Compounds halt SARS-CoV-2 replication by targeting key viral enzyme

Four promising antiviral drug candidates identified and analyzed by a University of Arizona-University of South Florida team in the preclinical study

UNIVERSITY OF SOUTH FLORIDA (USF HEALTH)

 

IMAGE: THREE CONFIGURATIONS OF ACTIVE SITES WHERE INHIBITOR GC-376 BINDS WITH THE COVID-19 VIRUS'S MAIN PROTEASE (DRUG TARGET MPRO), AS DEPICTED BY 3D COMPUTER MODELING. view more 

CREDIT: IMAGE GENERATED BY YU CHEN, UNIVERSITY OF SOUTH FLORIDA HEALTH, USING X-RAY CRYSTALLOGRAPHY

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.

Leap in lidar could improve safety, security of new technology

UNIVERSITY OF COLORADO AT BOULDER

 

IMAGE: A SILICON CHIP WITH A TILED ARRAY OF SERPENTINE OPTICAL PHASED ARRAY (SOPA) TILES. THE 32 TILES IN THE 8-BY-4 ARRAY HAVE SLIGHTLY DIFFERING GRATING DESIGNS, SHOWING HERE TWO MATCHING... view more 

CREDIT: BOHAN ZHANG AND NATHAN DOSTART

Whether it's on top of a self-driving car or embedded inside the latest gadget, Light Detection and Ranging (lidar) systems will likely play an important role in our technological future, enabling vehicles to 'see' in real-time, phones to map three-dimensional images and enhancing augmented reality in video games.

The challenge: these 3-D imaging systems can be bulky, expensive and hard to shrink down to the size needed for these up-and-coming applications. But University of Colorado Boulder researchers are one big step closer to a solution.

In a new paper, published in Optica, they describe a new silicon chip--with no moving parts or electronics--that improves the resolution and scanning speed needed for a lidar system.

"We're looking to ideally replace big, bulky, heavy lidar systems with just this flat, little chip," said Nathan Dostart, lead author on the study, who recently completed his doctorate in the Department of Electrical and Computer Engineering.

Current commercial lidar systems use large, rotating mirrors to steer the laser beam and thereby create a 3-D image. For the past three years, Dostart and his colleagues have been working on a new way of steering laser beams called wavelength steering--where each wavelength, or "color," of the laser is pointed to a unique angle.

They've not only developed a way to do a version of this along two dimensions simultaneously, instead of only one, they've done it with color, using a "rainbow" pattern to take 3-D images. Since the beams are easily controlled by simply changing colors, multiple phased arrays can be controlled simultaneously to create a bigger aperture and a higher resolution image.

"We've figured out how to put this two-dimensional rainbow into a little teeny chip," said Kelvin Wagner, co-author of the new study and professor of electrical and computer engineering.

The end of electrical communication

Autonomous vehicles are currently a $50 billion dollar industry, projected to be worth more than $500 billion by 2026. While many cars on the road today already have some elements of autonomous assistance, such as enhanced cruise control and automatic lane-centering, the real race is to create a car that drives itself with no input or responsibility from a human driver. In the past 15 years or so, innovators have realized that in order to do this cars will need more than just cameras and radar--they will need lidar.

Lidar is a remote sensing method that uses laser beams, pulses of invisible light, to measure distances. These beams of light bounce off everything in their path, and a sensor collects these reflections to create a precise, three-dimensional picture of the surrounding environment in real time.

Lidar is like echolocation with light: it can tell you how far away each pixel in an image is. It's been used for at least 50 years in satellites and airplanes, to conduct atmospheric sensing and measure the depth of bodies of water and heights of terrain.

While great strides have been made in the size of lidar systems, they remain the most expensive part of self-driving cars by far--as much as $70,000 each.

In order to work broadly in the consumer market one day, lidar must become even cheaper, smaller and less complex. Some companies are trying to accomplish this feat using silicon photonics: An emerging area in electrical engineering that uses silicon chips, which can process light.

The research team's new finding is an important advancement in silicon chip technology for use in lidar systems.

"Electrical communication is at its absolute limit. Optics has to come into play and that's why all these big players are committed to making the silicon photonics technology industrially viable," said Miloš Popovi?, co-author and associate professor of engineering at Boston University.

The simpler and smaller that these silicon chips can be made--while retaining high resolution and accuracy in their imaging--the more technologies they can be applied to, including self-driving cars and smartphones.

