NIST Develops Genetic Material for Validating Monkeypox Tests

A vial of the positive control material from NIST that can be used to help ensure the accuracy of tests for monkeypox.   
Credit: R. Press/NIST

In an effort to help speed the expansion of monkeypox testing in the U.S., the National Institute of Standards and Technology (NIST) has produced a material that can help ensure the accuracy of tests for the disease. NIST is making the material, which contains gene fragments from the virus that causes the disease but is noninfectious and safe to handle, freely available for use by test manufacturers and testing laboratories.

Monkeypox is spread by close contact and can cause fever, flu-like symptoms and skin lesions. More than 3,500 cases of monkeypox have been confirmed in the United States since the outbreak began in late May, and the World Health Organization has declared monkeypox to be a global health emergency.

Testing is necessary to identify the extent of an outbreak and contain it, and to properly care for people who have caught the disease and those who may have been exposed. The monkeypox test, like the most sensitive test for COVID-19, uses a technique called polymerase chain reaction, or PCR, to detect genetic sequences from the virus that causes the disease.

Because the material from NIST contains those genetic sequences, laboratories can use it as a positive control — that is, a sample that should cause a positive result if their test is working properly. As the U.S. Centers for Disease Control and Prevention (CDC) works to expand the nation’s testing capacity, the material from NIST will fill a growing need.

A Souped-Up Gene Promoter Stops Heat from Sapping Plant Defenses

The immune system of plants relies on the hormone salicylic acid, which helps fine-tune their defenses against infections and insect infestations. But at warm temperatures, plants turn off their salicylic acid production. New research from HHMI Investigators reveals why and uses genetic engineering to boost immune function during warm spells.
Credit: Lesley Warren Design Group, ON, Canada

Plants’ immune defenses falter during heat waves, rendering them more vulnerable to insects and pathogens under climate change. HHMI scientists have now figured out why high temperatures knock out a key defense system and they’ve come up with a strategy that bolsters plant immunity.

Plants feeling the heat face risks beyond wilting. During heat waves, plants’ defenses falter, rendering them more vulnerable to infection and infestation. This is especially worrisome as climate change is making heat waves more frequent and intense.

Sheng Yang He
Duke University
Plant Sciences Microbiology

“Plants actually have a very powerful innate immune system that explains why they’ve survived so long on Earth,” says plant scientist Sheng Yang He, who is a Howard Hughes Medical Institute (HHMI) Investigator at Duke University. “But now we know that this immune system may not function so well in a hot climate, especially for many cool-weather crops. Continued warming of the climate may exacerbate this reduction of innate immunity and increase diseases and insect infestations in the future.”

He’s team has unearthed new clues to why heat saps plants’ immunity. That allowed them to find a genetic solution to keep a key plant defense system online during warm spells, the researchers report June 29, 2022, in Nature.

Plants’ immune function requires the hormone salicylic acid, which helps coordinate which defenses plants raise or lower. But sweltering plants throttle back on their production of salicylic acid, and researchers haven’t known why.

Home Sweet Home: A Study of the ‘Chemical Soup’ in our Houses

Chances are very good that as you read this, you are seated somewhere indoors. The surfaces around you are covered in microbes and you are also covered in microbes. All those microbes are busy excreting molecules and responding to the rest of the molecules in the mix. What does all of this mean for your health?

“We are living in a soup of chemistry,” says UConn Department of Chemistry researcher Alexander Aksenov, who is working to understand this microbial and molecular soup in our indoor environments and how it could be impacting our health. He and a multidisciplinary team of researchers, including from the University of California, San Diego, Colorado State University, and the University of Colorado published a paper today in Science Advances exploring these under-studied questions, with some surprising findings that could help inform us how to live healthier lives indoors.

Accounting for our full day, including time spent in cars, on average we spend over 90% of our time indoors, says Aksenov, so the indoor environment is by far the most important for us.

