Culture

Atherosclerosis progresses rapidly in healthy people from the age of 40

image: Asterisks indicate the presence of an atherosclerotic plaque in the common carotid artery detected by 3D ultrasound. The plaque does not cause significant obstruction of the artery (

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CNIC

Almost half of apparently healthy people between the ages of 40 and 50 could be accumulating fatty plaques--atheromas--in their arteries at a much faster rate than was previously thought. The Journal of American College of Cardiology (JACC) has today published new data from the PESA-CNIC-Santander study demonstrating that atheroma plaques extend rapidly through the arteries of 40% of asymptomatic individuals aged between 40 and 50 years.

Researchers at the Centro Nacional de Investigaciones Cardiovasculares (CNIC), led by Dr Valentín Fuster, Director of the CNIC and lead investigator on the PESA-CNIC-Santander study, have also found that the progression of atherosclerosis is directly related to classical cardiovascular risk factors: age, sex, hypertension, cholesterol, smoking, and diabetes.

PESA ('Progression of early subclinical atherosclerosis') is a partnership between the CNIC and Santander Bank. The study has been monitoring 4200 healthy middle-aged men and women with noninvasive imaging technology and omics biomarkers for more than 10 years. The use of noninvasive imaging technologies, says Dr Fuster, "allows us to identify the progression of the disease earlier than is possible with classical markers, such as the presence of coronary calcium detected by computed tomography (CT), thus allowing us to identify individuals at higher risk who could benefit from early intervention."

The simpler imaging techniques like 2D and 3D ultrasound are accessible and do not involve exposure to radiation. With these techniques, explains CNIC Clinical Research Director Dr Borja Ibañez, "we can detect and quantify the burden and volume of atherosclerotic disease and precisely monitor its progression, thus identifying individuals who stand to benefit from earlier and more intensive prevention."

The 2019 European Prevention Guidelines recognize the utility of imaging techniques to evaluate cardiovascular risk in individuals beyond the conventional risk factors of age, sex, hypertension, cholesterol, smoking, and diabetes. "The recommended technique is low dose radiation CT, which evaluates the presence of calcium in the coronary arteries as an indirect measure of the presence of atherosclerotic plaques. But the guidelines also highlight the value of ultrasound to evaluate the burden of atherosclerosis in the carotid and femoral arteries."

The JACC article presents a 3-year follow-up study of the PESA cohort that makes the first direct comparison between these two imaging-based risk markers: coronary calcium by CT and atherosclerosis burden in the carotid and femoral arteries by 2D and 3D ultrasound. "The results show that ultrasound of the peripheral arteries is a more efficient method for detecting atherosclerosis progression than the study of coronary calcium by CT," said lead author Dr Beatriz López-Melgar.

Atherosclerosis is characterized by the accumulation of fatty deposits in the artery walls. The disease is normally detected at an advanced stage, when it has already caused clinical events such as a heart attack or stroke. Treatment of the disease at this symptomatic stage is of limited effectiveness, and most patients experience a decline in quality of life. The treatment of these patients, moreover, places a significant burden on health care resources.

"This study is the first to analyze the progression of atherosclerosis at frequent intervals. The previous view was that the disease progressed very slowly throughout life. However, the new results show that the disease progressed very rapidly in 40% of the individuals analyzed," said Dr Ibañez. "Future data from the PESA study will show whether this progression is associated with subsequent cardiovascular events. Until now, the speed of atherosclerosis progression has not been a factor in assessing individual risk."

A previous PESA analysis had already shown that atherosclerosis is generally present in young middle-aged individuals. "With the new study, we have shown how atherosclerosis progresses in its initial phases, before the development of symptoms," emphasized Dr Fuster.

"The key finding of the study is that over a short follow-up of just 3 years, 40% of individuals aged between 40 and 50 years showed major progression of atherosclerosis in distinct locations, including the carotid, femoral, and coronary arteries," emphasized Dr López-Melgar. "This rapid disease progression could make these individuals more vulnerable to developing symptoms or having clinical events such as a heart attack or stroke."
The researchers conclude that the findings, while they await validation from the occurrence of events in the PESA cohort in the future, will be of great value for the identification of strategies to stall the epidemic of cardiovascular disease.

Credit: 
Centro Nacional de Investigaciones Cardiovasculares Carlos III (F.S.P.)

A new antiviral drug heading into clinical trials offers hope for COVID-19 treatment

image: Dr. Timothy Sheahan in 2017 works in a lab at the UNC-Chapel Hill Gillings School of Global Public Health.

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Photo Courtesy of Mary Lide Parker

Scientists are hopeful that a new drug -- called EIDD-2801 -- could change the way doctors treat COVID-19. The drug shows promise in reducing lung damage, has finished testing in mice and will soon move to human clinical trials.

As of April 3, the novel coronavirus SARS-CoV-2 had infected more than 1 million people with COVID-19 and caused more than 58,000 deaths in a worldwide pandemic. Currently, no antiviral drugs have been approved to treat SARS-CoV-2 or any of the other coronaviruses that cause human disease.

Researchers at the UNC-Chapel Hill Gillings School of Global Public Health are playing a key role in the development and testing of EIDD-2801. Virologists in the lab of William R. Kenan Jr. Distinguished Professor of epidemiology Ralph Baric, are working with colleagues in the lab of Mark Denison, Edward Claiborne Stahlman Professor of pediatrics at Vanderbilt University Medical Center (VUMC), and with George Painter, chief executive officer of the nonprofit DRIVE (Drug Innovation Ventures at Emory) and director of the Emory Institute for Drug Development (EIDD), where EIDD-2801 was discovered.

The results of the team's most recent study were published online April 6 by the journal Science Translational Medicine. The paper includes data from cultured human lung cells infected with SARS-CoV-2, as well as mice infected with the related coronaviruses SARS-CoV and MERS-CoV.

