New research on hagfish provides insight into evolutionary origin of the eye

U of A biologists studying hagfish eyes uncover unexpected similarities to those of other vertebrates, including humans.

UNIVERSITY OF ALBERTA

Research News

 

IMAGE: AN ADULT HAGFISH IN A CONTAINER FILLED WITH SEA WATER. NEW U OF A RESEARCH REVEALS UNEXPECTED SIMILARITIES BETWEEN THE EYES OF HAGFISH AND THOSE OF OTHER VERTEBRATES INCLUDING HUMANS,... view more 

CREDIT: RYAN WAYNE

The answer to the age-old mystery of the evolutionary origins of vertebrate eyes may lie in hagfish, according to a new study by biologists at the University of Alberta.

"Hagfish eyes can help us understand the origins of human vision by expanding our understanding of the early steps in vertebrate eye evolution," explained lead author Emily Dong, who conducted the research during her graduate studies with Ted Allison, a professor in the Faculty of Science and member of the U of A's Neuroscience and Mental Health Institute. "Our findings solidify the hagfish's place among vertebrates and open the door to further research to uncover the finer details of their visual system."

For years, hagfish eyes were thought to be different from those of vertebrates--so the researchers were surprised to discover hagfish eyes contain many of the same features. These include neurons that connect light-sensitive photoreceptors to ganglion cells, continued growth of the eye late into adulthood, and a hidden layer of support cells that are prominent in other vertebrates and are key to photoreceptor function.

"This is important because it broadens the picture of early vertebrate eye evolution," explained Dong. "The fossil record can only provide us limited information, because soft tissues like eyes do not preserve well. And so we look to living members of these early lineages, such as the hagfish."

Hagfish are the most ancient line of vertebrates still living today, representing vertebrates before the evolutionary appearance of the jaw or paired fins, such as limbs. As a result, studying hagfish provides important information about early evolution in vertebrates, setting the foundation for what scientists can learn by studying other animal models such as zebrafish and mice.

"The data shed light on the confusing and dimly lit evolutionary origins of the vertebrate eye," added Allison, professor in the Department of Biological Sciences and Dong's master's supervisor.

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Dong is now a PhD student at the University of Toronto. The research was funded by the Natural Sciences and Engineering Research Council of Canada and the Bamfield Marine Sciences Centre.

The study, "Vertebrate features revealed in the rudimentary eye of the Pacific hagfish (Eptatretus stoutii)," was published in Proceedings of the Royal Society B.

Zebra finches choose nest materials based on past experience, new research shows

U of A scientists find that learning and past success play a role in how birds build their nests

UNIVERSITY OF ALBERTA

Research News

 

IMAGE: A FEMALE (LEFT) AND MALE ZEBRA FINCH. NEW U OF A RESEARCH SHOWS THAT THE BIRDS' PRIOR EXPERIENCE RAISING CHICKS INFLUENCES WHETHER THEY STICK WITH TRIED-AND-TRUE MATERIALS OR TRY SOMETHING... view more 

CREDIT: ANIMAL COGNITION RESEARCH GROUP

When building a nest, previous experience raising chicks will influence the choices birds make, according to a new study by University of Alberta scientists.

The results show that birds that have successfully raised families stick with tried-and-true methods when building their nests, whereas less successful birds will try something new.

"We found that when presented with a choice between a familiar material, coconut fibre, and a never-before-encountered material, white string, zebra finches who had successfully raised chicks preferred to stick with the same material they had previously used. Birds who failed to raise chicks built nests with equal amounts of familiar and novel material," explained Andrés Camacho-Alpízar, a PhD student in the Faculty of Science.

Male Zebra Finch selecting string

The research shows that nest building is a behaviour based on learning and past experiences, and sheds new light on the decision-making processes birds use when creating nests.

"Much like human architecture is ever-adapting--from changing styles to improved construction materials--birds also adapt their nest-building behaviour based on trial-and-error learning," added Camacho-Alpízar, who conducted the study under the supervision of Lauren Guillette, assistant professor in the Department of Psychology.

The study also showed that all birds took fewer days to complete their second nests compared with their first nest.

Zebra Finch nests

Nests built by previously successful (left) and unsuccessful (right) zebra finches. The nest on the left is built mainly with coconut fibre, a familiar material type for the birds. The nest on the right was built with a more equal proportion of familiar and new material, in this case white string. (Photo: Animal Cognition Research Group)

"This study adds to the small but growing area of research about nest-building behaviour that challenges long-held assumptions about why animals do what they do," said Guillette.

