Immune Protein Orchestrates Daily Rhythm Of Squid-bacteria Symbiotic Relationship (Biology)

Nearly every organism hosts a collection of symbiotic microbes–a microbiome. It is now recognized that microbiomes are major drivers of health in all animals, including humans, and that these symbiotic systems often exhibit strong daily rhythms.

A 63x magnification image showing the 4-week-old light organ during the day showing EsMIF (magenta) surrounding the crypt spaces. Host DNA is labeled in blue and the bacteria are labeled in green. ©Eric Koch

New research led by University of Hawai’i at Manoa scientists revealed that, in the mutually beneficial relationship between with the Hawaiian bobtail squid, Euprymna scolopes, and the luminescent bacterium, Vibrio fischeri, an immune protein called “macrophage migration inhibitory factor” or “MIF,” is the maestro of daily rhythms. This finding, published in the Proceedings of the National Academy of Sciences, could provide important clues on factors affecting human microbiome rhythms, as the MIF protein is also found in abundance in mammalian symbiotic tissues.

To survive, the nocturnal Hawaiian bobtail squid depends on V. fischeri, which gives it the ability to mimic moonlight on the surface of the ocean and deceive monk seals and other predators, as it forages for food. The symbiotic bacteria also require nutrition, especially at night when they are more numerous and their light is required for the squid’s camouflage.

The research team, led by Eric Koch, who was a graduate researcher at the Pacific Biosciences Research Center (PBRC) in the UH Manoa School of Ocean and Earth Science and Technology (SOEST) at the time of the study, determined the squid regulates production of MIF as a way to control the movement of specialized immune cells, called hemocytes, which provide chitin for bacteria to feed on.

At night, when the team found MIF was low in the squid’s light organ, hemocytes were allowed into the regions where the bacteria reside and chitin was delivered. During the day, MIF was very high, which inhibits the hemocytes from coming into the symbiotic tissues and dumping their chitin at the wrong time.

This cycling of nutrients has cascading effects on all of the other rhythms associated with the symbiotic system–perhaps affecting overall health, development or reproduction.

For nearly three decades, professors Margaret McFall-Ngai and Edward Ruby at PBRC have used the squid-bacterial symbiosis system to characterize animal microbiomes.

“We had recognized daily rhythms in the squid-vibrio symbiosis since 1996, but how the rhythm is controlled was not known,” said McFall-Ngai. “This study brought the whole thing into sharp focus, allowing us to understand how the rhythm works and how it matures in the animal.”

Such discoveries can pave the way for understanding how microbiomes function–what they do and how they do it–in other organisms and environments.

“A recent study of the mammalian, and human, gut microbiome has shown that MIF is present at high levels and controls the interactions of the microbes with the host cell,” said McFall-Ngai. “As has happened with other phenomena, such a developmental inducers, the simplicity of the squid-vibrio system has provided a window into the mechanisms of symbiosis. Because these mechanisms appear to be highly conserved among all animals, including humans, understanding how they function promises to give us the tools to foster healthy people and resilient ecosystems.”

References: Eric J. Koch, Clotilde Bongrand, Brittany D. Bennett, Susannah Lawhorn, Silvia Moriano-Gutierrez, Marko Pende, Karim Vadiwala, Hans-Ulrich Dodt, Florian Raible, William Goldman, Edward G. Ruby, Margaret McFall-Ngai, “The cytokine MIF controls daily rhythms of symbiont nutrition in an animal–bacterial association”, Proceedings of the National Academy of Sciences Oct 2020, 202016864; DOI: 10.1073/pnas.2016864117 link:

Provided by University Of Hawaii At Manao

Study Discovers Gene That Helps Us Know When It’s Time To Urinate (Biology)

Results suggest ‘sixth sense’ PIEZO2 gene may help body sense a full urinary bladder.

In a National Institutes of Health (NIH)-funded study involving both mice and patients who are part of an NIH Clinical Center trial, researchers discovered that a gene, called PIEZO2, may be responsible for the powerful urge to urinate that we normally feel several times a day. The results, published in Nature, suggest that the gene helps at least two different types of cells in the body sense when our bladders are full and need to be emptied. These results also expand the growing list of newly discovered senses under the gene’s control.

NIH funded researchers discovered that a gene called PIEZO2 may help us sense when our bladders are full, and it is time to urinate. Above is an example of a mouse bladder used in the study. ©Courtesy of Patapoutian lab, Scripps Researcher Institute, La Jolla, CA.

“Urination is essential for our health. It’s one of the primary ways our bodies dispose of waste. We show how specific genes and cells may play critical roles in initiating this process,” said Ardem Patapoutian, Ph.D., professor, Scripps Research Institute, La Jolla, CA and a senior author of the paper. “We hope that these results provide a more detailed understanding of how urination works under healthy and disease conditions.”

Urine is produced when the kidneys extract waste and excess water from the blood and send it to the bladder. Over time, it fills up and expands like a balloon, putting tension on the bladder muscles. Then, at a certain point, the body senses that it is reaching a limit, which triggers the urge to urinate.

