Friday, September 30, 2016

Emory's 'Rolosense' rolling to finals of Collegiate Inventors Competition

“I think the advantage we have with our technology is that it's so simple," says Aaron Blanchard, left (a PhD student in Emory's Laney Graduate School and Coulter Department of Biomedical Engineering at Georgia Tech and Emory), shown using the Rolosense with his advisor, Emory chemist Khalid Salaita. 

By Carol Clark

The first rolling DNA motor – the biological equivalent of the invention of the wheel for the field of DNA machines – is headed from its origins in an Emory University chemistry lab to the finals of the 2016 Collegiate Inventors Competition in Washington D.C.

Kevin Yehl and Aaron Blanchard make up one of six teams of graduate students who will be flown to the finals in early November. Yehl and Blanchard developed the DNA motor (dubbed Rolosense), and its application as a chemical sensor, in the laboratory of their advisor – Emory chemist Khalid Salaita.

Blanchard is a PhD student in Emory's Laney Graduate School and the Coulter Department of Biomedical Engineering (BME) at Georgia Tech and Emory, while Yehl recently graduated from Emory with a PhD in chemistry.

The entries of the elite student teams represent the most promising inventions from U.S. universities. “Their ideas will shape the future,” wrote Michael Oister, CEO of the National Inventors Hall of Fame, in a letter announcing the finalists.

The Collegiate Inventors Competition annually gives out about $100,000 in cash prizes and is considered the foremost program in the country encouraging invention and creativity in undergraduate and graduate students. The competition also promotes entrepreneurship, by rewarding ideas that hold value for society.

The Rolosense is 1,000 times faster than any other synthetic DNA motor. Its speed means a simple iPhone microscope can capture its movement through video, giving it potential for real-world applications, such as disease diagnostics.

Kevin Yehl sets up a smart-phone microscope to get a readout for the particle motion of the rolling DNA-based motor.

"It's exciting," Yehl says. "Previous winners have gone on to start companies with their inventions and become successful scientists. It will be great to get feedback from the judges on the Rolosense."

The judges will include inductees to the National Inventors Hall of Fame, officials from the U.S. Patent and Trademark Office, and scientists from the global healthcare firm AbbVie.

Some of the best discoveries involve serendipity, and that was the case for the Rolosense. Yehl was working last year as a post-doctoral fellow in the Salaita lab, which specializes in visualizing and measuring mechanical forces at the nano-scale. He was conducting experiments using enzymatic nano-particles – micron-sized glass spheres. “We were originally just interested in understanding the properties of enzymes when they’re confined to a surface,” Yehl says.

During the experiments, however, he learned by accident that the nano-particles roll. That gave him the idea of constructing a rolling DNA-based motor using the glass spheres.

The field of synthetic DNA-based motors, also known as nano-walkers, is about 15 years old. Researchers are striving to duplicate the action of nature’s nano-walkers. Myosin, for example, are tiny biological mechanisms that “walk” on filaments to carry nutrients throughout the human body. 

So far, however, mankind’s efforts have fallen far short of nature’s myosin, which speeds effortlessly about its biological errands. Some synthetic nano-walkers move on two legs. They are essentially enzymes made of DNA, powered by the fuel RNA. These nano-walkers tend to be extremely unstable, due to the high levels of Brownian motion at the nano-scale. Other versions with four, and even six, legs have proved more stable, but much slower. In fact, their pace is glacial: A four-legged DNA-based motor would need about 20 years to move one centimeter.

 A cell phone app is in the works.
The Rolosense design mows over these limitations. Hundreds of DNA strands, or “legs,” are allowed to bind to the sphere. These DNA legs are placed on a glass slide coated with the reactant: RNA.

The DNA legs are drawn to the RNA, but as soon as they set foot on it they destroy it through the activity of an enzyme called RNase H. As the legs bind and then release from the substrate, they guide the sphere along, allowing more of the DNA legs to keep binding and pulling.

“The Rolosense can travel one centimeter in seven days, instead of 20 years, making it 1,000 times faster than other synthetic DNA motors,” Salaita says. “In fact, nature’s myosin motors are only 10 times faster than the Rolosense, and it took them billions of years to evolve.”

The researchers next demonstrated the Rolosense could be used to detect a single DNA mutation by measuring particle displacement. Yehl simply glued lenses from two inexpensive laser pointers to the camera of an iPhone to turn the phone’s camera into a microscope and capture videos of the particle motion.

