Tracking COVID-19 across Europe

INTERNATIONAL INSTITUTE FOR APPLIED SYSTEMS ANALYSIS

Research News

IMAGE: COVID-19 CUMULATIVE CASES PER 10,000 POP (15 JAN 2020-26 APR 2021) view more 

CREDIT: A. NAQVI (2021)

According to the World Health Organization, a third wave of COVID infections is now all but inevitable in Europe. A COVID tracker developed by IIASA researcher Asjad Naqvi, aims to identify, collect, and collate various official regional datasets for European countries, while also combining and homogenizing the data to help researchers and policymakers explore how the virus spreads.

While many comparisons have been made between the COVID-19 pandemic and similar events in history, one thing sets this pandemic apart from others: the unprecedented amount of knowledge and data that is constantly being generated to understand how the pandemic is unfolding. For a high-income region like Europe, the quality of information made available on a daily basis is exceptionally high compared to the rest of the world. Using this information to make comparisons between different European countries is however not a simple task.

Almost all European countries make COVID-19 data available in the form of maps and trend graphs, but access to data behind these visualizations varies from country to country, with most allowing some form of access to regional data, while others do not release this information publicly. European countries also tend to define regions differently. The European Commission and Eurostat - the statistical office of the European Union - for instance, use homogenous units known as Nomenclature of Territorial Units for Statistics (NUTS), where NUTS 0 denotes countries, NUTS 1 are typically provinces, NUTS 2 are districts, and NUTS 3 are sub-districts. In addition, differences in testing practices and how COVID-19 related hospital admissions and deaths are recorded, further complicate the comparison of data. Lastly, not all European countries are part of the European Union, and therefore are not subject to Eurostat reporting or data sharing requirements.

To overcome some of these challenges, IIASA researcher Asjad Naqvi has developed a COVID-19 tracker that presents data on daily COVID-19 cases at the sub-national level for 26 European countries from January 2020 until the present. Although several innovative datasets that collect unique COVID-19 related information, such as the Oxford COVID-19 Government Response Tracker and the Complexity Science Hub (CSH) Tracker have come onto the scene since the start of the pandemic, Naqvi's tracker aims to identify, collect, and collate various official regional datasets for European countries, while also combining and homogenizing the data at the NUTS 3 or NUTS 2 level. This homogenized dataset makes it possible to explore how the virus spreads in terms of cumulative cases, daily cases, and cases per capita in Europe at a daily resolution.

"One of my aims in developing this tracker was to ensure data transparency, while also making the data consistent and ready for analysis. The paper identifies sources of COVID-19 datasets for 26 European countries and how to access each of them. The data set currently contains over 0.5 million data points at the NUTS 3 or NUTS 2 level," Naqvi explains.

The tracker's data, which is discussed in a new paper published in the journal Scientific Data, can be merged with country or continent-level datasets, such as primary surveys, data from national statistical offices, or data from Eurostat, to conduct comprehensive analyses on the causes and implications of COVID-19. The paper contains a detailed discussion of data sources in each country, including their strengths and weaknesses, and the raw country-level files are provided in an online repository. According to Naqvi, this is one of the very few datasets that has been continuously updated since August 2020 to provide consistent daily information on a regional level for Europe.

The map, for example, clearly illustrates that Germany, on the whole, insulated itself well against the virus and that Sweden and Czechia were particularly hard hit since the start of the pandemic.

Naqvi notes that the tracker can be used for a host of different research questions. It can, for instance, be mapped onto NUTS-level regional data including various economic, demographic, health, tourism, and labor related indicators, some of which also have a monthly or even a weekly frequency. Since data for individual countries are provided, a detailed country-specific analysis can also be done if regional or micro data are available for analysis. Other datasets catalogued on platforms such as the Oxford COVID-19 Supertracker, provides a range of interesting information on various policies put in place by countries during the pandemic. The tracker data can be combined with several innovative global datasets containing NUTS-level information for European countries. As the data for the tracker has a Creative Commons Attribution 4.0 International License (CC-BY), anyone can access it at any time. The data base will continue to be updated regularly until countries stop publishing regional COVID-19 data.

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Reference

Naqvi, A. (2021). COVID-19 European regional tracker. Scientific Data DOI: 10.1038/s41597-021-00950-7

Further information

https://doi.org/10.5281/zenodo.4244878

 

Study highlights how resilience is dynamic, not a static character trait

NORTH CAROLINA STATE UNIVERSITY

Research News

A new study finds that resilience is a dynamic process, rather than a fixed trait - and suggests this may have significant ramifications for the business world.

"Organizations are interested in cultivating a resilient workforce, because they want people who are able to remain committed to an organization and its goals over time," says Patrick Flynn, corresponding author of the study and an assistant professor of human resources management at North Carolina State University's Poole College of Management.

