Plastic-eating worms may offer solution to mounting waste, Stanford researchers discover

An ongoing study by Stanford engineers, in collaboration with researchers in China, shows that common mealworms can safely biodegrade various types of plastic.

Mealworms munch on Styrofoam, a hopeful sign that solutions to plastics pollution exist. Wei-Min Wu, a senior research engineer in the Department of Civil and Environmental Engineering, discovered the larvae can live on polystyrene. (Photo: Yu Yang)

Consider the plastic foam cup. Every year, Americans throw away 2.5 billion of them. And yet, that waste is just a fraction of the 33 million tons of plastic Americans discard every year. Less than 10 percent of that total gets recycled, and the remainder presents challenges ranging from water contamination to animal poisoning.

Enter the mighty mealworm. The tiny worm, which is the larvae form of the darkling beetle, can subsist on a diet of Styrofoam and other forms of polystyrene, according to two companion studies co-authored by Wei-Min Wu, a senior research engineer in the Department of Civil and Environmental Engineering at Stanford. Microorganisms in the worms' guts biodegrade the plastic in the process – a surprising and hopeful finding.

"Our findings have opened a new door to solve the global plastic pollution problem," Wu said.

The papers, published in Environmental Science and Technology, are the first to provide detailed evidence of bacterial degradation of plastic in an animal's gut. Understanding how bacteria within mealworms carry out this feat could potentially enable new options for safe management of plastic waste.

"There's a possibility of really important research coming out of bizarre places," said Craig Criddle, a professor of civil and environmental engineering who supervises plastics research by Wu and others at Stanford. "Sometimes, science surprises us. This is a shock."

Plastic for dinner

In the lab, 100 mealworms ate between 34 and 39 milligrams of Styrofoam – about the weight of a small pill – per day. The worms converted about half of the Styrofoam into carbon dioxide, as they would with any food source.

Within 24 hours, they excreted the bulk of the remaining plastic as biodegraded fragments that look similar to tiny rabbit droppings. Mealworms fed a steady diet of Styrofoam were as healthy as those eating a normal diet, Wu said, and their waste appeared to be safe to use as soil for crops.

Researchers, including Wu, have shown in earlier research that waxworms, the larvae of Indian mealmoths, have microorganisms in their guts that can biodegrade polyethylene, a plastic used in filmy products such as trash bags. The new research on mealworms is significant, however, because Styrofoam was thought to have been non-biodegradable and more problematic for the environment.

Researchers led by Criddle, a senior fellow at the Stanford Woods Institute for the Environment, are collaborating on ongoing studies with the project leader and papers' lead author, Jun Yang of Beihang University in China, and other Chinese researchers. Together, they plan to study whether microorganisms within mealworms and other insects can biodegrade plastics such as polypropylene (used in products ranging from textiles to automotive components), microbeads (tiny bits used as exfoliants) and bioplastics (derived from renewable biomass sources such as corn or biogas methane).

As part of a "cradle-to-cradle" approach, the researchers will explore the fate of these materials when consumed by small animals, which are, in turn, consumed by other animals.

Marine diners sought

Another area of research could involve searching for a marine equivalent of the mealworm to digest plastics, Criddle said. Plastic waste is a particular concern in the ocean, where it fouls habitat and kills countless seabirds, fish, turtles and other marine life.

More research is needed, however, to understand conditions favorable to plastic degradation and the enzymes that break down polymers. This, in turn, could help scientists engineer more powerful enzymes for plastic degradation, and guide manufacturers in the design of polymers that do not accumulate in the environment or in food chains.

Criddle's plastics research was originally inspired by a 2004 project to evaluate the feasibility of biodegradable building materials. That investigation was funded by the Stanford Woods Institute's Environmental Venture Projects seed grant program. It led to the launch of a company that is developing economically competitive, nontoxic bioplastics.

Co-authors of the papers, "Biodegradation and Mineralization of Polystyrene by Plastic-Eating Mealworms. 1. Chemical and Physical Characterization and Isotopic Tests" and "Biodegradation and Mineralization of Polystyrene by Plastic-Eating Mealworms. 2. Role of Gut Microorganisms," include Yu Yang, Jun Yang, Lei Jian, Yiling Song and Longcheng Gao of Beihang University, and Jiao Zhao and Ruifu Yang of BGI-Shenzhen.

For more Stanford experts on engineering and other topics, visit Stanford Experts.

ORIGINAL: Stanford

BY ROB JORDAN

September 29, 2015

This Is The First Biofluorescent Turtle Ever Found

photo credit: The turtle was found by accident. David Gruber/National Geographic.

For the first time, scientists have found a reptile that exhibits biofluorescence – which means it can emit light in a varying degree of colours. The creature, known as a hawksbill sea turtle, was spotted off the Solomon Islands by marine biologist David Gruber of the City University of New York.

As reported by National Geographic, the creature reflects incoming blue light in a variety of colours – green, red, and orange – to give off its ghostly appearance. Gruber and his team discovered the animal by accident, while out looking for crocodiles and studying coral.

Speaking to National Geographic, Gruber said the turtle “came out of nowhere,” but they let it go without hassling it so as not to disturb it. These turtles are critically endangered, with just a few thousand breeding females remaining in some locations – but it seems the hawksbill has much more of a story to tell.

Why the turtle uses biofluorescence, such as for mating or other reasons, is not known. Gruber noted that the red on the turtle may have been from biofluorescent algae, but the green was definitely from the turtle. Such abilities are starting to look more commonplace in marine animals though, with eels and jellyfish included in those that can glow in the dark. Now the hawksbill turtlte will have to be added to the list, too.

