Tech

Layered van der Waals materials are of high interest for electronic and photonic applications, according to researchers at Penn State and SLAC National Accelerator Laboratory, in California, who provide new insights into the interactions of layered materials with laser and electron beams.

Two-dimensional van der Waals materials are composed of strongly bonded layers of molecules with weak bonding between the layers.

The researchers used a combination of ultrafast pulses of laser light that excite the atoms in a material lattice of gallium telluride, followed by exposing the lattice to an ultrafast pulse of an electron beam. This shows the lattice vibrations in real time using electron diffraction and could lead to a better understanding of these materials.

"This is a quite unique technique," said Shengxi Huang, assistant professor of electrical engineering and corresponding author of a paper in ACS Nano that describes their work. "The purpose is to understand fully the lattice vibrations, including in-plane and out-of-plane."

One of the interesting observations in their work is the breaking of a law that applies to all material systems. Friedel's Law posits that in the diffraction pattern, the pairs of centrosymmetric Bragg peaks should be symmetric, directly resulting from Fourier transformation. In this case, however, the pairs of Bragg peaks show opposite oscillating patterns. They call this phenomenon the dynamic breaking of Friedel's Law. It is a very rare if not unprecedented observation in the interactions between the beams and these materials.

"Why do we see the breaking of Friedel's Law?" she said. "It is because of the lattice structure of this material. In layered 2D materials, the atoms in each layer typically align very well in the vertical direction. In gallium telluride, the atomic alignment is a little bit off."

When the laser beam shines onto the material, the heating generates the lowest-order longitudinal acoustic phonon mode, which creates a wobbling effect for the lattice. This can affect the way electrons diffract in the lattice, leading to the unique dynamic breaking of Friedel's law.

This technique is also useful for studying phase change materials, which absorb or radiate heat during phase change. Such materials can generate the electrocaloric effect in solid-state refrigerators. This technique will also be interesting to people who study oddly structured crystals and the general 2D materials community.

Climate - Predicting fire risk

Researchers at Oak Ridge National Laboratory developed a method that uses machine learning to predict seasonal fire risk in Africa, where half of the world's wildfire-related carbon emissions originate.

Their approach draws on data about underlying environmental drivers such as ocean temperatures and land surface changes in addition to more commonly used atmospheric and socioeconomic indicators. The method allows scientists to gain a deeper understanding of the relative importance of different variables such as soil moisture and leaf area.

"We found that oceanic and terrestrial dynamics are the most critical factors influencing the accuracy of seasonal fire prediction for these vulnerable ecosystems," said ORNL's Jiafu Mao. "Disturbances like fire can have a lasting impact on regional environments and global carbon cycling."

The scientists' computational framework could be applied to other regions or generalized to assess global fire risk and inform fire management practices that address environmental and safety concerns.

Media contact: Kim Askey, 865.576.2841, askeyka@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-07/firms3-Africa-NASA.jpg

Caption: Oak Ridge National Laboratory developed a method that uses machine learning to predict seasonal fire risk in Africa, which contains about 70% of the global burned area, shown in red. Credit: NASA

Batteries - Solid state stability check

Oak Ridge National Laboratory scientists seeking the source of charge loss in lithium-ion batteries demonstrated that coupling a thin-film cathode with a solid electrolyte is a rapid way to determine the root cause.

In a study, researchers prepared a lithium nickel manganese cobalt oxide cathode as dense, thin-films free from binders and additives. The cathode's charging and discharging cycles were compared in cells with a standard liquid electrolyte versus a sputtered-deposited solid electrolyte. The capacity of both cells faded quickly and, within a few cycles, the cathode showed physical instability.

Further analysis confirmed that resistance at the cathode interface with the liquid electrolyte grows with cycling leading to charge capacity loss while the solid electrolyte was stable.

"Charge loss was related to the inherent structural instability of the cathode's crystalline structure, a key finding for designing high capacity, high voltage cathodes in solid state batteries," ORNL's Gabriel Veith said.

Media Contact: Jennifer Burke, 865.414.6835, burkejj@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-07/solid_state_stability_check-batteries.jpg

Caption: ORNL researchers coupled a thin-film cathode with a solid electrolyte to rapidly determine the cause of charge loss in higher voltage lithium-ion batteries, a key finding for designing high capacity, high voltage cathodes in solid-state batteries. Credit: Nathan Phillip/ORNL, U.S. Dept. of Energy

Microscopy - Images in a flash

Oak Ridge National Laboratory researchers have built a novel microscope that provides a "chemical lens" for viewing biological systems including cell membranes and biofilms. The tool could advance the understanding of complex biological interactions, such as those between microbes and plants.

The noninvasive instrument, detailed in Optics Letters, allows researchers to capture images using ultrashort laser pulses. These intense pulses illuminate large areas of a sample, generating colors of light that allow detection of different chemical species. The approach quickly produces images over a wide field of view with chemical details.

"Because you're getting the whole image all in the same shot, you're able to study changes in space and in time," ORNL's Benjamin Doughty said.

Unlike common bioimaging techniques that can destroy or disturb samples, this label-free tool can be used on unaltered, living cells. The microscope is made with commonly available components, which may accelerate its implementation.