The PIEZO2 gene contains instructions for making proteins that are activated when cells are stretched or squeezed. In this study, the researchers found that patients who are born with a genetic deficiency in PIEZO2 have trouble sensing bladder filling while experiments in mice suggested the gene plays two critical roles in this process. It may help certain bladder cells gauge expansion while also sparking neurons to relay tension signals to the rest of the nervous system.

The study was a collaboration between Dr. Patapoutian’s team and researchers working in NIH labs led by Alex Chesler, Ph.D., senior investigator, at the NIH’s National Center for Complementary and Integrative Health (NCCIH) and a senior author of the paper, and Carsten Bönnemann, M.D., senior investigator at the NIH’s National Institute of Neurological Disorders and Stroke (NINDS).

In 2010, Dr. Patapoutian’s team discovered the PIEZO2 gene along with a similar gene called PIEZO1 in a line of mouse brain tumors. Before then, scientists knew of only a few rare examples from flies, worms, and mice in which a gene helped tissue, such as hairy skin cells, sense changes in shape and pressure. Since the discovery, Dr. Patapoutian’s team and others have primarily shown in mice that the PIEZO2 gene may play many roles throughout the body including controlling the sense of touch, vibration, pain, and proprioception, the unconscious awareness of one’s body in space.

NIH funded researchers showed how the PIEZO2 gene may help dorsal root ganglion neurons relay full bladder signals to the brain. Above is a picture of mouse DRGs colored purple. The PIEZO2 gene is colored light blue. ©Courtesy of Patapoutian lab, Scripps Researcher Institute, La Jolla, CA.

More recently Dr. Patapoutian’s and Dr. Chesler’s teams had been exploring whether PIEZO2 played a role in urination.

“There were a lot of reasons to think that PIEZO2 could be important for urination. Theoretically, it made sense as it is a pressure sensor for other internal sensory processes,” said Kara L. Marshall, Ph.D., a post-doctoral fellow on Dr. Patapoutian’s team and the lead author of the study.

Then in 2015, a breakthrough happened. The NIH researchers discovered people who were born with disabling mutations in their PIEZO2 genes. Initial evaluations of these PIEZO2 deficient individuals at the NIH’s Clinical Center reproduced some of the mouse results. They had no sense of proprioception and could not feel some forms of touch and pain. They also had something else in common.

“We were really struck by what we heard during background interviews with patients and their families. Almost everyone mentioned that the patients had problems with urination. As children, they had trouble potty training. They would often have urinary tract infections. And most of them follow a daily urination schedule,” said Dimah Saade, M.D., a clinical fellow on Dr. Bönnemann’s team and an author of the paper. “After seeing a consistent pattern, we decided to take a closer look.”

The researchers examined medical records, performed ultrasound scans, administered questionnaires, and conducted detailed interviews with 12 patients, 5 to 43 years of age, and their families.

Nearly all the patients claimed they could go an entire day without feeling the need to urinate and most urinated less than the normal five to six times per day. In fact, three patients reported only going once or twice a day. Five patients reported that when they finally do feel a need, it comes on as an abrupt urge. Seven patients reported that the act of urinating was difficult. They either had to wait for it to happen or needed to press their lower abdomen for it to start.

“These results strongly suggested that PIEZO2 plays a role in urination,” said Dr. Marshall. “We wanted to know how it may do this.”

In-depth experiments in mice helped them address this question.

Initially, the researchers found that the PIEZO2 gene was highly active in a few dorsal root ganglion (DRG) neurons that send nerve signals from the mouse bladder to the brain. Aided by an advanced, real-time imaging system, they saw that the cells lit up with activity when a mouse’s bladder filled with fluid. They also found that the PIEZO2 gene was turned on in some “umbrella” cells which are found among the cells that line the inside of a bladder.

“These were the first clues to understanding where in the urinary tract PIEZO2 worked. They suggested that it may help control the bladder,” said Nima Ghitani, Ph.D., a post-doctoral fellow in Dr. Chesler’s lab and an author of the study.

Next, they found that deleting the gene from the neurons and umbrella cells not only reduced the cells’ responses to bladder filling but also caused the mice to have problems with urination. The mutant mice showed some signs of incontinence and urinated randomly in their cages instead of in a corner as seen with control mice. Meanwhile, mutant mouse bladders required more fluid and greater pressure than normal to trigger urination which was reminiscent of the patient reports.

They also found that deleting the gene from the two cell types had longer lasting effects. For instance, the muscles of the mutant bladders were thicker than controls, suggesting the loss of sensation remodeled the bladder.

“Neurologists have always known that there’s a strong link between the nervous system and bladder control, both on a conscious as well as on an automatic level,” said Dr. Bönnemann. “Our patients together with the results in the mouse models teach us how the loss of the critical sensor PIEZO2 profoundly disrupts the wiring behind normal bladder control, ultimately reshaping the bladder itself.”

Finally, the researchers found that deleting the PIEZO2 gene from either the umbrella cells or the DRG neurons produced similar results as deleting it from both cell types simultaneously. Eliminating the gene from either cell lengthened the time that mice would take before feeling the need to squeeze their bladders and it increased the pressure applied during each squeeze.

“Our results show how the PIEZO2 gene tightly coordinates urination,” said Dr. Chesler. “This is a major advance in our understanding of interoception – or the sense of what’s going inside our bodies.”