Check out the amazing video of the turtle below.

ORIGINAL: IFLScience
by Jonathan O'Callaghan
September 29, 2015

First Optical Rectenna – Combined Rectifier and Antenna – Converts Light to DC Current

Using nanometer-scale components, researchers have demonstrated the first optical rectenna, a device that combines the functions of an antenna and a rectifier diode to convert light directly into DC current.

Using nanometer-scale components, researchers have demonstrated the first optical rectenna, a device that combines the functions of an antenna and a rectifier diode to convert light directly into DC current. 

Based on multiwall carbon nanotubes and tiny rectifiers fabricated onto them, the optical rectennas could provide a new technology for photodetectors that would operate without the need for cooling, energy harvesters that would convert waste heat to electricity – and ultimately for a new way to efficiently capture solar energy.

In the new devices, developed by engineers at the Georgia Institute of Technology, the carbon nanotubes act as antennas to capture light from the sun or other sources. As the waves of light hit the nanotube antennas, they create an oscillating charge that moves through rectifier devices attached to them. The rectifiers switch on and off at record high petahertz speeds (10¹⁵ Hz = 1Million GHz), creating a small direct current.

Optical rectenna converts laser light. A carbon nanotube optical rectenna converts green laser light to electricity in the laboratory of Baratunde Cola at the Georgia Institute of Technology. (Credit: Rob Felt, Georgia Tech)

Billions of rectennas in an array can produce significant current, though the efficiency of the devices demonstrated so far remains below one percent. The researchers hope to boost that output through optimization techniques, and believe that a rectenna with commercial potential may be available within a year.

“We could ultimately make solar cells that are twice as efficient at a cost that is ten times lower, and that is to me an opportunity to change the world in a very big way” said Baratunde Cola, an associate professor in the George W. Woodruff School of Mechanical Engineering at Georgia Tech. “As a robust, high-temperature detector, these rectennas could be a completely disruptive technology if we can get to one percent efficiency. If we can get to higher efficiencies, we could apply it to energy conversion technologies and solar energy capture.”

The research, supported by the Defense Advanced Research Projects Agency (DARPA), the Space and Naval Warfare (SPAWAR) Systems Center and the Army Research Office (ARO), was reported September 28 in the journal Nature Nanotechnology.

Developed in the 1960s and 1970s, rectennas have operated at wavelengths as short as ten microns, but for more than 40 years researchers have been attempting to make devices at optical wavelengths. There were many challenges:

• making the antennas small enough to couple optical wavelengths, and 
• fabricating a matching rectifier diode small enough and 
• able to operate fast enough to capture the electromagnetic wave oscillations. 

But the potential of high efficiency and low cost kept scientists working on the technology.

“The physics and the scientific concepts have been out there,” said Cola. “Now was the perfect time to try some new things and make a device work, thanks to advances in fabrication technology.”

Using metallic multiwall carbon nanotubes and nanoscale fabrication techniques, Cola and collaborators Asha Sharma, Virendra Singh and Thomas Bougher constructed devices that utilize the wave nature of light rather than its particle nature. They also used a long series of tests – and more than a thousand devices – to verify measurements of both current and voltage to confirm the existence of rectenna functions that had been predicted theoretically. The devices operated at a range of temperatures from 5 to 77 degrees Celsius.

Optical rectenna schematic. This schematic shows the components of the optical rectenna developed at the Georgia Institute of Technology. (Credit: Thomas Bougher, Georgia Tech)

Fabricating the rectennas begins with 

• growing forests of vertically-aligned carbon nanotubes on a conductive substrate.
• Using atomic layer chemical vapor deposition, the nanotubes are coated with an aluminum oxide material to insulate them. 
• Finally, physical vapor deposition is used to deposit optically-transparent thin layers of calcium 
• then aluminum metals atop the nanotube forest. 

The difference of work functions between the nanotubes and the calcium provides a potential of about two electron volts, enough to drive electrons out of the carbon nanotube antennas when they are excited by light.

In operation, oscillating waves of light pass through the transparent calcium-aluminum electrode and interact with the nanotubes. The metal-insulator-metal junctions at the nanotube tips serve as rectifiers switching on and off at femtosecond (10^-15s = 1 millionth of nanosecond) intervals, allowing electrons generated by the antenna to flow one way into the top electrode. Ultra-low capacitance, on the order of a few attofarads (10^-6 Picofarads) , enables the 10-nanometer diameter diode to operate at these exceptional frequencies.

“A rectenna is basically an antenna coupled to a diode, but when you move into the optical spectrum, that usually means a nanoscale antenna coupled to a metal-insulator-metal diode,” Cola explained. “The closer you can get the antenna to the diode, the more efficient it is. So the ideal structure uses the antenna as one of the metals in the diode – which is the structure we made.”

The rectennas fabricated by Cola’s group are grown on rigid substrates, but the goal is to grow them on a foil or other material that would produce flexible solar cells or photodetectors.

Measuring output from optical rectenna. Georgia Tech associate professor Baratunde Cola measures the power produced by converting green laser illumination to electricity using the carbon nanotube optical rectenna. (Credit: Rob Felt, Georgia Tech)

Cola sees the rectennas built so far as simple proof of principle. He has ideas for how to improve the efficiency by changing the materials, opening the carbon nanotubes to allow multiple conduction channels, and reducing resistance in the structures.