Rumor has it that the upcoming iPhone 12 will incorporate a lidar camera, like that currently in the iPad Pro. This technology could not only improve its facial recognition security, but one day assist in creating climbing route maps, measuring distances and even identifying animal tracks or plants.

"We're proposing a scalable approach to lidar using chip technology. And this is the first step, the first building block of that approach," said Dostart, who will continue his work at NASA Langley Research Center in Virginia. "There's still a long way to go."

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Additional co-authors of this study include Michael Brand and Daniel Feldkhun of CU Boulder; Bohan Zhang, Anatol Khilo, Kenaish Al Qubaisi, Deniz Onural and Milos A. Popovic of Boston University.

RESEARCHERS FORESEE LINGUISTIC ISSUES DURING SPACE TRAVEL
Mon, 07/06/2020


LAWRENCE — It lacks the drama of a shape-shifting alien creature, but another threat looms over the prospect of generations-long, interstellar space travel: Explorers arriving on Xanadu could face problems communicating with previous and subsequent arrivals, their spoken language having changed in isolation along the way.

Therefore, a new paper co-written by a University of Kansas linguistics researcher and published in a journal affiliated with the European Space Agency recommends that such crews include, if not a linguist, members with knowledge of what is likely to occur and how to adapt.

Andrew McKenzie, associate professor of linguistics at KU, and Jeffrey Punske, assistant professor of linguistics at Southern Illinois University, co-wrote the article “Language Development During Interstellar Travel” in the April edition of Acta Futura, the journal of the European Space Agency’s Advanced Concepts Team.

In it, they discuss the concept of language change over time, citing such earthbound examples of long-distance voyages as the Polynesian island explorers and extrapolating from there.

It might seem far-fetched, but the authors cite language change even during their own lifetimes with the rise – no pun intended – of uptalk.

They write that “it is increasingly common for speakers to end statements with a rising intonation. This phenomenon, called uptalk (or sometimes High Rising Terminal), is often mistaken for a question tone by those without it in their grammars, but it actually sounds quite distinct and indicates politeness or inclusion. Uptalk has only been observed occurring within the last 40 years but has spread from small groups of young Americans and Australians to most of the English-speaking world, even to many baby boomers who had not used it themselves as youth.”

“Given more time, new grammatical forms can completely replace current ones.”

Imagine trying to chat with Chaucer today. Even improvements in translation technology might not be enough.

“If you're on this vessel for 10 generations, new concepts will emerge, new social issues will come up, and people will create ways of talking about them,” McKenzie said, “and these will become the vocabulary particular to the ship. People on Earth might never know about these words, unless there's a reason to tell them. And the further away you get, the less you're going to talk to people back home. Generations pass, and there's no one really back home to talk to. And there's not much you want to tell them, because they'll only find out years later, and then you'll hear back from them years after that.

“The connection to Earth dwindles over time. And eventually, perhaps, we'll get to the point where there's no real contact with Earth, except to send the occasional update.

“And as long as the language changes on the vessel, and then at an eventual colony, the question becomes, ‘Do we still bother learning how to communicate with people on Earth?’ Yes. So if we have Earth English and vessel English, and they diverge over the years, you have to learn a little Earth English to send messages back, or to read the instruction manuals and information that came with the ship.

“Also, keep in mind that the language back on Earth is going to change, too, during that time. So they may well be communicating like we'd be using Latin — communicating with this version of the language nobody uses.”

The authors also point out that an adaptation in the form of sign language will be needed for use with and among crew members who, genetics tell us, are sure to be born deaf.

In any case, they write, “Every new vessel will essentially offload linguistic immigrants to a foreign land. Will they be discriminated against until their children and grandchildren learn the local language? Can they establish communication with the colony ahead of time to learn the local language before arrival?

“Given the certainty that these issues will arise in scenarios such as these, and the uncertainty of exactly how they will progress, we strongly suggest that any crew exhibit strong levels of metalinguistic training in addition to simply knowing the required languages. There will be need for an informed linguistic policy on board that can be maintained without referring back to Earth-based regulations.”

If a study of the linguistic changes aboard ship could be performed, it would only “add to its scientific value,” McKenzie and Punske concluded.