Media Contact: Abby Bower, 865.323.9943, bowerae@ornl.gov

Image: https://www.ornl.gov/sites/default/files/2020-07/Lily_CH%20and%20CO.png

Caption: A novel ORNL microscope captured an image of lily pollen, which is colorized to show the distribution of two molecular groups. The instrument quickly shows chemical details. Credit: Uvinduni Premadasa/ORNL, U.S. Dept. of Energy

Image: https://www.ornl.gov/sites/default/files/2020-07/Lily_BF.png

Caption: An image of lily pollen, captured using bright-field microscopy developed by ORNL, reveals only the presence of material without information about its composition. Credit: Uvinduni Premadasa/ORNL, U.S. Dept. of Energy

In an effort to improve large touchscreens, LED light panels and window-mounted infrared solar cells, researchers at the University of Michigan have made plastic conductive while also making it more transparent.

They provide a recipe to help other researchers find the best balance between conductivity and transparency by creating a three-layer anti-reflection surface. The conductive metal layer is sandwiched between two "dielectric" materials that allow light to pass through easily. The dielectrics reduce the reflection from both the plastic and metal layer between them.

"We developed a way to make coatings with high transparency and conductivity, low haze, excellent flexibility, easy fabrication and great compatibility with different surfaces," said Jay Guo, U-M professor of electrical engineering and computer science, who led the work.

Previously, Guo's team had shown that it was possible to add a layer of metal onto a plastic sheet to make it conductive--a very thin layer of silver that, by itself, reduced the transmission of light by roughly 10%.

Light transmission through plastic is a little lower than through glass, but its transparency can be improved with anti-reflection coatings. Guo and his colleague Dong Liu, a visiting professor at U-M from Nanjing University of Science and Technology, realized that they could make an anti-reflection coating that was also conductive.

"It was taken for granted that the transmittance of the conductor is lower than that of the substrate, but we show that this is not the case," said Chengang Ji, first author of the study in Nature Communications, who worked on the project as a Ph.D. student in electrical and computer engineering. Ji received his doctorate from U-M in 2019.

The dielectrics chosen by the team in this case are aluminum oxide and zinc oxide. On the side closest to the light source, the aluminum oxide reflects less light back to the source than the plastic surface would. Then comes the metal layer, composed of silver with a tiny amount of copper in it, just 6.5 nanometers thick, and then zinc oxide helps guide the light into the plastic surface. Some light still gets reflected back where the plastic meets the air on the opposite side, but overall, the light transmission is better than the plastic alone. The transmittance is 88.4%, up from 88.1% for the plastic alone.

With the theory results, the team anticipates that other researchers will be able to design similar sandwich-style flexible, highly transparent conductors, which allow even more light through than the plastic alone.

"We tell people how transparent a dielectric-metal-dielectric conductor could be, for a target electrical conductance. We also tell them how to achieve this high transmittance step-by-step," Liu said.

The tricks are selecting the right dielectrics and then figuring out the right thickness for each to suppress the reflection of the thin metal. In general, the material between the plastic and metal should have a higher refractive index, while the material nearest the display or light source should have a lower refractive index.

Guo is continuing to move the technology forward, collaborating on a project that uses transparent conductors in solar cells for mounting on windows. These could absorb infrared light and convert it to electricity while leaving the visible spectrum to brighten the room. He also proposes large panel interactive displays and car windshields that can melt ice the way rear windows can.

(Boston)--Researchers from Boston University School of Medicine (BUSM) have developed and implemented a new way to better understand how human cells communicate with each other, how this communication is disrupted in human diseases and how this can be corrected pharmacologically.

Their method consists of a suite of "biosensors", which are artificial genes that can be introduced in cells to report in real time when an important group of signaling molecules is turned on. These signaling molecules, "G-proteins," are molecular on/off switches inside cells. They are turned on by a large family of receptor proteins that sense a very wide range of stimuli, including light, odors, neurotransmitters and hormones.

This signaling mechanism has been studied over the course of several decades. However, what is new about these "biosensors" is that they were developed to study G-proteins with an accuracy that was not possible before. "These biosensors are good 'spies' in the sense that they can tell us what G-proteins are doing in real time with a resolution of tens of milliseconds, but without interfering with the signaling process that is being observed," explained corresponding author Mikel Garcia-Marcos, PhD, associate professor of biochemistry at BUSM. "Moreover, our biosensors have the advantage of easy implementation, which allows us to study G-proteins directly in experimental systems that were previously unavailable."

The researchers used molecular engineering to create their biosensors by borrowing parts from existing genes, including genes that encode fluorescent proteins from jellyfish, shape-changing proteins that make muscles contract, light-emitting proteins from deep sea shrimp and proteins known to specifically recognize active G-proteins. They then introduced the engineered genes that make the biosensors into several different types of cells and studied how they responded to stimulation by natural stimuli, like neurotransmitters or clinically used drugs.

According to the researchers, more than one-third of FDA-approved drugs work by activating or inhibiting signaling by G-proteins including common allergy medications, nasal decongestants, highly prescribed drugs for blood pressure, first-line treatment for Parkinson's, analgesics, anti-psychotics as well as cannabis and opioids.

Lead author Marcin Maziarz, PhD, post-doc in the Garcia-Marcos' laboratory, believes these biosensors can be instrumental in drug discovery and drug development and in characterizing the mode of action of many existing medications. "What we're doing today is important because it will allow researchers to more easily and accurately identify drugs more likely to be successful in clinical trials since many drugs that initially show promise in experimental systems eventually fail to deliver clinical results," he said.

The findings appear online in the journal Cell.

Over the past few years, fuel cells have become a focal point of research in eco-friendly technology because of their superior abilities to store and produce renewable energy and clean fuel. A typical type of fuel cell gaining ground is the proton-conducting fuel cell, which is primarily made of materials through which hydrogen ions (protons: H+), can easily move. Proton-conducting materials provide a number of advantages over commonly used fuel cells that comprise oxide-ion conductors for electrolytes, such as higher conductivity at low and intermediate temperatures, longer lifetimes, and lower costs.