The study found that, when used as a prophylactic, EIDD-2801 can prevent severe lung injury in infected mice. EIDD-2801 is an orally available form of the antiviral compound EIDD-1931; it can be taken as a pill and can be properly absorbed to travel to the lungs.

When given as a treatment 12 or 24 hours after infection has begun, EIDD-2801 can reduce the degree of lung damage and weight loss in mice. This window of opportunity is expected to be longer in humans, because the period between coronavirus disease onset and death is generally extended in humans compared to mice.

"This new drug not only has high potential for treating COVID-19 patients, but also appears effective for the treatment of other serious coronavirus infections," said senior author Baric.

Compared with other potential COVID-19 treatments that must be administered intravenously, EIDD-2801 can be delivered by mouth as a pill. In addition to ease of treatment, this offers a potential advantage for treating less-ill patients or for prophylaxis -- for example, in a nursing home where many people have been exposed but are not yet sick.

"We are amazed at the ability of EIDD-1931 and -2801 to inhibit all tested coronaviruses and the potential for oral treatment of COVID-19. This work shows the importance of ongoing National Institutes of Health (NIH) support for collaborative research to develop antivirals for all pandemic viruses, not just coronaviruses" said Andrea Pruijssers, the lead antiviral scientist in the Denison Lab at VUMC.

Denison was senior author of a December 2019 study that first reported that EIDD-1931 blocked the replication of a broad spectrum of coronaviruses.

These interinstitutional collaborators, supported by an NIH grant through the University of Alabama at Birmingham, also performed the preclinical development of remdesivir, another antiviral drug currently in clinical trials of patients with COVID-19. In the new Science Translational Medicine paper, Maria Agostini, a postdoctoral fellow in the Denison lab, demonstrated that viruses that show resistance to remdesivir experience higher inhibition from EIDD-1931.

"Viruses that carry remdesivir resistance mutations are actually more susceptible to EIDD-1931 and vice versa, suggesting that the two drugs could be combined for greater efficacy and to prevent the emergence of resistance," said Painter.

Clinical studies of EIDD-2801 in humans are expected to begin later this spring. If they are successful, the drug could not only be used to limit the spread of SARS-CoV-2, but also could control future outbreaks of other emerging coronaviruses.

"With three novel human coronaviruses emerging in the past 20 years, it is likely that we will continue to see more," said first author Timothy Sheahan, a Gillings assistant professor of epidemiology and a collaborator in the Baric Lab. "EIDD-2801 holds promise to not only treat COVID-19 patients today, but to treat new coronaviruses that may emerge in the future."

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University of North Carolina at Chapel Hill

Lifestyle trumps geography in determining makeup of gut microbiome

image: Kingo, a silverback Western lowland gorilla, is about 40 years old and lives in a remote area neighboring Nouabalé-Ndoki National Park in the Republic of Congo. Researchers from Washington University in St. Louis studied the gut microbiomes of wild apes in the Republic of Congo, of captive apes in zoos in the U.S., and of people from around the world and discovered that lifestyle is more important than geography or even species in determining the makeup of the gut microbiome.

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GOUALOUGO TRIANGLE APE PROJECT

Apes in U.S. zoos host bacterial communities in their intestinal tracts that are more similar to those of people who eat a non-Western diet than to the gut makeup of their wild ape cousins, according to a new study from Washington University in St. Louis. Further, even wild apes that have never encountered antibiotics harbor microbes with antibiotic resistance genes.

The findings suggest that contact with people shapes the gut microbial communities, or microbiomes, of gorillas and chimpanzees, and that the gut microbiomes of wild apes provide clues to human-ape interactions that could inform efforts to protect the endangered species. The study also highlights a way to identify new antibiotic resistance genes before they become widely established in bacteria in people, giving researchers time to develop tools to counter such genes before they threaten human health.

The study is available online in The ISME Journal.

The gut microbiome supplies us with vitamins, helps digest food, regulates inflammation and keeps disease-causing microbes in check. Antibiotics can change the makeup of the gut microbiome in lasting ways.

"It's difficult to figure out exactly how antibiotics affect the human gut microbiome when almost everyone is born with bugs that already have antibiotic resistance genes," said senior author Gautam Dantas, PhD, a professor of pathology and immunology, of molecular microbiology, and of biomedical engineering at Washington University School of Medicine. "Wild apes are the closest thing we have to pre-antibiotics humans. Luckily, we got the opportunity to work with two highly respected primatologists."

Co-authors Crickette Sanz, PhD, an associate professor of biological anthropology in Arts & Sciences at Washington University, and David Morgan, PhD, a research fellow at the Lester E. Fisher Center for the Study and Conservation of Apes at Lincoln Park Zoo in Chicago and an honorary research scientist at Washington University, study wild chimpanzees and gorillas in a remote area of Nouabalé-Ndoki National Park in the Republic of Congo. The park is managed by the Wildlife Conservation Society and the Congolese government. To learn about the apes' gut microbiomes, Sanz, Morgan and their field teams followed apes in known groups and discreetly collected fecal samples from 18 wild chimpanzees and 28 wild gorillas. The noninvasive sampling method allowed the researchers to collect data on the apes without disturbing them.

The samples were stored in liquid nitrogen, carried to the park headquarters, and transported by dugout canoe down the Sangha River and then by truck to Brazzaville, the capital of the Republic of Congo, where they were held in a freezer until they could be shipped to Dantas' lab. The researchers also collected and shipped fecal samples from 81 people who lived on the outskirts of the park.

Meanwhile, Dantas and first author Tayte Campbell, PhD - then a graduate student in Dantas' lab - arranged to obtain fecal samples from 18 chimpanzees and 15 gorillas living at either the Saint Louis Zoo or the Lincoln Park Zoo. The researchers identified the kinds of bacteria and the antibiotic genes present in the gorilla, chimpanzee and human samples, and compared the results to publicly available data on people who live in the U.S., Peru, El Salvador, Malawi, Tanzania, or Venezuela and follow hunter-gatherer, rural agriculturalist, or urban lifestyles.

