Scientists Demonstrate Basics of Nucleic Acid Computing Inside Cells

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DETAILS: Using strands of nucleic acid, scientists have demonstrated basic computing operations inside a living mammalian cell. Shown examining a cellular “AND” gate are associate professor Philip Santangelo and research scientist Chiara Zurla. (Credit: Rob Felt, Georgia Tech)

Using strands of nucleic acid, scientists have demonstrated basic computing operations inside a living mammalian cell. The research could lead to an artificial sensing system that could control a cell’s behavior in response to such stimuli as the presence of toxins or the development of cancer.

The research uses DNA strand displacement, a technology that has been widely used outside of cells for the design of molecular circuits, motors and sensors. Researchers modified the process to provide both “AND” and “OR” logic gates able to operate inside the living cells and interact with native messenger RNA (mRNA).

The tools they developed could provide a foundation for bio-computers able to sense, analyze and modulate molecular information at the cellular level. Supported by the Defense Advanced Research Projects Agency (DARPA) and the National Science Foundation (NSF), the research was reported December 21 in the journal Nature Nanotechnology.

“The whole idea is to be able to take the logic that is used in computers and port that logic into cells themselves,” said .Philip Santangelo, an associate professor in the .Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “These devices could sense an aberrant RNA, for instance, and then shut down cellular translation or induce cell death.”

Strand displacement reactions are the biological equivalent of the switches or gates that form the foundation for silicon-based computing. They can be programmed to turn on or off in response to an external stimuli such as a molecule. An “AND” gate, for example, would switch when both conditions were met, while an “OR” gate would switch when either condition was met.

In the switches the researchers used, a fluorophore reporter molecule and its complementary quenching molecule were placed side-by-side to create an “off” mode. Binding of RNA in one of the strands then displaced a portion of nucleic acid, separating the molecules and allowing generation of a signal that created an “on” mode. Two “on” modes on adjacent nucleic acid strands created an “AND” gate.

“Demonstrating individual logic gates is only a first step,” said Georg Seelig, assistant professor of computer science and engineering and electrical engineering at the University of Washington. “In the longer term, we want to expand this technology to create circuits with many inputs, such as those we have constructed in cell-free settings.”

The researchers used ligands designed to bind to specific portions of the nucleic acid strands, which can be created as desired and produced by commercial suppliers.

“We sensed molecules and showed that we could respond to them,” said Santangelo. “We showed that we could utilize native molecules in the cell as part of the circuit, though we haven’t been able to control a cell yet.”

Getting basic computing operations to function inside cells was no easy task, and the research required a number of years to accomplish. Among the challenges were getting the devices into the cells without triggering the switches, providing operation rapid enough to be useful, and not killing the human cell lines that researchers used in the lab.

“We had to chemically change the probes to get them to work inside the cell and to make them stable enough inside the cells,” said Santangelo. “We found that these strand displacement reactions can be slow within the cytosol, so to get them to work faster, we built scaffolding onto the messenger RNA that allowed us to amplify the effects.”

The nucleic acid computers ultimately operated as desired, and the next step is to use their switching to trigger the production of signaling chemicals that would prompt the desired reaction from the cells. Cellular activity is normally controlled by the production of proteins, so the nucleic acid switches will have to be given the ability to produce enough signaling molecules to induce a change.

“We need to generate enough of whatever final signal is needed to get the cell to react,” Santangelo explained. “There are amplification methods used in strand displacement technology, but none of them have been used so far in living cells.”

Even without that final step, the researchers feel they’ve built a foundation that can be used to attain the goal.

“We were able to design some of the basic logical constructs that could be used as building blocks for future work,” Santangelo said. “We know the concentrations of chemicals and the design requirements for individual components, so we can now start putting together a more complicated set of circuits and components.”

Cells, of course, already know how to sense toxic molecules and the development malignant tendencies, and to then take action. But those safeguards can be turned off by viruses or cancer cells that know how to circumvent natural cellular processes.

