Brain

Within the past decade, next-generation sequencing technologies have revolutionized the way in which genetic data are generated and analyzed. In the field of phylogenetics, this has meant that researchers are rapidly reconstructing the tree of life, a goal that biologists have been working toward since Darwin sketched the first phylogeny in his notebook in 1837.

Yet despite the relative ease with which DNA can now be sequenced in large quantities, scientists must first extract that DNA from an organism, often relying on vast numbers of curated specimens in museums and herbaria. With over 250,000 species in the plant kingdom alone, the acquisition and documentation of specimen material is now by far the most time-consuming and error-prone process in large studies.

In a research article published in a recent issue of Applications in Plant Sciences, researchers undertook the goal of automating the collecting process by using a combination of unique object identifiers, QR codes, and citizen science.

"Our goal was to create a resource for the scientific community," said lead author Ryan Folk, an assistant professor and herbarium curator at Mississippi State University. "In the future, we hope that all such collection information will be available online, where it's easy to find and the work won't need to be repeated."

Folk and his colleagues are working to create a partial -- 50 percent coverage -- phylogeny of seed plants that harbor nitrogen-fixing bacteria in specialized root nodules. This symbiotic relationship spans several disparate seed plant groups that collectively contain more than 30,000 species, for which the team relied entirely on herbarium specimens.

For a project of this scale, that meant members of the team worked for weeks at a time at multiple herbaria, focusing their efforts primarily at the New York and Missouri Botanical Gardens and the California Academy of Sciences.

Ordinarily, this would involve sifting through specimen material and manually transcribing or copying voucher information (such as the specimen locality, date, and name of the collector(s)) into a spreadsheet, as well as manually copying labels onto the samples themselves.

This process is absolutely essential for downstream analyses, but it requires large amounts of time and creates the potential for error. The biggest drawback, however, is the information garnered at this stage is typically only useful to the researchers who collected it and cannot be easily shared between groups. If a different group of researchers wanted to extract DNA from the same specimens, they would have to re-collect all of the same data.

Folk and his colleagues, wanting to curtail this duplication of effort, devised a digitization workflow whereby voucher information would only need to be collected once.

"Our workflow is made up of essentially several strategies -- more or less connected -- that takes you straight from walking into a museum all the way through data analysis and publication," said Folk.

At a glance, the process has three steps. First, a unique object identifier is assigned and physically attached to each herbarium voucher, and the specimen is photographed with the identifier clearly visible.

To transcribe the data from the roughly 15,000 specimens they used for the study, they used the citizen science platform Notes From Nature, which offers an online, interactive workspace where volunteers can join specific projects from home and communicate with researchers involved in the study.

By itself, this digitization of specimen information with unique object identifiers will be a valuable tool for researchers in the future and may ultimately complement the monumental effort being undertaken in museums around the world to digitize collections. But the researchers didn't stop there.

In the third step, QR codes were assigned to each specimen to further streamline data collection. This meant that when extracting and amplifying DNA in the lab, the researchers no longer had to manually enter specimen data into spreadsheets. Instead, that information was auto-populated when they scanned a given QR code.

"Scanning QR codes was basically effortless and didn't require any training or set up," said study co-author Heather Kates, a post-doctoral associate at the University of Florida. "But more important than the time-saving aspect of this approach was the reduction of errors. The errors introduced through illegibility and typos are a pain when you're doing a set of 20 extractions; you can imagine how important it is with 15,000 that those errors are avoided as much as possible."

Rather than keeping all of this information in spreadsheets, which have limited utility for specialized queries or data analysis, the team also created their own database using Python scripts.

The detailed workflow and Python scripts have been made freely available online so that researchers can access and fine-tune them for personalized use in their own studies.

"Although we have seen large DNA datasets published in recent years, reuse of data from many projects has been minimal due to the difficulty of accessing data online," said Folk. "In the long-term, we will release the data to the community in a form more easily amenable to future researchers. My hope is that our efforts will jump-start major projects focused on other organisms as well as establish a new baseline for biodiversity in the nitrogen-fixing clade of seed plants."

EUGENE, Ore. -- April 29, 2021 -- An analysis of Twitter activity between March 1 and Aug. 1, 2020, found strong support by U.S. users for wearing face coverings and that a media focus on anti-mask opinions fueled the rhetoric of those opposed, report University of Oregon researchers.

The study, published April 28 in the journal PLOS ONE, initially focused on linguistics, zeroing in on the language associated with hashtags during the study period, which began a month before the Centers for Disease Control and Prevention recommended mask-wearing to protect against COVID-19 infection.

However, to better understand that semantics, which were found to be polarized, angry and emotionally loaded, the research team had to take an interdisciplinary journey into politics and media, said Zhuo Jing-Schmidt, a professor and linguist in the UO's Department of East Asian Languages and Literatures.

"There was polarization that was strong and at a rhetorical level, but when we looked at the participatory process there was a huge imbalance in the numbers," Jing-Schmidt said. "After breaking down this imbalance, our findings provide a cautious optimism. Most Americans stepped up in support of mask-wearing, even though the media gave us the impression that there was a huge resistance."

The data analyzed consisted of 149,110 Twitter posts involving 35 distinct types of hashtags, 26 of which were associated with mask supporters. Of the total posts, 138,796 users tweeted pro-mask hashtags and 7,771 posted anti-mask hashtags.

Jing-Schmidt's doctoral student Jun Lang and Wesley W. Erickson, who earned a doctorate in physics from the UO in 2020, then applied their interest in big data to complete multilayer analyses to explore polarizing rhetoric, the pro-mask majority and a possible echo-chamber effect of participants merely engaging with like-minded people.

The analyses also explored public opinion polls on overall acceptance of wearing face coverings and connected Twitter posts with the headlines of continual mainstream media coverage of anti-mask sentiment, including the common opposing rhetoric of the former president and other conservative politicians.