"Our work here does a couple things," Flynn says. "First it finds that resilience is more of a process than a characteristic. Second, it identifies some of the characteristics that can contribute to that process in a meaningful way. Taken together, we think the findings can inform recruitment, hiring, operations and training practices."

At the heart of the study is the idea that resilience fluctuates, because it encompasses the way that an individual responds to a variety of circumstances over time.

"It's impossible to assess dynamic resilience at any given moment," Flynn says. "Dynamic resilience is demonstrated across time. How does people's behavior change over time? What influences that? Those are the sorts of questions we wanted to answer with this study."

To that end, researchers worked with 314 members of a university marching band. Study participants were surveyed weekly for 12 weeks. The surveys were designed to collect data on individual participants and their emotional and personal characteristics. To assess how resilience is functioning in individuals over time, the researchers also asked study participants about their commitment to the marching band as an organization, as well as their feelings of "burnout" - specifically, emotional exhaustion related to their work in the organization.

"Tracking the trajectories of commitment and burnout helped us see how resilience played out in real world terms," Flynn says.

The researchers found that, on average, emotional exhaustion increased over time and commitment decreased over time. However, there were factors that influenced those effects.

For example, experience within the organization exacerbated the effects of emotional exhaustion and decreased commitment. In other words, newcomers appeared to be more resilient over the study period.

The researchers also found that people who scored higher on assessments of emotional stability were better able to maintain higher levels of commitment.

Lastly, the researchers also looked at the trajectory of each individual's commitment to the organization to see if it predicted "retention." They found that positive commitment trajectories were associated with a greater likelihood of both planning to return to the organization for another year and then subsequently doing so.

"One takeaway here is that annual employee surveys may not be the best way to assess employee resilience and commitment to an organization," Flynn says.

That's because annual surveys provide snapshots, while resilience is a dynamic process that fluctuates.

"Since resilience affects things like employee retention, which are important to a company's bottom line, we really need to be touching base with employees more often," Flynn says.

The work also shows that resilience can wear down over time, even if people are only exposed to mild stressors.

"Chronic stress can wear down resilience, with ramifications for employee retention and, in all likelihood, job performance," Flynn says.

"However, we also feel that thinking about resilience as a dynamic process creates opportunities to foster resilience in employees not only through recruitment, but through training, and even job design. In short, it's not as simple as hiring the right person and assuming things will work out. Fostering resilience is going to be an ongoing task for management and human resources professionals."

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The paper, "Tracking the Process of Resilience: How Emotional Stability and Experience Influence Exhaustion and Commitment Trajectories," is published in the journal Group & Organization Management. The paper was co-authored by Paul Bliese, Audrey Korsgaard and Cormac Cannon of the University of South Carolina. The work was done with support from the Riegel and Emory HR Center at USC's Darla Moore School of Business.

 

The virus trap

Hollow nano-objects made of DNA could trap viruses and render them harmless

TECHNICAL UNIVERSITY OF MUNICH (TUM)

VIDEO: FOR THE DNA PLATES TO ASSEMBLE INTO LARGER GEOMETRICAL STRUCTURES, THE EDGES MUST BE SLIGHTLY BEVELED. THE CORRECT CHOICE AND POSITIONING OF BINDING POINTS ON THE EDGES ENSURE THAT THE... view more 

CREDIT: CHRISTIAN SIGL / DIETZLAB / TUM

To date, there are no effective antidotes against most virus infections. An interdisciplinary research team at the Technical University of Munich (TUM) has now developed a new approach: they engulf and neutralize viruses with nano-capsules tailored from genetic material using the DNA origami method. The strategy has already been tested against hepatitis and adeno-associated viruses in cell cultures. It may also prove successful against corona viruses.

There are antibiotics against dangerous bacteria, but few antidotes to treat acute viral infections. Some infections can be prevented by vaccination but developing new vaccines is a long and laborious process.

Now an interdisciplinary research team from the Technical University of Munich, the Helmholtz Zentrum München and the Brandeis University (USA) is proposing a novel strategy for the treatment of acute viral infections: The team has developed nanostructures made of DNA, the substance that makes up our genetic material, that can trap viruses and render them harmless.

DNA nanostructures

Even before the new variant of the corona virus put the world on hold, Hendrik Dietz, Professor of Biomolecular Nanotechnology at the Physics Department of the Technical University of Munich, and his team were working on the construction of virus-sized objects that assemble themselves.

In 1962, the biologist Donald Caspar and the biophysicist Aaron Klug discovered the geometrical principles according to which the protein envelopes of viruses are built. Based on these geometric specifications, the team around Hendrik Dietz at the Technical University of Munich, supported by Seth Fraden and Michael Hagan from Brandeis University in the USA, developed a concept that made it possible to produce artificial hollow bodies the size of a virus.