“Our mechanism would just give cells a hand at doing this,” Santangelo said. “The idea is to add to the existing machinery to give the cells enhanced capabilities.”

Applying an engineering approach to the biological world sets this example apart from other efforts to control cellular machinery.

“What makes DNA strand displacement circuits unique is that all components are fully rationally designed at the level of the DNA sequence,” said Seelig. “This really makes this technology ideal for an engineering approach. In contrast, many other approaches to controlling the cellular machinery rely on components that are borrowed from biology and are not fully understood.”

Beyond those already mentioned, the research team included Benjamin Groves, Yuan-Jyue Chen and Sergii Pochekailov from the University of Washington and Chiara Zurla and Jonathan Kirschman from Georgia Tech and Emory University.

This material is based on work supported by the Defense Advanced Research Projects Agency (DARPA) under contract W911NF-11-2-0068 and by National Science Foundation CAREER award 1253691. The content is solely the responsibility of the authors and does not necessarily represent the official views of DARPA or the NSF.

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Image shows activation of “AND” gates in cells as observed by fluorescence microscopy.
(Credit: Chiara Zurla, Georgia Tech)

CITATION: Benjamin Groves, et al., “Computing in mammalian cells with nucleic acid strand exchange,” (Nature Nanotechnology, 2015)..http://dx.doi.org/10.1038/nnano.2015.278

Research News

Georgia Institute of Technology

177 North Avenue

Atlanta, Georgia 30332-0181 USA

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

Writer: John Toon

ORIGINAL: .Geogia Tech
January 19, 2016

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

177 North Avenue

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

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

Watch a human musician and his robots improvise together

This performance by Shimon and the Shimi Robots showcases the PhD research of Georgia Tech doctoral student Mason Bretan on machine improvisation, path planning and embodied cognition. (Mason Bretan/YouTube)

This is a performance showcasing part of my PhD research in robotic musicianship at Georgia Tech including 

• machine improvisation, 
• path planning, and 
• embodied cognition. 

The smaller Shimi robots figure out how to move based on an analysis of the music and Shimon generates an improvisation given a precomposed chord progression using a generative algorithm that jointly optimizes for higher level musical parameters and its physical constraints.

The piece is called “What You Say” and is inspired by the high energy funk piece, “What I Say”, from Miles Davis’ Live-Evil album. The incredible brilliance of the musicians on that album (as well as the numerous other great musicians around the world) are not only an inspiration to me and my own musical and instrumental aspirations, but also set the standard for the level of musicianship that I hope machines will one day achieve. And through the power of artificial intelligence, signal processing, and engineering I firmly believe it is possible for machines to be artistic, creative, and inspirational.

I hope you enjoy!

To use this video in a commercial player or in broadcasts, please email licensing@storyful.com

Rest assured that when our future robotic overlords come on the scene, they'll have a sweet sense of rhythm.

The Robotic Musicianship Group at Georgia Tech has been working on Shimon, a musical robot that can improvise melodic accompaniment, for about six years now. And for three years, they've added Shimi — a small, smartphone-connected bot that can respond to music with dance and sound — to the mix.

Shimi shimmies. (Mason Bretan via The Washington Post)

Shimon and the Shimis (which is a great band name, by the way) are showcased in the above video, in which they jam along with one of their creators, PhD student Mason Bretan. He gave them an arrangement of what he'd be playing and recorded some tracks and cues for them, but in between (when you hear funky electronic noises) they're doing their own thing based on his chord progressions. And the mallet solo in the middle is completely robot-improvised.

(Mason Bretan via The Washington Post)

When Bretan joined the lab five years ago, Shimon was being taught how to compose jazz music on the fly based on music theory. "I jumped right in," Bretan said. "And with Shimi — which don't just generate music, we call them 'robotic musical companions' because you can talk to them and use them to interact with your playlist — with Shimi I've been there from the start."

"I'm always trying something new with the robots, and sometimes they surprise me with something that's sort of out there or pretty cool," he added.