The simple, low-tech method could come in handy for doing diagnostic sensing in the field, or anywhere with limited resources.

Nature Nanotechnology published the work on the rolling DNA motor. The researchers have filed an invention disclosure patent for the concept of using the particle motion of the Rolosense as a sensor for everything from a single DNA mutation in a biological sample to heavy metals in water.

Yehl has since left Emory for a position at MIT, but he continues to work with Salaita and Blanchard on refining the Rolosense.

Blanchard, who has a background in computer coding, is integrating the data analysis of the Rolosense into a smart phone app that will provide a readout of the results.

“I feel really fortunate as a graduate student to be working on this project,” Blanchard says. “As the molecular detection field grows, I think that Rolosense will grow with it.”

For their demonstration during the finals, Yehl and Blanchard plan to hand the judges smart phones and samples of water (including some containing lead), and let the judges use Rolosense to test the samples.

“It can be easy to dazzle with complex technologies like a robot,” Blanchard says, “but I think the advantage that we have with our technology is that it’s so simple. We can let the judges see for themselves how they can use Rolosense to quickly learn something useful, like whether a water source is contaminated with a heavy metal.”

Nano-walkers take speedy leap forward with first rolling DNA motor
Chemists reveal the force within you
Molecular beacons shine light on how cells crawl

Wednesday, September 28, 2016

Psychologists create 'listicle' of unlikely study authors

Long before he became famous for landing a plane on the Hudson River, Chesley Sullenberger III published a scientific paper on humor and vision. Image shows a detail from the new movie "Sully."

Benedict Carey writes in The New York Times about how Emory psychologist Scott Lilienfeld and a colleague created a "listicle" of psychology studies by unlikely authors. Below is an excerpt:

"The study was almost laughably arcane: Air Force cadets’ pupils tended to dilate more when they read cartoons they thought were funny than for ones they didn’t think were funny.

"But the real punch line of this 1978 experiment — 'Pupillary size as an indicator of preference in humor,' published in the journal Perceptual and Motor Skills — is what became of one of the authors, listed as Sullenberger, C. B.

"Chesley B. Sullenberger III is the retired airline captain who safely landed US Airways Flight 1549 in the Hudson River in 2009 and the hero of the new Clint Eastwood-directed movie 'Sully.' By virtue of publishing his small experiment, he is also a member of an unusual club. Call it the you’ll-never-guess-who-wrote-that collection of authors of psychology studies."

Read the whole article in The New York Times.

Wednesday, September 21, 2016

Status drives men's reproductive success across non-industrial world

The reproductive benefits of status reached their peak in pre-modern empires. A genetic study, for instance, found that 8 percent of men in populations spanning Asia shared nearly identical Y-chromosome sequences with Mongolian ruler Genghis Khan (shown entering the city of Beijing).

By Carol Clark

The reproductive success of men in non-industrialized societies is closely tied to their social status, finds a new meta-analysis published in the Proceedings of the National Academy of Sciences.

The analysis looked at studies of 33 non-industrial societies from around the globe, including hunter-gatherers, nomadic pastoralists and agriculturalists.

“We were surprised to learn that the correlation held up for a range of societies and their different measures for status,” says Adrian Jaeggi, an anthropologist at Emory University focused on primate and human behavioral ecology. “It doesn’t matter whether a man is a better hunter, owns more land or more livestock – men with high social status had more children compared to men with low status.”

Jaeggi co-authored the study with Christopher von Rueden, an anthropologist specialized in leadership studies at the University of Richmond in Richmond, Virginia.

Their findings go against the egalitarian hypothesis, the idea that status was a relatively weak target of selection for modern humans, since most of that evolutionary period involved living as egalitarian hunter-gatherers.

The !Kung bushmen of the Kalahari serve as a classic example of the egalitarianism associated with hunter-gatherer societies. “They are not allowed to brag about their hunting success, it’s not culturally acceptable,” Jaeggi says. “When one of them kills a large animal, he comes back to camp and sits down quietly by the fire and he is modest about it. Their society is built on mutual help. Sometimes a hunter may only be successful one out of every 10 days. But if they all support each other and share their game, on average they eat every day.”