The gut microbiomes of people whose data was included in the study fell into two groups. In one were hunter-gatherers and rural agriculturalists who typically eat a diet heavy in vegetables and light in meat and fat; this group included the people from the outskirts of the national park in the Republic of Congo. In the second group were urban people who eat a meat-rich Western diet. Wild gorillas and chimpanzees formed a third group distinct from both human groups. But captive apes fell into the first group; they were most similar to people who ate non-Western diets.

"Chimpanzees are endangered, and Western lowland gorillas are critically endangered; their main threats are habitat destruction, poaching and disease," Sanz said. "Measuring the gut microbiome could be a way to monitor apes' exposure to anthropogenic threats so we can identify areas of concern and develop effective, evidence-based mitigation strategies."

The researchers also identified several previously unknown antibiotic resistance genes in the wild apes and people from the Republic of Congo, including one that confers resistance to colistin, an antibiotic of last resort. For now, the genes reside in bacteria harmless to humans. But bacteria have the ability to share genes, so any antibiotic resistance gene could find its way into a more dangerous species of bacteria.

"Rare sampling opportunities of wild apes like in this study gives us a look into the future," Campbell said. "When we find these novel antibiotic resistance genes in the environment, we can study them and possibly find ways to inhibit them before they show up in human pathogens and make infections very difficult to treat."

"It would be very interesting to expand this research across a broader range of conservation contexts, such as commercial logging zones and tourist operations," Morgan added. "With the arrival of human activities and associated anthropogenic disturbances, wild apes may be exposed to antibiotic resistance genes. We don't know much about how antibiotic resistance spreads through natural environments, so that could have implications for human public health that we don't yet understand. That's something we'd like to investigate."

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Washington University School of Medicine

Potential therapy for rare neurologic disease

image: Xiaoyang Qi, PhD, professor in the Division of Hematology Oncology, UC Department of Internal Medicine,

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Colleen Kelley/ UC Creative + Brand

A targeted therapy, currently being studied for treatment of certain cancers including glioblastoma, may also be beneficial in treating other neurologic diseases, a study at the University of Cincinnati shows.

The study, being published online April 6 in the journal EBioMedicine, revealed that the effects of a therapy delivery system using microscopic components of a cell (nanovesicles) called SapC-DOPS may be able to provide targeted treatment without harming healthy cells. This method could even prove to be successful in treating other neurologic conditions, like Parkinson's disease.

This study is led by Xiaoyang Qi, professor in the Division of Hematology Oncology, UC Department of Internal Medicine, and Ying Sun, research professor in the UC Department of Pediatrics and a member of the Division of Human Genetics at Cincinnati Children's Hospital Medical Center.

One neurological challenge that may benefit from the therapy, Gaucher disease, is "a serious and rare genetic condition in which a type of lipid accumulates in cells and certain organs. The disorder can cause bruising, fatigue, anemia, low blood platelet count and enlargement of the liver and spleen, as well as poor coordination, seizures and cognitive problems in some patients; it is caused by a hereditary deficiency of a certain enzyme," says Qi, who is a corresponding author on the study. "Patients need enzyme replacement therapy to treat this condition, but a major limitation of FDA-approved enzyme replacement therapy is failure to cross the blood-brain barrier in the body. Therefore, the treatments available are only effective for patients who have Gaucher's affecting their internal organs, like their livers and spleens, but not their brain or nervous system.

"[Certain] nanovesicles have the ability to cross the blood-brain barrier and selectively target brain tissue, providing a biological vehicle for delivering the enzyme replacement therapy."

In the early 2000s, Qi developed SapC-DOPS, a combination of a cell protein, SapC, and a phospholipid, DOPS, that assembled into tiny cavities can selectively target cells and deliver therapies while sparing all other unaffected cells and tissues. In the past, he has studied that nanovesicle in cancer animal models looking at brain, lung, skin, prostate, blood, breast and pancreatic cancers. Results were promising, and now the human version of this nanovesicle is now being studied in clinical trials for treatment of glioblastoma.

This study shows its penetration into the brain is through a specific receptor and the lymphatic circulation system, which helps rid the body of toxins and waste.

"In this study, we showed that the nanovesicle was able to deliver the enzyme to the necessary tissues in animal models, especially the brain," Sun says. "This novel therapeutic approach corrects the deficiency of the enzyme in central nervous system cells and tissues and is efficient in reducing inflammation and neurological issues in animal models with [some types of] Gaucher disease."

"Our study presents a new targeted use for our nanovesicle and provides a new strategy for treating this type of Gaucher disease," Qi adds. "This is the tip of the iceberg when thinking about applications and it could mean promising treatments for other neurologic conditions.

"Although this study was focused on a rare disease, there may be implications for similar but vastly more common conditions such as Parkinson's disease where decreased activity of the same enzyme have been documented in the patients' brains. Without improvements in treatment, this type of Gaucher disease will remain lethal. This has the potential to improve patient care."

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University of Cincinnati

Which healthy lifestyle factors associated with more years free of chronic disease?

What The Study Did: What combination of healthy lifestyle factors were associated with the most years lived without chronic diseases was the focus of this analysis that included data from more than 100,000 adults who were participants in 12 European studies. Participants' levels of smoking, weight, physical activity and alcohol consumption were compared with the number of years from age 40 to 75 that they were without chronic disease, including type 2 diabetes, coronary heart disease, stroke, cancer, asthma and chronic obstructive pulmonary disease.

Authors: Solja T. Nyberg, Ph.D., of the University of Helsinki, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamainternmed.2020.0618)

Editor's Note: The article includes conflict of interest and funding/support disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, conflicts of interest and financial disclosures, and funding and support.

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JAMA Network

Changes in marijuana vaping, edible use among US 12th-graders

What The Study Did: About 2,400 students in the 12th grade were surveyed about the frequency and mode of use (smoking, vaping and edibles) of marijuana from 2015 to 2018.

