions of bacteria in a given test tube, and now we can start leveraging more of that population for memory storage and for computing, it might be interesting to do highly parallelized computing. It might be slow, but it could also be energy-efficient,” he says.

Another possible application is engineering brain cells of living animals or human cells grown in a petri dish to allow researchers to track whether a certain disease marker is expressed or whether a neuron is active at a certain time. “If you could turn the DNA inside a cell into a little memory device on its own and then link that to something you care about, you can write that information and then later extract it,” Lu says.

This Worm Is Genetically Engineered to Spin Spider Silk

Excellent long read by Brian Barth on Modern Farmer about genetically engineered spider silk worms and the future of green synthetically bioengineered superfabrics:

Feeding silkworms artificial colorants has produced ‘pre-dyed’ silk threads that preclude the need for the costly and toxic silk dyeing process (apparently with no harm done to the worms). Researchers in Japan have engineered silkworms to spin glow-in-the dark thread for use in high-end fashion design in hopes of building a niche silk market that will put a dent in China’s global dominance of the silk trade.

But the holy grail of silkworm gene splicing is to make the little larva pump out spider silk, a substance that can be woven into products that make Kevlar look flimsy. Interested parties have been salivating for years over the potential applications, which go far beyond fabrics: The U.S. Navy wants spider silk for its ability to adhere to any material, even underwater; the Department of Energy is hoping to make vehicles lighter and thus more fuel efficient by integrating silk proteins into the manufacture of door panels; and the Air Force is envisioning lightweight, bulletproof body armor that is easier to maneuver in during combat. The medical applications are all over the map: artificial skin for burn patients, better Band-Aids, synthetic ligaments, micro-sutures for delicate organs like the eyes and host of surgical implants and drug delivery mechanisms.

Currently the worms produce about five percent spider silk and ninety-five percent silkworm silk in their cocoons. If they reach 20 to 30 percent, bulletproof-silk vests could be a commercially viable reality. Not bad. “Synthetic spider silk worm farmer” is a job with a bright future. Watch out for silkworm vivariums.

[read more] [more about synthetic spider silk] [silkworm picture by Fastily / wikimedia]

lovehurtslifekills asked:

Hey mind helping me out? Whenever I ask my science teacher he just changes the subject and doesn't answer me for some weird reason o.O Anyways it's what exactly is gene cell therapy And how is this 'technology' used. I really wanna know because I've been interested in the Mars One 'adventure' that's gonna happen. Thanks heaps

Very briefly, gene therapy is an experimental technology that uses DNA as a pharmaceutical substance. With this technique, genes or fragments of genes are inserted into a body with the purpose of preventing or treating a disease. The gene transfer in the human organism is achieved by non-viral or viral vectors. Cell therapy has the same purpose, but in this case the preparations contain living cells. The most commonly used cells are adult stem cells: unspecialised cells that can be selected from various tissues of the body and can differentiate into specialized cells.

The topic is extremely interesting, but these, experimental (and still risky) therapies require more years of study to become effective and safe. So, if you decide to contribute to their development, for whatever reason, I wish you good luck and a good (hard, healthy, professional) work.

More info here

Scientists create GM organisms reliant on artificial compounds for survival Genetically recoded organisms could be safe enough to use outside, for example to clean up oil spills-In a drive to improve the environmental safety of genetically modified organisms, scientists have created the first GM microbes that can only survive in the presence of designer compounds not found in nature. The work represents a major step towards the creation of GM lifeforms that are completely reconfigured to perform an important job and then die without trace when their task is done. Vats of GM microbes are already used to make various chemicals, drugs and dairy products, but the newly designed organisms could be safe enough to use outside, for example to clean up oil spills or break down toxic chemicals on contaminated land. Other bugs based on the same procedure might be put in drinks as probiotics to cure diseases. Scientists at Harvard and Yale universities made changes throughout the genome of E coli bugs to make them resistant to viruses and reliant upon designer amino acids to survive. Amino acids are the building blocks of proteins that the organisms need to live and multiply. The researchers call the new microbes “genetically recoded organisms”, or GROs, because they have a new kind of genetic code that ensures they can only thrive when they are fed the synthetic amino acids. A similar procedure could be used to improve GM crops, but the task is far tougher because plants have about 10 times as many genes that are used to make proteins.

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Nanobots in Your Brain Could Be the Future of Learning

MIT Media Lab founder Nicholas Negroponte predicts that we might learn by injecting nanobots into the bloodstream, altering the brain at the level of the neuron.