Photo: An image from NASA's Spitzer Space Telescope shows the Tarantula Nebula in three wavelengths of infrared light, each represented by a different color. Credit: NASA / JPL-Caltech


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Yellow pond-lily prefers cyclic flowers to spiral ones

And helps in understanding the structure of Earth's oldest flowers

NATIONAL RESEARCH UNIVERSITY HIGHER SCHOOL OF ECONOMICS

Biologists from Lomonosov Moscow State University and HSE University have studied the patterns of flower development in yellow water-lily (Nuphar lutea). They found out that all the floral organs are arranged in cycles (whorls) rather than inserted sequentially in a spiral, as is the case in some other basal angiosperms. The ancestors of yellow pond-lily were among the first to diverge from the root of the angiosperm evolutionary tree, which is why it can be used to hypothesize about the structure of the first flowers. The study has been published in Frontiers in Cell and Developmental Biology journal.

The flower is one of the key evolutionary innovations of angiosperms. It helps attract various pollinators, protect the seeds inside the fruit, and adds some new means of distribution that do not exist in gymnosperms. Thanks to these advantages, flowering plants have settled across the planet and have become the most numerous group of land plants.

How flowers evolved and how they looked initially remains a mystery. The appearance of the ancestral flowers can be inferred with the help of plants that have preserved the greatest degree of similarity to the first angiosperms. It makes sense to look for them among the basal groups, whose ancestors diverged from the phylogenetic root of flowering plants earlier than the others. It is highly probable that the flower structure in such organisms will be similar to the initial one.

Among extant flowering plants, Nymphaeales are rather close to the root of angiosperms. Yellow pond-lily (Nuphar lutea) is widespread in Eurasia; it is also sometimes seen in North America, which is why it could be a convenient model object. But detailed studies of its flower structure using modern research methods are lacking.

Researchers from Lomonosov Moscow State University and HSE University have collected several dozen rhizomes of Nuphar lutea with leaves and flowers. Some of them were dissected to prepare specimens for light and scanning electron microscopy.

The researchers focused on shoot tips, where new leaves and flowers form. Young flowers at different stages of development were selected for the study. To determine their architecture, the researchers measured the angles between similar organs of the flower.

Elements of shoots in plants--leaves, flowers, lateral buds and lateral branches developing from them--are frequently arranged in a spiral. It had previously been assumed that plants similar to basal angiosperm type, including Nuphar, have a similar arrangement of organs. But the researchers discovered that in Nuphar lutea, the angles between the sepals differed from the spiral insertion (85° and 55°, rather than 137.5°). It looked like sepals and petals form cycles--two whorls for sepals and a single whorl for petals--although they are not always initiated simultaneously within a whorl.

Nuphar lutea develops five sepals. If they all were in one whorl, the angle between adjacent sepals would be 72°. In fact, they were placed at such angles that de-facto formed two circles: three elements in the external circle, and two in the internal one. The number of petals usually varied from 14 to 15, but they also formed a cycle rather than a spiral. And even the numerous stamens tended to arrange in alternating whorls.

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What ethical models for autonomous vehicles don't address - and how they could be better

NORTH CAROLINA STATE UNIVERSITY

There's a fairly large flaw in the way that programmers are currently addressing ethical concerns related to artificial intelligence (AI) and autonomous vehicles (AVs). Namely, existing approaches don't account for the fact that people might try to use the AVs to do something bad.

For example, let's say that there is an autonomous vehicle with no passengers and it is about to crash into a car containing five people. It can avoid the collision by swerving out of the road, but it would then hit a pedestrian.

Most discussions of ethics in this scenario focus on whether the autonomous vehicle's AI should be selfish (protecting the vehicle and its cargo) or utilitarian (choosing the action that harms the fewest people). But that either/or approach to ethics can raise problems of its own.

"Current approaches to ethics and autonomous vehicles are a dangerous oversimplification - moral judgment is more complex than that," says Veljko Dubljevi?, an assistant professor in the Science, Technology & Society (STS) program at North Carolina State University and author of a paper outlining this problem and a possible path forward. "For example, what if the five people in the car are terrorists? And what if they are deliberately taking advantage of the AI's programming to kill the nearby pedestrian or hurt other people? Then you might want the autonomous vehicle to hit the car with five passengers.

"In other words, the simplistic approach currently being used to address ethical considerations in AI and autonomous vehicles doesn't account for malicious intent. And it should."

As an alternative, Dubljevi? proposes using the so-called Agent-Deed-Consequence (ADC) model as a framework that AIs could use to make moral judgements. The ADC model judges the morality of a decision based on three variables.

First, is the agent's intent good or bad? Second, is the deed or action itself good or bad? Lastly, is the outcome or consequence good or bad? This approach allows for considerable nuance.