Authors: Megan E. Patrick, Ph.D., of the University of Minnesota in Minneapolis, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamapediatrics.2020.0175)

Editor's Note: The article includes conflict of interest and funding/support disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, conflicts of interest and financial disclosures, and funding and support.

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JAMA Network

Bedroom air filters help asthmatic children breathe easier

DURHAM, N.C. - Using a bedroom air filter that traps fine particles of pollution with diameters smaller than 2.5 micrometers can significantly improve breathing in asthmatic children, a new study by American and Chinese scientists shows.

It's the first study to document that physiological improvements occur in the childrens' airways when air filters are in use, and it suggests that with consistent use, the filters may help prevent, not just alleviate, asthmatic flare-ups.

While using the filters daily for two weeks, children in the study experienced decreased airway resistance and lung inflammation and increased airway elasticity, among other benefits.

"Pharmaceutical companies have spent large amounts to develop drugs that can work on lower airways, but they are very expensive. Our results show that using an air purifier to reduce the exposure of lower airways to pollutants could help asthmatic children breathe easier without those costly drugs," said Junfeng Zhang, professor of global and environmental health at Duke University's Nicholas School of the Environment.

"This warrants a clinical trial to confirm findings," he said. Zhang and his colleagues published their paper April 6 in JAMA Pediatrics, a journal of the American Medical Association.

Fine particulate matter (PM2.5) is a ubiquitous air pollutant originating from fossil fuel emissions, wildfires and other biomass burning, industrial sources, and gasoline- and diesel-powered vehicles. Thirty times smaller in diameter than a human hair, the particles are easily inhaled and can penetrate deep into the small, or lower, airways where they can trigger or exacerbate asthma symptoms. Inhalers don't help, since they are only designed to open upper airways.

The researchers conducted the double-blind crossover study in a Shanghai suburb during a period of moderately high PM2.5 pollution in 2017. They gave 43 children with mild to moderate asthma two air filters to use in their bedrooms. One was a high-efficiency particulate air (HEPA) filter capable of removing PM2.5; the other was a sham filter. Each filter was used for two weeks in random order with a two-week interval in between. Neither the children nor their families knew which filter was which.

Results showed that PM2.5 concentrations inside the children's bedrooms were a third to two-thirds lower when the real air filters were in use than when the sham ones were being used, said Michael H. Bergin, professor of civil and environmental engineering at Duke's Pratt School of Engineering.

This drop coincided with significant improvements in how easily air flowed in and out of the children's small airways and lungs, Bergin said. These improvements included a 24% average reduction in total airway resistance, a 43.5% average reduction in small airway resistance, a 73.1% average increase in airway elasticity, and a 27.6% average reduction in exhaled nitric oxide, a biomarker of lung inflammation.

Although the benefits lasted only as long as the real air filters were in use, "it's probable that if children use the filters on an ongoing daily basis they will see continued benefits," Zhang said.

If clinical trials confirm the new study's findings, the filters could serve as a practical preventive measure for asthma management in polluted outdoor or indoor environments worldwide, he said.

They could also be lifesavers in areas near wildfires.

"Look at the high PM2.5 pollution levels that occurred in San Francisco last year as a result of smoke from the California wildfires, and at the air-quality problems happening this year from the bushfires in Australia," he said. "People should really consider using one of these devices during wildfires."

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Duke University

RIKEN group leads world in single-cell transcriptome profiling

With the goal of ensuring that single-cell RNA sequencing, a current focus of intense research, makes use of the best possible methods, an international group has benchmarked 13 different methods. The group, led by Holger Heyn of the Centro Nacional de Análisis Genómico (CNAG-CRG) in Spain, found that the Quartz-seq2 method, developed by a team in the RIKEN Center for Biosystems Dynamics Research, was overall the best method developed to sequence single-cell RNA. The research was published in Nature Biotechnology.

The group began the project based on the concern that in the past, lack of benchmarking on methods used for genomic analysis has given rise to problems later in the process, as different groups were using different methods that had varying standards and came up with different results. With this in mind, a number of groups working on the analysis of single cell RNA came together to evaluate different methods to ensure that there is good reproducibility.

Single-cell DNA sequencing is seen as the next major project in genomic research. Initially, genomic research, exemplified by the Human Genome Project, sought to determine the DNA sequence that is found in all the cells in any organism. But what makes things complicated is that although the cells in an organism share the same DNA code, in fact the cells are all phenotypically different because different genes are expressed or not expressed based on epigenetic factors. There are enormous differences in the expression of genetic regions known as promoters and enhancers, which do not code proteins directly but act on other genetic regions. Understanding the genetic makeup of individual cells would make it possible to identify how individual cells differ in conditions such as cancer and how cells change during the development process. Currently, researchers participating in the Human Cell Atlas are working to develop a comprehensive atlas of gene expression in different cell types.

To make the comparison, the group used the 13 methods to analyze a set of approximately 3,000 cells selected to fulfill four conditions: it included a variety of cell types, some of the cells were very similar, with only subtle differences in gene expression, the cells had trackable markers, and they included cells from different species. The cells were mostly human peripheral blood cells and mouse colon cells, but also included a small set of dog cells.

The methods were evaluated based on how precisely they could detect cell profiles and marker expression. The group evaluated the methods using six key metrics: gene detection, overall level of expression in transcriptional signatures, cluster accuracy, classification probability, cluster accuracy after integration, and mixability. These metrics were selected to compare the methods in terms of their accuracy, applicability to various cell types, ability to distinguish between closely related cell types, ability to produce reproducible profiles, ability to detect population markers, compatibility with other methods, and have good predictive value for cell mapping.

As a result, they found that the Quartz-seq2 method, developed by researchers at RIKEN in Japan, was particularly accurate, scoring highest on the benchmark. According to Itoshi Nikaido, leader of the group that developed the method, "We were very happy that our method was selected as overall best, and plan to further improve it so that we can achieve the best results in projects such as the Human Atlas Project."

According to Dr. Heyn, "The protocols showed profound performance differences and we hope that our work contributes to developing standards and guidelines towards the production of high-quality datasets for the Human Cell Atlas and broader single-cell community."