In the future, the researchers will continue to examine the role PIEZO2 plays in urination and other interoceptive senses while also exploring the clinical implications of their discovery for the millions suffering from urinatory control problems.

References: Marshall, K.L., Saade, D., Ghitani N et al., PIEZO2 in sensory neurons and urothelial cells coordinate urination in humans and in mice. Nature, October 14, 2020
DOI: 10.1038/s41586-020-2830-7.

Provided by National Center for Complementary and Integrative Health (NCCIH)

NASA’s Perseverance Rover Bringing 3D-Printed Metal Parts to Mars (Planetary Science)

For hobbyists and makers, 3D printing expands creative possibilities; for specialized engineers, it’s also key to next-generation spacecraft design.

This video clip shows a 3D printing technique where a printer head scans over each layer of a part, blowing metal powder which is melted by a laser. It’s one of several ways parts are 3D printed at NASA’s Jet Propulsion Laboratory, but was not used to create the parts aboard the Perseverance rover.

If you want to see science fiction at work, visit a modern machine shop, where 3D printers create materials in just about any shape you can imagine. NASA is exploring the technique – known as additive manufacturing when used by specialized engineers – to build rocket engines as well as potential outposts on the Moon and Mars. Nearer in the future is a different milestone: NASA’s Perseverance rover, which lands on the Red Planet on Feb. 18, 2021, carries 11 metal parts made with 3D printing.

Instead of forging, molding, or cutting materials, 3D printing relies on lasers to melt powder in successive layers to give shape to something. Doing so allows engineers to play with unique designs and traits, such as making hardware lighter, stronger, or responsive to heat or cold.

“It’s like working with papier-mâché,” said Andre Pate, the group lead for additive manufacturing at NASA’s Jet Propulsion Laboratory in Southern California. “You build each feature layer by layer, and soon you have a detailed part.”

Curiosity, Perseverance’s predecessor, was the first mission to take 3D printing to the Red Planet. It landed in 2012 with a 3D-printed ceramic part inside the rover’s ovenlike Sample Analysis at Mars (SAM) instrument. NASA has since continued to test 3D printing for use in spacecraft to make sure the reliability of the parts is well understood.

As “secondary structures,” Perseverance’s printed parts wouldn’t jeopardize the mission if they didn’t work as planned, but as Pate said, “Flying these parts to Mars is a huge milestone that opens the door a little more for additive manufacturing in the space industry.”

The outer shell of PIXL, one of the instruments aboard NASA’s Perseverance Mars rover, includes several parts that were made of 3D-printed titanium. The inset shows the front half of the two-piece shell part it was finished. Credits: NASA/JPL-Caltech

A Shell for PIXL

Of the 11 printed parts going to Mars, five are in Perseverance’s PIXL instrument. Short for the Planetary Instrument for X-ray Lithochemistry, the lunchbox-size device will help the rover seek out signs of fossilized microbial life by shooting X-ray beams at rock surfaces to analyze them.

PIXL shares space with other tools in the 88-pound (40-kilogram) rotating turret at the end of the rover’s 7-foot-long (2-meter-long) robotic arm. To make the instrument as light as possible, the JPL team designed PIXL’s two-piece titanium shell, a mounting frame, and two support struts that secure the shell to the end of the arm to be hollow and extremely thin. In fact, the parts, which were 3D printed by a vendor called Carpenter Additive, have three or four times less mass than if they’d been produced conventionally.

“In a very real sense, 3D printing made this instrument possible,” said Michael Schein, PIXL’s lead mechanical engineer at JPL. “These techniques allowed us to achieve a low mass and high-precision pointing that could not be made with conventional fabrication.”

This X-ray image shows the interior of a 3D-printed heat exchanger in Perseverance’s MOXIE instrument. X-ray images like these are used to check for defects within parts. Credits: NASA/JPL-Caltech

MOXIE Turns Up the Heat

Perseverance’s six other 3D-printed parts can be found in an instrument called the Mars Oxygen In-Situ Resource Utilization Experiment, or MOXIE. This device will test technology that, in the future, could produce industrial quantities of oxygen to create rocket propellant on Mars, helping astronauts launch back to Earth.

To create oxygen, MOXIE heats Martian air up to nearly 1,500 degrees Fahrenheit (800 degrees Celsius). Within the device are six heat exchangers – palm-size nickel-alloy plates that protect key parts of the instrument from the effects of high temperatures.

While a conventionally machined heat exchanger would need to be made out of two parts and welded together, MOXIE’s were each 3D-printed as a single piece at nearby Caltech, which manages JPL for NASA.

“These kinds of nickel parts are called superalloys because they maintain their strength even at very high temperatures,” said Samad Firdosy, a material engineer at JPL who helped develop the heat exchangers. “Superalloys are typically found in jet engines or power-generating turbines. They’re really good at resisting corrosion, even while really hot.”

Although the new manufacturing process offers convenience, each layer of alloy that the printer lays down can form pores or cracks that can weaken the material. To avoid this, the plates were treated in a hot isostatic press – a gas crusher – that heats material to over 1,832 degrees Fahrenheit (1,000 degrees Celsius) and adds intense pressure evenly around the part. Then, engineers used microscopes and lots of mechanical testing to check the microstructure of the exchangers and ensure they were suitable for spaceflight.