“We think we can reduce the resistance by several orders of magnitude just by improving the fabrication of our device structures,” he said. “Based on what others have done and what the theory is showing us, I believe that these devices could get to greater than 40 percent efficiency.”

Professor Baratunde Cola (left) holds a carbon nanotube optical rectenna device. With him are Asha Sharma (center) and Virendra Singh from his group, who are collaborators on the development. (Credit: Candler Hobbs, Georgia Tech)

This work was supported by the Defense Advanced Research Projects Agency (DARPA), the Space and Naval Warfare (SPAWAR) Systems Center, Pacific under YFA grant N66001-09-1-2091, and by the Army Research Office (ARO), through the Young Investigator Program (YIP), under agreement W911NF-13-1-0491. The statements in this release are those of the authors and do not necessarily reflect the official views of DARPA, SPAWAR or ARO. Georgia Tech has filed international patent applications related to this work under PCT/US2013/065918 in the United States (U.S.S.N. 14/434,118), Europe (No. 13847632.0), Japan (No. 2015-538110) and China (No. 201380060639.2)

CITATION: Asha Sharma, Virendra Singh, Thomas L. Bougher and Baratunde A. Cola, “A carbon nanotube optical rectenna,” (Nature Nanotechnology, 2015). http://dx.doi.org/10.1038/nnano.2015.220

Research News

Georgia Institute of Technology

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Atlanta, Georgia 30332-0181 USA

Media Relations Contact: John Toon (jtoon@gatech.edu) (404-894-6986)

Writer: John Toon

ORIGINAL: Georgia Tech
By John Toon

September 28, 2015

How Your Brain Is Wired Reveals the Real You

The Human Connectome Project finds surprising correlations between brain architecture and behavior

©iStock.com

The brain’s wiring patterns can shed light on a person’s positive and negative traits, researchers report in Nature Neuroscience. The finding, published on September 28, is the first from the Human Connectome Project (HCP), an international effort to map active connections between neurons in different parts of the brain.

The HCP, which launched in 2010 at a cost of US$40 million, seeks to scan the brain networks, or connectomes, of 1,200 adults. Among its goals is to chart the networks that are active when the brain is idle; these are thought to keep the different parts of the brain connected in case they need to perform a task.

In April, a branch of the project led by one of the HCP's co-chairs, biomedical engineer Stephen Smith at the University of Oxford, UK, released a database of resting-state connectomes from about 460 people between 22 and 35 years old. Each brain scan is supplemented by information on approximately 280 traits, such as the person's age, whether they have a history of drug use, their socioeconomic status and personality traits, and their performance on various intelligence tests.

Axis of connectivity

Smith and his colleagues ran a massive computer analysis to look at how these traits varied among the volunteers, and how the traits correlated with different brain connectivity patterns. The team was surprised to find a single, stark difference in the way brains were connected. People with more 'positive' variables, such as more education, better physical endurance and above-average performance on memory tests, shared the same patterns. Their brains seemed to be more strongly connected than those of people with 'negative' traits such as smoking, aggressive behaviour or a family history of alcohol abuse.

Marcus Raichle, a neuroscientist at Washington University in St Louis, Missouri, is impressed that the activity and anatomy of the brains alone were enough to reveal this 'positive-negative' axis. “You can distinguish people with successful traits and successful lives versus those who are not so successful,” he says.

But Raichle says that it is impossible to determine from this study how different traits relate to one another and whether the weakened brain connections are the cause or effect of negative traits. And although the patterns are clear across the large group of HCP volunteers, it might be some time before these connectivity patterns could be used to predict risks and traits in a given individual. Deanna Barch, a psychologist at Washington University who co-authored the latest study, says that once these causal relationships are better understood, it might be possible to push brains toward the 'good' end of the axis.

Van Wedeen, a neuroscientist at Massachusetts General Hospital in Boston, says that the findings could help to prioritize future research. For instance, one of the negative traits that pulled a brain farthest down the negative axis was marijuana use in recent weeks. Wedeen says that the finding emphasizes the importance of projects such as one launched by the US National Institute on Drug Abuse last week, which will follow 10,000 adolescents for 10 years to determine how marijuana and other drugs affect their brains.

Wedeen finds it interesting that the wiring patterns associated with people's general intelligence scores were not exactly the same as the patterns for individual measures of cognition—people with good hand–eye coordination, for instance, fell farther down the negative axis than did those with good verbal memory. This suggests that the biology underlying cognition might be more complex than our current definition of general intelligence, and that it could be influenced by demographic and behavioural factors. “Maybe it will cause us to reconsider what [the test for general intelligence] is measuring,” he says. “We have a new mystery now.”

Much more connectome data should emerge in the next few years. The Harvard Aging Brain Study, for instance, is measuring active brain connections in 284 people aged between 65 and 90, and released its first data earlier this year. And Smith is running the Developing Human Connectome Project in the United Kingdom, which is imaging the brains of 1,200 babies before and after birth. He expects to release its first data in the next few months. Meanwhile, the HCP is analysing genetic data from its participants, which include a large number of identical and fraternal twins, to determine how genetic and environmental factors relate to brain connectivity patterns.

This article is reproduced with permission and was first published on September 28, 2015.