"While one can find many references in both the scientific and lay literature that suggest nest building in birds is entirely pre-programmed, our work shows that birds learn and modify the material they put into their nest based on past breeding experiences with that or similar material."

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This research was funded by the Natural Sciences and Engineering Council of Canada.

The study, "If it ain't broke don't fix it: breeding success affects nest-building decisions," was published in Behavioural Processes.

Population of critically endangered Bahama Oriole is much larger than previously thought

New study suggests there are at least 10 times as many Bahama Orioles as previously believed, and offers insights that could inform future conservation efforts for the orioles and other Caribbean bird species

UNIVERSITY OF MARYLAND BALTIMORE COUNTY

Research News

 

IMAGE: THIS BAHAMA ORIOLE IS PERCHED IN A PINE TREE ON ANDROS ISLAND IN THE BAHAMAS, THE ONLY PLACE THESE BIRDS LIVE. NEW RESEARCH HAS DEMONSTRATED THAT THESE ORIOLES FREQUENTLY INHABIT... view more 

CREDIT: MATTHEW KANE

On a low-lying island in the Caribbean, the future of the critically endangered Bahama Oriole just got a shade brighter. A new study led by researchers at the University of Maryland, Baltimore County (UMBC) estimates the population of these striking black and yellow birds at somewhere between 1300 and 2800 individuals in the region they surveyed, suggesting the overall population is likely several thousand. Older studies estimated the entire population at fewer than 300, so the new results indicate there are at least 10 times as many Bahama Orioles as previously understood. The research appeared this week in Avian Conservation and Ecology.

The research team is sharing its findings with Birdlife International, the organization that makes recommendations to the International Union for the Conservation of Nature (IUCN) about birds on its Red List of threatened species. The new findings may influence IUCN to down-list the Bahama Oriole, which only lives on Andros Island in the Bahamas, from critically endangered to endangered.

The new result "is a step forward for conservation," says Michael Rowley, a 2018 UMBC alumnus and one of two co-lead authors on the study. "This makes the world a bit more informed about what we should be putting our efforts toward. There are other birds that could use attention as well."

A fresh look

In addition to freeing up resources to protect other threatened birds in the Caribbean, details of the study revealed new avenues for protecting the still-endangered Bahama Oriole. Earlier work had largely discounted the pine forest, which covers approximately 20 percent of the island, as important habitat for the Bahama Oriole. Instead researchers focused on human-dominated habitats such as villages and agricultural lands.

However, a 2018 study led by 2017 UMBC alumnus Daniel Stonko upended that understanding of Bahama Oriole ecology. Stonko and colleagues reported the first three Bahama Oriole nests ever recorded in the pine forest. A follow-up study led by 2019 UMBC alumna Briana Yancy, published in December 2020, further detailed nest site characteristics for the orioles on Andros, finding they prefer pine forest containing thatch palms.

Supporting local efforts

The latest study builds on both of those projects. The research team conducted bird counts at 467 sites across 713 square kilometers in the northern 25 percent of the island. They chose sites along abandoned and previously unmapped logging roads, to strike a balance between ease of access and lack of human influence on the birds' presence. The team found the strongest predictor of oriole abundance was the presence of pine forest. Nesting habitat studies, including Yancy's, suggest that during the breeding season the birds may be most common in pine forest with plenty of thatch palms in the understory.

"The orioles seem to be able to nest in quite a few different habitats, which is really good for the orioles and important to know," says Kevin Omland, professor of biological sciences at UMBC and senior author on all three studies. "It gives us really useful information on what the nesting habitat is like, so we can tell the IUCN."

The new findings also supply important information for local conservation efforts led by the Bahamas National Trust (BNT), which has been a key partner to Omland's research group throughout its long-standing work in the Caribbean.

"If the BNT is able to create or expand national parks, they might try to include more of the pine forest with these tall thatch palm trees in the understory," Omland says.

Lasting impact

The other co-lead author, Richard Stanley at the University of Florida, conducted most of the in-person bird counts for the new study, using maps developed by the Omland team. Then Rowley took the lead on a complicated statistical analysis with support from Colin Studds, professor of geography and environmental systems at UMBC, and scientists at the Smithsonian Migratory Bird Center.

The highly impactful findings are particularly exciting for a researcher like Rowley, who completed the research as an undergraduate and is still quite early in his scientific career. Before joining Omland's group, "I'd never been outside of the contiguous U.S.," Rowley says. "It was an incredible privilege, and it really opened me up to my current interest in conservation work."