However, only a limited number of such materials are known and their application to developing fuel cells has largely remained at the laboratory scale. To truly achieve a sustainable energy economy, new proton conductors with high conductivity need to be discovered that can allow the low-cost and efficient scaling up of these technologies.

Scientists from Tokyo Tech and ANSTO set out to address this need, and in a recent study, identified a new proton-conducting material that may be a representative of an entire family of proton conductors.

The material in question has the chemical formula Ba5Er2Al2ZrO13 and is classified as a "hexagonal perovskite-related oxide." Prof Masatomo Yashima, who led the study, explains: "Proton conduction in oxides typically occurs via the hopping of protons between oxide ions. Therefore, the crystal structure and the local environment around oxide ions have a tremendous impact on the possible conducting pathways. This explains why high proton conductivity has been reported in only a limited number of materials."*

Prof Yashima and his team noted that the structure of Ba5Er2Al2ZrO13 contains oxygen-deficient layers and its proton conductivity is higher than those of representative proton conductors, which are created by artificially introducing oxygen deficiencies in the crystal structures of certain materials. They realized that this intrinsic oxygen deficiency of Ba5Er2Al2ZrO13 could give it a remarkable advantage over conventional proton conductors, eliminating a major issue in them: their instability and the difficulty of synthesizing compositionally homogeneous samples.

They conducted a series of experiments to elucidate the mechanisms underlying this property. Initial investigations showed that the proton conductivity of Ba5Er2Al2ZrO13 is high at intermediate and low temperatures that are key to potential industrial applications. Upon further experimentation, it turned out that water molecules (H2O) in air can dissolve into the oxygen-deficient layers of the crystal, where the oxygen from the water is separated from hydrogen to produce mobile H+. These H+ then "hop across oxide ions" within the oxygen-deficient layers, allowing for high proton conductivity.

This phenomenon is not restricted to this particular material. The team synthesized other materials with similar structures and conducted preliminary tests on their electrical conductivity. They found comparable results to those for Ba5Er2Al2ZrO13. Assistant Dr Taito Murakami, first author of the study, explains: "Our results suggest that the oxygen-deficient layers in hexagonal perovskite-related oxides could be a general structural block that confers high proton conductivity. These layers can be found in a number of oxides besides Ba5Er2Al2ZrO13."*

This discovery of a whole new range of intrinsically high proton-conducting materials, and the mechanism of their proton conductivity, could take research in this field to new horizons. Dr James R. Hester from ANSTO, who also participated in the study, remarks: "Our work presents a potential strategy to design superior proton conductors based on the oxygen-deficient layers of some perovskite-related oxides."* This work hopefully represents a step toward a cleaner future.

Currently, low-alloy aluminium is widely used in electrical engineering and machine building. At the same time, it should be noted that modern electrical engineering places very high and in some cases mutually exclusive requirements to aluminium alloys.

For example, conductive aluminium alloys must have both high electrical conductivity and strength, and sometimes also long term thermal stability, if they are to be used in conditions of long term exposure to certain temperatures. Typically, high strength and thermal stability of aluminium alloys is provided by means of complex alloying, which leads to a sharp decrease in electrical conductivity of the materials.

In 2017, a research team of the Physics and Technology Research Institute at Lobachevsky University in Nizhny Novgorod, on the initiative of the Moscow Plant for Special Alloys Processing, took up the task of improving the performance of aluminium alloys. To obtain new low-alloy aluminium alloys, Nizhny Novgorod researchers used the technology of induction casting in vacuum.

According to Professor Alexey Nokhrin, Head of the Materials Diagnostics Laboratory at the UNN Physics and Technology Research Institute, one of the main tasks was to develop the regimes of casting for new aluminium alloys.

"The structure of the cast metal is very heterogeneous, it has a needle-like dendrite structure and contains large particles that resulted from casting. Because of this, it is very difficult to form the cast metal. In order to achieve the required results, it was necessary first to determine very precisely the metal casting regimes that would help to get rid of large particles, and then, by using plastic deformation, to refine the cast dendrite structure. The second step was especially difficult, since it was not possible to process the alloy at elevated temperatures, as it is usually done at factories. An increase in temperature would have resulted in the precipitation of large particles, which would have caused the wire with a diameter of less than 0.5 mm to rupture", explains Alexey Nokhrin.

To solve the problem of obtaining thin wire, a large amount of research has been conducted by UNN scientists to study the effect of casting regimes on the homogeneity of the structure and properties of aluminium alloys containing magnesium and scandium microadditives. Intensive plastic deformation technologies, including equal channel angular pressing and rotary forging, were used as the key methods for controlling the structure of aluminium alloys.

As a result, a homogeneous highly plastic structure was obtained in the alloys where nanoparticles were formed by annealing, which provided the required level of strength and thermal resistance of the wires manufactured.

The new alloys have demonstrated a number of unique characteristics. Lobachevsky University researchers managed to solve the difficult task of increasing simultaneously electrical conductivity, strength and thermal resistance of the alloys while ensuring a very high level of plasticity at elevated temperatures.

The research shows that new alloys possess superplasticity: during tensile testing at 500 degrees Celsius and at high rates of deformation the samples showed the elongation of more than 1000%, and after cooling became very strong and electrically conductive again.

"This will allow the producers to manufactire the wire using the superplasticity regime, when special deformation mechanisms are activated and the metal "flows" like liquid glass", concludes Alexey Nokhrin.

