Commercial approaches to ultrasensitive protein detection are starting to become available, but they are based on expensive optics and fluid handlers, which make them relatively bulky and expensive and constrain their use to laboratory settings.

Knowing that having this sort of diagnostic system available as a point-of-care device would be critical for many conditions, especially traumatic brain injury, engineers at the University of Pennsylvania have developed a test that uses off-the-shelf components and can detect single proteins with results in a matter of minutes, compared to the traditional workflow, which can take days.

Using a standard cellphone camera and a set of strobing LED lights, combined with their lab’s microfluidic droplet generators, the team has developed a system that is a thousand times more sensitive than the standard protein assay, is handheld, and considerably less expensive than the current state-of-the-art single-protein tests first coming to market.

The researchers, led by David Issadore, assistant professor in Penn Engineering’s Department of Bioengineering, and graduate student Venkata R. Yelleswarapu, demonstrated their system in a study published in the Proceedings of the National Academy of Sciences.

The standard protein detection assay, ELISA, involves attaching antibodies to the proteins in question, then measuring how much the sample’s color changes in response to enzymes linked to the antibodies. This process is fast and simple enough to be incorporated in point-of-care devices, like home HIV tests, but only works when the proteins are in large concentrations.

There are currently very few biomarkers for traumatic brain injury because very few of the protein markers of those injuries make their way through the blood-brain barrier. Medical researchers have only recently confirmed that any such markers could be used for a blood test, and given their ultra-low concentrations, that test would need to be much more sensitive than the standard ELISA array.

“By a thousand times more sensitive,'” Issadore says, “we mean that if we had a vial of blood with only a few of the relevant proteins, we can accurately count those proteins, whereas a traditional test couldn’t reliably tell the difference between that vial of blood and one with none of the protein in it. As you keep increasing the number of proteins, the traditional test will eventually be able to detect them, but we can quantify the number of proteins at concentrations a thousand times less than they can.”

Issadore’s approach works by measuring one protein at a time, by breaking apart the sample into microdroplets, each of which contain either a single protein or none at all. His lab’s expertise in microfluidics has produced microchips etched with hundreds of microdroplet generators, all working in parallel.

“Normally, you’d have to measure very precisely how much a sample changes color or fluoresces, but here we’re turning it into tens of millions of yes-or-no questions,” Issadore says. “Digitizing that question brings down the cost of the camera and the surrounding fluid handling equipment, but shifts the problem into how to process tens of millions of those questions, in a way that is reproducible, accurate, inexpensive and portable.”

While an off-the-shelf camera can detect whether a microdroplet contains a fluorescent-marker-bound protein or not, the big challenge was to speed up the process. Existing digital droplet detectors line the droplets up so they can be measured one at a time. Such systems are accurate, but bulky and expensive. They also have limited throughput, because of the need to look at millions of droplets one at a time.

“A thousand droplets a second, the throughput of conventional technologies, is still pretty slow if you need to measure 50 million,” Yelleswarapu says.

Rather than having a single channel, the researchers flow droplets into hundreds of channels that pass by the camera at the same time. The bottleneck, however, is how fast a camera can capture the data.

“Conventionally, that wouldn’t work since the exposure time you’d get from a regular camera is such that the signals from two droplets next to each other would overlap,” Yelleswarapu says. “A cellphone camera takes about a hundred images a second, and that’s far too slow to be useful for us to resolve these droplets. But you can use that camera if the light source you’re using to illuminate the droplet strobes a thousand times faster than the framerate of the camera.”

The trick that makes the Issadore team’s approach work was to encode this strobing light with a signal that would allow them to tease apart one microdroplet from its neighbors.

“We’re strobing the light in a very specific pattern that never repeats itself, which is a technique we borrowed from radar,” Issadore says. “As the signals are going across the screen they get imprinted with this barcode. So even though they overlap with one another, we can tell them apart by which strobe pulse illuminated each droplet.”

Issadore’s group has previously published on traumatic brain injury markers, and has an ongoing research project with Presbyterian Hospital with brain injury patients. They also have a spin-off company, Chip Diagnostics, based at the Pennovation Center, which aims to produce test kits for early cancer diagnostics and traumatic brain injury.

The researchers have developed a ball-shaped VR display that supports up to two users at a time, using advanced calibration and graphics rendering techniques that produce a complete, distortion-free 3D image even when viewed from multiple angles.

Most spherical VR displays in the market are capable of showing a correct image only from a single viewpoint, said lead researcher Sidney Fels, an electrical and computer engineering professor at UBC.

“When you look at our globe, the 3D illusion is rich and correct from any angle,” explained Fels. “This allows two users to use the display to do some sort of collaborative task or enjoy a multiplayer game, while being in the same space. It’s one of the very first spherical VR systems with this capability.”

The system, which the researchers are calling Crystal, includes a 24-inch (600 millimetre) hollow ball-shaped display. The display surface was custom-made to specifications in Ottawa, while four high-speed projectors and one camera used for creating the images, calibration and touch sensing were purchased off-the-shelf.