Bushmen in Botswana demonstrate how to start a fire by rubbing sticks together. Such hunter-gatherer societies do not amass material wealth and are built on mutual help and support. Photo by Ian Sewell.

The egalitarian hypothesis posits that it was not until humans shifted from primarily hunter-gatherer societies toward pastoralism, agriculture and industrialization that status became a key driver for male reproductive success. “Once you start acquiring property and other forms of material wealth, you have assets to transmit to your offspring, so you would expect to see status more closely tied to reproductive success,” Jaeggi explains.

In humans, these reproductive benefits of status reached their peak in pre-modern states and empires that enabled powerful rulers to have access to large numbers of women. A genetic study, for instance, found that 8 percent of men in populations spanning Asia shared nearly identical Y-chromosome sequences with Genghis Khan, the Mongolian ruler who died in 1227.

The current meta-analysis suggests that status-seeking was not just a consequence of more formal social hierarchies and the rise of greater inequalities, but an evolved trait.

While a good hunter may not have material wealth, he carries “embodied capital,” measured by qualities like intelligence, skill, good health and reliable social connections, Jaeggi explains.

“Hunter-gatherer societies may actively work towards leveling any hierarchy, but at the same time people are aware of which men are better hunters and that appears to give them a reproductive edge,” he says. “And the relationship between status and reproductive success is as strong for a hunter as it is for a farmer or pastoralist. That indicates a biological basis for striving for status: It’s universally rewarded with the only currency that matters in biology – children.”

Wealthy men across most of the modern, industrialized world, however, tend to have fewer children than poor men. The link between male status and reproductive success is broken, due to women’s rights and access to contraception.

“Women can be more independent and successful in modern society,” Jaeggi says. “They get to decide if they want to continue to reward status-seeking in men by allowing them to have more children. Or whether they want to reward men who are more compliant with what women want.”

Conspicuous consumption may drive fertility down

Thursday, September 15, 2016

Sensory connections spill over in synesthesia

One of the most common forms of synesthesia is when people involuntarily see particular colors in connection with letters, numbers or sounds.

By Quinn Eastman
Woodruff Health Sciences Center

Neuroscientists at Emory University have found that people who experience a mixing of the senses, known as synesthesia, are more sensitive to associations everyone has between the sounds of words and visual shapes. The results are published in the European Journal of Neuroscience.

Synesthesia is a stable trait, and estimated to be present in 1 to 4 percent of people. It can be inherited, although the precise genes have not been identified. One of the most common forms of synesthesia is when people involuntarily see particular colors in connection with letters, numbers or sounds.

Many artists and composers have described their experiences with synesthesia. Children with synesthesia say sometimes that it is distracting when they are trying to read. Thus, understanding the origins of synesthesia may help people with dyslexia or other learning differences, or people who have lost their sight or hearing and are trying to engage in sensory substitution for rehabilitation.

Researchers led by neurologist Krish Sathian recruited 17 people with synesthesia, and asked them to take a form of the IAT (implicit association test). Known for its use probing social attitudes such as racial prejudice, the IAT can also assess "cross-modal correspondences."

An example of a cross-modal correspondence is that we describe musical notes as being "high" or "low" – words that also signify relative positions in space. Another is that we think of some sounds such as "m" and "l" as soft, and are more likely to associate them with rounded shapes. Similarly, we connect hard sounds such as "k" and "t" with angular shapes.

"There's been a debate about synesthesia," Sathian says. "Are the associations synesthetes have just extreme versions of cross-modal correspondences that other people have, or are they qualitatively different?"

Sathian and his colleagues found that people with synesthesia were more sensitive to correspondences between the sounds of pseudowords -- words without meaning in English -- and rounded or angular shapes.

"It shows that something about their synesthesia is spilling over into another domain," he says. "But that spillover is limited to a correspondence that is post-perceptual and symbolic – it's not purely sensory."

Such correspondences are called "sound-symbolic," and may be relevant to the evolutionary origins of language, Sathian adds.

People with synesthesia were not significantly more sensitive to purely sensory associations between the pitch of a sound and the size or position of a shape, compared to non-synesthetes. In this situation, sensitivity on the IAT means that study participants would have a greater difference in response times to congruent pairings of shape and sound (a high position in space, and a high pitch, for example) in comparison to incongruent pairings.