The study's findings supported the overall support of wearing face coverings found in polling by the Pew Research Center.

"We found that there is polarization, but you have to look at it at two different levels," Jing-Schmidt said. "One was the rhetorical, where we saw stark polarization that is angry and shouty. Secondly, we showed that the mask-resisters were a small cluster of users compared to a huge majority of mask supporters."

Media coverage, she said, magnified anti-mask rhetoric. The peak use of polarizing hashtags, the researchers found, was associated with headlines of stories that focused on anti-mask-wearing sentiments.

"We find that the media played a part in the polarization, magnifying the anti-mask rhetoric," she said. "This led us to understand how the anti-mask minority can seem to be so powerful in the public's perception."

That connection, she said, was not unexpected.

"That's the nature of news," she said. "Journalists in a democracy have this responsibility to hold people accountable, and that leads to negative events being covered. We're doing fine, generally, but we must account for these negative cognitive biases amplified by the media in our political discourse. We are still in the pandemic, so there is no reason to celebrate."

Interestingly, Jing-Schmidt said, it was pro-mask Twitter posters who fitted into an echo chamber. Most pro-maskers ignored the rhetoric of the anti-mask minority, especially disinformation that anti-maskers attempted to spread in their responses to tweets of pro-maskers.

"Our results demonstrate that the digital discourse on Twitter about mask wearing was rhetorically polarized whereby the rallying calls of the mask supporters were amplified by other mask supporters, and the battle cries of the mask resistors resonated with other mask resistors but were drowned out and ignored by a vocal and overwhelming pro-mask majority," her team wrote.

In an interdisciplinary research project carried out at Tel Aviv University, researchers from the School of Plant Sciences affiliated with the George S. Wise Faculty of Life Sciences collaborated with their colleagues from the Sackler Faculty of Medicine in order to study the course of plant root growth. The plant researchers were aided by a computational model constructed by cancer researchers studying cancer cells, which they adapted for use with plant root cells.

The fascinating and groundbreaking findings: For the first time in the world, it has been demonstrated, at the resolution of a single cell, that the root grows with a screwing motion - just like a drill penetrating a wall. In the wake of this study, the cancer researchers conjecture that cancer cells, too, are assisted by a spiral motion in order to penetrate healthy tissue in the environment of the tumor, or to create metastases in various organs of the body.

The research was led by Prof. Eilon Shani from the School of Plant Sciences and Food Security and Prof. Ilan Tsarfaty from the Department of Clinical Microbiology and Immunology at Tel Aviv University, and was conducted in collaboration with researchers from the USA, Austria and China. The article was published in March 2021 in the acclaimed journal Nature Communications.

The researchers in Prof. Shani's group, led by Dr. Yangjie Hu, used as a model the plant known as Arabidopsis. They marked the nuclei of the root cells with a fluorescent protein and observed the growing process and movement of the cells at the root tip through a powerful microscope - approximately 1000 cells in each movie. Furthermore, in order to examine what causes and controls the movement, they focused on a known hormone named auxin, which regulates growth in plants. They built a genetic system that enables activation of auxin production (like a switch) in a number of selected cells-types, and then monitored the influence of the on/off mechanism, in four dimensions - the three spatial dimensions and the dimension of time. After each instance of auxin biosynthesis, each of the thousand cells was video recorded for a period of 6 to 24 hours, thus an enormous amount of data accumulated.

For the next stage, the researchers were aided by the computational tools provided by Prof. Tsarfaty, which had been developed in his laboratory for the purpose of monitoring the development of cancerous growths. They used these tools to analyze the imaging data obtained in the study. Thus they were actually able, for the first time, to observe with their own eyes the corkscrew movement of the root, as well as to precisely quantify and chart some 30 root growth parameters relating to time and space - including acceleration, length, changes in cell structure, coordination between cells during the growth process and velocity - for each one of the thousand cells at the root tip. Using fluorescent reporters, the findings even allowed them to precisely assess the movement and the influence of the auxin on the root, and the way in which it controls the growth process.

Prof. Shani: "Plants present special challenges to researchers. For example, half of the plant (the hidden half), namely, the root system, is buried beneath the ground. The computational tools that were developed for cancer research have enabled us, for the first time, to precisely measure and quantify the kinetics of growth and to reveal the mechanisms that control it at the resolution of a single cell. By this they have significantly advanced plant research, an area of utmost importance for society - both from an environmental point of view and in terms of agriculture and feeding the population."

Prof. Shani adds: "In the course of our study we discovered a fascinating phenomenon that had not been previously observed 'live': we saw that the cells at the root tip move in a spiral motion, like a drill penetrating the earth. We also recognized that the hormone auxin controls the screwing process of the root tip. We learned and measured the directions of the auxin hormone's movement, passing from one cell to another in the root, in order to control the growth of the root and the corkscrew motion."

Prof. Tsarfaty adds: "This was a synergetic collaboration that benefited and enlightened both parties. In plants, processes take place much more rapidly, and therefore constitute an excellent model for us. In consequence of the findings provided by this plant study, we are presently examining the possibility of a similar screw-like motion in cancer cells and in metastases, in the course of their penetration into adjacent healthy tissues."

Researchers at the University of Bonn and the research center caesar have succeeded in ultra-fast freezing proteins after a precisely defined period of time. They were able to follow structural changes on the microsecond time scale and with sub-nanometer precision. Owing to its high spatial and temporal resolution, the method allows tracking rapid structural changes in enzymes and nucleic acids. The results are published in the Journal of the American Chemical Society.