Read more at BigThink.com: http://goo.gl/O7Jo9t

By: Big Think.

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Biohackers are engineering baker’s yeast to produce Real Vegan Cheese. No cows needed!

Citizen Science rocks!!!!!

Check them out at. 

Life on the Edge: The Coming of Age of Quantum Biology
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Life is the most extraordinary phenomenon in the known universe; but how does it work? Even in this age of cloning and synthetic biology, the remarkable truth remains: nobody has ever made anything living entirely out of dead material. Life remains the only way to make life. Are we missing a vital ingredient in its creation? Like Richard Dawkins’ The Selfish Gene, which provided a new perspective on how evolution works, Life on the Edge alters our understanding of life’s dynamics. Bringing together first-hand experience of science at the cutting edge with unparalleled gifts of exposition and explanation, Jim Al-Khalili and Johnjoe Macfadden reveal the hitherto missing ingredient to be quantum mechanics and the strange phenomena that lie at the heart of this most mysterious of sciences. Drawing on recent ground-breaking experiments around the world, they show how photosynthesis relies on subatomic particles existing in many places at once, while inside enzymes, those workhorses of life that make every molecule within our cells, particles vanish from one point in space and instantly materialize in another. Each chapter in Life on the Edge opens with an engaging example that illustrates one of life’s puzzles – How do migrating birds know where to go? How do we really smell the scent of a rose? How do our genes manage to copy themselves with such precision? – and then reveals how quantum mechanics delivers its answer. Guiding the reader through the maze of rapidly unfolding discovery, Al-Khalili and McFadden communicate vividly the excitement of this explosive new field of quantum biology, with its potentially revolutionary applications, and also offer insights into the biggest puzzle of all: what is life? (via Life on the Edge: The Coming of Age of Quantum Biology | KurzweilAI)

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Bionic Legs Help Spinal Cord Patient Walk

A powered exoskeleton from Ekso allows stroke victims and partial spinal cord injury patients, like Shane Mosko, to walk farther, aiding rehabilitation.

By: Live Science Videos.

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Bioluminescent trees could light up our streets

Dutch designer Daan Roosegaarde from Studio Roosegaarde (they developed the smart highway concept) explains how biomimicry techniques inspired his project to swap streetlights with giant light-emitting plants.

[Studio Roosegaarde] [more on earthweareone]

ieet.org

The concerns of anti-GMO activists would be addressed better by offering support to an alternative in the form of “do-it-yourself” biotechnology, rather than rejecting sciences and industries that are already destined to be a fundamental part of humanity’s future. What needs to be made is a case for popular technology, in hope that we can reject the portrayal of all advanced technology as an ally of powerful states and corporations and instead unlock its future as a means of liberation from global exploitation and scarcity.

I agree that the arguments tend to be a mix of the effects of the greedy or evil corporations and the dangers of GMO. But there is an important point here about when we have opened the bottle and let out the Gini we can’t put it back. We therefore have to approach the GMO issue with a strategy where we can minimize the negative effects for the future. Does that strategy include supporting the biotech hacking movement? Maybe… 

"Imagine this. A killer is put on trial, and the jury, in a surprise verdict, finds him not guilty. Afterwards, reporters interview this killer. He says, “The jury freed me. It’s up to them. They decide. That’s what justice is all about.”

Then the press moves along to members of the jury, who say: Well, we had to take the defendant’s word. He said he was innocent, so that’s what we ruled.

That’s an exact description of the FDA and Monsanto partnership.

When you cut through the verbiage that surrounded the introduction of GMO food into America, you arrive at two key statements. One from Monsanto and one from the FDA, the agency responsible for overseeing, licensing, and certifying new food varieties as safe.

Quoted in the New York Times Magazine (October 25, 1998, “Playing God in the Garden”), Philip Angell, Monsanto’s director of corporate communications, famously stated: “Monsanto shouldn’t have to vouchsafe the safety of biotech food. Our interest is in selling as much of it as possible. Assuring its safety is the FDA’s job.”

From the Federal Register, Volume 57, No.104, “Statement of [FDA] Policy: Foods Derived from New Plant Varieties,” here is what the FDA had to say on this matter: “Ultimately, it is the food producer who is responsible for assuring safety.”

The direct and irreconcilable clash of these two statements is no accident. It’s not a sign of incompetence or sloppy work or a mistake or a miscommunication. It’s a clear signal that the fix was in.”