“I really love microstructures,” Firdosy said. “For me to see that kind of detail as material is printed, and how it evolves to make this functional part that’s flying to Mars – that’s very cool.”

More About the Mission

A key objective of Perseverance’s mission on Mars is astrobiology, including the search for signs of ancient microbial life. The rover will characterize the planet’s geology and past climate, pave the way for human exploration of the Red Planet, and be the first mission to collect and cache Martian rock and regolith (broken rock and dust).

Subsequent missions, currently under consideration by NASA in cooperation with ESA (the European Space Agency), would send spacecraft to Mars to collect these cached samples from the surface and return them to Earth for in-depth analysis.

The Mars 2020 mission is part of a larger program that includes missions to the Moon as a way to prepare for human exploration of the Red Planet. Charged with returning astronauts to the Moon by 2024, NASA will establish a sustained human presence on and around the Moon by 2028 through NASA’s Artemis lunar exploration plans.

JPL, which is managed for NASA by Caltech in Pasadena, Southern California, built and manages operations of the Perseverance and Curiosity rovers.

Provided by NASA

Clumpy, Recycled Gas From Stars Surrounds Milky Way (Astronomy)

The Milky Way galaxy is in the recycling business. Our galaxy is surrounded by a clumpy halo of hot gases that is continually being supplied with material ejected by birthing or dying stars, according to a NASA-funded study in the journal Nature Astronomy.

The Milky Way Galaxy is seen in this illustration.
Credits: NASA/JPL-Caltech/R. Hurt (SSC/Caltech)

A halo is a large region filled with hot gas that surrounds a galaxy, also known as a “circumgalactic medium.” The heated gaseous halo around the Milky Way was the incubator for the Milky Way’s formation some 13 billion years ago and could help solve a longstanding puzzle about where the missing matter of the universe might reside.

HaloSat is a small satellite that looks at the hot gas around the Milky Way. Credits: Blue Canyon Technologies, Inc.
HaloSat, a CubeSat mission to study the halo of hot gas surrounding the Milky Way, was released from the International Space Station in 2018. Credits: NanoRacks/NASA

The new findings come from observations made by a small spacecraft called HaloSat. It is in a class of minisatellites called CubeSats and is roughly the size of a toaster, measuring 4-by-8-by-12 inches (about 10-by-20-by-30 centimeters) and weighing about 26 pounds (12 kilograms). Built by the University of Iowa, HaloSat was launched from the International Space Station in May 2018 and is the first CubeSat funded by NASA’s Astrophysics Division.

While tiny compared to NASA’s Chandra X-ray Observatory, HaloSat’s X-ray detectors view a much wider piece of the sky at once and therefore are optimized to doing the sort of wide-area survey needed to measure the galactic halo.

Because of their small size, CubeSats allow NASA to conduct low-cost scientific investigations in space. Six CubeSats to date have been selected in this Astrophysics Division series.

In the new study, researchers conclude the circumgalactic medium has a disk-like geometry, based on the intensity of X-ray emissions coming from it.

“The X-ray emissions are stronger above the parts of the Milky Way where star formation is more vigorous,” says Philip Kaaret, professor in the Department of Physics and Astronomy at Iowa and corresponding author on the study. “That suggests the circumgalactic medium is related to star formation, and it is likely we are seeing gas that previously fell into the Milky Way, made stars, and now is being recycled into the circumgalactic medium.”

Every galaxy has a circumgalactic medium, and these regions are crucial to understanding not only how galaxies formed and evolved but also how the universe progressed from a kernel of helium and hydrogen to a cosmological expanse teeming with stars, planets, comets, and all other sorts of celestial constituents.

HaloSat searches for baryonic matter — that is, the same kind of particles that compose the visible world — believed to be missing since the universe’s birth nearly 14 billion years ago. The satellite has been observing the Milky Way’s circumgalactic medium for evidence that the missing baryonic matter may reside there. Baryonic matter is distinct from dark matter, which is invisible and does not interact through any force except gravity. Scientists can only account for about two-thirds of the baryonic matter that should be present in the universe.

To do look for the missing matter, Kaaret and his team wanted to get a better handle on the circumgalactic medium’s configuration.

More specifically, the researchers wanted to find out how big the circumgalactic medium really is. If it’s a huge, extended halo that is many times the size of our galaxy, it could house enough material to solve the missing baryon question. But if the circumgalactic medium is mostly comprised of recycled material, it would be a relatively thin, puffy layer of gas and an unlikely host of the missing baryonic matter.

“What we’ve done is definitely show that there’s a high-density part of the circumgalactic medium that’s bright in X-rays,” Kaaret says. “But there still could be a really big, extended halo that is just dim in X-rays. And it might be harder to see that dim, extended halo because there’s this bright emission disk in the way.

“So it turns out with HaloSat alone, we really can’t say whether or not there really is this extended halo” around the Milky Way, Kaarat says.

Kaaret says he was surprised by the circumgalactic medium’s clumpiness, expecting its geometry to be more uniform. The denser areas are regions where stars are forming, and where material is being traded between the Milky Way and the circumgalactic medium.