At present, the team is working on the next stage of the project. The researchers are studying the possibilities of replacing expensive scandium with other alloying additives (Zr, Yb, etc.). The aim is to maintain high characteristics of the alloys produced while sharply reducing their cost.

TAMPA, Fla. (July 6, 2020) — As the death toll from the COVID-19 pandemic mounts, scientists worldwide continue their push to develop effective treatments and a vaccine for the highly contagious respiratory virus.

University of South Florida Health (USF Health) Morsani College of Medicine scientists recently worked with colleagues at the University of Arizona College of Pharmacy to identify several existing compounds that block replication of the COVID-19 virus (SARS-CoV-2) within human cells grown in the laboratory. The inhibitors all demonstrated potent chemical and structural interactions with a viral protein critical to the virus’s ability to proliferate.

The research team’s drug discovery study appeared June 15 in Cell Research, a high-impact Nature journal.

The most promising drug candidates – including the FDA-approved hepatitis C medication boceprevir and an investigational veterinary antiviral drug known as GC-376 – target the SARS-CoV-2 main protease (Mpro), an enzyme that cuts out proteins from a long strand that the virus produces when it invades a human cell. Without Mpro, the virus cannot replicate and infect new cells. This enzyme had already been validated as an antiviral drug target for the original SARS and MERS, both genetically similar to SARS-CoV-2.

“With a rapidly emerging infectious disease like COVID-19, we don’t have time to develop new antiviral drugs from scratch,” said Yu Chen, PhD, USF Health associate professor of molecular medicine and a coauthor of the Cell Research paper. “A lot of good drug candidates are already out there as a starting point. But, with new information from studies like ours and current technology, we can help design even better (repurposed) drugs much faster.”

Before the pandemic, Dr. Chen applied his expertise in structure-based drug design to help develop inhibitors (drug compounds) that target bacterial enzymes causing resistance to certain commonly prescribed antibiotics such as penicillin. Now his laboratory focuses its advanced techniques, including X-ray crystallography and molecular docking, on looking for ways to stop SARS-CoV-2.

Mpro represents an attractive target for drug development against COVID-19 because of the enzyme’s essential role in the life cycle of the coronavirus and the absence of a similar protease in humans, Dr. Chen said. Since people do not have the enzyme, drugs targeting this protein are less likely to cause side effects, he explained.

The four leading drug candidates identified by the University of Arizona-USF Health team as the best (most potent and specific) for fighting COVID-19 are described below. These inhibitors rose to the top after screening more than 50 existing protease compounds for potential repurposing:

Boceprevir, a drug to treat Hepatitis C, is the only one of the four compounds already approved by the FDA. Its effective dose, safety profile, formulation and how the body processes the drug (pharmacokinetics) are already known, which would greatly speed up the steps needed to get boceprevir to clinical trials for COVID-19, Dr. Chen said.

GC-376, an investigational veterinary drug for a deadly strain of coronavirus in cats, which causes feline infectious peritonitis. This agent was the most potent inhibitor of the Mpro enzyme in biochemical tests, Dr. Chen said, but before human trials could begin it would need to be tested in animal models of SARS-CoV-2. Dr. Chen and his doctoral student Michael Sacco determined the X-ray crystal structure of GC-376 bound by Mpro, and characterized molecular interactions between the compound and viral enzyme using 3D computer modeling.

Calpain inhibitors II and XII, cysteine inhibitors investigated in the past for cancer, neurodegenerative diseases and other conditions, also showed strong antiviral activity. Their ability to dually inhibit both Mpro and calpain/cathepsin protease suggests these compounds may include the added benefit of suppressing drug resistance, the researchers report.

All four compounds were superior to other Mpro inhibitors previously identified as suitable to clinically evaluate for treating SARS-CoV-2, Dr. Chen said.

A promising drug candidate – one that kills or impairs the virus without destroying healthy cells — fits snugly, into the unique shape of viral protein receptor’s “binding pocket.” GC-376 worked particularly well at conforming to (complementing) the shape of targeted Mpro enzyme binding sites, Dr. Chen said. Using a lock (binding pocket, or receptor) and key (drug) analogy, “GC-376 was by far the key with the best, or tightest, fit,” he added. “Our modeling shows how the inhibitor can mimic the original peptide substrate when it binds to the active site on the surface of the SARS-CoV-2 main protease.”

Instead of promoting the activity of viral enzyme, like the substrate normally does, the inhibitor significantly decreases the activity of the enzyme that helps SARS-CoV-2 make copies of itself.

Visualizing 3-D interactions between the antiviral compounds and the viral protein provides a clearer understanding of how the Mpro complex works and, in the long-term, can lead to the design of new COVID-19 drugs, Dr. Chen said. In the meantime, he added, researchers focus on getting targeted antiviral treatments to the frontlines more quickly by tweaking existing coronavirus drug candidates to improve their stability and performance.

Dr. Chen worked with lead investigator Jun Wang, PhD, UA assistant professor of pharmacology and toxicology, on the study. The work was supported in part by grants from the National Institutes of Health.

Journal

Cell Research

DOI

10.1038/s41422-020-0356-z

GAINESVILLE, Fla. --- In a surprise twist, a major group of flowering plants is evolving twice as quickly in temperate zones as the tropics. The finding runs counter to a long-held hypothesis that tropical regions, home to the planet's richest biological diversity, outpace their temperate counterparts in producing new species.

The tropics are the birthplace of most species of rosids, a group that makes up more than a quarter of flowering plants, ranging from mangroves to roses to oaks. But in an analysis of about 20,000 rosid species, researchers found the speed of tropical rosid evolution lags far behind that of younger communities in temperate habitats.