As for the findings themselves, "It's amazing. How many people get to work on a project when they're an undergrad that has such a real world impact, while also being able to do field work, and work with animals, and get involved in the community?" Rowley says. "It's really great to know that the work we've done is having such an exciting impact."

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Tiny crustaceans' show fastest repeatable movements ever seen in marine animals

New research shows that amphipod claws make snapping movements at 100 kilometres per hour and can accelerate nearly as fast as a bullet.

UNIVERSITY OF ALBERTA

Research News

 

IMAGE: AMPHIPODS CAN SNAP THEIR OUTSIZED CLAWS AT 100 KILOMETRES AN HOUR. AS IT SNAPS SHUT, THE PINCER ACCELERATES NEARLY AS FAST AS A BULLET, ACCORDING TO NEW RESEARCH. (PHOTO: ARTHUR... view more 

CREDIT: ARTHUR ANKER

A group of crustaceans called amphipods can accelerate as fast as a bullet--literally, according to a new study by biologists at the University of Alberta and Duke University.

This study shows that a tiny and unusual species is responsible for making the fastest repeatable movements yet known for any animal in water.

"The high speeds of these repeatable movements reach nearly 30 metres per second or more than 100 kilometres per hour," explained Richard Palmer, professor emeritus in the Department of Biological Sciences and co-author on the study.

"They have the highest accelerations of any animal in water, reaching more than 0.5 million metres per second squared, which is close to the acceleration of a bullet."

A high-speed video camera captures footage of an amphipod's claw snapping at 300,000 frames per second. (Video: Sheila Patek, Duke University)

Amphipods are a type of crustacean related to marine beach hoppers and freshwater scuds. Male amphipods use their large claws to make ultra-fast, repeatable snapping motions. The snaps make a popping sound and create rapid water jets that may be used to defend their territory.

"Each new discovery of extreme movements in a novel group of organisms raises fascinating questions about how such extreme adaptations are achieved in terms of biomechanics and functional behaviour, and how they evolved from more common, slower-moving relatives," said Palmer.

Though faster movements have been seen in other creatures, these movements only happen once and cannot be repeated. As Palmer noted, the mechanism that allows amphipods to create such high-speed movements repeatedly could inspire human engineering efforts.

"This may suggest novel engineering solutions to design and build small structures that can move extremely fast over and over."

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This research was led by Sarah Longo and Sheila Patek at Duke University, in collaboration with Palmer in the U of A's Faculty of Science. Funding was provided by the Natural Sciences and Engineering Research Council of Canada.

The study, "Tiny snaps of an amphipod push the boundary of ultrafast, repeatable movement," was published in Current Biology.

Eating human food could mean trouble for urban coyotes, study shows

New U of A research illustrates link between anthropogenic diet, human-like gut bacteria and poor health.

UNIVERSITY OF ALBERTA

Research News

 

IMAGE: URBAN COYOTES THAT SUBSIST ON HUMAN FOOD HAVE MORE HUMAN-LIKE GUT BACTERIA--WHICH COULD AFFECT THEIR HEALTH, IMMUNE FUNCTION AND POSSIBLY EVEN THEIR BEHAVIOUR, ACCORDING TO A U OF A STUDY.... view more 

CREDIT: COLLEEN CASSADY ST. CLAIR

A diet rich in human food may be wreaking havoc on the health of urban coyotes, according to a new study by University of Alberta biologists.

The research team from the Faculty of Science examined the stomach contents, gut microbiome and overall health of nearly 100 coyotes in Edmonton's capital region. Their results also show coyotes that consume more human food have more human-like gut bacteria--with potential impact on their nutrition, immune function and, based on similar findings in dogs, even behaviour.

"If eating human food disturbs the 'natural' coyote gut bacteria, it is possible that eating human food has the potential to affect all these other aspects of coyote health and behaviour as well," said Scott Sugden, lead author and recent master's graduate from the Department of Biological Sciences.

"The gut microbiome has been consistently related to various aspects of human health and behaviour, and the same is true for animals," Sugden noted.

The research also shows that urban coyotes, which eat more human food, also have lower body fat, stressed immune systems and more parasites. The study builds on Sugden's previous research into the relationship between an anthropogenic, or human, diet and the health of urban coyotes.

Urban coyotes that subsist on human food have more human-like gut bacteria--which could affect their health, immune function and possibly even their behaviour, according to a U of A study. (Photo: Colleen Cassady St. Clair)

"If access to human food has the potential to affect coyote health and behaviour by disturbing the gut microbiome, it's important to address the root of the issue by limiting their access to protein-poor human food," explained Sugden.