ORIGINAL: Scientific American

By Sara Reardon and Nature magazine

September 28, 2015

NASA Confirms Evidence That Liquid Water Flows on Today’s Mars

These dark, narrow, 100 meter-long streaks called recurring slope lineae flowing downhill on Mars are inferred to have been formed by contemporary flowing water. Recently, planetary scientists detected hydrated salts on these slopes at Hale crater, corroborating their original hypothesis that the streaks are indeed formed by liquid water. The blue color seen upslope of the dark streaks are thought not to be related to their formation, but instead are from the presence of the mineral pyroxene. The image is produced by draping an orthorectified (Infrared-Red-Blue/Green(IRB)) false color image (ESP_030570_1440) on a Digital Terrain Model (DTM) of the same site produced by High Resolution Imaging Science Experiment (University of Arizona). Vertical exaggeration is 1.5.

Credits: NASA/JPL/University of Arizona

New findings from NASA's Mars Reconnaissance Orbiter (MRO) provide the strongest evidence yet that liquid water flows intermittently on present-day Mars.

Using an imaging spectrometer on MRO, researchers detected signatures of hydrated minerals on slopes where mysterious streaks are seen on the Red Planet. These darkish streaks appear to ebb and flow over time. They darken and appear to flow down steep slopes during warm seasons, and then fade in cooler seasons. They appear in several locations on Mars when temperatures are above minus 10 degrees Fahrenheit (minus 23 Celsius), and disappear at colder times.

“Our quest on Mars has been to ‘follow the water,’ in our search for life in the universe, and now we have convincing science that validates what we’ve long suspected,” said John Grunsfeld, astronaut and associate administrator of NASA’s Science Mission Directorate in Washington. “This is a significant development, as it appears to confirm that water -- albeit briny -- is flowing today on the surface of Mars.”

These downhill flows, known as recurring slope lineae (RSL), often have been described as possibly related to liquid water. The new findings of hydrated salts on the slopes point to what that relationship may be to these dark features. The hydrated salts would lower the freezing point of a liquid brine, just as salt on roads here on Earth causes ice and snow to melt more rapidly. Scientists say it’s likely a shallow subsurface flow, with enough water wicking to the surface to explain the darkening.

Dark narrow streaks called recurring slope lineae emanating out of the walls of Garni crater on Mars. The dark streaks here are up to few hundred meters in length. They are hypothesized to be formed by flow of briny liquid water on Mars. The image is produced by draping an orthorectified (RED) image (ESP_031059_1685) on a Digital Terrain Model (DTM) of the same site produced by High Resolution Imaging Science Experiment (University of Arizona). Vertical exaggeration is 1.5.

Credits: NASA/JPL/University of Arizona

"We found the hydrated salts only when the seasonal features were widest, which suggests that either the dark streaks themselves or a process that forms them is the source of the hydration. In either case, the detection of hydrated salts on these slopes means that water plays a vital role in the formation of these streaks," said Lujendra Ojha of the Georgia Institute of Technology (Georgia Tech) in Atlanta, lead author of a report on these findings published Sept. 28 by Nature Geoscience.

Ojha first noticed these puzzling features as a University of Arizona undergraduate student in 2010, using images from the MRO's High Resolution Imaging Science Experiment (HiRISE). HiRISE observations now have documented RSL at dozens of sites on Mars. The new study pairs HiRISE observations with mineral mapping by MRO’s Compact Reconnaissance Imaging Spectrometer for Mars (CRISM).

The spectrometer observations show signatures of hydrated salts at multiple RSL locations, but only when the dark features were relatively wide. When the researchers looked at the same locations and RSL weren't as extensive, they detected no hydrated salt.

Ojha and his co-authors interpret the spectral signatures as caused by hydrated minerals called perchlorates. The hydrated salts most consistent with the chemical signatures are likely a mixture of magnesium perchlorate, magnesium chlorate and sodium perchlorate. Some perchlorates have been shown to keep liquids from freezing even when conditions are as cold as minus 94 degrees Fahrenheit (minus 70 Celsius). On Earth, naturally produced perchlorates are concentrated in deserts, and some types of perchlorates can be used as rocket propellant.

Perchlorates have previously been seen on Mars. NASA's Phoenix lander and Curiosity rover both found them in the planet's soil, and some scientists believe that the Viking missions in the 1970s measured signatures of these salts. However, this study of RSL detected perchlorates, now in hydrated form, in different areas than those explored by the landers. This also is the first time perchlorates have been identified from orbit.

MRO has been examining Mars since 2006 with its six science instruments.

"The ability of MRO to observe for multiple Mars years with a payload able to see the fine detail of these features has enabled findings such as these: first identifying the puzzling seasonal streaks and now making a big step towards explaining what they are," said Rich Zurek, MRO project scientist at NASA's Jet Propulsion Laboratory (JPL) in Pasadena, California.

For Ojha, the new findings are more proof that the mysterious lines he first saw darkening Martian slopes five years ago are, indeed, present-day water.

"When most people talk about water on Mars, they're usually talking about ancient water or frozen water," he said. "Now we know there’s more to the story. This is the first spectral detection that unambiguously supports our liquid water-formation hypotheses for RSL."

The discovery is the latest of many breakthroughs by NASA’s Mars missions.

“It took multiple spacecraft over several years to solve this mystery, and now we know there is liquid water on the surface of this cold, desert planet,” said Michael Meyer, lead scientist for NASA’s Mars Exploration Program at the agency’s headquarters in Washington. “It seems that the more we study Mars, the more we learn how life could be supported and where there are resources to support life in the future.” 

This animation simulates a fly-around look at one of the places on Mars where dark streaks advance down slopes during warm seasons, possibly involving liquid water. This site is within Hale Crater. The streaks are roughly the length of a football field.