In the summer of 2019, the team asked whether such hollow bodies could also be used as a kind of "virus trap". If they were to be lined with virus-binding molecules on the inside, they should be able to bind viruses tightly and thus be able to take them out of circulation. For this, however, the hollow bodies would also have to have sufficiently large openings through which viruses can get into the shells.

"None of the objects that we had built using DNA origami technology at that time would have been able to engulf a whole virus - they were simply too small," says Hendrik Dietz in retrospect. "Building stable hollow bodies of this size was a huge challenge."

The kit for a virus trap

Starting from the basic geometric shape of the icosahedron, an object made up of 20 triangular surfaces, the team decided to build the hollow bodies for the virus trap from three-dimensional, triangular plates.

For the DNA plates to assemble into larger geometrical structures, the edges must be slightly beveled. The correct choice and positioning of binding points on the edges ensure that the panels self-assemble to the desired objects.

"In this way, we can now program the shape and size of the desired objects using the exact shape of the triangular plates," says Hendrik Dietz. "We can now produce objects with up to 180 subunits and achieve yields of up to 95 percent. The route there was, however, quite rocky, with many iterations."

Viruses are reliably blocked

By varying the binding points on the edges of the triangles, the team's scientists can not only create closed hollow spheres, but also spheres with openings or half-shells. These can then be used as virus traps.

In cooperation with the team of Prof. Ulrike Protzer, head of the Institute for Virology at TUM and director of the Institute for Virology at the Helmholtz Zentrum München, the team tested the virus traps on adeno-associated viruses and hepatitis B virus cores.

"Even a simple half-shell of the right size shows a measurable reduction in virus activity," says Hendrik Dietz. "If we put five binding sites for the virus on the inside, for example suitable antibodies, we can already block the virus by 80 percent, if we incorporate more, we achieve complete blocking."

To prevent the DNA particles from being immediately degraded in body fluids, the team irradiated the finished building blocks with UV light and treated the outside with polyethylene glycol and oligolysine. The particles were thus stable in mouse serum for 24 hours.

CAPTION

Lined on the inside with virus-binding molecules, nano-shells made of DNA material bind viruses tightly and thus render them harmless.

CREDIT

Elena-Marie Willner / DietzLab / TUM

A universal construction principle

Now the next step is to test the building blocks on living mice. "We are very confident that this material will also be well tolerated by the human body," says Dietz.

"Bacteria have a metabolism. We can attack them in different ways, " says Prof. Ulrike Protzer. "Viruses, on the other hand, do not have their own metabolism, which is why antiviral drugs are almost always targeted against a specific enzyme in a single virus. Such a development takes time. If the idea of simply mechanically eliminating viruses can be realized, this would be widely applicable and thus an important breakthrough, especially for newly emerging viruses.

The starting materials for the virus traps can be mass-produced biotechnologically at a reasonable cost. "In addition to the proposed application as a virus trap, our programmable system also creates other opportunities," says Hendrik Dietz. "It would also be conceivable to use it as a multivalent antigen carrier for vaccinations, as a DNA or RNA carrier for gene therapy or as a transport vehicle for drugs."

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The research was funded by the European Community's Horizon 2020 Research and Innovation Program under the FET-Open project VIROFIGHT (grant no. 899619), the European Research Council (ERC) under a Consolidator Grant, the German Research Foundation (DFG) through SFB863 and TRR179, and by grants of the Gottfried Wilhelm Leibniz Program, the German Federal Ministry of Education and Research (BMBF) through the StabVacB project and the German Center for Infection Research (DZIF), the Netherlands Organization for Scientific Research (NWO), the National Science Foundation of the USA via the Brandeis University Materials Research Science and Engineering Center, the National Institute of General Medical Sciences (NIGMS) of the USA, and the Alexander von Humboldt Foundation (AvH).

 

Silicon in drinking water caused irreversible lung pathologies in rodents

Scientists of Immanuel Kant Baltic Federal University examined the effect of long-term silicon intake on the health of mice and rats.

IMMANUEL KANT BALTIC FEDERAL UNIVERSITY

Research News

Bone density, skin and hair health, and the mobility of joints depend to a great extent on the microelement of silicon. We mostly get it with food, but silicon is also consumed with some biologically active additives that promise beauty, longevity, and youth. The element can also be found in drinking water of a natural origin: usually, it is included in the compound of sodium salt and metasiliconic acid. However, in the case of microelements, one should be extremely careful: a deficiency could lead to diseases, but an overdose could bring negative effects too.

Together with colleagues from the Chuvash State University and the Hamburg Medical University, scientists of Immanuel Kant Baltic Federal University studied the effect of prolonged silicon consumption in relatively small doses. They experimented on laboratory rats and mice. For several months the animals were given water with sodium metasilicate, one of the most common compounds of silicon; the concentration was ten milligrams per liter.