For example, most people would agree that running a red light is bad. But what if you run a red light in order to get out of the way of a speeding ambulance? And what if running the red light means that you avoided a collision with that ambulance?

"The ADC model would allow us to get closer to the flexibility and stability that we see in human moral judgment, but that does not yet exist in AI," says Dubljevi?. "Here's what I mean by stable and flexible. Human moral judgment is stable because most people would agree that lying is morally bad. But it's flexible because most people would also agree that people who lied to Nazis in order to protect Jews were doing something morally good.

"But while the ADC model gives us a path forward, more research is needed," Dubljevi? says. "I have led experimental work on how both philosophers and lay people approach moral judgment, and the results were valuable. However, that work gave people information in writing. More studies of human moral judgment are needed that rely on more immediate means of communication, such as virtual reality, if we want to confirm our earlier findings and implement them in AVs. Also, vigorous testing with driving simulation studies should be done before any putatively 'ethical' AVs start sharing the road with humans on a regular basis. Vehicle terror attacks have, unfortunately, become more common, and we need to be sure that AV technology will not be misused for nefarious purposes."

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The paper, "Toward Implementing the ADC Model of Moral Judgment in Autonomous Vehicles," is published in the journal Science and Engineering Ethics.

Nematode has potential to reduce cotton yields by 50 percent

AMERICAN PHYTOPATHOLOGICAL SOCIETY

 

IMAGE: TRIAL PLOT CONTAINING CROPLAN 3885 B2XF CULTIVAR 43 DAYS AFTER PLANTING IN 2018. THE LEFT TWO ROWS SHOWN IN THE PICTURE ARE THE CULTIVAR PLANTED WITHOUT THE APPLICATION OF A... view more 

CREDIT: KATHY LAWRENCE

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.

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To learn more about this study, read "Yield Loss of Cotton Cultivars Due to Rotylenchulus reniformis and the Added Benefit of a Nematicide" in the May issue of Plant Health Progress

New room-temperature liquid-metal battery could be the path to powering the future

UNIVERSITY OF TEXAS AT AUSTIN

 

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.

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Community science birding data does not yet capture global bird trends

More observations and more focus on common birds could fill the data gap

UNIVERSITY OF UTAH

 

IMAGE: QUECHUA WOMAN LOOKING FOR BIRDS THROUGH A BIRDWATCHING TELESCOPE IN MONTANE RAINFOREST, SAN MIGUEL POLYLEPIS FOREST, COCHABAMBA, BOLIVIA. view more 

CREDIT: ÇA?AN ?EKERCIO?LU.

Binoculars in hand, birders around the world contribute every day to a massive database of bird sightings worldwide. But while community science observations of birds can be useful data, it may not be enough to fill the data gaps in developing countries where professional bird surveys are insufficient or absent.

Ornithologists at the University of Utah say that community science bird data shows different trends in bird populations than professional bird surveys do, especially in developing countries. Researchers look for trends to know whether the number of individuals in a species is increasing, stable or decreasing--with the latter as a warning sign that the species is in trouble. Their results are published in Biological Conservation. More observations are needed, the researchers say, both by birders and professionals.

"We hope that this study will encourage birdwatchers to be more conscientious in their recording," says Monte Neate-Clegg, doctoral student and lead author of the study, "to think of these data not just as a personal record but as contributing to a wider cause."

Birding is a long tradition, but as paper guidebooks and life lists have given way to digital records and mobile apps, birders have become more connected, compiling their data into near real-time global snapshots of where and when birders are seeing species. For this study, the authors accessed data from eBird.

Developed by the Cornell Lab of Ornithology, eBird is the world's largest biodiversity-related community science project, the lab says, with more than 100 million bird sightings contributed each year. Birders submit sightings and checklists to eBird, which reaches out to birding experts when a sighting seems out of the ordinary.

U ornithologist Çağan Şekercioğlu is a world-class eBirder, currently ranked fifth in the world for spotting more than 8,000 bird species--more than 76% of all the species that eBirders have ever reported.

In 2018, former Şekercioğlu lab member JJ Horns found that eBird trend data matched the U.S. Breeding Bird Survey to within 0.4%. The results of the three-year project were encouraging--maybe eBird, they hoped, could serve to accurately fill in data for countries that didn't have the same level of governmental or professional surveys.

So, to compare eBird trends with worldwide trends, they turned to BirdLife International, an independent global partnership of conservation organizations.