“It seems as if the Milky Way and other galaxies are not closed systems,” Kaaret says. “They’re actually interacting, throwing material out to the circumgalactic medium and bringing back material as well.”

The next step is to combine the HaloSat data with data from other X-ray observatories to determine whether there’s an extended halo surrounding the Milky Way, and if it’s there, to calculate its density. That, in turn, could solve the missing baryonic matter puzzle.

“Those missing baryons better be somewhere,” Kaaret says. “They’re in halos around individual galaxies like our Milky Way or they’re located in filaments that stretch between galaxies.”

The study is titled, “A disc-dominated and clumpy circumgalactic medium of the Milky Way seen in X-ray emission.” Study co-authors include Jesse Bluem, graduate student in physics at Iowa; Hannah Gulick, graduate student in astronomy at the University of California, Berkeley who graduated from Iowa last May; Daniel LaRocca, who earned his doctorate at Iowa last July and is now a postdoctoral researcher at Pennsylvania State University; Rebecca Ringuette, a postdoctoral researcher with Kaaret who joined NASA’s Goddard Space Flight Center this month; and Anna Zayczyk, a former postdoctoral researcher with Kaaret and a research scientist at both NASA Goddard and University of Maryland, Baltimore County.

HaloSat is a NASA CubeSat mission led by the University of Iowa in Iowa City. Additional partners include NASA’s Goddard Space Flight Center in Greenbelt, Maryland, NASA’s Wallops Flight Facility on Wallops Island, Virginia, Blue Canyon Technologies in Boulder, Colorado, Johns Hopkins University in Baltimore and with important contributions from partners in France. HaloSat was selected through NASA’s CubeSat Launch Initiative as part of the 23rd installment of the Educational Launch of Nanosatellites missions.

References: Kaaret, P., Koutroumpa, D., Kuntz, K.D. et al. A disk-dominated and clumpy circumgalactic medium of the Milky Way seen in X-ray emission. Nat Astron (2020).

Provided by NASA

Sandia Developed New Device From The House Paint Material To More Efficiently Process Information (Computer Science)

The development of a new method to make non-volatile computer memory may have unlocked a problem that has been holding back machine learning and has the potential to revolutionize technologies like voice recognition, image processing and autonomous driving.

Researchers at Sandia National Laboratories have developed an array of processors coated with titanium oxide that has the potential to revolutionize technologies like voice recognition, image processing and autonomous driving. © (Photo courtesy of Sandia National Laboratories)

A team from Sandia National Laboratories, working with collaborators from the University of Michigan, published a paper in the peer-reviewed journal Advanced Materials that details a new method that will imbue computer chips that power machine-learning applications with more processing power by using a common material found in house paint in an analog memory device that enables highly energy-efficient machine inference operations.

“Titanium oxide is one of the most commonly made materials. Every paint you buy has titanium oxide in it. It’s cheap and nontoxic,” explains Sandia materials scientist Alec Talin. “It’s an oxide, there’s already oxygen there. But if you take a few out, you create what are called oxygen vacancies. It turns out that when you create oxygen vacancies, you make this material electrically conductive.”

Those oxygen vacancies can now store electrical data, giving almost any device more computing power. Talin and his team create the oxygen vacancies by heating a computer chip with a titanium oxide coating above 302 degrees Fahrenheit (150 degree Celsius), separate some of the oxygen molecules from the material using electrochemistry and create vacancies.

“When it cools off, it stores any information you program it with,” Talin said.

Energy efficiency a boost to machine learning

Right now, computers generally work by storing data in one place and processing that data in another place. That means computers have to constantly transfer data from one place to the next, wasting energy and computing power.

The paper’s lead author, Yiyang Li, is a former Truman Fellow at Sandia and now an assistant professor of materials science at the University of Michigan. He explained how their process has the potential to completely change how computers work.

“What we’ve done is make the processing and the storage at the same place,” Li said. “What’s new is that we’ve been able to do it in a predictable and repeatable manner.”

Both he and Talin see the use of oxygen vacancies as a way to help machine learning overcome a big obstacle holding it back right now — power consumption.

“If we are trying to do machine learning, that takes a lot of energy because you are moving it back and forth and one of the barriers to realizing machine learning is power consumption,” Li said. “If you have autonomous vehicles, making decisions about driving consumes a large amount of energy to process all the inputs. If we can create an alternative material for computer chips, they will be able to process information more efficiently, saving energy and processing a lot more data.”

Research has everyday impact

Talin sees the potential in the performance of everyday devices.

“Think about your cell phone,” he said. “If you want to give it a voice command, you need to be connected to a network that transfers the command to a central hub of computers that listen to your voice and then send a signal back telling your phone what to do. Through this process, voice recognition and other functions happen right in your phone.”

Talin said the team is working on refining several processes and testing the method on a larger scale. The project is funded through Sandia’s Laboratory Directed Research and Development program.

References: Li, Y., Fuller, E. J., Sugar, J. D., Yoo, S., Ashby, D. S., Bennett, C. H., Horton, R. D., Bartsch, M. S., Marinella, M. J., Lu, W. D., Talin, A. A., Filament‐Free Bulk Resistive Memory Enables Deterministic Analogue Switching. Adv. Mater. 2020, 2003984.