In the first phase of their experiment, the researchers took rats and mice pulmonary tissue samples two and three months after the introduction of silicon-contaminated water and didn't find any pathological changes. Then, they decided to triple the time of influence. Nine months later, the results were very different -- the animals' health greatly deteriorated. Their weight reduced in half, and the animals showed signs of lung fibrosis (the transformation of functional tissues into non-functional connective) of varying severity, and deformation of the bronchial tree. The epithelial walls between their alveoli were so depleted that in some cases they conjoined, and the total number and diameter of the alveoli decreased. Histological studies showed the presence of giant multinuclear Pirogov-Langhans cells that are common in tuberculosis and other severe lung diseases.

Remarkably, the negative impact on animals from the first phase of the experiment occurred six months after they were transferred from silicon-contaminated to clean water. Zones of increased density developed inside their lungs and along the bronchial tree areas. High concentration of lymphocytes (the main cells of the immune system) in these zones was indicative of inflammation.

"What we've seen during our experiment with rats and mice was very similar to silicosis, a chronic occupational disease that mostly affects miners and foundry workers. The constant use of silicon, whether in water or dietary supplements, may at first appear safe, although the damage increases unnoticeably. Research like this has been going on for years and is aimed to form an evidence base. The results are already included in the guidelines on microelement additives, which means we are actively changing the minds of the scientific community. Perhaps, lovers of "miracle pills" would be next", noted the head of research Valentina Gordova, a Candidate of Medical Sciences, and an Assistant Professor at the Department of Fundamental Medicine of the Immanuel Kant Medical Institute.

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Looking beyond the numbers to see pandemic's effect on nursing home residents

REGENSTRIEF INSTITUTE

 VIDEO: REGENSTRIEF INSTITUTE RESEARCH SCIENTIST KATHLEEN UNROE, M.D. DISCUSSES PANDEMIC'S EFFECT ON NURSING HOME RESIDENTS. view more 

CREDIT: REGENSTRIEF INSTITUTE

INDIANAPOLIS -- Nursing homes throughout the United States have been devastated by the COVID-19 pandemic with many perceptions and misperceptions but little documentation about what has happened on a day-by -day basis to residents in these facilities. A study from Regenstrief Institute and Indiana University School of Medicine research scientists is one of the first to describe and identify patterns in the course of COVID-19 in the typically frail individuals who reside in nursing homes.

Much has been written about number of deaths, vaccine uptake and other topics related to the impact of COVID on nursing homes, yet prior to the Regenstrief-IU School of Medicine study, there has been little known about how the disease has clinically affected individuals residing in nursing homes. A full understanding of the disease burden and trajectories of COVID-19 in nursing home residents - those who died and those who survived COVID - will aid medical and public health professionals immediately, will help them prepare for outbreaks of variants and may inform efforts to confront outbreaks of other diseases.

"When the COVID outbreak occurred, we [physicians who care for nursing home residents] didn't know, because we weren't armed with knowledge or clinical experience, what to expect - who would do well and who wouldn't," said Regenstrief Institute Research Scientist Kathleen Unroe, M.D., senior author of the study. "This is a population that by their very need to reside in a nursing home, has complex medical conditions and is at high risk. And it's a different population than younger adults. For example, some older adults may not experience fever in response to infection; persons with dementia may be unable to report symptoms."

The researchers studied the electronic medical records (EMRs) of 74 nursing home residents infected with COVID of whom half were women, 57 percent were Caucasian and 43 percent were African American. One third (25) died; with 23 of the deaths considered related to COVID-19 infection. Hypertension was the most common comorbidity (81 percent) followed by dementia (51 percent), diabetes (50 percent) and non-dementia mental illness (43 percent). The most common symptoms were fever, hypoxia (low oxygen level in the blood), anorexia, and fatigue/malaise. None reported headaches. The duration of symptoms was extended, with an average of more than three weeks.

The 74 nursing home residents with COVID-19 infection appeared to fall into four disease trajectory categories:

• minimal to no symptoms (17)

• residents who survived but experienced significant symptoms (32),

• residents who died after a rapidly progressive course (less than seven days) (5)

• residents who died after a prolonged course with significant symptom burden (20)

"For many of nursing home residents who survive COVID-19, the duration of symptoms is long and arduous; most will survive the disease but may not get back to baseline," said Dr. Unroe. "The effect of COVID on nursing home residents goes beyond the mortality numbers we saw."

CAPTION

A study from Regenstrief Institute and Indiana University School of Medicine research scientists is one of the first to describe and identify patterns in the course of COVID-19 in the typically frail individuals who reside in nursing homes. Previously, little was known about how the disease has clinically affected individuals residing in nursing homes.

CREDIT

Regenstrief Institute

In addition to Dr. Unroe, authors of "COVID-19 Disease Trajectories Among Nursing Home Residents," published online ahead of print in the Journal of the American Geriatrics Society, are corresponding author Regenstrief Institute Research Scientist and IU School of Medicine faculty member Jennifer Carnahan, M.D., MPH, MA, and IU School of Medicine student Lauren Albert. Additional co-authors are Kristi M Lieb M.D.; Kamal Wagle M.D., MPH; Ellen Kaehr M.D., all of IU School of Medicine and Richard L. Roudebush VA Medical Center.