"BirdLife amasses data and expert opinion across the world," Neate-Clegg says. Their methods for assessing bird populations and trends vary, though. "Some estimates are based on complete population counts or interpolated surveys," he says. "Most are indirectly assessed via changes in habitat or other impacts, such as hunting or wildlife trade."

Downloading and analyzing eBird data is not an Excel-scale task. The U's Center for High Performance Computing assisted in processing the data, which includes more than 800 million records. Using observations from the past 20 years, Neate-Clegg further filtered the data to focus on the best-quality observations and to match the list of species with those reported by BirdLife International. Calculating the trends in bird counts over time, Neate-Clegg rated them as increasing, decreasing or stable.

For the final list of 8,121 species, BirdLife listed 624 (7.7%) as increasing, 3,616 (44.5%) as stable and 3,881 (47.8%) as decreasing.  The eBird trends differed: 1,974 (24.3%) species were rated as increasing, 4,942 (60.9%) as stable, and 1,205 (14.8%) as decreasing. Only a little more than a third of the species displayed trends that agreed between the two data sources. Unfortunately, that's not much better than would have been expected by chance.

"This isn't particularly reassuring," Neate-Clegg says.

Part of the disagreement is due to the different experience of birdwatching in the tropics as compared to the U.S.

"Birdwatchers in the tropics tend to be more targeted in their approach," Neate-Clegg says, "meaningfully searching for particular species. This may mean that, although a species is declining, eBirders are still finding them reliably and so we do not detect that decline in the eBird data."

"In some cases," Şekercioğlu adds, "the rarer bird species can be seen more often by birders who may overlook the common species nearby that they have already seen before."

Some results of the study were encouraging, though.

As in the earlier study, Neate-Clegg's study shows that the rate of agreement with BirdLife trends for a species increases as the number of eBird checklists for that species increases. "This suggests that our accuracy will increase as more people gather data in the tropics," he says. The rate of agreement is also higher for species where population trends are directly estimated rather than indirectly inferred. "This suggests that we still need in situ population trend estimation by experts to validate eBird trends," he adds.

Neate-Clegg says that the results of this study are far from the end of the story. "It is really important that we carry out studies such as these to validate the use of eBird data," he says. "It would be great to get to the point where we can successfully leverage what will soon exceed 1 billion bird records to estimate population trends."

With a need for more quality data, Neate-Clegg encourages eBirders to include as much additional information in their checklists as possible. For example, he says, eBirders have the option of recording all species seen or counts of every species, as well as associated metadata such as the duration of the birdwatching period and the distance traveled.

"All of these data are important for maximizing the number of checklists we can use while controlling for variation in effort," he says.

Birding in many different places, and not just hotspots with high species numbers, is also important. "You should be birding everywhere you go," Şekercioğlu says, "which also has the personal satisfaction of being a pioneer as you are adding data from places with little or no bird data."

In other words, keep watching the skies. And the trees. And the wetlands. Birders' efforts do not go unnoticed. The researchers express their gratitude to the Cornell Lab of Ornithology, BirdLife International and the millions of birders who contribute to eBird and other community science efforts like iNaturalist. "The centuries-long symbiosis between birdwatchers and ornithologists is the best example of the collaboration of community scientists, professional scientists and conservationists," Şekercioğlu says.

Find this release here.

Find the full study here.

Conservation agriculture increases carbon sequestration in extensive crops

UNIVERSITY OF CÓRDOBA

IMAGE: CROPS SOWN UNDER NO TILL FARMING. view more 

CREDIT: UNIVERSITY OF CORDOBA

Agricultural activity is responsible for about 12% of the total emissions of greenhouse gases in Spain. Nevertheless, adopting good agricultural practices can help reverse this situation, by increasing the sequestration of organic carbon in soil. With the goal of compensating for CO2 emissions produced by agricultural activity by means of fixing organic carbon in soil, the 4perMille initiative came about, in the framework of the Paris Climate Agreement (adopted at the COP21 in 2015).

Conservation Agriculture uses practices such as no-till farming (sowing without having previously tilled the soil), making use of the organic soil cover and rotating crops, which are beneficial in decreasing greenhouse gas emissions. In this vein, Rural Engineering Department Professor, at the School of Agricultural and Forestry Engineering, University of Cordoba, Emilio J. González, in the GI AGR 126 Mechanization and Rural Technology group, participated in the project working with Dr. Rafaela Ordóñez's team, from the Agriculture and the Environment Area at the Institute of Agricultural Research and Training. They analyzed the potential of Conservation Agriculture to reach the aim of increasing organic carbon in soil by 0.4% yearly, which is the main goal of the 4perMille initiative. Applying the Carbon Benefit Project model, designed by the UN Environment Programme, they concluded that by using no-till farming for extensive crops, carbon sequestration levels could reach up to three times the goal amount in the agreement.