The researchers are working on a four-person system and see many potential uses for their display in the future, including multiplayer virtual reality games, virtual surgery and VR-aided learning. However, they are focusing on teleconferencing applications and computer-aided design for now.

“Imagine a remote user joining a meeting of local users. At either location you can have a Crystal globe, which is great for seeing people’s heads and faces in 3D,” said Ian Stavness, a computer science professor at the University of Saskatchewan and a member of the research team. “Or you can have a team of industrial designers in a room, perfecting a design with the help of VR and motion tracking technology.”

While the technology is young, the researchers are forecasting a good future for it.

“We’re not saying that spherical VR will replace flat screens or headsets,” said Fels, adding “but we think it can be a good option for VR activities where you still want to see and talk to other people — be it at home or in the office, for work or play.”

The research, described here, was supported by the Natural Sciences and Engineering Research Council of Canada and B-Con Engineering.

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Materials provided by University of British Columbia. Note: Content may be edited for style and length.

Geologists have long known that 42 of Stonehenge’s smaller stones, known as ‘bluestones’, came from the Preseli hills in Pembrokeshire, west Wales. Now a new study published in Antiquity pinpoints the exact locations of two of these quarries and reveals when and how the stones were quarried.

The discovery has been made by a team of archaeologists and geologists from UCL, Bournemouth University, University of Southampton, University of the Highlands and Islands and National Museum of Wales, which have been investigating the sites for eight years.

Professor Mike Parker Pearson (UCL Archaeology) and leader of the team, said: “What’s really exciting about these discoveries is that they take us a step closer to unlocking Stonehenge’s greatest mystery — why its stones came from so far away.”

“Every other Neolithic monument in Europe was built of megaliths brought from no more than 10 miles away.

We’re now looking to find out just what was so special about the Preseli hills 5,000 years ago, and whether there were any important stone circles here, built before the bluestones were moved to Stonehenge.”

The largest quarry was found almost 180 miles away from Stonehenge on the outcrop of Carn Goedog, on the north slope of the Preseli hills.

“This was the dominant source of Stonehenge’s spotted dolerite, so-called because it has white spots in the igneous blue rock. At least five of Stonehenge’s bluestones, and probably more, came from Carn Goedog,” said geologist Dr Richard Bevins (National Museum of Wales).

In the valley below Carn Goedog, another outcrop at Craig Rhos-y-felin was identified by Dr Bevins and fellow geologist Dr Rob Ixer (UCL Archaeology) as the source of one of the types of rhyolite — another type of igneous rock — found at Stonehenge.

According to the new study, the bluestone outcrops are formed of natural, vertical pillars. These could be eased off the rock face by opening up the vertical joints between each pillar. Unlike stone quarries in ancient Egypt, where obelisks were carved out of the solid rock, the Welsh quarries were easier to exploit.

Neolithic quarry workers needed only to insert wedges into the ready-made joints between pillars, then lower each pillar to the foot of the outcrop.

Although most of their equipment is likely to have consisted of perishable ropes and wooden wedges, mallets and levers, they left behind other tools such as hammer stones and stone wedges.

“The stone wedges are made of imported mudstone, much softer than the hard dolerite pillars. An engineering colleague has suggested that hammering in a hard wedge could have created stress fractures, causing the thin pillars to crack. Using a soft wedge means that, if anything were to break, it would be the wedge and not the pillar,” said Professor Parker Pearson.

Archaeological excavations at the foot of both outcrops uncovered the remains of human-made stone and earth platforms, with each platform’s outer edge terminating in a vertical drop of about a metre.

“Bluestone pillars could be eased down onto this platform, which acted as a loading bay for lowering them onto wooden sledges before dragging them away,” said Professor Colin Richards (University of the Highlands and Islands), who has excavated Britain’s only other identified megalith quarry in the Orkney islands, off the north coast of Scotland.

An important aim of Professor Parker Pearson’s team was to date megalith-quarrying at the two outcrops. In the soft sediment of a hollowed-out track leading from the loading bay at Craig Rhos-y-felin, and on the artificial platform at Carn Goedog, the team recovered pieces of charcoal dating to around 3000 BC.

The team now thinks that Stonehenge was initially a circle of rough, unworked bluestone pillars set in pits known as the Aubrey Holes, near Stonehenge, and that the sarsens (sandstone blocks) were added some 500 years later.

The new discoveries also cast doubt on a popular theory that the bluestones were transported by sea to Stonehenge.

“Some people think that the bluestones were taken southwards to Milford Haven and placed on rafts or slung between boats and then paddled up the Bristol Channel and along the Bristol Avon towards Salisbury Plain. But these quarries are on the north side of the Preseli hills so the megaliths could have simply gone overland all the way to Salisbury Plain,” said Professor Kate Welham (Bournemouth University).