If you want to know what the spatial structure of a biomolecule looks like, you have a formidable arsenal of tools at your disposal. The most popular ones are electron microscopy and X-ray diffraction, which can reveal even the smallest details of a protein. However, a significant limitation of those methods is that they usually deliver static images, which are often insufficient to understand biomolecular processes in precise mechanistic terms. Therefore, a long-term goal of many research groups worldwide has been to track the movements within a macromolecule such as a protein over time while it carries out its work, just like in a movie. The research groups led by Prof. Dr. Olav Schiemann from the Institute of Physical and Theoretical Chemistry at the University of Bonn and Prof. Dr. Benjamin Kaupp from the research center caesar of the Max Planck Society have now come a step closer to achieving this goal.

They chose an ion channel for their investigation. This is a protein that forms miniscule pores in the cell membrane that are permeable to charged particles called ions. "This channel is normally closed," Schiemann explains. "It only opens when a cellular messenger, called cAMP, binds to it. We wanted to know how exactly this process works."

Mini magnets to measure distances

To do so, the researchers first mixed the channel protein and cAMP and then rapidly froze the solution. In the frozen state, the protein structure can now be analyzed. For their method to work, they had attached molecular electromagnets at two points in the channel. The distance between these magnets can be determined with a precision of a few Angstrom (ten billionths of a millimeter) using a sophisticated method called PELDOR, which works like a molecular ruler. In recent years, the method was significantly refined and improved in Schiemann's group.

"However, this only gives us a static image of cAMP binding to the ion channel," Schiemann says. "We therefore repeated the freezing process at different times after mixing the two molecules. This allowed reconstructing the movements in the protein after cAMP binding - just like a movie, which is also made up of a sequence of images."

At the center of this procedure is a sophisticated method that allows samples to be mixed and frozen very quickly at a precise point in time. The technique, called "microsecond freeze hyperquenching" (abbreviated MHQ), was originally developed at Delft University, but later fell into disuse. It was rediscovered and decisively refined by Kaupp's group.

"In the MHQ device, the cAMP molecule and the ion channel are mixed at ultrafast speed," Kaupp explains. "Then the mixture is shot as a hair-thin stream onto a very cold metal cylinder at -190 °C, which rotates 7,000 times per minute. It was particularly challenging to transfer the frozen samples for the PELDOR measurement from the metal plate into thin glass tubes, and to keep them frozen meanwhile. We had to design and build special tools for that."

Deep-freezing in 82 millionths of a second

The entire mixing and freezing process takes only 82 microseconds (one microsecond equals a millionth of a second). "This allows us to visualize very rapid changes in the spatial structure of proteins," explains Tobias Hett, one of the two doctoral students who contributed significantly to the success. The advantage of the method is its combination of high spatial and temporal resolution. "This represents a major step forward in studying dynamic processes in biomolecules," Kaupp emphasizes.

The researchers now plan to use their method to take a closer look at other biomolecules. They hope to gain new insights, for example into the functioning of enzymes and nucleic acids. The importance of such insights is best illustrated by the recent worldwide surge of structural research on the SARS coronavirus-2: The so-called spike protein of the virus also undergoes a structural change when human cells are infected. Clarifying this mechanism will provide valuable information how to target the infection mechanism with new drugs.

The preparation of the samples, the experimental execution, and the analysis of the data is very complex. The results of the study therefore also reflect a successful scientific cooperation with researchers led by Prof. Dr. Helmut Grubmüller of the Max Planck Institute for Biophysical Chemistry in Göttingen and Prof. Dr. Heinz-Jürgen Steinhoff of the University of Osnabrück.

The ability to turn on and off a physical process with just one photon is a fundamental building block for quantum photonic technologies. Realizing this in a chip-scale architecture is important for scalability, which amplifies a breakthrough by City College of New York researchers led by physicist Vinod Menon. They've demonstrated for the first time the use of "Rydberg states" in solid state materials (previously shown in cold atom gases) to enhance nonlinear optical interactions to unprecedented levels in solid state systems. This feat is a first step towards realizing chip-scale scalable single photon switches.

In solid state systems, exciton-polaritons, half-light half-matter quasiparticles, which result from the hybridization of electronic excitations (excitons) and photons, are an attractive candidate to realize nonlinearities at the quantum limit. "Here we realize these quasiparticles with Rydberg excitons (excited states of excitons) in atomically thin semiconductors (2D materials)," said Menon, chair of physics in City College's Division of Science. "Excited states of excitons owing to their larger size, show enhanced interactions and therefore hold promise for accessing the quantum domain of single-photon nonlinearities, as demonstrated previously with Rydberg states in atomic systems."

According to Menon, the demonstration of Rydberg exciton-polaritons in two-dimensional semiconductors and their enhanced nonlinear response presents the first step towards the generation of strong photon interactions in solid state systems, a necessary building block for quantum photonic technologies.

Jie Gu, a graduate student working under Menon's supervision, was the first author of the study entitled: "Enhanced nonlinear interaction of polaritons via excitonic Rydberg states in monolayer WSe2," which appears in "Nature Communications." The team also included scientists from Stanford, Columbia, Aarhus and Montreal Polytechnic universities.

The research of Professor Menon and his co-workers could have a tremendous impact on Army goals for ultra-low energy information processing and computing for mobile Army platforms such as unmanned systems," said Dr. Michael Gerhold, program manager at the U.S. Army Combat Capabilities Development Command, known as DEVCOM, Army Research Laboratory. "Optical switching and nonlinearities used in future computing paradigms that use photonics would benefit from this advancement. Such strong coupling effects would reduce energy consumption and possibly aid computing performance.

PHILADELPHIA (April 27, 2021) - Nurses and other clinicians rely heavily upon the electronic health record (EHR) to provide patient care. This includes clinical decision-making, care planning, patient surveillance, medication ordering and administration, and communication with other health care team members. While data show that EHR technology usability can put added burden on clinicians, the relationships between EHR usability and the job outcomes of hospital staff nurses and surgical patient outcomes have not been explored.