The study was funded by the National Institutes of Health's National Institute on Aging (K23AG062797) and Centers for Medicare and Medicaid Services (1E1CMS331488).

About Regenstrief Institute

Founded in 1969 in Indianapolis, the Regenstrief Institute is a local, national and global leader dedicated to a world where better information empowers people to end disease and realize true health. A key research partner to Indiana University, Regenstrief and its research scientists are responsible for a growing number of major healthcare innovations and studies. Examples range from the development of global health information technology standards that enable the use and interoperability of electronic health records to improving patient-physician communications, to creating models of care that inform practice and improve the lives of patients around the globe.

Sam Regenstrief, a nationally successful entrepreneur from Connersville, Indiana, founded the institute with the goal of making healthcare more efficient and accessible for everyone. His vision continues to guide the institute's research mission.

About IU School of Medicine

IU School of Medicine is the largest medical school in the U.S. and is annually ranked among the top medical schools in the nation by U.S. News & World Report. The school offers high-quality medical education, access to leading medical research and rich campus life in nine Indiana cities, including rural and urban

Kathleen Unroe, M.D., MHA, M.S.

In addition to being a research scientist at Regenstrief Institute, Kathleen Unroe, M.D., MHA, is an associate professor at Indiana University School of Medicine and a practicing geriatrician.

Jennifer Carnahan, M.D., MPH, M.A.

In addition to her role as a research scientist at Regenstrief, Jennifer Carnahan, M.D., MPH, M.A., is an assistant professor of medicine at Indiana University School of Medicine.

 

UK Government's latest pandemic plan recklessly exposes millions to effects of mass infection

Strategy of infection over vaccination is 'unethical and unscientific' warn experts

BMJ

Research News

The UK government's latest pandemic plan involves recklessly exposing millions of people to the acute and long-term effects of mass infection, warn experts in The BMJ today.

A strategy that chooses mass infection in the young now over vaccination in order to achieve greater population immunity to protect the vulnerable in winter, is "unethical and unscientific" say Dr Deepti Gurdasani and colleagues.

Instead of allowing infections to rise, they urge the government to take urgent actions to inform and protect the public and prepare for autumn.

These include outlining a long-term strategy for pandemic control, keeping basic measures such as masks and physical distancing until cases return to low levels, investing in workplaces, schools and public transport to make them safer, and providing the means for extensive testing and support for people to isolate.

The prime minister's argument that it is better to accept mass infection now than to postpone until winter, when 'the virus has an advantage' is deeply flawed and misleading, they write. Instead, this strategy will place around 48% of the population (children included) who are not yet fully vaccinated, including the clinically vulnerable and those with compromised immune systems, at unacceptable risk.

This approach is already putting intense pressure on struggling healthcare services and will lead to many avoidable deaths and long-term illness, they add. It also provides a fertile environment for selection of escape variants which could have huge consequences for the UK and countries globally.

They point out that more than 1,000 scientists have already signed a letter to the Lancet setting out why allowing mass infection this summer is a 'dangerous and unethical experiment'. The British Medical Association, Directors of Public Health, SAGE, the Academy of Medical Royal Colleges, the Royal College of Nursing and NHS leaders have all highlighted the dangers inherent in allowing mass infection.

Opening the UK up further is billed as "freedom day," but for too many people, removing mandated measures such as wearing masks and physical distancing restrict, rather than enable, freedom.

This, they say, is unlikely to bolster public confidence and engagement in economic activity. And if the government strategy leads us into yet another lockdown, they warn that this could have an even more devastating impact on the economy.

What's more, the public overwhelmingly supports sensible public health measures such as masking indoors. "This begs the question why dangerous public health decisions that are neither in the public interest, or in line with public sentiment, have been made in the midst of a raging pandemic," they write.

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Externally peer reviewed? No

Evidence type: Opinion

Subject: UK government pandemic plan

 

Life-saving snake venom

Researchers create reptile-derived 'super glue' that stops bleeding in seconds using visible light

UNIVERSITY OF WESTERN ONTARIO

Research News

Indiana Jones hates snakes. And he's certainly not alone. The fear of snakes is so common it even has its own name: ophidiophobia.

Kibret Mequanint doesn't particularly like the slithery reptiles either (he actually hates them too) but the Western University bioengineer and his international collaborators have found a novel use for snake venom: a body tissue 'super glue' that can stop life-threatening bleeding in seconds.

Over the past 20 years, Mequanint has developed a number of biomaterials-based medical devices and therapeutic technologies - some of which are either licensed to medical companies or are in the advanced stage of preclinical testing.