The research was funded by the British Academy, the Natural Environment Research Council (NERC), the National Geographic Society, the Society of Antiquaries, the Royal Archaeological Institute and the Cambrian Archaeological Association.

In a major scientific step to understand the biology of this iconic apex predator and sharks in general, the entire genome of the white shark has now been decoded in detail.

A team led by scientists from Nova Southeastern University’s (NSU) Save Our Seas Foundation Shark Research Center and Guy Harvey Research Institute (GHRI), Cornell University College of Veterinary Medicine, and Monterey Bay Aquarium, completed the white shark genome and compared it to genomes from a variety of other vertebrates, including the giant whale shark and humans.

The findings are reported in the ‘Latest Articles’ section of the journal Proceedings of the National Academy of Sciences.

Decoding the white shark’s genome revealed not only its huge size — one-and-a-half times the size of the human genome — but also a plethora of genetic changes that could be behind the evolutionary success of large-bodied and long-lived sharks.

The researchers found striking occurrences of specific DNA sequence changes indicating molecular adaptation (also known as positive selection) in numerous genes with important roles in maintaining genome stability ¬¬- the genetic defense mechanisms that counteract the accumulation of damage to a species’ DNA, thereby preserving the integrity of the genome.

These adaptive sequence changes were found in genes intimately tied to DNA repair, DNA damage response, and DNA damage tolerance, among other genes. The opposite phenomenon, genome instability, which results from accumulated DNA damage, is well known to predispose humans to numerous cancers and age-related diseases.

“Not only were there a surprisingly high number of genome stability genes that contained these adaptive changes, but there was also an enrichment of several of these genes, highlighting the importance of this genetic fine-tuning in the white shark,” said Mahmood Shivji, Ph.D., director of NSU’s Save Our Seas Foundation Shark Research Center and GHRI. Shivji co-led the study with Michael Stanhope, Ph.D., of Cornell University College of Veterinary Medicine.

Also notable was that the white shark genome contained a very high number of “jumping genes” or transposons, and in this case a specific type, known as LINEs. In fact this is one of the highest proportions of LINEs (nearly 30%) discovered in vertebrates so far.

“These LINEs are known to cause genome instability by creating double stranded breaks in DNA,” said Stanhope. “It’s plausible that this proliferation of LINEs in the white shark genome could represent a strong selective agent for the evolution of efficient DNA repair mechanisms, and is reflected in the positive selection and enrichment of so many genome stability genes.”

The international research team, which also included scientists from California State University, Monterey Bay, Clemson University, University of Porto, Portugal, and the Theodosius Dobzhansky Center for Genome Bioinformatics, Russia, also found that many of the same genome stability genes in the white shark were also under positive selection and enriched in the huge-bodied, long-lived whale shark.

The discovery that the whale shark also had these key genome stability adaptations was significant because theoretically, the risk of developing cancer should increase with both the number of cells (large bodies) and an organism’s lifespan — there is statistical support for a positive relationship of body size and cancer risk within a species. Interestingly, this does not tend to hold up across species.

Contrary to expectations, very large-bodied animals do not get cancer more often than humans, suggesting they have evolved superior cancer-protective abilities. The genetic innovations discovered in genome stability genes in the white and whale shark could be adaptations facilitating the evolution of their large bodies and long lifespans.

“Decoding the white shark genome is providing science with a new set of keys to unlock lingering mysteries about these feared and misunderstood predators — why sharks have thrived for some 500 million years, longer than almost any vertebrate on earth” said Dr. Salvador Jorgensen, a Senior Research Scientist at the Monterey Bay Aquarium, who co-authored the study.

But the innovations did not end there.

The shark genomes revealed other intriguing evolutionary adaptations in genes linked to wound healing pathways. Sharks are known for their impressively rapid wound healing.

“We found positive selection and gene content enrichments involving several genes tied to some of the most fundamental pathways in wound healing, including in a key blood clotting gene,” said Stanhope. “These adaptations involving wound healing genes may underlie the vaunted ability of sharks to heal efficiently from even large wounds.”

The researchers say they have just explored the “tip of the iceberg” with respect to the white shark genome.

“Genome instability is a very important issue in many serious human diseases; now we find that nature has developed clever strategies to maintain the stability of genomes in these large-bodied, long-lived sharks,” said Shivji. “There’s still tons to be learned from these evolutionary marvels, including information that will potentially be useful to fight cancer and age-related diseases, and improve wound healing treatments in humans, as we uncover how these animals do it.”

Decoding the white shark genome will also assist with the conservation of this and related sharks, many of which have rapidly declining populations due to overfishing,” said Steven O’Brien, a conservation geneticist at NSU, who co-conceived this study. “The genome data will be a great asset for understanding white shark population dynamics to better conserve this amazing species that has captured the imagination of so many.”

This research was funded by NSU’s Save Our Seas Foundation, the Guy Harvey Ocean Foundation, the Hai Stiftung/Shark Foundation, the Monterey Bay Aquarium, and in-kind support from Illumina, Inc., and Dovetail Genomics.