A new study from the University of Pennsylvania School of Nursing's Center for Health Outcomes and Policy Research (CHOPR) has investigated associations between EHR usability and nurse job outcomes (burnout, job dissatisfaction, and intention to leave) and surgical patient outcomes (inpatient mortality and 30-day readmission). The study found that employing EHR systems with suboptimal usability was associated with higher odds of adverse nurse job outcomes and surgical patient mortality and readmission. EHR usability may be more important to nurse job and patient outcomes than comprehensive EHR adoption. The results have been published in the journal Medical Care.

"When the EHR system does not allow work to be performed efficiently and effectively, nurse burden increases, and patient outcomes are threatened," says Ann Kutney-Lee, PhD, RN, FAAN, Adjunct Associate Professor, Department of Biobehavioral Health Sciences at Penn Nursing and lead investigator of the study. "Improving EHR usability may be critical to reducing nurse burnout and to realizing the full potential of EHRs to improve the quality and safety of health care."

The study's findings have implications for nurse turnover and its associated costs. The findings can also help EHR vendors and hospital leadership teams better understand the critical importance of nurse involvement in developing, selecting, implementing, and modifying EHR systems.

Aromatics are major building blocks of polymers, or plastics, that turn up as everything from PET bottles for water to breathable, wrinkle-resistant polyester clothing. These petrochemicals comprise a specialized, value-added sector of the energy industry. The process for refining crude oil into useful aromatic streams for derivative use often involves the usage of a catalyst to facilitate chemical reactions. Among the various types of catalysts, many are zeolites - porous aluminosilicates - such as ZSM-5, a unique synthetic zeolite prolifically used in the upgrading of chemicals in alkylation and isomerization. Petrochemicals producers are constantly looking to minimize overhead costs to weather the volatility in commodity markets and provide a competitive end product to the average person.

Jeffrey Rimer, Abraham E. Dukler Professor at the University of Houston Cullen College of Engineering and Javier Garcia-Martinez, professor of inorganic chemistry at the University of Alicante, have uncovered a seeding method that simplifies the synthesis process and results in spontaneous pillaring of zeolites. The work is published in Advanced Materials. The process results in more aluminum concentrate in the zeolite and a unique crystal structure to facilitate chemical reactions with reduced carbon build up.

"This novel technique has the advantage of producing thicker well-formed sheets, which is important to produce highly stable materials - an important feature in most industrially relevant applications," said Martinez.

"These hierarchical catalysts show unprecedented improvement in catalyst performance with 4-fold lower rates of deactivation, five-fold increases in activity and nearly two-fold increases in selectivity," according to Rimer.

In industry, petrochemical producers often must take turnarounds every two years or so to regenerate a catalyst or replace it altogether. In the US, late first quarter to early second quarter usually sees several refiners take a two-week to two-month maintenance period to accommodate this. During that time, production and profit are lost, and while these improved hierarchical zeolite catalysts will not end turnarounds altogether, their smaller but stable 30-60 nanometer size supplies aluminum - active sites for catalysis - comparable to commercial ZSM-5. However, their small size simultaneously improves selectivity and reduces carbon build up. This hints at longer periods between costly turnarounds and increased yield.

The implications of this study extend to an improved understanding of zeolite nucleation - or first observation of a crystal - and point toward a new process for creating pillared zeolites without costly organic structure-directing agents (OSDA). Zeolites with hierarchical (pillared) structures have been prepared previously only with OSDAs, which operate as templates to form these unique structures.

"Until now, OSDAs were believed to be critical to synthesis of pillared zeolites, acting as templates to facilitate the formation of thin interconnecting nanosheets," Rimer said." But as we observed in this seeding process, these 30-60 nanometer nanosheets emerged from amorphous material and formed pillars without any template."

"Previous attempts to produce these catalysts required costly organic agents and low yields were typically obtained, which greatly limited their commercial application," Martinez said.

Seeding proved to be instrumental in synthesizing pillared zeolites with improve catalytic performance in Friedel-Craft alkylation and methanol to hydrocarbon reactions. This synthesis approach bypasses the typical energy intensive process of utilizing OSDAs. Organics previously thought essential for creating zeolites that can be utilized commercially are ultimately no longer necessary.

Next steps for this project include scaling up the process to show whether this improved zeolite catalyst can replicate its performance on industry scale. This research also functions as a springboard for further exploring the implications of seeding to produce other zeolites with unique structures and exceptional performance in commercial applications.

Corals are part of a highly complex ecosystem, but it remains a mystery if and how they might communicate within their biological community. In a new study, researchers found evidence of sound-related genes in corals, suggesting that the marine invertebrates could use sound to interact with their surroundings.

Coral reefs make up less than 1% of the ocean floor yet support more than 25% of all marine life. Around the world, coral reefs are being threatened by climate change, ocean acidification, diseases, overfishing and pollution. A better understanding of coral communication could help inform policies that aim to protect this critical ecosystem.

"A growing number of studies have shown that trees can communicate, and that this communication is important for ecosystems such as rain forests," said Camila Rimoldi Ibanez, a high school student in the dual enrollment program at South Florida State College. "Coral reefs are often referred to as the rainforests of the sea because of the habitat they provide for a wide variety of plants and animals. Thus, we wanted to find out how coral communicates."

Ibanez will present the new findings at the American Society for Biochemistry and Molecular Biology annual meeting during the virtual Experimental Biology (EB) 2021 meeting, to be held April 27-30. Her mentor is James Hawker, PhD, dean of arts and sciences at South Florida State College.

Many organisms that live in coral reefs perceive sound and use it to find their way to the reefs. Based on this information, the researchers decided to look for the presence of genes related to the reception and/or emission of sound in the coral Cyphastrea. Using PCR amplification, the researchers found probable evidence that two of the four genes they examined may be present in coral DNA. The genes they found -- TRPV and FOLH-1 -- are used for sound emission or reception in sea anemones and freshwater polyps, respectively.