Participants in the study were recruited through advertisements on the Emory campus and screened with an online test called the Synesthesia Battery. This test confirms whether people who report they have synesthesia have consistent associations.

A connection between letters or other symbols and colors, also known as "grapheme-color" synesthesia, was the most common type in the Emory study. It may represent the presence of idiosyncratic wrinkles in how people learned their letters or other symbols during childhood. Indeed, Sathian notes that one study suggests that a popular brand of refrigerator magnets had an influence on what letter-color associations people with this form of synesthesia developed.

To be sure, people with synesthesia are not all the same, says senior research associate Simon Lacey, the first author of the paper. Some describe experiencing connections between shapes and tastes, or porous boundaries between self and non-self (so-called "mirror touch")."

Brain imaging studies have shown that people with synesthesia tend to be wired differently: they display hyperconnectivity between parts of their brains related to their synesthetic experiences. Scientists have proposed that synesthesia represents alterations in pruning, the process of editing connections between brain cells.

Sathian is professor of neurology, rehabilitation medicine and psychology at Emory University and executive director of the Rehabilitation R&D Center for Visual and Neurocognitive Rehabilitation at the Atlanta Veterans Affairs Medical Center. Sathian and collaborator Lynne Nygaard, professor of psychology, are exploring the neural bases of cross-modal correspondences and of synesthesia using brain imaging studies.

Uncovering secrets of sound symbolism

Wednesday, September 7, 2016

Set phasers to stun: Star Trek turns 50

Star Trek blasted audiences with important social messages and fired up enthusiasm for space exploration and science. Among the iconic characters in the series are, from left: Spock (Leonard Nimoy), Captain Kirk (William Shatner) and Montgomery “Scotty” Scott (James Doohan). 

Sidney Perkowitz, Emory emeritus professor of physics, wrote an article for Nature about the impacts of Star Trek on science, technology and society as the science fiction series turns 50. Below is an excerpt:

“Half a century ago, in September 1966, the first episode of Star Trek aired on the US television network NBC. NASA was still three years short of landing people on the Moon, yet the innovative series was soon zipping viewers light years beyond the Solar System every week. After a few hiccups it gained cult status, along with the inimitable crew of the starship USS Enterprise, led by Captain James T. Kirk (William Shatner). It went into syndication and spawned 6 television series up to 2005; there are now also 13 feature films, with Star Trek Beyond debuting in July this year.

“Part of Star Trek's enduring magic is its winning mix of twenty-third-century technology and the recognizable diversity and complexity enshrined in the beings — human and otherwise — created by the show's originator Gene Roddenberry and his writers. As Roddenberry put it, ‘We stress humanity.’ The series wore its ethics on its sleeve at a time when the Vietnam War was raging and anti-war protests were proliferating, along with racial tensions that culminated in major US urban riots in 1967–68.”

Read the whole article in Nature.

Fantastic light: From science fiction to fact

Tuesday, September 6, 2016

Pistil-packing science: Pollen genetics could help fight crime

A European honey bee collects nectar, gathering pollen on its body in the process. Emory biologists Karen Bell and Berry Brosi, who study pollen to monitor the health of ecosystems, say that pollen analysis also holds potential to help with forensic investigations.

By Karen Bell, Berry Brosi and Kevin Burgess

Bell is a post-doctoral fellow in the lab of Brosi, an evolutionary biologist in Emory's Department of Environmental Sciences, focused on the study of bees. Burgess is a biologist at Columbia State University. This article originally ran in The Conversation.

Imagine you're a detective working on a murder case. You have a body, but you believe it was moved from another location. Now what? There's one unexpected tool you might use to follow up on this suspicion: forensic palynology. That's the application of palynology – the study of pollen – to crime investigation.

But how does pollen have any bearing on forensics? While usually unseen, pollen is essentially ubiquitous in terrestrial habitats, and it is extremely tough. In fact, pollen is so durable that paleontologists can examine fossilized pollen grains in ancient sediments to see what plants grew during prehistoric times. And the “signature” of which pollen grains are present is specific to a particular place (because different plant species occur in different areas) and time (because different plant species flower at different times).

All of that makes pollen an ideal biomarker for linking people and objects to particular places and times, a central need in forensic investigations. Despite this potential utility, forensic palynology has been underutilized, because of its reliance on specialized experts to meticulously identify pollen visually under the microscope.