Provided by DOE/Sandia National Laboratory

Nanophotonics Researchers Demonstrated Ultrafast Polarization Switching (Physics)

U.S. and Italian engineers have demonstrated the first nanophotonic platform capable of manipulating polarized light 1 trillion times per second.

A pictorial schematic depicts the structure and action of a nanopatterned plasmonic metasurface that modulates polarized light at terahertz frequencies. An ultrashort laser pulse (green) excites cross-shaped plasmonic structures, which rotate the polarity of a second light pulse (white) that arrives less one picosecond after the first. ©Image courtesy of A. Assié

“Polarized light can be used to encode bits of information, and we’ve shown it’s possible to modulate such light at terahertz frequencies,” said Rice University’s Alessandro Alabastri, co-corresponding author of a study published this week in Nature Photonics.

“This could potentially be used in wireless communications,” said Alabastri, an assistant professor of electrical and computer engineering in Rice’s Brown School of Engineering. “The higher the operating frequency of a signal, the faster it can transmit data. One terahertz equals 1,000 gigahertz, which is about 25 times higher than the operating frequencies of commercially available optical polarization switches.”

The research was a collaboration between experimental and theoretical teams at Rice, the Polytechnic University of Milan (Politecnico) and the Italian Institute of Technology (IIT) in Genoa. This collaboration started in the summer of 2017, when study co-first author Andrea Schirato was a visiting scholar in the Rice lab of physicist and co-author Peter Nordlander. Schirato is a Politecnico-IIT joint graduate student under the supervision of co-corresponding author Giuseppe Della Valle of Politecnico and co-author Remo Proietti Zaccaria of IIT.

A scanning electron microscope image of the nanopatterned plasmonic metasurface that engineers from Rice University, the Polytechnic University of Milan and the Italian Institute of Technology created to modulate polarized light at terahertz frequencies. ©Image courtesy of Andrea Toma/IIT

Each of the researchers work in nanophotonics, a fast-growing field that uses ultrasmall, engineered structures to manipulate light. Their idea for ultrafast polarization control was to capitalize on tiny, fleeting variations in the generation of high-energy electrons in a plasmonic metasurface.

Metasurfaces are ultrathin films or sheets that contain embedded nanoparticles that interact with light as it passes through the film. By varying the size, shape and makeup of the embedded nanoparticles and by arranging them in precise two-dimensional geometric patterns, engineers can craft metasurfaces that split or redirect specific wavelengths of light with precision.

“One thing that differentiates this from other approaches is our reliance on an intrinsically ultrafast broadband mechanism that’s taking place in the plasmonic nanoparticles,” Alabastri said.

The Rice-Politecnico-IIT team designed a metasurface that contained rows of cross-shaped gold nanoparticles. Each plasmonic cross was about 100 nanometers wide and resonated with a specific frequency of light that gave rise to an enhanced localized electromagnetic field. Thanks to this plasmonic effect, the team’s metasurface was a platform for generating high-energy electrons.

“When one laser light pulse hits a plasmonic nanoparticle, it excites the free electrons within it, raising some to high-energy levels that are out of equilibrium,” Schirato said. “That means the electrons are ‘uncomfortable’ and eager to return to a more relaxed state. They return to an equilibrium in a very short time, less than one picosecond.”

Despite the symmetric arrangement of crosses in the metasurface, the nonequilibrium state has asymmetric properties that disappear when the system returns to equilibrium. To exploit this ultrafast phenomenon for polarization control, the researchers used a two-laser setup. Experiments performed by study co-first author Margherita Maiuri at Politecnico’s ultrafast spectroscopy laboratories — and confirmed by the team’s theoretical predictions — used an ultrashort pulse of light from one laser to excite the crosses, allowing them to modulate the polarization of light in a second pulse that arrived less than a picosecond after the first.

“The key point is that we could achieve the control of light with light itself, exploiting ultrafast electronic mechanisms peculiar of plasmonic metasurfaces,” Alabastri said. “By properly designing our nanostructures, we have demonstrated a novel approach that will potentially allow us to optically transmit broadband information encoded in the polarization of light with unprecedented speed.”

References: Schirato, A., Maiuri, M., Toma, A. et al. Transient optical symmetry breaking for ultrafast broadband dichroism in plasmonic metasurfaces. Nat. Photonics (2020).

Provided by Rice University

Cheaters Don’t Always Win: Species That Work Together Do Better (Biology)

Extinction may be prevented by diverse communities of mutually beneficial species

The sign of a healthy personal relationship is one that is equally mutual – where you get out just as much as you put in. Nature has its own version of a healthy relationship. Known as mutualisms, they are interactions between species that are mutually beneficial for each species. One example is the interaction between plants and pollinators, where your apple trees are pollinated and the honeybee gets nectar as a food reward. But what makes these mutualisms persist in nature? If rewards like nectar are offered freely, does this make mutualisms more susceptible to other organisms that take those rewards without providing a service in return?

Wells of yeast in the top tray with only two mutualist species and a cheater showed higher extinction (indicated by the many dark wells). Yeast strains of complex communities and a cheater in the bottom tray showed better growth and less extinction. ©Syracuse University

A team of researchers from the College of Arts and Sciences at Syracuse University, including co-principal investigators Kari Segraves, professor of biology, and David Althoff, associate professor of biology, along with postdoctoral researcher Mayra Vidal, former research assistant professor David Rivers, and Sheng Wang ’20 Ph.D., recently researched that question and the results have been published in this month’s edition of the prestigious journal Science.