There are eight co-authors of the Nature Geoscience paper, including Mary Beth Wilhelm at NASA’s Ames Research Center in Moffett Field, California and Georgia Tech; CRISM Principal Investigator Scott Murchie of the Johns Hopkins University Applied Physics Laboratory in Laurel, Maryland; and HiRISE Principal Investigator Alfred McEwen of the University of Arizona Lunar and Planetary Laboratory in Tucson, Arizona. Others are at Georgia Tech, the Southwest Research Institute in Boulder, Colorado, and Laboratoire de Planétologie et Géodynamique in Nantes, France.

The agency’s Jet Propulsion Laboratory (JPL) in Pasadena, California manages the Mars Reconnaissance Orbiter Project for NASA's Science Mission Directorate, Washington. Lockheed Martin built the orbiter and collaborates with JPL to operate it.

More information about NASA's journey to Mars is available online at:

https://www.nasa.gov/topics/journeytomars

For more information about the Mars Reconnaissance Orbiter, visit:

http://www.nasa.gov/mro

ORIGINAL: NASA

The War Over Genome Editing Just Got A Lot More Interesting

The cutting circle GETTY IMAGES

IF YOU WANT to drop some real DNA editing knowledge—like, I don’t know, at a party!—here’s a tip. Instead of calling the much hyped precise genome-editing tool CRISPR, call it CRISPR/Cas9. CRISPR, you see, just refers to stretches of repeating DNA that sit near the gene for Cas9, the actual protein that does the DNA editing.

Well, at least for now. Today, gene-editing scientists dropped some curious news: They’ve found a CRISPR system involving a different protein that also edits human DNA, and, in some cases, it may work even better than Cas9.

The discovery comes at a time when CRISPR/Cas9 is sweeping through biology labs. So revolutionary is this new genome editing technique that rival groups, who each claim to have been first to the tech, are bitterly fighting over the CRISPR/Cas9 patent. This new gene-editing protein called Cpf1—and maybe even others yet to be discovered—means that one patent may not be so powerful after all.

And there’s good reason to think more useful CRISPR proteins are out there. CRISPR sequences are a part of primordial immune systems, found in some 40 percent of bacteria and 90 percent of archaea. In a study published today in Cell, Feng Zhang (no relation to this writer) and colleagues trawled through bacterial genomes looking for different versions of Cpf1. They found two, from Acidominococcus and Lachnospiraceae, that can snip DNA when scientists insert them into human cells.

“There are definitely many more defense systems out there, and maybe some of them might even have spectacular applications like with the Cas9 system,” says John van der Oost, a microbiologist at Wageningen University who is a co-author on the paper. “We have the feeling it’s just the tip of the iceberg.”

Zhang and van der Oost’s search was deliberate, but the initial discovery of CRISPR/Cas9 as a gene-editing tool was not. Back in the 1980s, microbiologists saw strange repeating sequences in the DNA of bacteria. Those clustered regularly interspaced short palindromic repeats became CRISPR, and scientists realized they were evidence of an immune system bacteria used to defend against viruses. The spacers between the repeats are in fact snippets of viral genomes, which CRISPR-associated proteins called Cas use as “mug shots” to recognize viruses and shred their DNA.

Many different proteins are associated with CRISPR. But in the early 2010s, Emmanuelle Charpentier, who was studying the flesh-eating bacteria Streptococcus pyogenes, stumbled onto one with special powers. Her bacteria happen to carry Cas9 proteins, which have the remarkable ability to precisely cut DNA based on a RNA guide sequence. In 2012, Charpentier and UC Berkeley biologist Jennifer Doudna published a paper describing the CRISPR/Cas9 system and speculated about its genome editing capabilities. And they filed a patent application. Much more on that patent later.

The Obscure Protein

While Cas9 has driven thousands of lab experiments and millions of dollars in funding for startups trying to capitalize on the technology, Cpf1 has remained relatively obscure. This study drags Cpf1 into the limelight. “It’s a very comparable to Cas9 and it has a few different features which could be quite useful,” says Dana Carroll, a biochemist at the University of Utah.

That’s because Cas9 isn’t perfect, despite its hype as a laser-precise genome editing tool. Cpf1 offers some slight advantages. For example, when it cuts double-stranded DNA, it snips the two strands in slightly different locations, resulting in overhang that molecular biologists call “sticky ends.” Sticky ends can make it easier to insert a snippet of new DNA—say, a different version of a gene—though the Cell paper does not actually show data directly comparing Cas9 and Cpf1 when inserting DNA.

Cpf1 is also physically a smaller protein, so it may be easier to put into human cells. It requires only one RNA molecule instead of two, with Cas9. But it’s not a rival so much as a complementary tool: The two proteins favor binding to different locations in the genome, so together, they might allow more flexibility in where scientist want to cut.

But Cpf1 has implications reaching far outside the lab.

Patent Wars

Not long after Doudna and UC Berkeley filed a patent, the Broad Institute and MIT filed their own patent on behalf of Zhang for the CRISPR/Cas9 system. Zhang had been working on actually showing that CRISPR/Cas9 can edit mammalian genomes in mammalian cells, an application he published in 2013 and says he came up with independently. The Broad’s and MIT’s attorney paid a fee to accelerate their application. Ultimately, the US Patent and Trademark Office awarded the patent to Zhang, MIT, and the Broad Institute. The University of California, obviously unhappy with the decision, filed an application for an interference proceeding to get the USPTO to reconsider. That process is ongoing.