(Mason Bretan via The Washington Post)

His dissertation, which he hopes to turn in by the end of 2015, centers around teaching the robots to understand their physical constraints and abilities.
"So the goal is that if you gave the same input to a robot with 20 arms, it would perform differently than an eight-armed robot because it would be optimizing its performance," he said."Combined with the new algorithm we have for jazz music improvisation, these skills really allow them to more optimally achieve musical goals."

And while he certainly doesn't want to replace human musicians like himself with robots, he's excited about the mechanical abilities they have that we don't.
"I mean, Shimon already has four arms and can hold eight mallets," he said, "So it can already do something a person can't."

ORIGINAL: Washington Post
By Rachel Feltman
Jan 14, 2015

Crazy! Spider Launches Slingshot Web to Snag Prey (Video)

The spider bunches up a silky string in its legs and waits till the right moment to release it. Credit: Jeff Cremer / Perunature.com

A new video has captured the remarkable tactic a tiny spider uses to catch insects: It uses its web as a slingshot to fling itself and the web at unsuspecting prey.

The video of the bizarre Amazonian spider was posted to YouTube on Jan. 8 and has garnered more than 250,000 views so far.

Georgia Institute of Technology graduate student Troy Alexander first noticed the unusual spider acrobatics at the Tambopata Research Center, an Amazon jungle lodge in Peru.

The tiny spider, which measures no more than 0.1 inch (3 millimeters) across, belongs to the family Theridiosomatidae, commonly known as Ray spiders. [In Photos: Spiders Hatched from Web Towers]

Though the spider family was identified about 80 years ago, very little is known about these tiny critters. The team thinks the particular spider may be the species Naatlo splendida but needs to collect specimens to be sure, Phil Torres, a Rice University ecology graduate student who has documented the spider's behavior, wrote in an email.

Spider acrobat

The miniscule spider builds a fairly ordinary web, about the size of the palm of a human hand. But in the middle, it creates a silk drawstring that it affixes to a nearby solid surface, but bunches up in the terminal hooks on its legs to pull the web off-center into a cone shape. The tiny hunter waits until it somehow senses the approaching bugs, and then releases the drawstring.

"The web goes flying, and so does Mr. Spider," said Jeff Cremer, the photographer who captured the spider's daredevil move. The flying web makes it much more likely that the hapless bug will become entangled in the silky lure.

The surprise attack works because the tension developed in the web is enough to launch the whole ensemble with high acceleration. (The hardy spiders aren't fazed by the speed.)

Other weird webs

The tactic may ensure that the webs can entangle even slow-flying insects such as mosquitoes, one of the spiders' preferred prey. Most spiders rely on the stickiness of their webs to trap flying insects, but at low speeds, the force of impact may not be enough to entrap the bugs.

"This method of flinging the web appears to make it much more likely that the prey will get tangled, as they seem to be getting slammed into its sticky web regardless of the prey's original flight speed," Torres said.

The tiny spider in its web. Credit: Lary Reeves / Perunature.com

The spider isn't looking at the prey when it releases its lure, so the researchers think the spider is waiting to sense the vibrations of the bug's wing beats, Cremer told LiveScience.

This isn't the only unusual method spiders use to attract prey. Some spiders create charged webs that suck prey in using electrostatic attraction. Others weave elaborate ladderlike webs.
Follow Tia Ghose on Twitter and Google+. Follow LiveScience @livescience, Facebook & Google+. Original article on LiveScience.



ORIGINAL: Live Science
By Tia Ghose, Staff Writer
January 14, 2014

What Is This? Mysterious Amazon Web Baffles Scientists

ORIGINAL: LiveScience
By Douglas Main, Staff Writer

September 04, 2013

This strange formation found in the Peruvian Amazon resembles a tiny spire surrounded by a webby picket fence and is about 2 centimeters (0.8 inches) wide. Credit: Troy Alexander / Tambopata Research Center

A bizarre-looking web structure has been found in the Peruvian Amazon, and apparently nobody knows what it is, not even scientists.