In addition to performing more testing, the researchers want to sequence the TRPV and FOLH-1 genes they found to add additional evidence that these genes, or genes related to them, are present in coral.

"As we learn more about the negative impacts of sound in different kinds of ecosystems, it is vital that we set policies to protect and manage human noises in natural environments," said Ibanez. "The more we know about how corals communicate, the better we can develop restoration and conservation projects to help corals as they face bleaching epidemics and other threats."

Camila Rimoldi Ibanez will present the findings in poster R4543 (abstract). Contact the media team for more information or to obtain a free press pass to access the meeting.

Images available.

Ship movements on the world's oceans dropped in the first half of 2020 as Covid-19 restrictions came into force, a new study shows.

Researchers used a satellite vessel-tracking system to compare ship and boat traffic in January to June 2020 with the same period in 2019.

The study, led by the University of Exeter (UK) and involving the Balearic Islands Coastal Observing and Forecasting System and the Mediterranean Institute for Advanced Studies (both in Spain), found decreased movements in the waters off more than 70 per cent of countries.

Global declines peaked in April 2020, but by June - as Covid restrictions were eased in many countries - ship movements began to increase.

"As lockdowns came into force, we heard stories and began to see early research findings that suggested reduced boat movements had allowed some marine ecosystems to recover," said lead-author Dr David March of the Centre for Ecology and Conservation on Exeter's Penryn Campus in Cornwall.

"There were reports of clearer water in Venice's canals, and a study showed a reduction in underwater noise at Vancouver."

Professor Brendan Godley, who leads the Exeter Marine research group, added: "The effects of ships and boats - from noise and pollution to fishing and collisions with animals - have a major impact on marine ecosystems across the world.

"Our study aimed to measure the impact of Covid on this traffic, and we are continuing to monitor this as the restrictions on human activity continue to change.

"Quantifying the changes in human activities at sea paves the way to research the impacts of Covid-19 on the blue economy and ocean health."

The study found:

Decreased ship movements in the Exclusive Economic Zones (up to 200 nautical miles offshore) of 70.2 per cent of the 124 countries included in the study.

Countries with stricter Covid restrictions saw sharper decreases in ship movements.

Global declines peaked in April, with decreases found across all ship categories (i.e. cargo, tankers, fishing, service, recreational and passenger vessels)

The largest and longest-lasting reductions were in passenger vessels, while tankers, cargo vessels and fishing boats were least affected.

A more detailed analysis of the Western Mediterranean (covering January to November 2020) showed reductions in boat movements reached a maximum of 62.2 per cent during mid-April, being one of the areas with the highest reduction. This included a 93.7 per cent reduction in movements of recreational boats.

"The long-term trend is for increased global ship movements, so a modest decrease may represent a more significant reduction compared to the amount of traffic we would otherwise have seen," Dr March concluded.

A study led by scientists at the American Museum of Natural History has resolved a long-standing controversy about an extinct "horned" crocodile that likely lived among humans in Madagascar. Based on ancient DNA, the research shows that the horned crocodile was closely related to "true" crocodiles, including the famous Nile crocodile, but on a separate branch of the crocodile family tree. The study, published today in the journal Communications Biology, contradicts the most recent scientific thinking about the horned crocodile's evolutionary relationships and also suggests that the ancestor of modern crocodiles likely originated in Africa.

"This crocodile was hiding out on the island of Madagascar during the time when people were building the pyramids and was probably still there when pirates were getting stranded on the island," said lead author Evon Hekkala, an assistant professor at Fordham University and a research associate at the American Museum of Natural History. "They blinked out just before we had the modern genomic tools available to make sense of the relationships of living things. And yet, they were the key to understanding the story of all the crocodiles alive today."

The arrival of modern humans in Madagascar between about 9,000 and 2,500 years ago preceded the extinction of many of the island's large animals, including giant tortoises, elephant birds, dwarf hippos, and several lemur species. One lesser-known extinction that occurred during this period was that of an endemic "horned" crocodile, Voay robustus. Early explorers to Madagascar noted that Malagasy peoples consistently referred to two types of crocodiles on the island: a large robust crocodile and a more gracile form with a preference for rivers. This suggests that both types persisted until very recently, but only the gracile form, now recognized as an isolated population of the Nile crocodile (Crocodylus niloticus), is currently is found on the island.

Despite nearly 150 years of investigation, the position of the horned crocodile in the tree of life has remained controversial. In the 1870s, it was first described as a new species within the "true crocodile" group, which includes the Nile, Asian, and American crocodiles. Then, in the early part of the 20th century, it was thought that the specimens simply represented very old Nile crocodiles. And finally, in 2007, a study based on physical characteristics of the fossil specimens concluded that the horned crocodile was actually not a true crocodile, but in the group that includes dwarf crocodiles.

"Teasing apart the relationships of modern crocodiles is really difficult because of the physical similarities," Hekkala said. "Many people don't even realize that there are multiple species of crocodiles, and they see them as this animal that's unchanging through time. But we've been trying to get to the bottom of the great diversity that exists among them."

To fully examine the horned crocodile's place in the evolutionary tree, Hekkala and her collaborators at the Museum made a number of attempts to sequence DNA from fossil specimens, including two well-preserved skulls that have been at the Museum since the 1930s.

"This a project we've tried to do on and off for many years, but the technology just hadn't advanced enough, so it always failed," said study co-author George Amato, emeritus director of the Museum's Institute for Comparative Genomics. "But in time, we had both the computational setup and the paleogenomic protocols that could actually fish out this DNA from the fossil and finally find a home for this species."