"This would likely be more effective, and easier to implement, than trying to manage aggressive coyotes and unhealthy coyotes as separate issues," he said, adding that another U of A project will more directly address bold urban coyotes.

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Sugden completed the research under the supervision of ecologist Colleen Cassady St. Clair and microbiologist Lisa Stein, both professors in the Department of Biological Sciences.

The research was funded by the Natural Sciences and Engineering Research Council of Canada. Collaborators include U of A undergraduate student Kyra Ford and Dana Sanderson from MacEwan University, as well as the City of Edmonton's Animal Care and Control Centre and Animal Damage Control in Sherwood Park.

The study, "An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health," was published in Scientific Reports.

Market design to accelerate COVID-19 vaccine supply

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE

 NEWS RELEASE 25-FEB-2021

Research News

 

Although the value of vaccines for COVID-19 may seem obvious, government action and investment in vaccines have not been commensurate with the enormous scale of benefits they offer, argue Juan Camilo Castillo and colleagues in this Policy Forum. Since even one extra month of exposure to COVID-19 kills hundreds of thousands, reduces global gross domestic product (GDP) by hundreds of billions of dollars, and generates large losses to human capital by harming education and health, expanding vaccine capacity even further would generate substantial global benefits. Castillo et al. report results of two related exercises: estimating the global benefits from vaccine capacity already in place, and estimating the benefits of undertaking additional capacity investment starting now. "The enormous estimates from both exercises provide a wake-up call relevant for the current [and future pandemics]," they say. For example, the results suggest that investing now in expanding capacity for an additional annual 1 billion courses of vaccine could accelerate completion of widespread immunization by over 4 months, providing additional global benefits of $576 to $989 per course. "This dwarfs prices of $6 to $40 per course seen in deals with vaccine producers," they say. They urge governments and international organizations to contract with vaccine producers to further expand capacity and encourage measures - such as delayed second doses, lower-dose regimens, or provision of only one dose to those previously infected - to "stretch" existing capacity. "These proposals could have large potential benefits; thus, investigating their medical appropriateness is worthwhile," they say. To avoid the issue of some countries ending up with vaccine allocations that are not optimally matched to their needs, the authors advocate for steps including a cross-country vaccine exchange. Such a mechanism is under consideration by COVAX, a global initiative to promote access to COVID-19 vaccines.

 

Chip simplifies COVID-19 testing, delivers results on a phone

Programmed magnetic nanobeads enable diagnostic device designed at Rice University

RICE UNIVERSITY

Research News

 

IMAGE: A SYSTEM DEVELOPED BY RICE UNIVERSITY ENGINEERS EMPLOYS A STAMP-SIZED MICROFLUIDIC CHIP THAT MEASURES THE CONCENTRATION OF SARS-COV-2 NUCLEOCAPSID PROTEIN IN BLOOD SERUM TO DIAGNOSE COVID-19 IN LESS THAN AN... view more 

CREDIT: LILLEHOJ RESEARCH GROUP/RICE UNIVERSITY

HOUSTON - (Feb. 25, 2021) - COVID-19 can be diagnosed in 55 minutes or less with the help of programmed magnetic nanobeads and a diagnostic tool that plugs into an off-the-shelf cell phone, according to Rice University engineers.

The Rice lab of mechanical engineer Peter Lillehoj has developed a stamp-sized microfluidic chip that measures the concentration of SARS-CoV-2 nucleocapsid (N) protein in blood serum from a standard finger prick. The nanobeads bind to SARS-CoV-2 N protein, a biomarker for COVID-19, in the chip and transport it to an electrochemical sensor that detects minute amounts of the biomarker.

The researchers argued their process simplifies sample handling compared to swab-based PCR tests that are widely used to diagnose COVID-19 and need to be analyzed in a laboratory.

"What's great about this device is that doesn't require a laboratory," Lillehoj said. "You can perform the entire test and generate the results at the collection site, health clinic or even a pharmacy. The entire system is easily transportable and easy to use."

The research appears in the American Chemical Society journal ACS Sensors.

Lillehoj and Rice graduate student and lead author Jiran Li took advantage of existing biosensing tools and combined them with their own experience in developing simple diagnostics, like a microneedle patch introduced last year to diagnose malaria.

The new tool relies on a slightly more complex detection scheme but delivers accurate, quantitative results in a short amount of time. To test the device, the lab relied on donated serum samples from people who were healthy and others who were COVID-19-positive.