Although rosids originated 93-115 million years ago, the rate at which the group diversified, or formed new species, dramatically increased over the last 15 million years, a period of global cooling and expanding temperate habitats. Today, rosids are diversifying far faster in places such as the southeastern U.S. than in equatorial rainforests, said study co-lead author Ryan Folk, assistant professor of biological sciences and herbarium curator at Mississippi State University.

"Everyone knows about the diversity of tropical rainforests. You would assume all the action in evolution is happening in them," said Folk, formerly a postdoctoral researcher at the Florida Museum of Natural History. "But we found out that it is really the temperate regions of the Earth - really our own backyards - where a lot of the recent action is taking place."

Charles Darwin once described the speed with which the earliest flowering plants evolved and spread across the planet as an "abominable mystery." Scientists are still tracing the driving forces behind these plants' runaway evolutionary success, with temperature emerging as a complex factor: Some studies have shown that flower evolution accelerates in warmer regions while others point to cooler climates. Research on higher and lower latitudes' influence on plant diversification produced similarly conflicting findings.

A team of evolutionary biologists selected rosids as the candidates for a closer look at the relationship between temperature and plant diversity in the first large-scale assessment of the group's evolution. Comprising an estimated 90,000-120,000 species, rosids live in nearly all land-based habitats, with rosid trees shaping most temperate and many tropical forests, said study co-author Douglas Soltis, Florida Museum curator and University of Florida distinguished professor.

"To me that was one of the biggest terrestrial evolutionary events - the rise of the rosid-dominated forests," he said. "Other lineages, such as amphibians, insects and ferns, diversified in the shadow of rosids."

The team's study shows rosids evolved by leaps and bounds after the Earth's hothouse climate began to cool and dry and as many tropical and subtropical habitats transformed into temperate ones - offering new real estate for evolutionarily enterprising organisms.

The diversity of tropical regions, in contrast, is not due to evolutionary mechanisms, but rather stability: Folk said tropical plant communities have "simply failed to go extinct, so to speak."

The findings echo a similar pattern the team uncovered in another group of plants known as Saxifragales, but the researchers are cautious about making conjectures on whether the pattern holds true for other plants or animals.

"It's difficult to say there is a universal pattern for how life responds to temperature," said study co-lead author Miao Sun, a postdoctoral researcher at Denmark's Aarhus University and a former Florida Museum postdoctoral researcher. "On the other hand, there seems to be a trend forming that, together with our study, shows a lower diversification rate in tropical regions compared with temperate zones. But it's still hard to tell to what extent this pattern is true across the tree of life."

If cooling temperature spurred rosid diversification, how might the group fare on a warming planet? The prognosis is not promising, the researchers said.

Rosids were able to fill cool ecological niches and now may not be able to adapt to a temperature hike, especially at the current rate of change, said study co-author Pamela Soltis, Florida Museum curator and UF distinguished professor.

"Warming temperatures will likely slow the rate of diversification, but even worse, we don't expect species currently living in arctic or alpine areas to be able to respond to quickly warming temperatures," she said. "The change is happening too rapidly, and we are already seeing species moving northward in the Northern Hemisphere or up mountains, with many more species facing extinction or already lost."

The team used genetic data from GenBank and natural history databases such as iDigBio and the Global Biodiversity Information Facility to assemble DNA data for 20,000 species and 3 million plant occurrence records - one of the largest investigations of this nature to date.

"This work would have been impossible without natural history collections data," said study co-lead and senior author Robert Guralnick, Florida Museum curator of bioinformatics. "Rosids are an enormously successful group of flowering plants. Look out your window, and you will see rosids. Those plants are there because of processes occurring over millions of years, and now we know something essential about why."

DALLAS - July 6, 2020 - UT Southwestern researchers have identified vast webs of small snippets of the genome that interact with each other and with genes to promote prostate cancer. Their findings, published June 22 in the Journal of Clinical Investigation, could lead to new ways to treat the most common type of malignancy in American men other than skin cancer.

Research over the past few decades has shown that genetic mutations trigger and encourage the growth and spread of many cancer types. However, prostate cancers typically have relatively few of these mutations, explains study leader Ram S. Mani, Ph.D., an assistant professor in the departments of pathology and urology at UTSW.

Instead, how prostate cancers regulate gene expression - which genes are turned off and on, and to what extent - tends to go awry. What causes this aberrant gene regulation has been a mystery. Although previous research had identified pieces of DNA throughout the genome that appeared to be connected to prostate cancer, many of these pieces weren't genes, so their role was unclear.

To help answer these questions, Mani and his colleagues focused on genetic enhancers, short pieces of DNA that help encourage genes to make proteins. However, explains Mani, it's not as simple as a one-to-one ratio of enhancer per gene target. One enhancer may target several genes, or multiple enhancers might target a single gene. Additionally, each enhancer could be up to a million base pairs away from its gene target on the same chromosome - a significant distance that makes it difficult to link enhancers with their genes.

To pair enhancers to their gene targets in prostate cancer, Mani and his team used a technique called ChIA-PET, short for chromatin interaction analysis by paired-end tag sequencing. This technique maps associations of particular proteins with DNA throughout the genome.

The researchers used ChIA-PET to find DNA targeted by a protein called RNA polymerase II, looking for differences between benign prostate cells and prostate cancer cells. RNA polymerase II not only binds to genes to start transcription - the process in which cells use the instructions in DNA to make RNA - but also enhancers for these genes. "When this technique identifies a gene, it also identifies all the enhancers that target that gene at the same time," says Mani, a member of UT Southwestern's Harold C. Simmons Comprehensive Cancer Center.