The strange formation resembles a tiny spire surrounded by a webby picket fence and is about 2 centimeters (0.8 inches) wide. Georgia Tech graduate student Troy Alexander first spotted one of these on the underside of a tarp near the Tambopata Research Center in the Peruvian Amazon. At first he thought it might have been an aborted moth cocoon, he wrote on Reddit. But then he found several more, all of which looked quite similar.

He posted the photos to Reddit and asked other scientists to help him out, besides making queries around the Tambopata Research Center, to no avail. His guess is that "there are eggs in the base of the maypole in the middle of the horse corral, though it might be something pupating," he wrote on Reddit. [See Images of Weird Amazon Web Structure]

Chris Buddle, an arachnologist at McGill University, said that neither he nor any of his associates know what it is. "I have no clue," he said. It's "a seriously fascinating mystery."

"I have no idea what animal made that," Norman Platnick, curator emeritus of spiders at the American Museum of Natural History in New York, told LiveScience.

The weird structure was first spotted on the underside of a tarp near the Tambopata Research Center in the Peruvian Amazon. Credit: Troy Alexander / Tambopata Research Center

So far, Redditors and others have guessed that it could be some kind of moth cocoon, an intricate defense for spider eggs, or even the fruiting body of some type of fungus.

Alexander fell in love with the Peruvian Amazon while on vacation there, he told Colossal, an art blog. So he asked his adviser if he could take a leave of absence to be a volunteer researcher. Shortly thereafter, Alexander flew back to Peru to work at the Tambopata Macaw Project, which focuses on parrot biology and conservation, he told Colossal.

If whatever produces this structure turns out to be a new species, it should come as no surprise — the world's rain forests are expected to perhaps contain millions of new species of arthropods (a group of animals with hard exoskeletons, which includes spiders and insects), according to various scientific estimates. One survey of arthropods in Panama's jungle, in an area about the size of Manhattan, found 25,000 species of insects, spiders and other arthropods, 70 percent of which were new to science. That study also found that there were 300 arthropod species for every one mammal species.

Email Douglas Main or follow him on Twitter or Google+. Follow us @livescience, Facebook or Google+. Article originally on LiveScience.

In college at 12, off to start her Ph.D. at 16, Tigard's Tesca Fitzgerald blazes new intellectual territory

ORIGINAL: Oregon Live
By Betsy Hammond, The Oregonian
June 12, 2013

 

At age 16, Tesca Fitzgerald will graduate with honors Sunday from Portland State University and head to a prestigious computer science Ph.D. program. Those who know her well say she is unfailingly fun to be around and always likes to try new things, whether tap dance, a new route to the bus stop or stretching software past what its designers thought were the limits. (Beth Nakamura/The Oregonian) 

During her first week in college, in a discrete mathematics class at Portland Community College, Tesca Fitzgerald sat in the back of the room trying not to call attention to herself. A diligent student, she soon raised her hand and asked a question.

Every head in the room swiveled. Why such a childlike-voice in advanced college math?

The pint-size pony-tailed 12-year-old would go on to ace the class.

Now 16, the self-possessed teen from Tigard will graduate Sunday from Portland State University with honors in computer science. Oregon's six other public universities will hold graduations Saturday and Monday.

After being heavily wooed by several of the nation's top computer science programs, Fitzgerald is headed to Georgia Tech to earn her Ph.D. with a specialty in artificial intelligence.

Over and over, she has turned heads by quietly pushing the envelope to pull off intellectual feats. Explaining one of them, with a simplicity that explains many, she says, "It was because I wanted to do something different that nobody had done before."

With her degree and know-how, Fitzgerald could easily have scored a high-paying job at her choice of Portland firms. Most of her fellow C.S. majors have done just that.

Her desire to stretch exploration of human and artificial intelligence explains her plans to instead move 2,600 miles from the parents and sisters she adores to spend six years or more earning a doctorate.

She chose Georgia Tech because it offers a computer science specialty called interactive computing that will allow her to delve into cognitive science, neuroscience and other interdisciplinary arenas.