They investigated the abilities of simple versus diverse communities of mutualists, comparing how each deal with cheaters. Cheaters are species that steal the benefits of the mutualism without providing anything in return. An example of one of nature’s cheaters are nectar robbers. Nectar-robbing bees chew through the side of flowers to feed on nectar without coming into contact with the flower parts that would result in pollination.

The research team wanted to test if having multiple mutualists with similar roles allows the community as a whole to persist when cheaters take away the mutualists’ resources. The idea was to examine whether having more species involved in a mutualism, such as many pollinator species interacting with many different plant species, made the mutualism less susceptible to the negative effects of cheaters. They also wanted to analyze whether increasing the number of mutualist species allowed all the mutualists to persist or if competition would whittle down the number of mutualists species over time. In essence, the team wanted to understand the forces governing large networks of mutualists that occur in nature.

A&S researchers tested their ideas by producing mutualisms in the lab using yeast strains that function as mutualistic species. These strains were genetically engineered to trade essential food resources. Each strain produced a food resource to exchange with a mutualist partner. They engineered four species of each type of mutualist as well as two cheater strains that were unable to make food resources.

The researchers assembled communities of yeast that differed both in the number of species and the presence of cheaters. They found that communities with higher numbers of mutualist species were better able to withstand the negative effects of cheaters because there were multiple species of mutualists performing the same task. If one species was lost from the community due to competing with a cheater, there were other species around to perform the task, showing that the presence of more species in a community can lessen the negative effects of cheaters.

“It’s similar to thinking about a plant that has many pollinator species,” says Segraves. “If one pollinator species is lost, there are other pollinator species around to pollinate. If a plant only has one species of pollinator that goes extinct, the mutualism breaks down and might cause extinction of the plant.”

Their results highlight the importance of having multiple mutualist species that provide similar resources or services, essentially creating a backup in case one species goes extinct. Segraves compares this phenomenon to the relationship between retailers and consumers. Communities typically have multiple banks, grocery stores, restaurants and hospitals to ensure that there are always goods and services available should something happen to one company or facility, or, as with COVID today, grocery stores now have multiple suppliers to fend off shortages.

Segraves says future research will explore the possibility of a mutualist species becoming a cheater. The group is testing if mutualists that perform the same function might set up an environment that allows one of those mutualist species to become a cheater since there are other mutualists around that can fill that role. They predict that the mutualist species that is experiencing the most competition from the other mutualists will be the species that switches to cheating. They also hope to determine how the mutualists and cheaters evolved over time to provide a deeper understanding of the actual changes that led to differing outcomes in the communities.

References: Mayra C. Vidal, Sheng Pei Wang, David M. Rivers, David M. Althoff, Kari A. Segraves, “Species richness and redundancy promote persistence of exploited mutualisms in yeast”, Science 16 Oct 2020: Vol. 370, Issue 6514, pp. 346-350
DOI: 10.1126/science.abb6703 link:

Provided by Syracuse University

Microscopy Beyond The Resolution Limit (Physics)

The Polish-Israeli team from the Faculty of Physics of the University of Warsaw and the Weizmann Institute of Science has made another significant achievement in fluorescent microscopy. In the pages of the Optica journal the team presented a new method of microscopy which, in theory, has no resolution limit. In practice, the team managed to demonstrate a fourfold improvement over the diffraction limit.

Image of microtubules in a fixed cell sample. A 3 microns x 3 microns confocal scan of microtubules in a fixed 3T3 cell labelled with quantum dots analyzed in two ways. Upper left: image scanning microscopy (ISM), lower right: super-resolution optical fluctuation image scanning microscopy (SOFISM) after Fourier-reweighting. (Source: UW Physics, A. Makowski). ©Source: UW Physics, A. Makowski

The continued development of biological sciences and medicine requires the ability to examine smaller and smaller objects. Scientists need to see into the structure of, and the mutual relationships between, for example, proteins in cells. At the same time, the samples being observed should not differ from the structures naturally occurring in biological organisms, which rules out the use of aggressive procedures and reagents. Although it revolutionised the natural sciences, the classical optical microscope is clearly insufficient today. Due to the wavelike nature of light, an optical microscope does not allow imaging structures smaller than about 250 nanometres. As a result, objects closer to each other than half the wavelength of light (which is about 250 nm for green light) cannot be discerned. This phenomenon, known as the diffraction limit, one of the main obstacles in observing the tiniest biological structures, scientists have long attempted to overcome. Electron microscopes provide orders of magnitude better resolution but only allow the examination of inanimate objects, which must be placed in a vacuum and bombarded by an electron beam. For this reason, electron microscopy cannot be used for studying living organisms and the natural processes occurring in them. This is where fluorescence microscopy steps in, hence the rapid development of super-resolution fluorescence microscopy as a field of physical sciences and the two Nobel Prizes already awarded for related research – in 2008 and 2014.