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RIKEN

Nanopore reveals shape-shifting enzyme linked to catalysis

image: Energy diagram of the four conformers (left) and the experimental setup showing the nanopore with the trapped enzyme in cross section (right). Underneath, there is a typical trace showing measurements during exchange within rotamers.

Image: 
Giovanni Maglia, University of Groningen

University of Groningen scientists observed the characteristics of a single enzyme inside a nanopore. This revealed that the enzyme can exist in four different folded states, or conformers, that play an active role in the reaction mechanism. These results will have consequences for enzyme engineering and the development of inhibitors. The study was published in Nature Chemistry on 6 April.

Enzymes are folded proteins that have a specific three-dimensional structure that creates an active site that can bind a substrate and catalyse a specific reaction. In recent years, it has become clear that enzymes are not rigid structures but that the folded proteins exist as an ensemble of conformations in equilibrium around an energetically stable ground state.

Wind tunnel

Studying the transition between states requires observing single enzymes for a prolonged period of time, which is challenging. University of Groningen Associate Professor of Chemical Biology Giovanni Maglia developed funnel-shaped nanopores that can trap proteins. By measuring the ionic current across such a nanopore, embedded in an artificial lipid membrane, Maglia was able to observe conformational changes in enzymes. 'You could compare it with studying a car in a wind tunnel,' he explains. 'Opening a window or a door will change the airflow. In a similar way, a change in the folding structure of the enzyme changes the ionic current through the pore.'

Maglia used his nanopore system to study the enzyme dihydrofolate reductase (DHFR), which converts dihydrofolate into tetrahydrofolate. 'We chose this enzyme because it has been studied as a model system for enzyme dynamics for over thirty years, using all available techniques. In addition, inhibitors of this enzyme, such as methotrexate, are used as anti-cancer drugs.

Efficient release

Measurements of DHFR revealed the presence of four different conformers, with different affinities for the substrates. Maglia: 'Switching between these four states was very slow. This means that you can only see them in these kinds of long-lasting single enzyme studies.'

Adding the reaction inhibitor methotrexate, which binds to the enzyme, caused a very rapid transition between states and changed the enzymes' affinity. 'Our conclusion is that the reactions of the enzyme with different compounds provide the free energy for conformational changes,' says Maglia. Furthermore, conformational change also changed the enzymes' affinity. This makes sense, as the enzyme needs to bind two substrates and, after completing the reaction, must release both. 'The substrate and the product are very similar molecules, so the enzyme needs to change its affinity for an efficient release.'

Two states

Based on these studies, Maglia can see the enzyme switching between two states: after binding the substrate, NADPH drives the reaction which then changes the conformation of the enzyme and thereby its affinity. Subsequently, binding a new substrate brings it back to the first state. 'This explains two of the four conformers that we observed; we cannot yet make sense of the other two,' Maglia admits. It is impossible to derive structural information from the measurements.

Nevertheless, the study shows the power of nanopore technology in determining the structural changes of enzymes. 'We also now know that this enzyme has four different ground states and must switch between them to function.' This adds a challenge to enzyme design: not only should this produce a reactive centre, but it should also allow the necessary conformational changes. Maglia: 'This may explain why artificially designed enzymes often do not work as efficiently as natural enzymes.' Finally, the study will also allow scientists to identify new inhibiting drugs that bind tighter to DHFR than methotrexate.

Credit: 
University of Groningen

Breakthrough in unlocking genetic potential of ocean microbes

image: Polar ice-floes contain some of the most important ocean photosynthetic microbes on the planet.

Image: 
James Raymond

Researchers have made a major breakthrough in developing gene-editing tools to improve our understanding of one of the most important ocean microbes on the planet.

The international project, co-led by scientists at the University of East Anglia (UEA) in the UK, unlocks the potential of the largest untapped genetic resource for the development of natural products such as novel antibacterial, antiviral, anti-parasitic and antifungal compounds.

Ocean microbes regulate global cycles of carbon and essential nutrients such as nitrogen and phosphorous. Despite their significance, government and industry funding is still largely used for research and development with non-marine organisms. This is partly due to a lack of awareness of the importance of marine microbes, limited understanding about their biology, as well as difficulties in accessing and sustainably exploiting them.

Addressing this requires genetic manipulation tools that have not been readily available for many different ecologically and biotechnologically important groups of marine microbes such as protists, which share a subcellular organisation similar to plants and animals.

Unlike plants and animals, they are unicellular and of remarkable diversity. Some represent the origins of complex life forms on land, others such as photosynthetic protists, called phytoplankton, contribute almost as much to global annual carbon fixation as land plants.

Published in the journal Nature Methods, this new study aims to improve understanding of the basic biology and evolution of marine protists, with potentially valuable outcomes for evolutionary studies, nanotechnology, biotechnology, medicine, and pharmacology.

The three-year collaborative project, supported primarily by the Gordon and Betty Moore Foundation, involved 53 international laboratories comprising more than 100 researchers. It has resulted in the development of new genetic model systems, summarised in a synthetic 'Transformation Roadmap'. This outlines DNA delivery methods, gene expression constructs and genome editing approaches, and is available as a resource for the wider research community.

Lead UK author Thomas Mock, professor of marine microbiology at UEA's School of Environmental Sciences, said the study builds on decades of research that have contributed to an increasingly coherent picture of the oceanic ecosystem.

"The oceans harbour the most significant microbial diversity on Earth in terms of maintaining habitability," said Prof Mock. "These organisms and how their genes function are therefore incredibly important to understand because of their vital role in the health of the planet. They also represent how life has evolved over the last 1.5 billion years. They are so old that it's not been possible to fully understand their cell biology and functional biodiversity.

"Our reported breakthroughs on genetic manipulation will allow the research community to dissect cellular mechanisms from a range of important protists, which will collectively provide insights into their reproduction, metabolism and signaling.