But biotech companies have raced ahead to develop therapeutics and techniques with the system. Feng and Doudna have since licensed their technology to rival companies, Editas and Caribou. Charpentier also cofounded Crispr Therapeutics in Switzerland. Whoever wins the patent dispute will have a monopoly on CRISPR/Cas9 technology, the hottest new thing in biotech.

But with Cfp1, the stakes of that specific patent dispute go down. A lab or company could use Cfp1 without infringing on the CRISPR/Cas9 patent. “It takes power away from whoever the winner is going to be,” says Jacob Sherkow, a professor at New York Law School1 (Zhang has indicated the rights to Cpf1 may not necessarily go to the company he cofounded, Editas.) Whether a CRISPR/Cfp1 system is patentable as a separate invention—Sherkow says it probably is—perhaps isn’t even relevant because its very existence means Cas9 is no longer the only game in town.

And if biologists keep trawling through bacterial genomes, they might find even more proteins to join Cfp1 and Cas9. Who knows what else is hiding in the genomes of microbes?

ORIGINAL: Wired

By SARAH ZHANG

09.25.15

Urban Barns | Farming of the future

Photo by Urban Barns

Our Story

We are an innovative Canadian food producer dedicated to growing consistent, healthy, and fresh vegetables year round. Grown in a completely controlled environment, our produce is grown from non-GMO seeds and free of pesticides, herbicides, and fungicides. Controlled environment means no contact with the outside world, eliminating the possibilities of contamination and infection. With careful consideration for food traceability, sustainability, and of course, taste, our produce is picked at the peak of ripeness, ensuring luscious plate ready food every time. We redefine what it means to be truly local and fresh.

The world's first commercial Cubic Farm™ opened in June 2014 in Mirabel, Quebec. 

Photo by Urban Barns

What Makes Us Different

Photo by Urban Barns

• Cutting edge LED technology.
• 24/7 and 365 days in production regardless of pests, disease or extreme weather.
• 100% controlled environment for maximized production and food safety.
• Lower labour costs with yields up to 400 times more than conventional farming.
• 94% less water-usage than conventional farming methods.
• Ability to locate and grow anywhere in the world. From the Arctic to the Sahara.
• Our Cubic Farming™ machines maximize any growing space in any sized building.
• Off-grid facilities using solar panels, wind turbines and dehumidification systems.
• Local = fresh.
• Low carbon footprint. No long-haul shipping.
• Higher nutritional values than conventional produce.
• Guaranteed pricing and product consistency.
• Strong R&D team with McGill University’s Bioresource Engineering Department.
• No GMOs or pesticides.
• Endless customization. We can easily grow thousands of varieties.

Urban Barns Foods says it's the future of agriculture. The company is growing food indoors, with an emphasis on efficiency and volume.

IBM's Watson Personality Insights service

How it works

Personality Insights extracts and analyzes a spectrum of personality attributes to help discover actionable insights about people and entities, and in turn guides end users to highly personalized interactions. 

The service outputs personality characteristics that are divided into three dimensions: 

• the Big 5
  • openness, 
  • conscientiousness, 
  • extraversion, 
  • agreeableness, and 
  • neuroticism
• Values, and 
• Needs. 

While some services are contextually specific depending on the domain model and content, Personality Insights only requires a minimum of 3500+ words of any text.

Intended UsePersonality Insights is great for brand analytics and can help measure a brand's personality and compare/contrast with your customers personalities. It can also help with market segmentation and individualizing marketing campaigns or promotions. Personality Insights can also be used to help recruiters or university admissions match candidates to companies or universities. Overall, Personality Insights individualizes customer care and infers personality traits to drive a more tailored response.

YOU INPUT:JSON, or Text or HTML (such as social media, emails, blogs, or other communication) written by one individual

SERVICE OUTPUT:A tree of cognitive and social characteristics in JSON or CSV format

The IBM Watson™ Personality Insights service provides an Application Programming Interface (API) that enables applications to derive insights from social media, enterprise data, or other digital communications. The service uses linguistic analytics to infer personality and social characteristics, including 

• Big Five (openness, conscientiousness, extraversion, agreeableness, and neuroticism), 
• Needs, and 
• Values, 

from text. 

These insights help businesses to understand their clients' preferences and improve customer satisfaction by anticipating customer needs and recommending future actions. Businesses can use these insights to improve client acquisition, retention, and engagement, and to strengthen relations with their clients.

You can see a quick demo of the Personality Insights service in action. The demo lets you analyze input text to develop a personality portrait for the author of the text. The applications 

• Speak Up, 
• NYC School Finder, and 
• Your Celebrity Match 

on the Watson Developer Cloud App Gallery also demonstrate the Personality Insights service.

We are always looking to improve and learn from your experience with our services. You can submit comments or ask questions about Personality Insights in the Watson forum. You can also read posts about Watson services that are written by IBM researchers, developers, and other experts on the Watson blog. 

Specifically, you might want to look at

• IBM Watson Personality Insights: The science behind the service,
• IBM Watson Personality Insights General Availability Announcement,
• Watson and the State of the Union, and
• Watson in the Wild from March 12 and 5, 2015.

The Personality Insights service is generally available (GA). For information about the pricing plans available for the service, see thePersonality Insights service in Bluemix.