"My passion lies in finding new solutions to new problems," she says.

Her talent for computing showed early, thanks in part to an unusual home environment. Her parents, both with MBAs, worked at home a lot, half time for her trust-manager mom, Ami, full time for her self-taught database designer dad, Mark.
He had a lot of computers, enough that all three daughters could bang around on them from infancy and got one of their own as preschoolers.

One scene from a plane, as recalled by Ami Fitzgerald: When Tesca was not yet 2, she and her mother took a flight, each with her own laptop, unusual for a toddler in the 1990s. While Ami worked, Tesca played a simple interactive game, appearing to deftly use the computer as she sucked on her pacifier. Other passengers gaped.

At landing time, mother told daughter to shut down her computer, and she did. But Ami struggled to get hers off, even after she yanked out the battery pack. A flustered flight attendant insisted she shut it down.

From the back of the plane, a chorus of voices shouted: "Ask the baby." Fitzgerald passed the laptop to Tesca, who did, indeed, turn it off.

"The whole back of the plane erupted," Ami Fitzgerald says.

The program Tesca played was a Reader Rabbit game designed to teach 4- to 6-year-olds letters, sounds and words. Her parents assumed she was just enjoying the goofy graphics and punching random keys.

When older sister Tayt was 5, her teacher declared her ready to read and sent home easy picture books. On her first try, Tayt did well.

Tesca, not yet 3, said what any little sister might: "My turn." Then, to her mother's astonishment, "She read and read and read. Every book you could put in front of her, she could read."

At age 2, with help only from Reader Rabbit, she had cracked the code.

On trips to and from Tayt's school, Ami Fitzgerald would strap 3-year-old Tesca in her car seat and hand her second-grade books. The toddler greedily consumed them.

"That's when I realized, 'Huh, we're going to have an issue,'" Ami Fitzgerald says.

At age 8, a pony-tailed Tesca Fitzgerald made a chess move in a game against her big sister, Tayt. The two super-smart sisters went through high school, Portland Community College and Portland State University together. Both graduate Sunday, Tayt with a degree in English, Tesca with hers in computer science. Bob Ellis / The Oregonian / 2005

She was a successful certified trust and financial adviser with a full-time career. She had barely heard of home schooling and had no idea how to teach.

But super-bright Tayt was being bullied at school. Ultra-bright Tesca was so far off the charts no regular classroom would fit.

So Ami Fitzgerald became a home-schooling mom, a role she still plays for 13-year-old Tylise.

Tesca Fitzgerald has a prodigious ability to memorize, lightning-fast learning skills and a passion for cutting-edge computing, says her senior thesis adviser, associate computer science professor Bart Massey. But his star student says another factor helps explain her trajectory: robotics team.

With its zany atmosphere, novel challenges and reward for smart coding, robotics taught her how much fun she could have writing software as part of a team, she says.

Almost by chance, Tesca got to take part at age 5 in an organized robotics program that has thousands of mostly middle-school-age Oregonians building and programming rudimentary robots for table-top contests each year.

Tayt was invited to help form a team. Tesca tagged along. On Day One, the woman guiding the team asked Tesca, "Do you want to learn how to program the robot?" She never looked back.

"I was the lead programmer that year," she says. "I loved the challenge, and I kept coming back to try to take it to the next level." As a member of the FIRST LEGO League's Fire-breathing Rubber Duckies, she programmed robots for seven years, culminating when she led the Duckies to the world competition as a 13-year-old PCC student.

Teams receive identical, easy-to-program kits. Tesca, naturally, found unprecedented ways to do more.

Tesca Fitzgerald, left, then a 14-year-old community college student, took part in a state robotics competition with friends Amiel Patton-Hall and Jevon Streicher. "Tesca is extremely smart and it's a ball to have conversations with her," says Patton-Hall, who took college physics at PSU with Fitzgerald this year. Randy Rasmussen/The Oregonian/2011 One year a new programmable box was introduced, with room to give the robot only five series of moves because the visual programming language took up so much space.