Using sophisticated analytical techniques, the scientists sorted out each of these complicated interactions unique to prostate cancer cells, finding vast hubs of enhancers that interact not just with genes but also with each other. They found that many enhancers interacted with tens of other enhancers or genes. These interactions explain the abnormal expression of several key prostate cancer genes, such as the androgen receptor gene that's over-expressed in many subtypes of prostate cancer and the oncogene MYC, which plays a role in many cancer types. Further investigation identified some "grammar rules" for enhancers in prostate cancer, grouping genes and enhancers into clusters that strictly interact with each other.

Mani notes that finding these hubs of enhancers and their genes also helps explain the long-standing mystery of the short pieces of DNA connected to prostate cancer that are scattered throughout the genome. This new research suggests that many of these pieces are enhancers.

Manipulating the interaction between these enhancers and their gene targets could eventually be used as a strategy to slow or stop prostate cancer spread or potentially prevent it from developing at all, he adds. "These findings open up a whole new field focused on enhancers," he says, "that could lead to novel prostate cancer treatments."

It images single atoms. It maps atomic-scale hills and valleys on metal and insulating surfaces. And it records the flow of current across atom-thin materials subject to giant magnetic fields. Scientists at the National Institute of Standards and Technology (NIST) have developed a novel instrument that can make three kinds of atom-scale measurements simultaneously. Together, these measurements can uncover new knowledge about a wide range of special materials that are crucial for developing the next generation of quantum computers, communications and a host of other applications.

From smartphones to multicookers, devices that perform several functions are often more convenient and potentially less expensive than the single-purpose tools they replace, and their multiple functions often work better in concert than separately. The new three-in-one instrument is a kind of Swiss Army knife for atom-scale measurements. NIST researcher Joseph Stroscio and his colleagues, including Johannes Schwenk and Sungmin Kim, present a detailed recipe for building the device in the Review of Scientific Instruments.

"We describe a blueprint for other people to copy," Stroscio said. "They can modify the instruments they have; they don't have to buy new equipment."

By simultaneously conducting measurements on scales ranging from nanometers to millimeters, the instrument can help researchers zero in on the atomic origins of several unusual properties in materials that may prove invaluable for a new generation of computers and communication devices. These properties include the resistance-less flow of electric current, quantum jumps in electrical resistance that could serve as novel electrical switches, and new methods to design quantum bits, which could lead to solid-state-based quantum computers.

"By connecting the atomic with the large scale, we can characterize materials in a way that we couldn't before," said Stroscio.

Although the properties of all substances have their roots in quantum mechanics -- the physical laws that govern the Lilliputian realm of atoms and electrons -- quantum effects can often be ignored on large scales such as the macroscopic world we experience every day. But for a highly promising class of materials known as quantum materials, which typically consist of one or more atomically thin layers, strong quantum effects between groups of electrons persist over large distances and the rules of quantum theory can dominate even on macroscopic length scales. These effects lead to remarkable properties that can be harnessed for new technologies.

To study these properties more precisely, Stroscio and his colleagues combined in a single instrument a trio of precision measuring devices. Two of the devices, an atomic force microscope (AFM) and a scanning tunneling microscope (STM), examine microscopic properties of solids, while the third tool records the macroscopic property of magnetic transport -- the flow of current in the presence of a magnetic field.

"No single type of measurement provides all the answers for understanding quantum materials," said NIST researcher Nikolai Zhitenev. "This device, with multiple measuring tools, provides a more comprehensive picture of these materials."

To build the instrument, the NIST team designed an AFM and a magnetic-transport-measuring device that were more compact and had fewer moving parts than previous versions. They then integrated the tools with an existing STM.

Both an STM and an AFM use a needle-sharp tip to examine the atomic-scale structure of surfaces. An STM maps the topography of metal surfaces by placing the tip within a fraction of a nanometer (billionth of a meter) of the material under study. By measuring the flow of electrons that tunnels out of the metal surface as the sharp tip hovers just above the material, the STM reveals the sample's atomic-scale hills and valleys.

In contrast, an AFM measures forces by changes in the frequency at which its tip oscillates as it hovers over a surface. (The tip is mounted on a miniature cantilever, which allows the probe to swing freely.) The oscillation frequency shifts as the sharp probe senses forces, such as the attraction between molecules, or the electrostatic forces with the material's surface. To measure magnetic transport, a current is applied across a surface immersed in a known magnetic field. A voltmeter records the voltage at different places on the device, revealing the electrical resistance of the material.

The ensemble is mounted inside a cryostat, a device that chills the system to one-hundredth of a degree above absolute zero. At that temperature, the random quantum jitter of atomic particles is minimized and large-scale quantum effects become more pronounced and easier to measure. The three-in-one device, which is shielded from external electrical noise, is also five to 10 times more sensitive than any previous set of similar instruments, approaching the fundamental quantum noise limit that can be achieved at low temperatures.

Although it's possible for three entirely independent instruments -- an STM, an AFM and a magnetic transport setup -- to make the same measurements, inserting and then retracting each tool can disturb the sample and diminish the accuracy of the analysis. Separate instruments can also make it difficult to replicate the exact conditions, such as the temperature and rotation angle between each ultrathin layer of the quantum material, under which previous measurements were made.

To achieve the goal of a three-in-one instrument with high sensitivity, the NIST team partnered with an international team of experts, including Franz Giessibl from the University of Regensburg, Germany, who invented a highly effective AFM known as the qPlus AFM. The team chose a compact design that increased the stiffness of the microscope and outfitted the system with a series of filters to screen out radio frequency noise. The atomically thin needle of the STM doubled as the force sensor for the AFM, which was based on a new force sensor design created by Giessibl for the three-in-one instrument.