The results place the horned crocodile right next to the true crocodile branch of the evolutionary tree, making it the closest species to the common ancestor of the crocodiles alive today.

"This finding was surprising and also very informative to how we think about the origin of the true crocodiles found around the tropics today," Amato said. "The placement of this individual suggests that true crocodiles originated in Africa and from there, some went to Asia and some went to the Caribbean and the New World. We really needed the DNA to get the correct answer to this question."

In a uniquely deep and detailed look at how the commonly used anesthetic propofol causes unconsciousness, a collaboration of labs at The Picower Institute for Learning and Memory at MIT shows that as the drug takes hold in the brain, a wide swath of regions become coordinated by very slow rhythms that maintain a commensurately languid pace of neural activity. Electrically stimulating a deeper region, the thalamus, restores synchrony of the brain's normal higher frequency rhythms and activity levels, waking the brain back up and restoring arousal.

"There's a folk psychology or tacit assumption that what anesthesia does is simply 'turn off' the brain," said Earl Miller, Picower Professor of Neuroscience and co-senior author of the study in eLife. "What we show is that propofol dramatically changes and controls the dynamics of the brain's rhythms."

Conscious functions, such as perception and cognition, depend on coordinated brain communication, in particular between the thalamus and the brain's surface regions, or cortex, in a variety of frequency bands ranging from 4 to 100 Hz. Propofol, the study shows, seems to bring coordination among the thalamus and cortical regions down to frequencies around just 1 Hz.

Miller's lab, led by postdoc Andre Bastos and former graduate student Jacob Donoghue, collaborated with that of co-senior author Emery N. Brown, who is Edward Hood Taplin Professor of Medical Engineering and Computational Neuroscience and an anesthesiologist at Massachusetts General Hospital. The collaboration therefore powerfully unified the Miller lab's expertise on how neural rhythms coordinate the cortex to produce conscious brain function with the Brown lab's expertise in the neuroscience of anesthesia and statistical analysis of neural signals.

Brown said studies that show how anesthetics change brain rhythms can directly improve patient safety because these rhythms are readily visible on the EEG in the operating room. The study's main finding of a signature of very slow rhythms across the cortex offers a model for directly measuring when subjects have entered unconsciousness after propofol administration, how deeply they are being maintained in that state, and how quickly they may wake up once propofol dosing ends.

"Anesthesiologists can use this as a way to better take care of patients," Brown said.

Brown has long studied how brain rhythms are affected in humans under general anesthesia by making and analyzing measurements of rhythms using scalp EEG electrodes and to a limited extent, cortical electrodes in epilepsy patients. Because the new study was conducted in animal models of those dynamics, the team was able to implant electrodes that could directly measure the activity or "spiking" of many individual neurons and rhythms in the cortex and thalamus. Brown said the results therefore significantly deepen and extend his findings in people.

For instance, the same neurons that they measured chattering away with spikes of voltage 7-10 times a second during wakefulness routinely fired only once a second or less during propofol-induced unconsciousnesss, a notable slowing called a "down state." In all, the scientists made detailed simultaneous measurements of rhythms and spikes in five regions: two in the front of the cortex, two toward the back, and the thalamus.

"What's so compelling is we are getting data down to the level of spikes," Brown said. "The slow oscillations modulate the spiking activity across large parts of the cortex."

As much as the study explains how propofol generates unconsciousness, it also helps to explain the unified experience of consciousness, Miller said.

"All the cortex has to be on the same page to produce consciousness," Miller said. "One theory about how this works is through thalamo-cortical loops that allow the cortex to synchronize. Propofol may be breaking the normal operation of those loops by hyper synchronizing them in prolonged down states. It disrupts the ability of the cortex to communicate."

For instance, by making measurements in distinct layers of the cortex, the team found that higher frequency "gamma" rhythms, which are normally associated with new sensory information like sights and sounds, were especially reduced in superficial layers. The increase in slow wave power during unconsciousness was especially strong in the deep layers of cortex, which Miller has shown tend to regulate the processing of the information carried by gamma rhythms.

In addition to the prevailing synchrony at very slow frequencies, the team noted other signatures of unconsciousness in the data. As Brown and others have observed in humans before, alpha and beta rhythm power was notably higher in posterior regions of the cortex during wakefulness, but after loss of consciousness power at those rhythms flipped to being much higher in anterior regions.

The team further showed that stimulating the thalamus with a high frequency pulse of current (180Hz) undid propofol's effects.

"Stimulation produced an awake-like cortical state by increasing spiking rates and decreasing slow-frequency power," the authors wrote in the study. "In all areas, there was a significant increase in spiking during the stimulation interval compared to pre-stimulation baseline."

Researchers have developed the first LiDAR-based augmented reality head-up display for use in vehicles. Tests on a prototype version of the technology suggest that it could improve road safety by 'seeing through' objects to alert of potential hazards without distracting the driver.

The technology, developed by researchers from the University of Cambridge, the University of Oxford and University College London (UCL), is based on LiDAR (light detection and ranging), and uses LiDAR data to create ultra high-definition holographic representations of road objects which are beamed directly to the driver's eyes, instead of 2D windscreen projections used in most head-up displays.

While the technology has not yet been tested in a car, early tests, based on data collected from a busy street in central London, showed that the holographic images appear in the driver's field of view according to their actual position, creating an augmented reality. This could be particularly useful where objects such as road signs are hidden by large trees or trucks, for example, allowing the driver to 'see through' visual obstructions. The results are reported in the journal Optics Express.

"Head-up displays are being incorporated into connected vehicles, and usually project information such as speed or fuel levels directly onto the windscreen in front of the driver, who must keep their eyes on the road," said lead author Jana Skirnewskaja, a PhD candidate from Cambridge's Department of Engineering. "However, we wanted to go a step further by representing real objects in as panoramic 3D projections."