After reading 100 pages of technical background, Tesca found an out: She would write lots of programs to direct the robot's movements in plain text programs that take up little room. She would write only one program in the bulky built-in visual language -- one that could translate her text commands into the visual programming that was the only language the robot could understand.

Her team advanced to the international meet but was nearly disqualified there, Ami Fitzgerald says. "They didn't think a 10-year-old could do that work. It was such a unique concept, even the (organizers) had never thought of it and were sure a grown-up must have come up with it."

But the teen confidently made her case to 15 dubious adults. It helped that she is an unusually poised public speaker who has, among other things, helped keynote a major Google science fair event in New York City. Even so, she was asked to submit to a software exam and show her transcript before they relented.

Two years later, she reached her mini-robot zenith: She spent 600-plus hours to write and perfect a complex artificial intelligence code so the robot could make its own decisions and operate itself. Designers of the robotics program flew in from Europe and talked to her for hours about how she pushed their software beyond what any had imagined possible.

"These adults learned from someone who had tested their software to the absolute limit," Ami Fitzgerald says.

Massey, the honors thesis adviser, says Tesca Fitzgerald is still enlightening her elders. The speed, versatility and creativity she's exhibited in creating a program to test-drive user interfaces, researching machine learning logarithms and other projects have wowed people more than twice her age, he says.

"That's how it should be with your best undergraduates. By the end, they're teaching you stuff."

--Betsy Hammond

Giving graphene the bends makes it transistor-ready

ORIGINAL: New Scientist

 by Douglas Heaven

23 November 2012

Transistor-ready (Image: Alfred Pasieka/Getty)

Sometimes bending something destroys it, but graphene grown on a rippling surface develops the semiconducting properties required for it to act as a transistor. The technique could be what's needed for the wonder material to finally replace silicon as the bedrock of computing.

Graphene is a sheet of carbon just one atom thick, with the atoms arranged in a hexagonal grid, like chicken wire. As well as being thin, super-strong and very flexible, this structure allows electrons to zip through at high speeds. It therefore seems poised to become the basis for ultra-fast computers.

But there's a problem. Materials used to make transistors have to be able to switch current on and off to create logic circuits. This switchability depends on there being a difference, known as a band gap, between the energy possessed by the material's free electrons, and the energy they would need to move around and conduct electricity. Only applying the right amount of external energy allows electrons to jump the band gap to become conducting.

Semiconductors like silicon have band gaps, making for good transistors. But because of its natural conductivity, graphene has a band gap of zero – making it unsuitable for transistors.

Nanoribbon solution

Various solutions have been proposed for turning graphene into a semiconductor, including adding an insulating layer between two layers of graphene to reduce its conductivity, or carving it into very narrow ribbons, which alters its structure, making it easier to turn current off.

However, both of these use conventional etching techniques, placing limits on just how small such graphene transistors could get. For example, creating ribbons any less than 10 nanometres wide has until now left them with edges so ragged that the band gap disappears.

Now Ed Conrad at the Georgia Institute of Technology in Atlanta and colleagues have found a way to create much narrower nanoribbons, without destroying their semiconductor capabilities, in a much simpler way.

The trick was to grow graphene sheets on a rippling surface covered in parallel trenches, each 18 nanometres deep. The team found that where the surface of the sheet dipped into a trench, the graphene's properties became semiconducting, with a band gap of 0.5 electronvolts, rather like the nanoribbons. Crucially, however, these strips of semiconductor were just 1.5 nanometres wide and sleek, not ragged.

Silicon replacement?

"The results are very important, because the existence of a band gap makes it possible to use graphene in nanoelectronics," says Luis Brey at the Materials Science Institute in Madrid, Spain. But the reason the gap exists is not yet clear. "More theoretical work is needed in order to understand how a 0.5 electronvolt gap appears in this structure," he says.

Chris Howard at University College London calls the work a strong development that opens up many potential applications, including high-performance electronics.