For Stroscio, a pioneer in building ever-more-sophisticated STMs, the new device is something of a pinnacle in a more than three-decade career in scanning probe microscopy. His team, he noted, had been struggling for several years to dramatically reduce the electrical noise in its measurements. "We have now achieved the ultimate resolution given by thermal and quantum limits in this new instrument," Stroscio said.

"This feels like I've climbed the highest peak of the Rocky Mountains," he added. "It's a nice synthesis of everything I've learned over the last 30-plus years."

The development of metasurfaces opened a horizon for the advance of planar optics. Among various metadevices, the metalens has attracted widespread attention for practical applications in imaging and spectroscopy, where it allows multifunctional wavefront manipulations for improved focus.

As part of the trend of miniaturization and integration of photonic systems, metalenses are replacing the traditional refractive lenses made of polished crystals or polymers. But their functions remain static. The prospect of realizing active metalenses has motivated the introduction of materials with special properties, such as switchable bifocals or discrete focal lengths. Until recently, dynamic manipulation of metalenses, especially tunable chromatic dispersion, has remained out of reach.

Dynamic focusing with a single metalens

Metalenses are plagued by failure to focus all colors to the same point, which is known as chromatic aberration. Overcoming chromatic aberration is a vital concern for improved resolution in full-color and hyperspectral imaging. On the contrary, for spectrographic analysis and tomographic applications, chromatic dispersion helps to separate focal spots for different frequencies, to avoid crosstalk.

The ability to manipulate chromatic dispersion dynamically with a single metalens would promote system integration and functional versatility.

Photo-patterned liquid crystal

A research team from Nanjing University recently demonstrated active manipulation of chromatic dispersion, achieving achromatic focusing within a designated broadband. As reported in the peer-reviewed, open access journal Advanced Photonics, the team integrated a photo-patterned liquid crystal into a dielectric metasurface. In their design, the metasurface generates a linear-resonant phase dispersion, which means that the phase front of the transmitted wave is delayed linearly by the dielectric metasurface. The liquid crystal (LC) is responsible for generating frequency-independent geometric phase modulation.

The team verified the chromatic aberration control of the combined lens and demonstrated a significant dynamic broadband imaging contrast effect. The design can be extended to other active metadevices; as an example, the team presented a beam deflector with controllable dispersion. "Combining the flexibility of metadevices with the broadband electro-optical characteristics of liquid crystals makes the design competent for wavefront control from the visible wavelengths to the THz and microwaves," remarked senior author Prof. Yanqing Lu, of the College of Engineering and Applied Sciences at Nanjing University.

Lu's colleague at the College of Engineering and Applied Sciences, fellow senior author Prof. Wei Hu notes, "We anticipate that liquid crystal integrated metadevices will give birth to a variety of active planar photonic elements to enhance the functional flexibility of optical systems."

"Running in Tarahumara (Rarámuri) Culture," just published in Current Anthropology (v61, no. 3 (June 2020): 356-379) studies the Tarahumara Native Americans of northern Mexico. For over a century, the Tarahumara have been famous for their long distance running traditions and abilities, with many accounts claiming they have superhuman athletic abilities that partly result from being uncontaminated by westernization. Now an international team of researchers (including a champion Tarahumara runner) combine their own observations with detailed interviews of elderly Tarahumara runners to dispel these stereotypical myths, which they term the "fallacy of the athletic savage." Lieberman and colleagues use accounts by Tarahumara runners to detail the various ways Tarahumara used to run for hours to hunt animals, and they describe how the Tarahumara still run traditional long distance races that, for men, involve chasing a small wooden ball and, for women, a hoop. While these many different kinds of running have important social dimensions, running is also a spiritually vital form of prayer for the Tarahumara. Further, contrary to the fallacy of the athletic savage, Tarahumara runners --both men and women-- struggle just as much as runners from other cultures to run long distances, and instead of being the natural "superathletes" that some journalists have claimed, they develop their endurance from regular hard work and other endurance physical activities such as lots of walking and dancing.

Researchers in the Cockrell School of Engineering at The University of Texas at Austin have built a new type of battery that combines the many benefits of existing options while eliminating their key shortcomings and saving energy.

Most batteries are composed of either solid-state electrodes, such as lithium-ion batteries for portable electronics, or liquid-state electrodes, including flow batteries for smart grids. The UT researchers have created what they call a "room-temperature all-liquid-metal battery," which includes the best of both worlds of liquid- and solid-state batteries.

Solid-state batteries feature significant capacity for energy storage, but they typically encounter numerous problems that cause them to degrade over time and become less efficient. Liquid-state batteries can deliver energy more efficiently, without the long-term decay of sold-state devices, but they either fall short on high energy demands or require significant resources to constantly heat the electrodes and keep them molten.

The metallic electrodes in the team's battery can remain liquefied at a temperature of 20 degrees Celsius (68 degrees Fahrenheit), the lowest operating temperature ever recorded for a liquid-metal battery, according to the researchers. This represents a major change, because current liquid-metal batteries must be kept at temperatures above 240 degrees Celsius.

"This battery can provide all the benefits of both solid- and liquid-state -- including more energy, increased stability and flexibility -- without the respective drawbacks, while also saving energy," said Yu Ding, a postdoctoral researcher in associate professor Guihua Yu's research group in the Walker Department of Mechanical Engineering. Ding is the lead author of a paper on the room-temperature battery the team published recently in Advanced Materials.