Lillehoj said a longer incubation yields more accurate results when using whole serum. The lab found that 55 minutes was an optimum amount of time for the microchip to sense SARS-CoV-2 N protein at concentrations as low as 50 picograms (billionths of a gram) per milliliter in whole serum. The microchip could detect N protein in even lower concentrations, at 10 picograms per milliliter, in only 25 minutes by diluting the serum fivefold.

Paired with a Google Pixel 2 phone and a plug-in potentiostat, it was able to deliver a positive diagnosis with a concentration as low as 230 picograms for whole serum.

"There are standard procedures to modify the beads with an antibody that targets a particular biomarker," Lillehoj said. "When you combine them with a sample containing the biomarker, in this case SARS-CoV-2 N protein, they bond together."

A capillary tube is used to deliver the sample to the chip, which is then placed on a magnet that pulls the beads toward an electrochemical sensor coated with capture antibodies. The beads bind to the capture antibodies and generate a current proportional to the concentration of biomarker in the sample.

The potentiostat reads that current and sends a signal to its phone app. If there are no COVID-19 biomarkers, the beads do not bind to the sensor and get washed away inside the chip.

Lillehoj said it would not be difficult for industry to manufacture the microfluidic chips or to adapt them to new COVID-19 strains if and when that becomes necessary.

CAPTION

Programmed magnetic nanobeads paired with an off-the-shelf cellphone and plug-in diagnostic tool can diagnose COVID-19 in 55 minutes or less, according to Rice University engineers.

CREDIT

Jeff Fitlow/Rice University

The National Institutes of Health, the National Science Foundation and the Rice University COVID-19 Research Fund supported the research.

Read the abstract at https://pubs.acs.org/doi/10.1021/acssensors.0c02561.

This news release can be found online at https://news.rice.edu/2021/02/25/chip-simplifies-covid-19-testing-delivers-results-on-a-phone/

Follow Rice News and Media Relations via Twitter @RiceUNews.

Related materials:

Lillehoj Research Group: http://lillehoj.rice.edu

Department of Mechanical Engineering: https://mech.rice.edu

George R. Brown School of Engineering: https://engineering.rice.edu

CAPTION

Rice University mechanical engineer Peter Lillehoj, left, and graduate student Jiran Li developed a system that uses programmable magnetic nanobeads, an off-the-shelf cellphone and a plug-in diagnostic tool to diagnose COVID-19 in 55 minutes or less.

CREDIT

Jeff Fitlow/Rice University

Images for download:

https://news-network.rice.edu/news/files/2021/02/0215_PHONE-1-WEB.jpg A system developed by Rice University engineers employs a stamp-sized microfluidic chip that measures the concentration of SARS-CoV-2 nucleocapsid protein in blood serum to diagnose COVID-19 in less than an hour. The system uses an off-the-shelf cellphone and potentiostat to deliver the results. (Credit: Lillehoj Research Group/Rice University)

https://news-network.rice.edu/news/files/2021/02/0215_PHONE-2-WEB.jpg Programmed magnetic nanobeads paired with an off-the-shelf cellphone and plug-in diagnostic tool can diagnose COVID-19 in 55 minutes or less, according to Rice University engineers. (Credit: Jeff Fitlow/Rice University)

https://news-network.rice.edu/news/files/2021/02/0215_PHONE-3-WEB.jpg Rice University mechanical engineer Peter Lillehoj, left, and graduate student Jiran Li developed a system that uses programmable magnetic nanobeads, an off-the-shelf cellphone and a plug-in diagnostic tool to diagnose COVID-19 in 55 minutes or less. (Credit: Jeff Fitlow/Rice University)

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,978 undergraduates and 3,192 graduate students, Rice's undergraduate student-to-faculty ratio is just under 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for lots of race/class interaction and No. 1 for quality of life by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger's Personal Finance.

First complete coronavirus model shows cooperation

Frontera, Anton 2 supercomputers simulate holistic model of SARS-CoV-2 virion

UNIVERSITY OF TEXAS AT AUSTIN, TEXAS ADVANCED COMPUTING CENTER

Research News

VIDEO: COARSE-GRAINED MOLECULAR DYNAMICS SIMULATION OF THE SARS-COV-2 VIRION USING LAMMPS FOR 10 × 106 CG TIME STEPS. view more 

CREDIT: GREGORY VOTH, UNIVERSITY OF CHICAGO.

The COVID-19 virus holds some mysteries. Scientists remain in the dark on aspects of how it fuses and enters the host cell; how it assembles itself; and how it buds off the host cell.