Silicon won't be replaced just yet, adds Conrad. "But graphene could push Moore's law to its limits."

Journal reference: Nature Physics, DOI: 10.1038/nphys2487

La extraña relación del ARN con el hierro

ORIGINAL: Noticias de la ciencia

Cuando comenzó la vida en la Tierra, el hierro pudo haber realizado en diversos aspectos el trabajo del magnesio, haciendo posible la vida en un entorno muy distinto del actual.

En la tabla periódica de los elementos, el hierro y el magnesio están alejados. Pero un nuevo hallazgo sugiere que hace tres mil millones de años, el hierro hizo el trabajo que el magnesio hace hoy para que el ácido ribonucleico (ARN), una molécula esencial para la vida, asuma las formas moleculares necesarias para la biología.

Hay bastantes indicios de que la evolución de la vida pasó por una etapa arcaica durante la cual el ARN desempeñó un papel protagonista, haciendo en muchos aspectos el trabajo del ADN y de las proteínas antes de su aparición. En aquel pasado remoto, hace más de tres mil millones de años, el entorno carecía de oxígeno , pero tenía gran cantidad de hierro disponible.

Tal como subraya Carl Pilcher, director del Instituto de Astrobiología de la NASA, uno de los mayores desafíos en la astrobiología es comprender cómo comenzó la vida en la Tierra hace miles de millones de años, cuando el entorno era muy diferente al de hoy. Los resultados del nuevo estudio sugieren de qué modo las condiciones en la Tierra primigenia pudieron ser propicias para el desarrollo de la vida.

En este estudio, el equipo de Loren Williams, del Instituto Tecnológico de Georgia (Georgia Tech) en Atlanta, Estados Unidos, realizó experimentos y cálculos numéricos para demostrar que en un escenario con las mismas condiciones de la Tierra primigenia, incluyendo una gran escasez de oxígeno, el hierro es capaz de sustituir al magnesio y permitir al ARN asumir las formas que necesita para catalizar las reacciones químicas de la vida simple. De hecho, aquel ARN primigenio catalizó las reacciones mejor con el hierro que con el magnesio.

La motivación principal de esta investigación fue atisbar la función del ARN bajo las condiciones más probables de la Tierra primitiva. La hipótesis de Williams y sus colegas es que el ARN evolucionó en presencia del hierro y está optimizado para funcionar con ese elemento.

Loren Williams. (Foto: Gary Meek / Georgia Tech)

El oxígeno gaseoso libre era casi inexistente en la atmósfera terrestre de hace más de tres mil millones de años. Cuando el oxígeno comenzó a entrar en el ambiente, como producto de la fotosíntesis, oxidó al hierro terrestre disponible, formando así masivos depósitos de hierro en bandas. El estudio reciente indica que el ARN empezó entonces a utilizar el magnesio, resultando ello en el desarrollo de la vida tal como la conocemos hoy.

En futuros estudios, los investigadores planean investigar qué funciones del ARN se pueden realizar con hierro y no con magnesio.

En la investigación, también han trabajado Shreyas Athavale, Anton Petrov, Roger Wartell, Stephen Harvey, Chiaolong Hsiao y Nicholas Hud, todos del Georgia Tech.

El estudio fue financiado por el Instituto de Astrobiología de la NASA, dirigido desde el Centro de Investigación Ames de la NASA, en Moffett Field, California.

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On early Earth, iron may have performed magnesium's RNA folding job

ORIGINAL: eScienceNews

May 31, 2012

Loren Williams, professor in the Georgia Tech School of Chemistry and Biochemistry, used experiments and numerical calculations to show that in plausible early earth conditions, iron can substitute for magnesium in RNA binding, folding and catalysis. Georgia Tech/Gary Meek.

Jessica Bowman (left) and Loren Williams from the Georgia Tech School of Chemistry and Biochemistry assess a gel showing that RNA is not degraded by iron if oxygen is omitted. Based on these results, Williams hypothesizes that RNA evolved on the early earth in the presence of iron and is optimized to work with iron. Georgia Tech/Gary Meek.