The battery includes a sodium-potassium alloy as the anode and a gallium-based alloy as the cathode. In the paper, the researchers note that it may be possible to create a battery with even lower melting points using different materials.

The room-temperature battery promises more power than today's lithium-ion batteries, which are the backbone of most personal electronics. It can charge and deliver energy several times faster, the researchers said.

Because of the liquid components, the battery can be scaled up or down easily, depending on the power needed. The bigger the battery, the more power it can deliver. That flexibility allows these batteries to potentially power everything from smartphones and watches to the infrastructure underpinning the movement toward renewable energy.

"We are excited to see that liquid metal could provide a promising alternative to replace conventional electrodes," Professor Yu said. "Given the high energy and power density demonstrated, this innovative cell could be potentially implemented for both smart grid and wearable electronics."

The researchers have spent more than three years on this project, but the job isn't done yet. Many of the elements that constitute the backbone of this new battery are more abundant than some of the key materials in traditional batteries, making them potentially easier and less expensive to produce on a large scale. However, gallium remains an expensive material. Finding alternative materials that can deliver the same performance while reducing the cost of production remains a key challenge.

The next step to increasing the power of the room-temperature battery comes in improving the electrolytes -- the components that allow the electrical charge to flow through the battery.

"Although our battery cannot compete with high-temperature, liquid-metal batteries at the current stage, better power capability is expected if advanced electrolytes are designed with high conductivity," Ding said.

The reniform nematode is one of the most commonly found pests of cotton, with the ability to cause severe economic damage. In order to assess exactly how much damage the reniform nematode can cause, plant pathologists at Auburn University conducted a field trial comparing a clean field to a reniform-infested field.

To get the most accurate data, the plant pathologists began with one field experiencing the same conditions, including soil type and irrigation system. They then split the field in half, leaving a 10-foot grass strip in the center, and inoculated one side with the reniform nematode and left the other half clean. They planted ten cotton varieties on each half. They found that, averaged over two years, the cotton yields were 50 percent lower in the reniform field compared to the clean field.

They also experimented with the nematicide Velum Total and found it to be effective dependent on the environment. The nematicide supported a 55 percent increase in yield in 2017 but only 6 percent in 2018, in part due to the dry spring.

"This trial is unique because we can test varieties and nematicides with and without the reniform nematode under almost identical conditions in the field. We can truly measure the reniform nematode effect on yield and the real benefit of the nematicide," said Kathy Lawrence, one of the plant pathologists involved in the study.

Lawrence advises growers to be careful not to allow the reniform nematode to establish in their fields. If they do discover nematodes, they should wash their equipment before moving to a clean field to prevent transfer.

Characteristics of palm trees differ from those of other tropical trees in many ways. In a major new study led by scientists at Uppsala University, Sweden, and University of Campinas, Brazil, they have surveyed the actual numbers of palms in tropical rainforests around the globe. The proportion of palm trees is important to include in calculations of forests' potential carbon storage and in estimates of forested areas' sensitivity to climate change.

Palm trees are iconic tropical forest plants. However, postcard images of coconut palms leaning over white sandy beaches do not capture the stunning diversity of palms and their importance to humans and ecosystems. There are over 2,500 palm species and many are used by humans for food, shelter, medicine and crafts. In some areas, palms are also entirely dominant and form natural monocultures. Palms are among the most common tree species in the Amazon rainforest, but in some tropical areas they are unusual, or conspicuously absent.

Before, variation in numbers of palm trees among tropical regions had not been quantified. Now a study led by Bob Muscarella at Uppsala University in Sweden and Thaise Emilio at University of Campinas in Brazil has made the first global assessment of their numbers. Over 200 co-authors from 48 countries contributed to the scientific article.

"To get a better understanding of tropical forests and reduce uncertainty about carbon balance in these ecosystems during climate change, we summarised data to show how the number of palms vary around the world compared with other tree species," Muscarella says.

Drawing from existing networks of forest plots (including forestplots.net, PPBio, Rainfor, AfriTRON), the researchers compiled a huge database of 2,548 plots and then quantified palm numbers relative to other tree species in the sample plots.

The study results show that in the Neotropical rainforests (such as Amazonia), palms are more than five times more numerous than in comparable Asian and African forests. Many palms were already known to prefer land with a good groundwater supply, and the new study confirmed that palm trees were more plentiful in wetter areas with less fertile soils and shallower groundwater.

Tropical rainforests are often seen as synonymous with biodiversity. However, this diversity is not evenly distributed, and most plants in a given area belong to only a handful of species. More than half of the total biomass in the Amazon rainforest is distributed among fewer than 300 tree species - including several species of palms.

"Understanding the dominant species in tropical forests is crucial to recognising how these forests function and how vulnerable they're going to be to disturbances and climate change in the future," Muscarella says.

Being monocotyledons (the seed produces only one first leaf, or cotyledon) palms are more closely related to grasses than to the deciduous trees of the tropics, for instance. Palms therefore differ in many fundamental ways, in anatomy and physiology, from other tropical trees. These differences may have far-reaching implications when it comes to estimating uptake and storage (sequestration) of carbon in tropical forests, as well as their resilience to climate change. The new study provides knowledge with a vital bearing on further research into both of these aspects.

"Impressive levels of palm abundance do not come as a surprise to many tropical forest researchers. Days of work may be necessary to measure all the palms of a single hectare in some places in the middle of Amazon. However, a fair representation of palms in studies of tropical forests functioning is yet to come. Showing where and when palms must be considered is a major contribution of our new study," Emilio says.