Developing a Personality Insights application

• To begin working with the Personality Insights service by creating and running applications that communicate with the service, see the following sections:
• To create and run an example Node.js application that works with the service from the command line, see Watson Quick Start for Node.js.
• To create and run a sample Node.js application that works with the service from a web browser, see Developing a Watson application in Node.js. You need the link to the source code for the Node.js application at the personality-insights-nodejs repository in the watson-developer-cloudnamespace on GitHub.
• To create and run a sample Java application that works with the service from a web browser, see Developing a Watson application in Java. You need the link to the source code for the Java application at thepersonality-insights-java repository in the watson-developer-cloud namespace on GitHub.
• For the sample applications available from GitHub, you can download a .zipfile that contains the source code or, if you are familiar with Git, fork the repository into your Git namespace or clone it to your local system. To learn about Git or to download Git for your operating system, see git-scm.com/documentation.
• For a language-independent introduction to working with Watson Developer Cloud services and Bluemix, see Developing Watson applications with Bluemix. That page provides an overview of working with Watson services with the Bluemix web interface, the Eclipse IDE, or the Cloud Foundry command-line tool.

ORIGINAL: IBM Watson™ Personality Insights

100 Years to Find a Cure: Can the Process be Accelerated?

Researchers quantify relationship between scientific discoveries and advances in medicine

SAN FRANCISCO, CA—Scientists from the Gladstone Institutes have provided a detailed map of how basic research translates into new treatments for deadly diseases. Charting the network of discoveries that led to the development of important therapeutic drugs, the investigators revealed that, up to now, the path to a cure has required thousands of scientists and many decades. Writing in the journal Cell, the authors propose that a clearer understanding of how past successes have come about can reveal ways to accelerate the process of finding future cures.

“We started with a big question: how do scientific discoveries lay the foundation for successful development of new drugs?” says author Alexander Pico, PhD, a staff research scientist at the Gladstone Institutes. “We all have an intuitive understanding that basic research provides the starting point for new drug development, but in this paper we wanted to quantify and illuminate features of that path. Our data show that it takes contributions from a surprisingly large and complex network of individual scientists working in many locales to reach a cure.”

Using newly developed, unbiased data modeling methods, the investigators retrospectively mapped the discovery path to two drugs that have been recently approved by the FDA and could be characterized as “cures”—ipilimumab for certain forms of cancer and ivacaftor for cystic fibrosis. The researchers relied on citations from published research findings, using “bibliometrics” to work backwards to uncover the stepwise scientific advances that led to the new medications. According to the networks of cited publications,

• ipilimumab resulted from research conducted by 7000 scientists from 5700 institutional affiliations over the course of 100 years, while 
• ivacaftor took 2900 scientists with 2500 different affiliations 60 years to develop.

A network map of all the publications that led to the discovery and FDA approval of a new life-saving drug. All papers related to the drug are shown in green, authors of the papers are shown in purple, and institutional affiliations of the authors are shown in blue. Yellow dots are "elite performers." [Image: Alex Pico]

To extract additional information from the data, the researchers developed new metrics—the Propagated In-Degree Rank (PIR) and Ratio of Basic Rankings (RBR)—to quantify the influence and selectiveness of each scientist in the network. These rankings identified “elite performers” who contributed disproportionately to the development of the drugs.

This work provides an initial step towards the development of new predictive metrics that may enhance decision-making in ways that would accelerate future research progress. Ascertaining—and then emulating—certain qualities of the elite performers may be one way to accelerate discovery and propel scientists more rapidly down the path toward cures.

What’s more, in light of waning public and governmental support for funding basic science, the researchers are hopeful that enhanced public understanding of how scientific research leads to urgently needed drugs will translate into increased and sustained Congressional support for the National Institutes of Health.

“As shown by our analysis, new treatments depend upon a broad base of scientific knowledge plus special contributions from a few exceptional scientists,” says first author R. Sanders Williams, MD, president of the Gladstone Institutes. “The ultimate goal of this work is to find ways to accelerate progress towards future cures for cruel diseases that remain unsolved: Alzheimer’s disease, Parkinson’s disease, heart failure, deadly viruses, diabetes, many cancers, and others.”

Samad Lotia and Alisha Holloway from the Gladstone Institutes also took part in this research. Funding was provided by the Schwab Foundation and Bruce and Martha Atwater.

About the Gladstone Institutes

To ensure our work does the greatest good, the Gladstone Institutes focuses on conditions with profound medical, economic, and social impact—unsolved diseases of the brain, the heart, and the immune system. Affiliated with the University of California, San Francisco, Gladstone is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease.

Contact Person

Dana Smith

Direct line: 415.734.2532

Mobile: 415.806.6245

ORIGINAL: Gladstone Institutes

Gladstone Press Release

September 24, 2015

Chatting With Bacteria To Save The World

Top Image Source: Stocktrek Images/Getty

The most recent E. coli epidemic in the U.S. struck late last year, when 33 people in Arizona, California and Nevada suffered from abdominal cramps, nausea and diarrhea after eating grab-and-go chicken salads. For two patients, the infection produced toxic substances that killed their red blood cells, which then clogged and damaged the tiny blood vessels in their kidneys, crucial for filtering out waste products and regulating blood pressure. Since treatments like dialysis often lead to a full recovery, no one died; but the conditon can lead to potentially fatal kidney failure, or long-term kidney damage that may require medication or dietary changes to keep blood pressure low.

The next step is to use a microprocessor to convert the light pulses emitted by bacteria into speech.

Foodborne illnesses affect 48 million — or 1 in 6 — Americans, and kill 3,000 each year, according to CDC estimates. Usually a quick sniff test or glance at the expiration date can reveal whether or not a food item is past its prime. But it’s tricky with E. coli contamination, which is impossible to detect by smell, taste or appearance alone.