Computational modeling combined with experimental data provides insights into these behaviors. But modeling over meaningful timescales of the pandemic-causing SARS-CoV-2 virus has so far been limited to just its pieces like the spike protein, a target for the current round of vaccines.

A new multiscale coarse-grained model of the complete SARS-CoV-2 virion, its core genetic material and virion shell, has been developed for the first time using supercomputers. The model offers scientists the potential for new ways to exploit the virus's vulnerabilities.

"We wanted to understand how SARS-CoV-2 works holistically as a whole particle," said Gregory Voth, the Haig P. Papazian Distinguished Service Professor at the University of Chicago. Voth is the corresponding author of the study that developed the first whole virus model, published November 2020 in the Biophysical Journal.

"We developed a bottom-up coarse-grained model," said Voth, "where we took information from atomistic-level molecular dynamics simulations and from experiments." He explained that a coarse-grained model resolves only groups of atoms, versus all-atom simulations, where every single atomic interaction is resolved. "If you do that well, which is always a challenge, you maintain the physics in the model."

The early results of the study show how the spike proteins on the surface of the virus move cooperatively.

"They don't move independently like a bunch of random, uncorrelated motions," Voth said. "They work together."

This cooperative motion of the spike proteins is informative of how the coronavirus explores and detects the ACE2 receptors of a potential host cell.

"The paper we published shows the beginnings of how the modes of motion in the spike proteins are correlated," Voth said. He added that the spikes are coupled to each other. When one protein moves another one also moves in response.

"The ultimate goal of the model would be, as a first step, to study the initial virion attractions and interactions with ACE2 receptors on cells and to understand the origins of that attraction and how those proteins work together to go on to the virus fusion process," Voth said.

Voth and his group have been developing coarse-grained modeling methods on viruses such as HIV and influenza for more than 20 years. They 'coarsen' the data to make it simpler and more computationally tractable, while staying true to the dynamics of the system.

"The benefit of the coarse-grained model is that it can be hundreds to thousands of times more computationally efficient than the all-atom model," Voth explained. The computational savings allowed the team to build a much larger model of the coronavirus than ever before, at longer time-scales than what has been done with all-atom models.

"What you're left with are the much slower, collective motions. The effects of the higher frequency, all-atom motions are folded into those interactions if you do it well. That's the idea of systematic coarse-graining."

The holistic model developed by Voth started with atomic models of the four main structural elements of the SARS-CoV-2 virion: the spike, membrane, nucleocapsid, and envelope proteins. These atomic models were then simulated and simplified to generate the complete course-grained model.

The all-atom molecular dynamics simulations of the spike protein component of the virion system, about 1.7 million atoms, were generated by study co-author Rommie Amaro, a professor of chemistry and biochemistry at the University of California, San Diego.

"Their model basically ingests our data, and it can learn from the data that we have at these more detailed scales and then go beyond where we went," Amaro said. "This method that Voth has developed will allow us and others to simulate over the longer time scales that are needed to actually simulate the virus infecting a cell."

Amaro elaborated on the behavior observed from the coarse-grained simulations of the spike proteins.

"What he saw very clearly was the beginning of the dissociation of the S1 subunit of the spike. The whole top part of the spike peels off during fusion," Amaro said.

One of the first steps of viral fusion with the host cell is this dissociation, where it binds to the ACE2 receptor of the host cell.

"The larger S1 opening movements that they saw with this coarse-grained model was something we hadn't seen yet in the all-atom molecular dynamics, and in fact it would be very difficult for us to see," Amaro said. "It's a critical part of the function of this protein and the infection process with the host cell. That was an interesting finding."

Voth and his team used the all-atom dynamical information on the open and closed states of the spike protein generated by the Amaro Lab on the Frontera supercomputer, as well as other data. The National Science Foundation (NSF)-funded Frontera system is operated by the Texas Advanced Computing Center (TACC) at The University of Texas at Austin.

"Frontera has shown how important it is for these studies of the virus, at multiple scales. It was critical at the atomic level to understand the underlying dynamics of the spike with all of its atoms. There's still a lot to learn there. But now this information can be used a second time to develop new methods that allow us to go out longer and farther, like the coarse-graining method," Amaro said.

"Frontera has been especially useful in providing the molecular dynamics data at the atomistic level for feeding into this model. It's very valuable," Voth said.

The Voth Group initially used the Midway2 computing cluster at the University of Chicago Research Computing Center to develop the coarse-grained model.