Skirnewskaja and her colleagues based their system on LiDAR, a remote sensing method which works by sending out a laser pulse to measure the distance between the scanner and an object. LiDAR is commonly used in agriculture, archaeology and geography, but it is also being trialled in autonomous vehicles for obstacle detection.

Using LiDAR, the researchers scanned Malet Street, a busy street on the UCL campus in central London. Co-author Phil Wilkes, a geographer who normally uses LiDAR to scan tropical forests, scanned the whole street using a technique called terrestrial laser scanning. Millions of pulses were sent out from multiple positions along Malet Street. The LiDAR data was then combined with point cloud data, building up a 3D model.

"This way, we can stitch the scans together, building a whole scene, which doesn't only capture trees, but cars, trucks, people, signs, and everything else you would see on a typical city street," said Wilkes. "Although the data we captured was from a stationary platform, it's similar to the sensors that will be in the next generation of autonomous or semi-autonomous vehicles."

When the 3D model of Malet St was completed, the researchers then transformed various objects on the street into holographic projections. The LiDAR data, in the form of point clouds, was processed by separation algorithms to identify and extract the target objects. Another algorithm was used to convert the target objects into computer-generated diffraction patterns. These data points were implemented into the optical setup to project 3D holographic objects into the driver's field of view.

The optical setup is capable of projecting multiple layers of holograms with the help of advanced algorithms. The holographic projection can appear at different sizes and is aligned with the position of the represented real object on the street. For example, a hidden street sign would appear as a holographic projection relative to its actual position behind the obstruction, acting as an alert mechanism.

In future, the researchers hope to refine their system by personalising the layout of the head-up displays and have created an algorithm capable of projecting several layers of different objects. These layered holograms can be freely arranged in the driver's vision space. For example, in the first layer, a traffic sign at a further distance can be projected at a smaller size. In the second layer, a warning sign at a closer distance can be displayed at a larger size.

"This layering technique provides an augmented reality experience and alerts the driver in a natural way," said Skirnewskaja. "Every individual may have different preferences for their display options. For instance, the driver's vital health signs could be projected in a desired location of the head-up display.

"Panoramic holographic projections could be a valuable addition to existing safety measures by showing road objects in real time. Holograms act to alert the driver but are not a distraction."

The researchers are now working to miniaturise the optical components used in their holographic setup so they can fit into a car. Once the setup is complete, vehicle tests on public roads in Cambridge will be carried out.

Proteins are undoubtedly some of the most fascinating biomolecules, and they perform many of the functions that (in our eyes) separate life from inanimate matter. Multi-molecular protein assemblies even have large-scale structural functions, as evidenced by feathers, hair, and scales in animals. It should come as no surprise that, with progress in advanced nanotechnology and bioengineering, artificial protein assemblies have found applications in a variety of fields, including catalysis, molecular storage, and drug delivery systems.

However, producing ordered protein assemblies remains challenging. It is particularly difficult to get monomers, the building blocks of proteins, to assemble stably into the desired structures; this generally requires very accurate design and control of synthesis conditions, such as pH (acidity) and temperature. Recent studies found ways to circumvent this problem by using protein crystals--solid molecular arrangements that occur naturally in some organisms--as precursor matrices to produce protein assemblies.

At Tokyo Institute of Technology, Japan, a team of scientists led by Professor Takafumi Ueno has been working on a promising approach for synthesizing protein assemblies from protein crystals. Their strategy involves introducing mutations into the genetic code of an organism that naturally produces protein crystals. These mutations cause disulfide bonds (S-S) to form between monomers in very specific locations in the crystals. The crystals are then dissolved, but instead of breaking down completely into their individual monomers as usual, the newly introduced S-S bonds hold groups of monomers together and the crystals split into many of the desired protein assemblies. With this approach, Ueno's team has managed to synthesize protein cages and tubes by essentially using living cells as nano-3D printers.

In their latest study, which was published in Angewandte Chemie International Edition, the team demonstrated yet another application of their novel strategy; this time for the synthesis of bundled protein filaments. They used a culture of insect cells (Spodoptera frugiperda) infected with a virus that caused overexpression of a monomer called "TbCatB." These monomers naturally aggregate inside the cells into protein crystals, which are held together there by the relatively weak non-covalent interactions between monomers. The scientists strategically introduced two mutations in the cells so that each monomer had two thiol groups (-SH) of cysteine at critical interface points with other monomers.

The crystals were extracted from the cells and left to oxidize at room temperature, which caused the thiol groups to change into strong S-S bonds between monomers adjacent along a single direction by autoxidation under air. When the crystals were dissolved, these disulfide bonds, together with some lingering non-covalent interactions, resulted in the formation of bundled protein filaments that were two monomers wide--about 8.3 nanometers. "With our strategy, we achieved a highly precise arrangement of protein molecules while suppressing random aggregation of monomers due to unwanted sulfide bonds, all in a relatively straightforward one-pot process," highlights Ueno.

Overall, the approach demonstrated by the team at Tokyo Tech stands as an innovative way to synthesize protein structures via rational genetic engineering and by using the tools naturally available to cells of certain organisms. "We consider our synthesis method a useful advance in nano-biomaterials science and supramolecular chemistry for producing desired stable assemblies from protein crystals," concludes Ueno. Only time will tell what other useful molecular structures can be produced using this strategy and what interesting applications they will find!

Fentanyl, oxycodone, morphine--these substances are familiar to many as a source of both pain relief and the cause of a painful epidemic of addiction and death.

Scientists have attempted for years to balance the potent pain-relieving properties of opioids with their numerous negative side effects--with mostly mixed results.

Work by John Traynor, Ph.D., and Andrew Alt, Ph.D., and their team at the University of Michigan Edward F. Domino Research Center, funded by the National Institute on Drug Abuse, seeks to side-step these problems by harnessing the body's own ability to block pain.