After comparing the situation of conventional agriculture based on heavy tilling to data from the model based on a no-till farming situation with extensive crops (grains, sunflower, legumes, forage crops), regions appeared where carbon sequestration could triple the amount fixed by the 4permille initiative, places such as the Guadalquivir valley, Navarre, Aragon and Catalonia. With this study, Conservation Agriculture's capacity to mitigate climate change has been scientifically contrasted, and in doing so, tools are offered up for agricultural management policies such as the European Union's Common Agricultural Policy (CAP), which is currently undergoing debate on green aims focused on mitigation and adaptation to climate change. This study is found within the European project called LIFE Agromitiga, whose objective is to contribute to shifting towards a low-carbon farming system.

Soil conservation

In addition to increasing organic carbon sequestration, using no-till farming and other Conservation Agriculture practices means reducing soil erosion by up to 95%. In this way, the main environmental problem in this country is also being dealt with. Soil loss is especially marked in the basins of the Guadalquivir and Ebro rivers.

Large communities devoted to agriculture, therefore, will benefit greatly from applying Conservation Agriculture, which has over 700,000 ha of extensive crops in Spain, making it the European country with the greatest amount of application of these techniques.

If we continue down this path, we will not only increase the environmental advantages for the surrounding area and society, but also increase the financial feasibility of farms, farms that will keep their key production asset, soil, and will also save on work and fuel costs.

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1.5 billion people will depend on water from mountains

UNIVERSITY OF ZURICH

IMAGE: THE ROSEGBACH RIVER IN THE UPPER ENGADINE, SWITZERLAND, IS PART OF THE DANUBE RIVER BASIN WHERE ROUGHLY ONE THIRD OF THE 46 MILLION PEOPLE LIVING DOWNSTREAM STRONGLY DEPEND ON WATER... view more 

CREDIT: D. VIVIROLI

Global water consumption has increased almost fourfold in the past 100 years, and many regions can only meet their water demand thanks to essential contributions from mountain regions. In 30 years, almost a quarter of the world's lowland population will strongly depend on runoff from the mountains. Only sustainable development can ensure the important function of mountain areas as Earth's "water towers".

Water is a key resource for the 21st century, and many lowland regions all over the world depend on water resources originating in mountain regions, not least when it comes to irrigating agricultural land. A study led by the University of Zurich has now quantified this dependence for the first time by comparing water supply and consumption in the world's lowland areas with runoff contributions from the mountains. Based on a high-resolution global model, the study provides detailed information on the dependence on mountain water resources around the globe. The comprehensive analyses were carried out using a regular grid and then compared for every river catchment area of at least 10,000 km2. This allowed for highly differentiated insights into regional characteristics and differences.

Increasing dependence despite declining per-capita consumption

"Until now, research has focused mainly on river basins that originate in High Mountain Asia," says Daniel Viviroli from the Department of Geography at the University of Zurich, first author of the study. "But in many other regions, irrigated agriculture is heavily dependent on water from mountainous areas, such as in the Middle East and North Africa, as well as parts of North America, South America and Australia."

This dependence has increased strongly since the 1960s - despite more efficient water use and thus declining per-capita water consumption. Whereas only 7 percent of the lowland population used to be strongly dependent on contributions from mountain areas at that time, this figure is projected to rise to 24 percent by mid-21st century. This corresponds to about 1.5 billion people in lowland areas. Particular focus is on catchment areas such as those of the Ganges-Brahmaputra-Meghna, Yangtze and Indus rivers in Asia, the Nile and Niger in Africa, the Euphrates and Tigris in the Middle East as well as the Colorado River in North America. For their analyses, the researchers assumed a middle-of-the-road scenario in terms of population growth as well as technological, economic and social development.

Functioning ecosystems and climate protection

"Ensuring the function of mountains as 'water towers' should be a major concern of the world's lowland populations," says Viviroli. Sustainable development of mountain regions is therefore essential, for example by preventing agricultural overuse and ensuring the functioning of ecosystems, the researchers say. In addition, climate action is of paramount importance: Due to the rising temperatures, meltwater peaks from snow-covered mountain regions sometimes already occur several weeks earlier and are thus not as useful for summer agriculture. Adjustments in water management will be necessary, and possibly also new infrastructure such as dams and water transfers.