"These insights will improve our understanding about their role in the oceans, and they are invaluable for biotechnological applications such as building factories for biofuel or the production of bioactive compounds."

The study involved attempting to introduce foreign DNA into the host genomes of 39 protist species, in order to understand their gene functions and how they adapt to changes. Of these, more than 50% were genetically manipulated successfully, which will now enable researchers to carry out functional studies of thousands of new genes carried in their genomes.

Credit: 
University of East Anglia

Neuroscientists find memory cells that help us interpret new situations

CAMBRIDGE, MA -- Imagine you are meeting a friend for dinner at a new restaurant. You may try dishes you haven't had before, and your surroundings will be completely new to you. However, your brain knows that you have had similar experiences -- perusing a menu, ordering appetizers, and splurging on dessert are all things that you have probably done when dining out.

MIT neuroscientists have now identified populations of cells that encode each of these distinctive segments of an overall experience. These chunks of memory, stored in the hippocampus, are activated whenever a similar type of experience takes place, and are distinct from the neural code that stores detailed memories of a specific location.

The researchers believe that this kind of "event code," which they discovered in a study of mice, may help the brain interpret novel situations and learn new information by using the same cells to represent similar experiences.

"When you encounter something new, there are some really new and notable stimuli, but you already know quite a bit about that particular experience, because it's a similar kind of experience to what you have already had before," says Susumu Tonegawa, a professor of biology and neuroscience at the RIKEN-MIT Laboratory of Neural Circuit Genetics at MIT's Picower Institute for Learning and Memory.

Tonegawa is the senior author of the study, which appears today in Nature Neuroscience. Chen Sun, an MIT graduate student, is the lead author of the paper. New York University graduate student Wannan Yang and Picower Institute technical associate Jared Martin are also authors of the paper.

Encoding abstraction

It is well-established that certain cells in the brain's hippocampus are specialized to store memories of specific locations. Research in mice has shown that within the hippocampus, neurons called place cells fire when the animals are in a specific location, or even if they are dreaming about that location.

In the new study, the MIT team wanted to investigate whether the hippocampus also stores representations of more abstract elements of a memory. That is, instead of firing whenever you enter a particular restaurant, such cells might encode "dessert," no matter where you're eating it.

To test this hypothesis, the researchers measured activity in neurons of the CA1 region of the mouse hippocampus as the mice repeatedly ran a four-lap maze. At the end of every fourth lap, the mice were given a reward. As expected, the researchers found place cells that lit up when the mice reached certain points along the track. However, the researchers also found sets of cells that were active during one of the four laps, but not the others. About 30 percent of the neurons in CA1 appeared to be involved in creating this "event code."

"This gave us the initial inkling that besides a code for space, cells in the hippocampus also care about this discrete chunk of experience called lap 1, or this discrete chunk of experience called lap 2, or lap 3, or lap 4," Sun says.

To further explore this idea, the researchers trained mice to run a square maze on day 1 and then a circular maze on day 2, in which they also received a reward after every fourth lap. They found that the place cells changed their activity, reflecting the new environment. However, the same sets of lap-specific cells were activated during each of the four laps, regardless of the shape of the track. The lap-encoding cells' activity also remained consistent when laps were randomly shortened or lengthened.

"Even in the new spatial locations, cells still maintain their coding for the lap number, suggesting that cells that were coding for a square lap 1 have now been transferred to code for a circular lap 1," Sun says.

The researchers also showed that if they used optogenetics to inhibit sensory input from a part of the brain called the medial entorhinal cortex (MEC), lap-encoding did not occur. They are now investigating what kind of input the MEC region provides to help the hippocampus create memories consisting of chunks of an experience.

Two distinct codes

These findings suggest that, indeed, every time you eat dinner, similar memory cells are activated, no matter where or what you're eating. The researchers theorize that the hippocampus contains "two mutually and independently manipulatable codes," Sun says. One encodes continuous changes in location, time, and sensory input, while the other organizes an overall experience into smaller chunks that fit into known categories such as appetizer and dessert.

"We believe that both types of hippocampal codes are useful, and both are important," Tonegawa says. "If we want to remember all the details of what happened in a specific experience, moment-to-moment changes that occurred, then the continuous monitoring is effective. But on the other hand, when we have a longer experience, if you put it into chunks, and remember the abstract order of the abstract chunks, that's more effective than monitoring this long process of continuous changes."

Tonegawa and Sun believe that networks of cells that encode chunks of experiences may also be useful for a type of learning called transfer learning, which allows you to apply knowledge you already have to help you interpret new experiences or learn new things. Tonegawa's lab is now working on trying to find cell populations that might encode these specific pieces of knowledge.

Credit: 
Massachusetts Institute of Technology

Alport syndrome severity can be predicted by causative protein genotype

image: Evaluation of mutant type IV collagen α5 gene with different severity levels and correspondence of severity levels by using split NanoLuc® cell-based type IV collagen trimer evaluation system.

Image: 
Assoc. Prof. Tsuyoshi Shuto

A Japanese research team has successfully developed a system to predict the severity of Alport syndrome, a serious hereditary kidney disease that occurs in about 1 out of 5,000 people in the US. Patients with Alport syndrome have abnormalities in the causative protein, type IV collagen, that often lead to chronic renal dysfunction requiring dialysis. Without a kidney transplant, this can eventually lead to kidney failure and death.

Estimating the severity of the disease has been difficult but researchers from Kumamoto University, in collaboration with Kobe University researchers, recently demonstrated that severity prediction can be made by analyzing a person's type IV collagen genotype. The researchers discovered this after studying the behavior of several genetic mutations using a proprietary type IV collagen trimer evaluation system that can predict the severity of nephropathy in Alport syndrome patients. They expect their development will contribute to the advancement of precision medicine for hereditary intractable diseases.

Type IV collagen forms a complex of three polypeptide chains (a trimer of fibrous proteins). Mutations in any of the chain genes cause abnormalities in the polypeptide chains, resulting in renal dysfunction. Several hundred mutations of type IV collagen have been reported so far and the severity of the disease varies depending on the mutation. Identification of these mutations is important to predict the severity of renal pathology.