But what if an alarm system could alert us to contamination?
It’s a possibility, thanks to research led by Manuel Porcar, a synthetic biology researcher at the University of Valencia in Spain. His group engineered harmless strains of E. colibacteria to emit different colors of light depending on its environment, from temperature to pH.
What’s next?
Convert the light waves into actual speech. That means we could add these engineered bacteria to food packaging, and if they detect enivronmental conditions that indicate contamination, they can tell us — literally — to avoid eating the package’s contents.

“It seems like science fiction,” Porcar says. “But it’s a simple idea, and it worked well.”

Manuel Porcar. Source: Via Twitter

And food safety is just one application. For example, pharmacists can place a sample of a drug containing the engineered bacteria in a special machine outfitted with a microprocessor, so the bacteria can let them know whether they made the drug correctly by producing proteins that emit different colors of fluorescent light depending on the amount of a certain ingredient. Distillers can use the engineered bacteria in a similar way to determine whether their alcohol is ready to bottle.

”The amount of light the bacteria emitted went up or down depending on their comfort level.”

The project, published online in Letters in Applied Microbiology, was Porcar and his students’ entry to the 2012 International Genetically Engineered Machine (iGEM) competition, in which undergraduate student teams build biological systems from a library of DNA sequences that encode specific biological parts.

One of Porcar’s students asked a simple yet tantalizing question: Can we talk to bacteria through light pulses?

To find out, the team engineered four strains of E. coli to produce proteins that emit different colors and amounts of fluorescent light depending on environmental factors considered crucial for survival. They designed

• one strain to glow cyan under low glucose conditions, 
• another to glow red with increasing temperature, and 
• a third to glow green with decreasing oxygen levels. Finally, they designed 
• a fourth strain to fluoresce yellow under low-nitrogen conditions

Sure enough, when the researchers tweaked the environment in which the E. coli bacteria were growing, the amount of light they emitted went up or down depending on their comfort level. For example, exposing the heat-sensitive strain to pulses of increasing temperatures caused it to glow red more brightly each time.

Are bacteria happy, are they stressed, will they refuse to obey?

The next step is to use a microprocessor to convert vocal questions into light pulses that stimulate the engineered E. coli to produce fluorescent light-emitting proteins. Then the microprocessor would convert that light into vocal responses, depending on its wavelength. So if the microprocessor detects wavelengths that result in bright red light, “the machine would say, ‘I’m very warm. Please refresh me,’” Porcar explained.

So far, the researchers have designed a microprocessor that can convert speech into light pulses, and vice-versa, but they haven’t integrated it into a complete system. Porcar has no plans to continue the project and, as far he knows, no one else has taken up the charge. But Victor de Lorenzo, a microbiologist at the Spanish National Center for Biotechnology, is engineering cells to command each other to perform sophisticated computations. These cells can then serve as building blocks for circuits to perform even more complex tasks, such as cleaning up toxic metals.

Schematic drawing of the Microbial Thermoelectric Cell (Auto-CAD).All dimensions are given in mm. Source: PLOS ONE

Nonetheless, Porcar’s study — the first-ever attempt to communicate with bacteria — highlights the importance of regular “check-ins” with bacteria to optimize their performance. “On one hand, the domesticated biological object must follow predictably the orders of the master,” de Lorenzo says. “But we have thus far not cared about the other direction — how bacteria feel while responding to our orders. Are they happy, are they stressed, will they refuse to obey?”

Today, Porcar is continuing to investigate bacteria’s potential. His group has developed a device that converts the heat that bacteria emit — for example, when they digest sugar during alcohol production — into electricity to power small electronics.

We might be unable to make bacteria behave exactly as we want by rational design.

But Porcar’s work also raises the controversial question of whether engineering principles can be applied to living systems— a central tenet of synthetic biology often trumpeted by the popular media. “The main reason is that, in my opinion, cells are not machines because they’re not designed,” he says. “They arise from natural selection and evolution.”

If living systems really were machines, then each part should behave independently of each other. But Porcar thinks the opposite is true. A major limitation of the “talking bacteria” project was that growing different strains together failed to provide readouts of multiple environmental conditions; for example, the strain designed to sense oxygen could no longer do so.

Porcar is testing his hypothesis for this year’s iGEM entry. The results might vastly change the way scientists approach synthetic biology. “We might be unable to make bacteria behave exactly as we want by rational design,” he says. Porcar thinks “rational design plus some room for fine-tuning with natural selection” might be more effective.

Typically, scientists insert one specific DNA sequence — encoding an anti-malarial protein, for example — into bacteria, allowing them to replicate, forming clones. Procar instead suggests allowing bacteria to naturally accumulate mutations in their DNA over the course of a few weeks, perhaps with the help of UV radiation, generating different variants of the protein and growing them with the malaria-causing parasite to select which one works best.

Porcar is challenging and stretching the way we think of bacteria. More than just cogs in a machine, they’re living systems themselves, meaning that our best chance of benefiting from them may be working with them — and even asking them how they’re doing.

* Editor’s note: An earlier version of this article did not adequately credit a source, The New Scientist blog.

MELISSA PANDIKA

OZY AUTHOR

Melissa Pandika is a lab rat-turned-journalist with an eye to all things science, medicine and more. Likes distance running, snails, late-night Korean BBQ + R&B slow jams.

ORIGINAL: OZY

BY MELISSA PANDIKA

MAY 19 2014