His latest collaborative research discovery is based on a blood clotting enzyme called reptilase or batroxobin found in the venom of lancehead snakes (Bothrops atrox), which are amongst the most poisonous snakes in South America.

Taking advantage of this clotting property, Mequanint and the international research team designed a body tissue adhesive that incorporates the special enzyme into a modified gelatin that can be packaged into a small tube for easy, and potentially life-saving, application.

"During trauma, injury and emergency bleeding, this 'super glue' can be applied by simply squeezing the tube and shining a visible light, such as a laser pointer, over it for few seconds. Even a smartphone flashlight will do the job," said Mequanint, a Western engineering professor.

Compared to clinical fibrin glue, considered the industry gold standard for clinical and field surgeons, the new tissue sealant has 10 times the adhesive strength to resist detachment or washout due to bleeding. The blood clotting time is also much shorter, cutting it in half from 90 seconds for fibrin glue to 45 seconds for the new snake venom 'super glue.'

This new biotechnology translates to less blood loss and more life-saving. The super-sealant was tested in models for deep skin cuts, ruptured aortae, and severely injured livers - all considered as major bleeding situations.

"We envision that this tissue 'super glue' will be used in saving lives on the battlefield, or other accidental traumas like car crashes," said Mequanint. "The applicator easily fits in first aid kits too."

In addition, the new snake venom 'super glue' can be used for suture-free, surgical wound closures.

Snake extract-laden hemostatic bioadhesive gel cross-linked by visible light was published today in the journal Science Advances. For the discovery, Mequanint collaborated with bioengineers, scientists and medical practitioners at the University of Manitoba and Army Medical University in Chongqing, China.

"The next phase of study which is underway is to translate the tissue 'super glue' discovery to the clinic," said Mequanint.

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Fossil rodent teeth add North American twist to Caribbean mammals' origin story

FLORIDA MUSEUM OF NATURAL HISTORY

Research News

IMAGE: TWO TEETH DISCOVERED IN PUERTO RICO PROVIDE THE FIRST EVIDENCE OF A CARIBBEAN RODENT WITH NORTH AMERICAN ROOTS. RESEARCHERS NAMED THE NEW GENUS AND SPECIES CARIBEOMYS MERZERAUDI. THIS ARTIST'S RECONSTRUCTION... view more 

CREDIT: JORGE VELEZ-JUARBE

GAINESVILLE, Fla. --- Two fossil teeth from a distant relative of North American gophers have scientists rethinking how some mammals reached the Caribbean Islands.

The teeth, excavated in northwest Puerto Rico, belong to a previously unknown rodent genus and species, now named Caribeomys merzeraudi. About the size of a mouse, C. merzeraudi is the Caribbean's smallest known rodent and one of the region's oldest, dating back about 29 million years.

It also represents the first discovery of a Caribbean rodent from a North American lineage, a finding that complicates an idea that has persisted since Darwin - that land-dwelling mammals colonized the islands from South America. The presence of C. merzeraudi in Puerto Rico suggests a second possibility: Some species may have rafted from North America.

The tiny rodent joins two other types of animals, an extinct rhinoceros-like species and bizarre, venomous shrews known as Solenodons, as the only known examples of Caribbean land-dwelling mammals with North American roots.

"This discovery demonstrates that overwater dispersal from North America was also a potential pathway to the Caribbean," said study co-author Jorge Velez-Juarbe, associate curator of mammalogy at the Natural History Museum of Los Angeles County. "This challenges what we thought we knew about the origins of Antillean terrestrial mammals."

While Caribbean ecotourism brochures generally don't feature splashy images of rats, the islands were once home to a rich representation of rodents, including spiny rats, chinchillas, rice rats and hutias - all descendants of South and Central American forebears.

Fossil and molecular evidence suggest these rodents arrived in the islands in multiple waves over time, though how they got there - whether by scurrying over an ancient land bridge, island-hopping or rafting - has been hotly contested. The paucity of fossils from the early years of the Caribbean Islands further obscures the picture of the region's past biodiversity.

Caribeomys merzeraudi's teeth were so unusual that researchers initially struggled to discern what kind of animal they had come from, said study co-author Lazaro Vinola Lopez, a doctoral student in vertebrate paleontology at the Florida Museum of Natural History.

"We didn't know what it was for several months," he said. "We wondered whether this could be some other rodent from the Caribbean or even some kind of strange fish. It was so puzzling because they're not similar to anything else we had found in that region."

The team eventually pinpointed several tooth characteristics that are hallmarks of rodents known as geomorphs, a group that includes kangaroo rats, pocket mice and gophers. Caribeomys merzeraudi is the first geomorph found outside North America.

An exceptionally thick layer of tooth enamel, among other features, sets C. merzeraudi apart from its relatives and could indicate these rodents belonged to a distinct West Indian branch that evolved in isolation over several million years, Vinola Lopez said.