The membrane and envelope protein all-atom simulations were generated on the Anton 2 system. Operated by the Pittsburgh Supercomputing Center (PSC) with support from National Institutes of Health, Anton 2 is a special-purpose supercomputer for molecular dynamics simulations developed and provided without cost by D. E. Shaw Research.

"Frontera and Anton 2 provided the key molecular level input data into this model," Voth said.

"A really fantastic thing about Frontera and these types of methods is that we can give people much more accurate views of how these viruses are moving and carrying about their work," Amaro said.

"There are parts of the virus that are invisible even to experiment," she continued. "And through these types of methods that we use on Frontera, we can give scientists the first and important views into what these systems really look like with all of their complexity and how they're interacting with antibodies or drugs or with parts of the host cell."

The type of information that Frontera is giving researchers helps to understand the basic mechanisms of viral infection. It is also useful for the design of safer and better medicines to treat the disease and to prevent it, Amaro added.

Said Voth: "One thing that we're concerned about right now are the UK and the South African SARS-CoV-2 variants. Presumably, with a computational platform like we have developed here, we can rapidly assess those variances, which are changes of the amino acids. We can hopefully rather quickly understand the changes these mutations cause to the virus and then hopefully help in the design of new modified vaccines going forward."

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The study, "A multiscale coarse-grained model of the SARS-CoV-2 virion," was published on November 27, 2020 in the Biophysical Journal. The study co-authors are Alvin Yu, Alexander J. Pak, Peng He, Viviana Monje-Galvan, Gregory A. Voth of the University of Chicago; and Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, and Rommie E. Amaro of the University of California, San Diego. Funding was provided by the NSF through NSF RAPID grant CHE-2029092, NSF RAPID MCB-2032054, the National Institute of General Medical Sciences of the National Institutes of Health through grant R01 GM063796, National Institutes of Health GM132826, and a UC San Diego Moore's Cancer Center 2020 SARS-COV-2 seed grant. Computational resources were provided by the Research Computing Center at the University of Chicago, Frontera at the Texas Advanced Computer Center funded by the NSF grant (OAC-1818253), and the Pittsburgh Super Computing Center (PSC) through the Anton 2 machine. Anton 2 computer time was allocated by the COVID-19 HPC Consortium and provided by the PSC through Grant R01GM116961 from the National Institutes of Health. The Anton 2 machine at PSC was generously made available by D. E. Shaw Research."

Survey reveals racial, political differences in COVID-19 responses

MICHIGAN STATE UNIVERSITY

Research News

 

America's stark racial disparities in health care have been exposed by COVID-19, but a new study from Michigan State University suggests that Black individuals are more likely than conservative White people to adhere to public health standards due to disparities.

The study, published in the Journal of Racial and Ethnic Health Disparities, used data from MSU's State of the State Survey that was captured during the initial COVID-19 outbreak from a representative group of 800 adults in Michigan.

"Our findings suggest that although COVID impacts all Michiganders, reactions to COVID are politicized. This is significant because if people base their response to COVID on politics rather than science, they may be placing themselves at risk," said Zachary Neal, MSU associate professor of psychology and study co-author.

What's more: Michigan residents' race impacted how much politics affected their views of COVID.

"When COVID was politicized, partisanship mattered more to White Michiganders than it did to Black Michiganders," Neal said. "This is significant because it could mean that White Michiganders are more likely to misjudge COVID risks due to politics. For example, although Black Michiganders on average said they would comply with stay-at-home orders, only the more liberal White Michiganders said they would comply."

In considering political ideology, the findings reveal that conservative White individuals were more likely to have noncompliance attitudes toward local and state COVID orders than more liberal White people and Black people who tend towards compliance.

Overall, Black Michiganders' attitudes toward the pandemic were more in line with public health recommendations around mask wearing and stay-at-home orders than views held by their White counterparts. Researchers point to a long history of health, social and economic disparities as the driving force. They found that Black Michiganders were more likely to contract COVID-19 or lose their job as a result of COVID-19 and thereby more likely to comply with regulations.

"Black Americans experience a disproportionately greater rate of preexisting conditions, such as hypertension and diabetes, that place them at an elevated COVID risk," said Kaston Anderson-Carpenter, MSU assistant professor of psychology and study lead author. "Since social determinants of health adversely impact Black Michiganders, adhering to the restrictions may also be perceived as a preventive health measure. Black people who work in essential jobs may also care for family members who have preexisting conditions, which may also influence their adherence to COVID restrictions."