Nowadays several techniques of fluorescence microscopy are available, and some of them have become widespread in biological imaging. Some methods, such as PALM, STORM or STED microscopy, are characterised by an ultra-high resolution and allow discerning objects located just a dozen or so nanometres from each other. However, these techniques require long exposure times and a complex procedure of biological specimen preparation. Other techniques, such as SIM or ISM microscopy, are easy to use, but offer a very limited resolution improvement, allowing to identify structures only half the size of the diffraction limit.

Aleksandra Sroda, Adrian Makowski and Dr. Radek Lapkiewicz from the Quantum Optics Lab at the Faculty of Physics of the University of Warsaw, in cooperation with Prof. Dan Oron’s team from the Weizmann Institute of Science in Israel, have introduced a new technique of super-resolution microscopy, called Super-resolution optical fluctuation image scanning microscopy (SOFISM). In SOFISM, the naturally occurring fluctuations in emission intensity of fluorescent markers are used to further enhance the spatial resolution of an image scanning microscope (ISM). ISM, an emerging super-resolution method, has already been implemented in commercial products and proven valuable for the bio-imaging community. Largely, since it achieves a modest improvement in lateral resolution (x2), with very few changes to the optical setup and without the common handicap of long exposure times. Thus, it enables a natural extension of the capabilities of a standard confocal microscope. ISM uses a confocal microscope in which a single detector is replaced with a detector array. In SOFISM correlations of intensities detected by multiple detectors are computed. In principle, the measurement of the n-th order correlation can lead to a factor of 2n resolution improvement with respect to the diffraction limit. In practice, the resolution achievable for higher-order correlations is limited by the signal-to-noise ratio of the measurements.

“SOFISM is a compromise between ease of use and resolution. We believe that our method will fill the niche between the complex, difficult-to-use techniques providing very high resolution and the easy-to-use lower-resolution methods. SOFISM does not have a theoretical resolution limit, and in our article, we demonstrate results which are four times better than the diffraction limit. We also show that the SOFISM method has a high potential in the imaging of three-dimensional biological structures,” said Dr. Radek Lapkiewicz.

Crucially, SOFISM is, in its technical aspects, highly accessible, as it only requires introducing a small modification to the widely-used confocal microscope – replacing its photomultiplier tube with a SPAD array detector. In addition, it is necessary to slightly increase the measurement time and change the data processing procedure. “Until recently, SPAD array detectors were expensive and their specifications were not sufficient for correlation-based microscopy. This situation has recently changed. The new SPAD detectors introduced last year removed both the technological and price-related barriers. This makes us think that fluorescence microscopy techniques such as SOFISM might, in a few years’ time, become widely used in the field of microscopic examination,” stressed Dr. Lapkiewicz.

References: Aleksandra Sroda, Adrian Makowski, Ron Tenne, Uri Rossman, Gur Lubin, Dan Oron, Radek Lapkiewicz: ”SOFISM: Super-resolution optical fluctuation image scanning microscopy”, Optica Vol. 7, Issue 10, pp. 1308-1316 (2020).
DOI: link:

Provided by Faculty Of Physics, University Of Warsaw

Scientists Map The First Draft Sequence Of The Human Proteome (Medicine)

Twenty years after the release of the human genome, the genetic “blueprint” of human life, an international research team, including the University of British Columbia’s Chris Overall, has now mapped the first draft sequence of the human proteome.

Their work was published Oct. 16 in Nature Communications and announced today by the Human Proteome Organization (HUPO). Overall is the only Canadian scientist involved in the Nature Communications paper.

“Today marks a significant milestone in our overall understanding of human life,” says Overall, a professor in the faculty of dentistry and a member of the Centre for Blood Research at UBC. “Whereas the human genome provides a complete ‘blueprint’ of human genes, the human proteome identifies the individual building blocks of life encoded by this blueprint: proteins. “Proteins interact to shape everything from life-threatening diseases to cellular structure in our bodies.”

With 90 per cent of the proteins in the human body now mapped, Overall says scientists have a deeper understanding of how individual proteins interact to influence human health, providing insights into disease prevention and individualized medicine.

Their work may have implications for scientists studying potential treatments for COVID-19.

“In COVID-19, for instance, there are two proteomes involved, that of the SARS-CoV-2 virus and that of the infected cells, both of which likely interact with, modify, and change the function of the other,” says Overall. “Understanding this relationship can shed light on why some cells and individuals are more resilient to COVID-19 and others more vulnerable, providing essential functional information about the human body that genomics alone cannot answer.”

As many human diseases result from changes in the composition or functions of proteins, mapping the proteome strengthens the foundation for disease diagnosis, prediction of outcomes, treatment, and precision medicine.

“Humans share 99.9 per cent of their DNA between individuals, yet deficiencies in the proteome ‘parts’ stemming from inherited genetic mutations can lead to genetic diseases, or defective or inadequate immune and cellular responses to environmental, nutritional and infection stressors,” says Overall. “Knowing which proteins are key to protection from disease, and the deficiencies in expression or activity that are hallmarks of disease, can inform individualized medicine and the development of new therapies.”

References: Adhikari, S., Nice, E.C., Deutsch, E.W. et al. A high-stringency blueprint of the human proteome. Nat Commun 11, 5301 (2020). link:

Provided by University Of British Columbia