Georgia Tech biology postdoctoral fellow Shreyas Athavale (left) and chemistry and biochemistry professor Loren Williams look at a gel showing the products of a ribozyme reaction that was run with iron instead of magnesium. Under identical anaerobic conditions, the activity of two enzymes was enhanced in the presence of iron, compared to their activity in the presence of magnesium . Georgia Tech/Gary Meek  .

On the periodic table of the elements, iron and magnesium are far apart. But new evidence suggests that 3 billion years ago, iron did the chemical work now done by magnesium in helping RNA fold and function properly. There is considerable evidence that the evolution of life passed through an early stage when RNA played a more central role before DNA and coded proteins appeared. During that time, more than 3 billion years ago, the environment lacked oxygen but had an abundance of soluble iron.

In a new study, researchers from the Georgia Institute of Technology used experiments and numerical calculations to show that iron, in the absence of oxygen, can substitute for magnesium in RNA binding, folding and catalysis. The researchers found that RNA's shape and folding structure remained the same and its functional activity increased when magnesium was replaced by iron in an oxygen-free environment.

"The primary motivation of this work was to understand RNA in plausible early earth conditions and we found that iron could support an array of RNA structures and catalytic functions more diverse than RNA with magnesium," said Loren Williams, a professor in the School of Chemistry and Biochemistry at Georgia Tech.

The results of the study were published online on May 31, 2012 in the journal PLoS ONE. The study was supported by the NASA Astrobiology Institute.

In addition to Williams, Georgia Tech School of Biology postdoctoral fellow Shreyas Athavale, research scientist Anton Petrov, and professors Roger Wartell and Stephen Harvey, and Georgia Tech School of Chemistry and Biochemistry postdoctoral fellow Chiaolong Hsiao and professor Nicholas Hud also contributed to this work.

Free oxygen gas was almost nonexistent more than 3 billion years ago in the early earth's atmosphere. When oxygen began entering the environment as a product of photosynthesis, it turned the earth's iron to rust, forming massive banded iron formations that are still mined today. The free oxygen produced by advanced organisms caused iron to be toxic, even though it was -- and still is -- a requirement for life.

This environmental transition triggered by the introduction of free oxygen into the atmosphere would have caused a slow, but dramatic, shift in biology that required transformations in biochemical mechanisms and metabolic pathways. The current study provides evidence that this transition may have caused a shift from iron to magnesium for RNA binding, folding and catalysis processes.

The researchers used quantum mechanical calculations, chemical footprinting and two ribozyme assays to determine that in an oxygen-free environment, iron, Fe2+, can be substituted for magnesium, Mg2+, in RNA folding and catalysis.

Quantum mechanical calculations showed that the structure of RNA was nearly identical when it included iron or magnesium. When large RNAs fold into native, stable structures, negatively charged phosphate groups are brought into close proximity. The researchers calculated one small difference between the activity of iron and magnesium structures: more charge was transferred from phosphate to iron than from phosphate to magnesium.

Chemical probing under anaerobic conditions showed that iron could replace magnesium in compacting and folding large RNA structures, thus providing evidence that iron and magnesium could be nearly interchangeable in their interactions with RNA.

Under identical anaerobic conditions, the activity of two enzymes was enhanced in the presence of iron, compared to their activity in the presence of magnesium. The initial activity of the L1 ribozyme ligase, an enzyme that glues together pieces of RNA, was 25 times higher in the presence of iron. Activity of the hammerhead ribozyme, an enzyme that cuts RNA, was three times higher in the presence of iron compared to magnesium.

"The results suggest that iron is a superior substitute for magnesium in these catalytic roles," said Williams, who is also director of the Center for Ribosomal Origins and Evolution at Georgia Tech. "Our hypothesis is that RNA evolved in the presence of iron and is optimized to work with iron."

In future studies, the researchers plan to investigate what unique functions RNA can possess with iron that are not possible with magnesium.

Source: Georgia Institute of Technology Research News