Using data from the State of the State survey, conducted by MSU's Institute for Public Policy and Social Research, Anderson-Carpenter and Neal measured 12 areas of COVID-19 sentiment across four categories: personal impacts, the perceived severity of the virus, the state of Michigan's response to rising caseloads and Michigan's initial stay-at-home order.

Beyond the politicization of the virus, Anderson-Carpenter and Neal's paper reinforces the national conversation about Black people being disproportionately affected by the virus.

"Very little has happened between May and now to reduce racial disparities or political divisions; if anything, both are now worse than before," Neal said. "Knowing now what was happening then -- and, now that we're experiencing another surge in cases -- more resources need to go to the Black communities to address both the health and economic impacts of COVID, particularly now that vaccines are available."

By highlighting the impact of partisan perceptions, the researchers hope their study stresses the extensive disparities related to COVID health care and encourage public health officials to focus on providing assistance to Black communities.

"It is imperative to understand how COVID has been politicized in Michigan as a microcosm of the nation, and we hope the study encourages politicians to make COVID a nonpartisan issue," Anderson-Carpenter said.

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(Note for media: Please include the following link to the study in all online media coverage: https://link.springer.com/article/10.1007/s40615-020-00939-9)

Getting ahead of climate change

Earth observation data could help the humanitarian community reduce the destruction of natural disasters

SPIE--INTERNATIONAL SOCIETY FOR OPTICS AND PHOTONICS

Research News

 

IMAGE: PHASES OF FORECAST-BASED EARLY ACTION EFFORTS: DESIGN, OPERATION, EVALUATION. view more 

CREDIT: NAUMAN ET AL.

As climate change increases the occurrence of catastrophic natural disasters around the world, international organizations are looking for ways to reduce the risk of such disasters. One approach under exploration is the humanitarian community's forecast-based early action (FbA), which seeks to enable pre-emptive actions based on forecasts of extreme events.

With FbA, disaster response shifts toward anticipating disasters to ameliorate their destructive effects. However, the development of data-based triggers and metrics for action rely on timely and accurate information. A group of researchers publishing in SPIE's Journal of Applied Remote Sensing believes that some of that information can be provided by Earth observation (EO). In "Perspectives on flood forecast-based early action and opportunities for Earth observations," Claire Nauman et al. focus on flood forecasts and identify opportunities to incorporate Earth observation data into flood FbA.

Efforts have been made to focus on risk reduction, but in the past two decades, only a small percentage of funding for disasters has been spent to decrease disaster risk. The overwhelming majority of funding has been spent on emergency response, reconstruction, and rehabilitation. However, preventive action to avoid disaster losses could provide significant return on investment, both by avoiding losses and by increasing economic activity in areas prone to destructive weather events. However, action often is not taken in response to early warning systems, but only after destruction has occurred. FbA systems are intended to change that fact, enabling pre-emptive action based on a forecast, even under uncertain conditions.

FbA programs often take one of two primary approaches - predefined triggers or real-time forecast-informed decision-making - to determine when action is needed. This paper focuses on predefined triggers because such triggers are a new aspect of FbA that differentiate them from early warning systems. "Triggers are defined by the danger level or magnitude of a forecasted event (e.g., 100 mm of rain over 24 h) and forecast probability (e.g., 80% chance of the event occurring)," the study says.

Recently, FbA triggers have also been defined based on impact, instead of hazard, in keeping with guidelines proposed for impact-based forecasting. For example, an impact-based trigger would prompt action if a defined percentage of homes are forecasted to flood.

CAPTION

Countries with FbA programs and their associated hazard focus implemented by the International Federation of Red Cross and Red Crescent Societies, Start Network, World Food Program, and the Food and Agriculture Organization.

CREDIT

Nauman et al.

As EO science advances and FbAs become more common, the two communities will find new ways to connect, not only regarding flood impacts but also for other destructive events, such as forest fires, droughts, heat waves, volcanic eruptions, and others. "Flood early warning systems are still many years away from producing forecasts of impact," Nauman says in the study, "but this should not discourage the design of impact-based triggers for early action today."

And as EO scientists and humanitarians continue to cooperate, the researchers say boundary organizations that can bridge the two communities will be key to facilitating the coordination required to help turn science into action and reduce the effects of floods. "For joint success, collaboration is crucial," Nauman said.

Read the open access paper: Claire Nauman et al., "Perspectives on flood forecast-based early action and opportunities for Earth observations," J. Appl. Rem. Sens. 15(3), 032002 (2021) doi:10.1117/1.JRS.15.032002

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