This study uses a system (Split NanoLuc®) developed by Professor Hirofumi Kai of Kumamoto University that is highly sensitive to abnormalities of type IV collagen trimers. Prof. Kai's group evaluated the intracellular trimer formation and extracellular trimer secretion of nine (four severe, four mild, one non-pathogenic) type IV collagen gene mutants. Severe mutations significantly reduced the formation and secretion of collagen IV trimers. Additionally, most of the mild mutations produced only a slight reduction of the extracellular secretory trimer. This shows that nephropathy severity is mostly determined by the ability of type IV collagen trimers to form intracellularly and secrete extracellularly. Furthermore, the non-pathogenic mutant collagen did not show any changes in trimer behavior.

These results demonstrate that it is possible to distinguish between pathogenic and non-pathogenic mutations with the Split NanoLuc® evaluation system. This can provide important data for estimating the pathological severity and identification of pathogenic mutations. In particular, it allows for the construction of a system to predict the severity of nephropathy using only the gene mutation information in Alport syndrome patients.

"The remarkable progress of genome analysis technology in recent years has enabled comprehensive analysis of disease-related genes. The momentum of precision medicine based on genetic information is increasing for various diseases," said Associate Professor Tsuyoshi Shuto, who co-authored this study. "In the field of hereditary kidney disease, large-scale genetic analysis has become widespread. Accurate diagnoses and new disease classifications through identification of causative gene mutations are being diligently conducted. We expect that this research will greatly advance the field of precision medicine for various hereditary diseases as well as Alport syndrome."

Credit: 
Kumamoto University

The human body as an electrical conductor, a new method of wireless power transfer

image: Image credits: BERG-UPF

Image: 
BERG-UPF

The project Electronic AXONs: wireless microstimulators based on electronic rectification of epidermically applied currents (eAXON, 2017-2022), funded by a European Research Council (ERC) Consolidator Grant awarded to Antoni Ivorra, head of the Biomedical Electronics Research Group (BERG) of the Department of Information and Communication Technologies (DTIC) at UPF principally aims to "develop very thin, flexible, injectable microstimulators to restore movement in paralysis", says Ivorra, principal investigator of the project.

A secondary goal of this project is to illustrate how volume conduction (also known as galvanic coupling) can be used to transfer power wirelessly to electronic implants. Volume conduction is considered an alternative to batteries or wireless power transfer based on inductive coupling since these two supply methods imply that implants must be relatively large to accommodate the components needed to obtain the energy required for operation.

One of the main parameters of interest to know if a technology has the potential to supply implants is to determine the maximum power implants can receive by using the proposed method. Thus, the main goal of the study published in the journal IEEE Access is to use equations to determine the maximum power an implant can receive by means of volume conduction when the currents applied are safe according to the electrical safety standards. Its authors are Marc Tudela, Laura Becerra-Fajardo, Aracelys García-Moreno, Jesus Minguillon and Antoni Ivorra.

"Today, the main element that hinders the development of minimally invasive implants is the way they get power. In this regard, we believe that volume conduction has the potential to solve this problem. Volume conduction allows us to develop thread-like devices that can be implanted by injection", Tudela explains.

Wireless Power Transfer (WPT)

The method of wireless energy transfer via volume conduction consists of using the body's own tissues as a channel for transferring electrical power. Using an external system, electrical currents are delivered through the human body and these currents flow through tissues and a small amount is drawn by the implants.

This is how the implants get the energy necessary for operating. The innovative aspect of the authors' approach is the thread-like form of the implants, which allows them to be injected without surgery, and the use of high frequency currents (> 5 MHz) applied in bursts, rendering them completely harmless and imperceptible.

To produce power to implants in the region of milliwatts, the authors propose applying currents with magnitudes of the order of a few amperes for which the external system must generate tensions of around a few hundred volts. These magnitudes would be most harmful if it they corresponded to alternating currents of a frequency like that of the grid (50 Hz). This completely avoids using higher frequencies. Specifically, the authors propose the use of alternating currents with a frequency of greater than 5 MHz.

The authors of the study published in IEEE Access obtained mathematical models that allowed them to determine the maximum local power that can be obtained by an implant using volume conduction according to the size of the implant, its electronic charge and the properties of the tissue where it will be placed. Finally, they validated these models in vitro using a saline solution that simulates the electrical properties of human tissue and obtained a good correlation between experimental and analytical results.

Devices that can be easily implanted by injection

Thus, the study results show that by applying high frequency electrical currents in a burst -harmless for the human body and that meet the main international safety standards- can yield powers of greater than 1 mW in very thin (section less than 1 mm), short (

"Another interesting result we have obtained is that the application of high frequency electrical currents in the form of bursts, rather than continuously, enables maximizing the power obtained in the implants", Tudela comments. And the researcher adds, "our results indicate that an implant with a section of only one millimetre and a length of about one centimetre could get 100 times the power currently required by a pacemaker".

Credit: 
Universitat Pompeu Fabra - Barcelona

New algorithm aims to protect surgical team members against infection with COVID-19 virus

image: Precautions for Operating Room Team Members during the COVID-19 Pandemic

Image: 
American College of Surgeons

CHICAGO (April 6, 2020): Researchers from Stanford University's department of surgery (Stanford, Calif.) have created an algorithm that aims to protect operating room team members who perform urgent and emergency operations from Coronavirus Disease 2019 (COVID-19) and rationally conserve the personal protective equipment (PPE) they wear. This best practice guideline is published as an "article in press" on the Journal of the American College of Surgeons website ahead of print. Stanford Health Care, verified as a Level 1 trauma center by the American College of Surgeons (ACS), serves Santa Clara and San Mateo Counties, which saw their first cases of COVID-19 infection in early March.