All opioid drugs--from poppy-derived opium to heroin--work on receptors that are naturally present in the brain and elsewhere in the body. One such receptor, the mu-opioid receptor, binds to natural pain-killers in the body called endogenous endorphins and enkephalins. Drugs acting on the mu-opioid receptor can cause addiction as well as unwanted side effects like drowsiness, problems with breathing, constipation and nausea.

"Normally, when you are in pain, you are releasing endogenous opioids, but they're just not strong enough or long lasting enough," says Traynor. The team had long hypothesized that substances called positive allosteric modulators could be used to enhance the body's own endorphins and enkephalins. In a new paper published in PNAS, they demonstrate that a positive allosteric modulator known as BMS-986122 can boost enkephalins' ability to activate the mu-opioid receptor.

What's more, unlike opioid drugs, positive allosteric modulators only work in the presence of endorphins or enkephalins, meaning they would only kick in when needed for pain relief. They do not bind to the receptor in the way that opioids do instead binding in a different location that enhances its ability to respond to the body's pain-relieving compounds.

"When you need enkephalins, you release them in a pulsatile fashion in specific regions of the body, then they are metabolized quickly," explains Traynor. "In contrast, a drug like morphine floods the body and brain and sticks around for several hours."

The team demonstrated the modulator's ability to stimulate the mu-opioid receptor by isolating the purified receptor and measuring how it responds to enkephalins. "If you add the positive allosteric modulator, you need a lot less enkephalin to get the response."

Additional electrophysiology and mouse experiments confirmed that the opioid receptor was more strongly activated by the body's pain-relieving molecules leading to pain relief. In contrast the modulator showed much reduced side effects of depression of breathing, constipation and addiction liability.

Their next goal is to measure their ability to enhance activation of endogenous opioids under conditions of stress or chronic pain, explains Traynor, to ensure that they are effective but don't lead to more dangerous responses like depression of breathing.

"While these molecules won't solve the opioid crisis," says Traynor, "they could slow it and prevent it from happening again because patients in pain could take this type of a drug instead of a traditional opioid drug."

A phenomenon of "photoexpansion" in hard plastic films with a high glass transition temperature in the dry state was established, which was essentially different from very soft actuators, such as elastomers or gels. The photoexpanding hard actuators were expected to apply in the wide fields because they do not contain vaporable matters such as solvents and were much more thermoresistant than conventional ones.

Ishikawa, April 22, 2021 - Polymers that exhibit their functions by light have been studied for a few decades because they enable device miniaturization, energy saving, and precise signal control. Polymers based on azobenzene, diarylethene, etc. are the pioneers, and many examples of light-driven motors and artificial muscles have been reported. On the other hand, cinnamic acid, which is a constituent of lignin in natural wood, also exhibit the function by ultraviolet (UV) rays, so that it has been applied to polymers. The deformation mechanism of these cinnamate-based polymers has not been clarified because the two reactions of double bond cis-trans isomerization and [2+2] cycloaddition occur almost simultaneously. Since the mechanism has not been clarified, its use as a photodeformable material has not received as much attention as the above-mentioned azobenzene and diarylethene.

To tackle these issues, a team of researchers from Japan Advanced Institute of Science and Technology (JAIST) are investigating photobending mechanism of bio-based polycinnamete films. Their latest study, published in ACS Applied Materials & Interfaces, was led by Professor Tatsuo Kaneko and Assistant Professor Kenji Takada also involved Professor Hideyuki Murata, Associate Professor Kosuke Okeyoshi, and Research Assistant Professor Amit Kumar.

In this study, polyesters were synthesized based on coumarates in which hydroxyl groups were substituted in the aromatics of cinnamate. Among them, those showing photodeformability were poly(3-hydroxycinnamic acid) (P3HCA) and poly(3,4-dihydroxycinnamic acid) (PdHCA). Although both films had a cinnamate unit, P3HCA showed convex deformation with respect to an UV source, and PdHCA showed concave deformation, respectively. These differences were analyzed by various spectral analyzes. First, when the fluorescence lifetime was measured, it was found that there are two excited states in P3HCA. Next, by time-resolved infrared (IR) spectroscopic measurement, the absorption of the double bond of the cinnamate unit was traced from the change in the IR spectrum during UV irradiation. In case of P3HCA, it was confirmed that the absorption of cis-formed -CH=CH- bond was increased by increasing the UV irradiation time. On the other hand, in PdHCA, no change in the absorption of cis-formed -CH=CH- was confirmed. To prove these photoexpansions, an experiment was conducted in which a P3HCA film was covered with a photomask and UV rays were irradiated from above. When the free-standing film was irradiated with UV through a photomask, the non-irradiated surface also showed a deformation. Therefore, when an irradiation experiment was conducted with the P3HCA film coated on the glass substrate, there was no deformation of the surface, opposite side, not irradiated with UV, and no deformation of the part covered with the photomask was observed. From the above results, it was found that P3HCA exhibits convex deformation by "expanding" with respect to UV owing to cis isomerization.

There is no other example that is bio-based and can control the deformation with respect to UV light. In addition, by elucidating the deformation mechanism of polycinnamates through this research, precise control of photodeformability based on a dense polymer design can be expected. The fact that the photodeformability differs depending on the "shape" of the molecule, as Prof. Kaneko explains: "even though they are the same constituents, deformation behaviors were different. These results strongly support the correlation between the structure and physical properties of the cinnamate-based polymers, and this study become the good perspective of the bio-based and photoresponsive polymers." In addition, they consider, it can be expected to greatly contribute to the development of new materials based on the molecular design.

Further progress in bio-based polycinnamate as photodeformable materials will hopefully get us closer to more precisely controllable actuator and a sustainable society.