But recently researchers developed a new technique for identifying pollen, using genetics. By making identification much easier and faster for large numbers of pollen samples, this development has the potential to transform forensic palynology, allowing us to harness the power of pollen to solve crimes.

"Pollen could be a great biomarker to work out where people have been, or where something they were carrying has been," says Emory biologist Karen Bell, shown in the field.

Forensic palynology has been particularly useful in cases where there is suspected movement of evidence, or where a crime has occurred in a location with distinct plant species. For example, following the Bosnian war, investigators uncovered mass graves where bodies had been moved from different locations. Pollen was one of the lines of evidence used to trace bodies to their original burial sites. In a case in New Zealand, a burglar was tracked to the scene of the crime when pollen grains on his clothing were matched to an uncommon plant species growing in front of the victim’s house.

There are many other types of cases where forensic palynology could be applied. Objects under examination in missing person cases could be traced to their origin. Analysts could tie individual criminals' travel histories together based on finding a similar pollen species composition on seized evidence, possibly linking their crimes and providing direction for further investigation. Officials could determine illegal imports' country of origin.

Traditionally, forensic palynology is done by examining pollen grains under a microscope and comparing them to known pollen morphology. This is a highly specialized skill, and there are few experts able to identify plant species based on the size, shape and color of the pollen grains. After all, researchers estimate almost 400,000 species of plants live on our planet today. There is currently only one person employed full-time as a forensic palynologist in the U.S.

Forensic palynology is further limited by the labor intensiveness of morphological identification. Frequently it's impossible to determine the exact species present; identification is typically to a genus or family of plants – a group of species, in other words. This limits the technique's utility, because while many plant species occur in a small geographic range, the genus or family in which they belong may cover a much broader area.

"Because pollinator species are declining so rapidly, we need high through-put methods of analyses," Bell says, noting that those same techniques may make pollen genetics practical for other uses.

In a recently published article in Forensic Science International Genetics, we revealed how identifying pollen through DNA barcoding, on its own or with traditional palynology, could be a practical alternative.

DNA barcoding is a way to identify species via their species-specific genetic signatures. To do this for pollen, scientists sequence the DNA from a genetic region known to occur in all plants, but which varies from species to species. There are two parts to the standardized sequence we use for plant DNA barcoding. One is a section of the large subunit of a gene called ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL for short). The other is a gene called maturase-K (matK). These genes are both essential for a plant to survive, and are thus present in all plants. Once an investigator sequences these gene regions from a sample, they can be compared to a database containing all the known DNA sequences of rbcL and matK to identify the species.

To DNA barcode pollen, the first step is to extract the DNA. Pollen grains produce the male reproductive cells (sperm) of the plant. Each pollen grain has a tough outer layer called the exine, made of a protein called sporopollenin. We need to break the exine in order to release the DNA that's protected inside. We do this by putting the pollen grains in a tube filled with small silica beads and shaking vigorously for several minutes. Once the cells release their DNA, it can be purified and then sequenced.

High-throughput DNA sequencing is a methodological advance that has made pollen DNA barcoding feasible. This new method allows researchers to sequence multiple pieces of DNA at the same time, without separating them first. It's a key innovation because forensic pollen samples typically contain a mixture of species. Without high-throughput sequencing, these species would first need to be painstakingly separated – and then we'd be back to the same efficiency problems of traditional morphological analysis. With high-throughput sequencing, the whole mixture of pollen grains can be ground up in one sample, the DNA isolated and sequenced, and matched to a database. This technique is known as DNA metabarcoding.

Although pollen DNA barcoding has not yet been applied to forensic palynology, similar techniques have been used to quality test honey, determining the plant species on which bees have been foraging. Pollen DNA barcoding has also contributed to air quality monitoring, when it's useful to know what allergens are present in the environment.

Optimizing these methods for forensics may require some small modifications, such as dealing with very few pollen grains in a sample. Ideally a standardized method should be developed for forensics, to enable comparisons between different cases, studied by different scientists. It will also be necessary to expand the reference databases, to include more species that might be of interest to forensics specialists.

But while there are still a few hurdles to overcome, eventually pollen DNA barcoding could become a common and scientifically rigorous technique in law enforcement and national security.

Pollinators vital to food supply facing extinction, U.N. report warns
Bees 'betray' their flowers when pollinator species decline The Conversation