Scientists found the teeth while screen-washing sediment collected from a river outcrop in San Sebastian, a site that has yielded fossil sharks and rays, fish, turtles, a gharial, sea cows and the oldest known frog in the Caribbean, a coqui. In 2019, the team excavated fossil evidence of two large chinchillas, which likely grew up to 30 pounds. These South American rodents once shared Puerto Rico with the humble C. merzeraudi, which weighed less than a quarter pound.

Today, hutias, bats and Solenodons are the "last survivors of what was once a much more diverse group of Caribbean mammals" that included sloths and primates, Velez-Juarbe said.

Discovering C. merzeraudi opens up the tantalizing possibility that Caribbean mammals with North American origins may not be as exceptional as previously thought, Vinola Lopez said. But there's only one way to find out: "Go back to the locality and see what else we can find."

CAPTION

The advanced state of wear on this Caribeomys merzeraudi fossil molar, seen from above in this CT image, leads researchers to believe it came from an old adult.

CREDIT

The Palaeontological Association

Laurent Marivaux of the University of Montpellier was the study's lead author. Other co-authors are Pierre-Henri Fabre of the University of Montpellier and the Natural History Museum; Francois Pujos of the Argentine Institute of Nivology, Glaciology and Environmental Sciences (IANIGLA); Hernan Santos-Merca, Eduardo Cruz, Alexandra Grajales Perez and James Padilla of the University of Puerto Rico; Kevin Velez-Rosado of the University of Michigan; and Jean-Jacques Cornee, Melody Philippon, Philippe Munch and Pierre-Olivier Antoine of the University of Montpellier.

CAPTION

Jorge Velez-Juarbe discovered a fossil site in San Sebastian, Puerto Rico, with fellow undergraduate students in 2006. Excavations have produced fossils from sharks and rays, fish, turtles, a gharial, sea cows and the oldest known frog and rodents in the Caribbean. From top, the paleontologists pictured here are Lazaro Vinola Lopez, Jorge Velez-Juarbe, Francois Pujos and Laurent Marivaux.

CREDIT

Pierre-Olivier Antoine

 

Modified yeast inhibits fungal growth in plants

External application could reduce agricultural reliance on fungicides

UNIVERSITY OF CALIFORNIA - RIVERSIDE

Research 

About 70-80% of crop losses due to microbial diseases are caused by fungi. Fungicides are key weapons in agriculture's arsenal, but they pose environmental risks. Over time, fungi also develop a resistance to fungicides, leading growers on an endless quest for new and improved ways to combat fungal diseases.

The latest development takes advantage of a natural plant defense against fungus. In a paper published in Biotechnology and Bioengineering, engineers and plant pathologists at UC Riverside describe a way to engineer a protein that blocks fungi from breaking down cell walls, as well as a way to produce this protein in quantity for external application as a natural fungicide. The work could lead to a new way of controlling plant disease that reduces reliance on conventional fungicides.

To gain entrance into plant tissues, fungi produce enzymes that use catalytic reactions to break down tough cell walls. Among these are polygalacturonases, or PGs, but plants are not helpless against this attack. Plants produce proteins called PG-inhibiting proteins, or PGIPs, that slow catalysis.

A group of UC Riverside researchers located the segment of DNA that tells the plant how to make PGIPs in common green beans. They inserted complete and partial segments into the genomes of baker's yeast to make the yeast produce PGIPs. The team used yeast instead of plants because yeast has no PGIPs of its own to muddy the experiment and grows quicker than plants.

After confirming the yeast was replicating with the new DNA, the researchers introduced it to cultures of Botrytis cinerea, a fungus that causes gray mold rot in peaches and other crops; and Aspergillus niger, which causes black mold on grapes and other fruits and vegetables.

Yeast that had both the complete and partial DNA segments that coded for PGIP production successfully retarded fungal growth. The result indicates the yeast was producing enough PGIPs to make the method a potential candidate for large-scale production.

"These results reaffirm the potential of using PGIPs as exogenous applied agents to inhibit fungal infection," said Yanran Li, a Marlan and Rosemary Bourns College of Engineering assistant professor of chemical and environmental engineering, who worked on the project with plant pathologist Alexander Putman in the Department of Microbiology and Plant Pathology. "PGIPs only inhibit the infection process but are likely not fatal to any fungi. Therefore, the application of this natural plant protein-derived peptide to crops will likely have minimal impact on plant-microbe ecology."

Li also said that PGIPs probably biodegrade into naturally occurring amino acids, meaning fewer potential effects for consumers and the environment when compared with synthetic small molecule fungicides.

"The generation of transgenic plants is time-consuming and the application of such transgenic crops in agricultural industry requires a long approval period. On the other hand, the engineered PGIPs that are derived from natural proteins are applicable as a fast-track product for FDA approval, if they can be utilized exogenously in a manner similar to a fungicide," Li said.