The Stanford algorithm is based on the urgency of the procedure, potential for aerosolization and release of virus droplets at the surgical site, and evidence that a patient has been infected. The algorithm aligns with the goals of the ACS Statement on PPE Shortages during the COVID-19 Pandemic, released April 1, 2020.

"We developed institutional guidelines based on how soon the surgical cases needed to be performed, the patient's condition, the risk that a surgeon would access an area of body where the amount of virus could be high, and the risk that a patient could be infected with COVID-19," said Joseph Forrester, MD, MSc, an assistant professor in general surgery and lead author of the algorithm article. Dr. Forrester was a field agent in Liberia during the 2014 Ebola outbreak where he conducted several investigations of the Ebola burden and preparedness as an Epidemic Intelligence Service officer with the Centers for Disease Control and Prevention.

At Stanford, a PPE task force of hospital and medical school leaders from interventional suites, including the operating room, interventional radiology, and endoscopy, as well as quality improvement and infectious disease experts, convened on March 19 to create institutional guidelines that could be implemented within 72 hours. At that time, Stanford Health Care had approximately 10 patients infected with COVID-19. Guidelines incorporated current data about COVID-19 transmission in hospital and non-hospital settings and operating room risk during outbreaks of severe acute respiratory syndrome (SARS) and Ebola.

Patients were triaged by severity of illness into urgent and emergency procedures. Urgent cases were stratified into high- and low-risk procedures depending on the expected viral burden at the surgical site. Procedures categorized as aerosol-generating (AGP) were classified as high-risk. These procedures include those that involve the aerodigestive tract, endoscopy, and open or laparoscopic surgery on the bowel with gross contamination.

The Stanford guideline assumes, above all, that any patient could be infected with COVID-19 unless proven otherwise by a negative RT-PCR test. When operating on COVID-19-postive patients or performing an AGP, the guideline requires operating room team members to be fitted with an N-95 respirator mask and wear a gown, gloves, and eye protection. Only when an RT-PCR test is negative for COVID-19 may surgical team members wear standard surgical clothing.

A surgeon may consider delaying an urgent or emergency procedure on a patient who exhibits viral symptoms (fever, cough, sore throat). If delay compromises the well-being of the patient, the surgeon orders in-house RT-PCR COVID-19 testing with a 24-hour turnaround. If the patient's status does not allow for a 24-hour wait, the case is considered to be an emergency and the patient is presumed to be COVID-19-positive.

Special considerations are made for the use of PPE during and after bag mask ventilation and endotracheal intubation, which both pose a high risk for viral transmission. All health care providers who are not directly involved with intubation are asked to leave the operating room beforehand. Anesthesiologists should be fitted with N-95 face masks and droplet-protective PPE because they are positioned at the head of the bed throughout the procedure. Cleaning staff should take droplet precautions when cleaning any operating room.

At the time the guideline was created at Stanford Health there was a nationwide shortage of N-95 face masks. To conserve the institution's supply, the algorithm requires a face shield to be placed over the mask. However, the federal government recently announced that millions of face masks, face shields, surgical masks, gloves, and gowns were entering the medical supply chain, which was encouraging, noted Dr. Forrester.

Dr. Forrester nevertheless recommends that surgical centers where urgent and emergency procedures are performed follow strategies that protect providers and conserve equipment. "You never know what's going to happen, and it's better to be prepared and use the right PPE at the right time and be careful not to waste PPE. Guidelines like ours show that health care providers on the frontline are trying to take care of every person with a serious surgical condition and make sure they have enough equipment to carry that mission through safely."

Credit: 
American College of Surgeons

Invasive species with charisma have it easier

image: Proposed control measures for introduced eastern grey squirrel (Sciurus carolinensis) populations in Italy were delayed and made ineffective by strong public opposition.

Image: 
Jonathan Jeschke

It's the outside that counts: Their charisma has an impact on the introduction and image of alien species and can even hinder their control. An international research team, led by the Biology Centre of the Czech Academy of Sciences and the Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), have investigated the influence of charisma on the management of invasive species.

More and more animals and plants are being taken from their habitat by humans - consciously and unconsciously. Many cannot adapt to the new living conditions, but some are becoming firmly established. "Some non-native species cause serious problems for native species - as predators, competitors for food and habitat, or vectors of diseases," explains Professor Jonathan Jeschke, researcher at IGB and Freie Universität Berlin, and head of the Invasion Dynamics Network which initiated the study.

As ornamental plants, aquarium inhabitants or exotic pets, charismatic species are probably more likely to be deliberately introduced than inconspicuous species. And "if a non-native species is introduced more frequently and in higher numbers, it is more likely to establish itself," says Jonathan Jeschke.

The social acceptance of attractive invasive species with charisma is higher than that of unattractive invasive species. This can hamper nature conservation measures designed to contain the spread of a species: "An appearance perceived as beautiful or cute can make the management of species invasions more difficult, because then public support is often lacking," regrets Ivan Jaric, lead author of the study and researcher at the Biology Centre of the Czech Academy of Sciences. For example, management actions in Italy to control the invasive grey squirrel - and to protect the native red squirrel - were prevented by protests from interest groups using cute cartoon characters of the animals.

Even research is taxonomically biased

The research priorities on invasive species are largely determined by their ecological and economic impacts. And yet there is a stronger focus on invasive vertebrates than on invertebrates and on large and charismatic species. "Public and also research interest is disproportionately concentrated on charismatic species. This can cause one-sided gaps in knowledge that lead to protective measures being wrongly prioritised," criticises IGB researcher Dr. Gregor Kalinkat, co-author of the study.

It is therefore important to be aware of the influence of charisma on the management of invasive species and to sensitise actors." This aspect is particularly important when planning and implementing management measures. Conflicts, especially when they affect charismatic species, can arise from the apparent incompatibility of two different ethical perspectives: between those who give priority to the protection of the ecosystem or the conservation of native species and those who are concerned about the welfare of the invasive species concerned," Ivan Jaric underlines the importance of the findings.

Credit: 
Forschungsverbund Berlin