"However, technical solutions go hand in hand with major ecological damage, and some rivers, such as the Indus, have little potential for expansion," says Viviroli. For the future, it will be crucial that lowland and mountain regions work closely together despite political, cultural, social and economic differences.

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Agriculture - a climate villain? Maybe not!

A proposal to rethink agriculture in the climate calculations

LINKÖPING UNIVERSITY NEWS RELEASE 7-JUL-2020

 

IMAGE: EVERY SECTOR IN SOCIETY EMITS GREENHOUSE GASES. BUT AGRICULTURE IS DIFFERENT FROM MOST OTHER SECTORS BECAUSE OF THE LARGE-SCALE PHOTOSYNTHESIS. CROPS PRODUCE OXYGEN (O2) AND EMIT IT TO THE ATMOSPHERE,... view more 

CREDIT: PER FRANKELIUS

The UN's Intergovernmental Panel on Climate Change (IPCC) claims that agriculture is one of the main sources of greenhouse gases, and is thus by many observers considered as a climate villain. This conclusion, however, is based on a paradigm that can be questioned, writes Per Frankelius, Linkoping University, in an article in Agronomy Journal.

The fundamental process in agriculture is large-scale photosynthesis, in which carbon dioxide is captured by crops and at the same time oxygen is produced. A fraction of the carbon is bound in the plant roots, while most of it is bound in the form of carbohydrates that are harvested and used in other sectors of society. This involves various form of cereal, oilseed crops, vegetables and grassland.

"The fact that the carbon is bound in the crops, which at the same time produce oxygen, just as growing forest does, is a positive effect that is not included in the IPCC calculations. These only consider the greenhouse gases that have a negative impact on the climate. This is also the case in The Greenhouse Gas Protocol, which is a well established standard for calculating the emission of greenhouse gases", says Per Frankelius, associate professor in business administration at Linköping University, who has recently written an article in the prestigious Agronomy Journal, published by the American Society of Agronomy.

"This view is based on a paradigm that has essentially never been questioned. Politicians and decision-makers must understand the complete range of the climate impact of agriculture, otherwise there is a risk that many decisions that influence long-term sustainability in a negative manner will be taken", says Per Frankelius.

The justification that crops are not included as a positive factor is probably that carbon dioxide is formed in the next step along the chain, when the crops are consumed by humans. "But that takes place in another sector: it's not part of agriculture", Per Frankelius points out.

Per Frankelius gives an example calculation in the article in Agronomy Journal:

Many different crops are cultivated as agricultural products, and all of them perform photosynthesis. One common crop is cereals, such as wheat, and in 2019, global production of cereals was 2.7 billion tonnes. This corresponds to approximately 1 billion tonnes of carbon, which in turn corresponds to 3.8 billion tonnes of carbon dioxide. The figure would be significantly higher if we included other crops such as oilseed crops and sugar beet.

"The total agricultural production has been estimated to be 9200 million tons by FAOSTAT. Different crops have different water content, but a good guess is that the total production corresponds to approximately 9100 million tonnes of carbon dioxide", adds Per Frankelius.

Agriculture produces also grasslands and grazing that bind carbon, and a further 2.7 billion tonnes of carbon is bound in the soil.

"So is agriculture one of the world's largest climate villains, or does the sector actually have a positive impact on climate?" asks Per Frankelius.

He does not question the fact that agriculture also produces a significant amount of negative greenhouse gases, and it is important to reduce this in a sustainable manner.

Per Frankelius, who is also process manager at Agtech 2030, an innovation platform at Linköping University, presents in the article no less than seven concrete measures that can both advance the sector and reduce emissions. The measures range from ensuring that fields are green throughout the year to the marketing of animal ecosystem services, the use of fossil-free mineral-based fertilisers, the spread of biochar, replacing diesel by fossil-free biodiesel, electricity, fuel cells or even steam to power engines, planting trees in rows along the edges of fields and placing solar panels there to follow the sun with a recently patented technology, and various ways to reduce soil compaction. He refers to concrete examples in all cases.

The conclusions Per Frankelius draws are unambiguous: in order to achieve long-term sustainability, all aspects of global agriculture must be developed, not wound down or given less advantageous economic conditions. One key to success is innovation.