By tweaking the yeast a slightly different way, the researchers were able to make it exude PGIPs for external application. Previous studies have shown freeze drying naturally occurring microbes on apples, then reconstituting them in a solution and spraying them on crops, greatly reduces fungal disease and loss during shipping. The authors suggest that PGIP-expressing yeast could be used the same way. They caution, however, that because plants also form beneficial relationships with some fungi, future research needs to ensure plants only repel harmful fungi.

Li will continue to engineer PGIPs for enhanced efficiency and broader spectrum against various pathogenic fungi. Meanwhile, Li and Putman will keep evaluating the potential of using engineered PGIPs to suppress fungi-induced pre-harvest and post-harvest disease.

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Li and Putman were joined in the research by doctoral student Tiffany Chiu and plant pathologist Anita Behari, both of whom are at UC Riverside, and Justin Chartron, who was a professor at UC Riverside when the research was conducted. The paper, "Exploring the potential of engineering polygalacturonase?inhibiting protein as an ecological, friendly, and nontoxic pest control agent," is available here. The work was supported by LG Chem Ltd. and the Frank G. and Janice B. Delfino Agricultural Technology Research Initiative and partially supported by the National Institutes of Health.

 

A new avenue for fighting drug-resistant bacteria

Targeting an RNA sequence in pathogenic bacteria could make them more sensitive to antibiotics

INSTITUT NATIONAL DE LA RECHERCHE SCIENTIFIQUE - INRS

Research News

 

IMAGE: INRS PROFESSOR CHARLES DOZOIS, SPECIALIST IN MICROBIOLOGY AND IMMUNOLOGY AND THE IDENTIFICATION AND CHARACTERIZATION OF BACTERIAL GENES AFFECTING HUMANS, POULTRY AND PIGS. view more 

CREDIT: CHRISTIAN FLEURY (INRS)

A small regulatory RNA found in many problematic bacteria, including Escherichia coli, appears to be responsible for managing the response of these bacteria to environmental stresses. Professor Charles Dozois from Institut national de la recherche scientifique (INRS) and doctoral student Hicham Bessaiah see a promising avenue for more effective treatment of antibiotic-resistant bacteria. Their results have been published in the journal PLOS Pathogens.

In conducting their work, the researchers and their team observed that the elimination of this regulatory RNA sequence had an effect on urinary tract infections related to E. coli. These infections are among the world's most common, especially in women, but they are sometimes hard to treat due to antibiotic resistance.

E. coli is normally found in the intestinal flora, but when it migrates to the bladder, the conditions there are completely different. The bacteria have to withstand the environmental stressors in order to cause a bladder infection. "Without the regulatory RNA, the bacteria is more sensitive to changes in the environment and loses its infectious capacity," explained the doctoral student.

Inhibiting the RNA sequence

The idea is to block the RNA and make the bacteria less infectious, especially in the case of chronic infection, which can lead to increased resistance to treatment. If the bacteria are less resistant to stress, it will be more vulnerable to the host's immune response. Regulation of the systems that make it virulent will also be disrupted.

"People with recurrent urinary tract infections take antibiotics regularly. This leads to resistance and limits treatment options, which is why it's important to find alternatives," explained Professor Dozois.

The relationship between virulence and stress isn't unique to urinary tract infections. The regulatory RNA sequence studied by the researchers is also found in a number of other major pathogenic bacteria. Given that the RNA seems to impact multiple functions, the research group is working to better understand the mechanisms of regulation before pursuing additional research on antibiotic-resistant strains of bacteria.

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About the study

The article "The RyfA small RNA regulates oxidative and osmotic stress responses and virulence in uropathogenic Escherichia coli" by Hicham Bessaiah, Pravil Pokharel, Hamza Loucif, Merve Kulbay, Charles Sasseville, Hajer Habouria, Sébastien Houle, Jacques Bernier, Éric Massé, Julien Van Grevenynghe, and Charles M. Dozois was published in PLOS Pathogens. The research group received financial support from the Natural Sciences and Engineering Research Council of Canada (NSERC), the Canadian Institutes of Health Research (CIHR), and the Swine and Poultry Infectious Diseases Research Centre (CRIPA) funded by Fonds de recherche du Québec - Nature et technologies (FRQNT).

About INRS

INRS is a university dedicated exclusively to graduate level research and training. Since its creation in 1969, INRS has played an active role in Québec's economic, social, and cultural development and is ranked first for research intensity in Québec and in Canada. INRS is made up of four interdisciplinary research and training centres in Québec City, Montréal, Laval, and Varennes, with expertise in strategic sectors: Eau Terre Environnement, Énergie Matériaux Télécommunications, Urbanisation Culture Société, and Armand-Frappier Santé Biotechnologie. The INRS community includes more than 1,500 students, postdoctoral fellows, faculty members, and staff.