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Frankelius, Per (2020). A proposal to rethink agriculture in the climate calculations, Agronomy Journal (published by American Society of Agronomy), vol 112, issue 4, pp. 3216-3221. DOI 10.1002/agj2.20286 https://acsess.onlinelibrary.wiley.com/doi/epdf/10.1002/agj2.20286

Contact: Per Frankelius, per.frankelius@liu.se, +46 13 28 15 96

Background:

According to the latest and Fifth Assessment Report (AR5) published in 2014, the IPPC argues that "Agriculture, forestry and other land use" (AFOLU) stands for 24% of the world's greenhouse gas emissions. Only the sector "Electricity and heat production" stands for slightly more, 25%. In the special report on land use published in 2019, the IPPC modified 24% to 23% but underlined: "Agriculture, forestry and other land use (AFOLU) is a significant net source of GHG emissions (high confidence), contributing to about 23% of anthropogenic emissions of carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) combined as CO2 equivalents in 2007-2016 (medium confidence)."

Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Core Writing Team, R.K. Pachauri and L.A. Meyer (eds.)]. IPCC, Geneva, Switzerland, 2014.

Climate change and land: An IPCC special report on climate change, desertification, land degradation, sustainable land management, food security, and greenhouse gas fluxes in terrestrial ecosystems. Geneva: The Intergovernmental Panel on Climate Change, IPCC, 2019. Page 45.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy

Engineers use electricity to clean up toxic water

Powerful electrochemical process destroys water contaminants, such as pesticides

UNIVERSITY OF SYDNEY

IMAGE: WATER BEFORE AND AFTER ELECTROCHEMICAL TREATMENT. view more 

CREDIT: JULIA CIARLINI JUNGERS SOARES, UNIVERSITY OF SYDNEY

A team of engineers may be one step closer to cleaning up heavily contaminated industrial wastewater streams.

Researchers from the School of Chemical and Biomolecular Engineering developed an electrochemical oxidation process with the aim of cleaning up complex wastewater that contained a toxic cocktail of chemical pollutants.

"Our study, published in Algal Research, involved industrial wastewater that had been heavily contaminated with a cocktail of organic and inorganic species during a biofuel production process", said Julia Ciarlini Jungers Soares, who is completing a PhD in Chemical and Biomolecular Engineering under the supervision of Dr Alejandro Montoya.

The wastewater, which contained carbon, nitrogen and phosphorus, was generated in a pilot plant, designed by the team for the production of biofuels using naturally abundant microalgae.

The process involved treating wastewater with electricity using specialised electrodes. They discharged electricity, then drove oxidation reactions near the electrode surfaces, transforming the organic contaminants into harmless gasses, ions or minerals.

The water before, during and after treatment. Photo credit: Julia Ciarlini Jungers Soares, University of Sydney

"We have employed an incredibly powerful process that eliminates even the most persistent non-biodegradable pollutants, such as pharmaceuticals and pesticides, as well as various classes of organic compounds that can be found in many industrial effluents," she said.

"The process is relatively simple, does not require the addition of chemicals or severe operation conditions, and does not produce additional waste streams."

"Wastewater is a significant issue for our environment, as well as for many industries who use substantial volumes of water in their processes, such as in reactions, transport, and washing and cooling. Finding suitable solutions for reuse or disposal is often very challenging and costly.

"The electrochemical method that we used can be readily applied to industries that must comply with strict regulations for wastewater disposal, such as pulp and paper processing, wineries, as well as pharmaceutical production facilities.

"Worldwide, researchers are investigating methods for the development of biofuels from algae. Developing alternatives for the treatment and reuse of this industrial effluent is a hot research topic and can bring opportunities for energy and resource recovery within a circular bio-economy framework."

The team will soon carry out research focused on specific contaminants to better understand the chemical transformations that take place during electrochemical oxidation and will upscale the process.

A 2017 UNESCO report found that the opportunities from exploiting wastewater as a resource were vast, and that safely managed wastewater is an affordable and sustainable source of water, energy, nutrients and other recoverable materials.

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DISCLOSURE:

The researchers have no conflicts of interest to declare. The research was supported by a University of Sydney Engineering and Information Technology Research Scholarship.

THE RESEARCH:

Please contact Luisa Low for a PDF copy of the research.

MEDIA CONTACT:

Luisa Low, Media and PR Adviser (Engineering), University of Sydney
luisa.low@sydney.edu.au