Previous studies show human activities impact our indoor environments, through things like gas stoves, chemical off-gassing, and the type of cleaning solutions we use. These studies usually looked at a limited number of molecules. For this study, the researchers sought to explore the full suite of molecules and microbes within a household environment.

How bacteria adhere to cells: Basis for the development of a new class of antibiotics

Adhesion of Bartonella henselae (blue) to human blood vessel cells (red). The bacterium's adhesion to the host cells could be blocked with the help of what are known as “anti-ligands".
Credit: Goethe University

Researchers from University Hospital Frankfurt and Goethe University Frankfurt have unraveled how bacteria adhere to host cells and thus taken the first step towards developing a new class of antibiotics.

The adhesion of bacteria to host cells is always the first and one of the decisive steps in the development of infectious diseases. The purpose of this adhesion by infectious pathogens is first to colonize the host organism (i.e., the human body), and then to trigger an infection, which in the worst case can end fatally. Precise understanding of the bacteria's adhesion to host cells is a key to finding therapeutic alternatives that block this critical interaction in the earliest possible stage of an infection.

COVID-19 Fattens Up Our Body’s Cells to Fuel Its Viral Takeover

Illustration of a SARS-CoV-2 viral particle entering a cell. The particle pierces through a cell’s membrane, made of two layers of lipids.  A PNNL-OHSU team has shown how lipids are key to the ability of the virus to replicate.
Credit: Illustration by Michael Perkins | Pacific Northwest National Laboratory

The virus that causes COVID-19 undertakes a massive takeover of the body’s fat-processing system, creating cellular storehouses of fat that empower the virus to hijack the body’s molecular machinery and cause disease.

After scientists discovered the important role of fat for SARS-CoV-2, they used weight-loss drugs and other fat-targeting compounds to try to stop the virus in cell culture. Cut off from its fatty fuel, the virus stopped replicating within 48 hours.

The authors of the recent paper in Nature Communications caution that the results are in cell culture, not in people; much more research remains to see if such compounds hold promise for people diagnosed with COVID. But the scientists, from Oregon Health & Science University and the Department of Energy’s Pacific Northwest National Laboratory, call the work a significant step toward understanding the virus.

“This is exciting work, but it’s the start of a very long journey,” said Fikadu Tafesse, the corresponding author of the study and assistant professor of molecular microbiology and immunology at OHSU. “We have an interesting observation, but we have a lot more to learn about the mechanisms of this disease.”

Highly antibiotic-resistant strain of MRSA that arose in pigs can jump to humans

Pig farm 
Credit: Mark Holmes

The strain, called CC398, has become the dominant type of MRSA in European livestock in the past fifty years. It is also a growing cause of human MRSA infections.

The study found that CC398 has maintained its antibiotic resistance over decades in pigs and other livestock. And it is capable of rapidly adapting to human hosts while maintaining this antibiotic resistance.

The results highlight the potential threat that this strain of MRSA poses to public health. It has been associated with increasing numbers of human infections, in people who have and have not had direct contact with livestock.

“Historically high levels of antibiotic use may have led to the evolution of this highly antibiotic resistant strain of MRSA on pig farms,” said Dr Gemma Murray, a lead author of the study, previously in the University of Cambridge’s Department of Veterinary Medicine and now at the Wellcome Sanger Institute.

She added: “We found that the antibiotic resistance in this livestock-associated MRSA is extremely stable – it has persisted over several decades, and also as the bacteria has spread across different livestock species.”

Virus Discovery Offers Clues About Origins of Complex Life

Comparison of all known virus genomes. Those viruses with similar genomes are grouped together including those that infect bacteria (on the left), eukaryotes (on the right and bottom center). The viruses that infect Asgard archaea are unique from those that have been described before.
Credit: University of Texas at Austin.

The first discovery of viruses infecting a group of microbes that may include the ancestors of all complex life has been found, researchers at The University of Texas at Austin report in Nature Microbiology. The discovery offers tantalizing clues about the origins of complex life and suggests new directions for exploring the hypothesis that viruses were essential to the evolution of humans and other complex life forms.

There is a well-supported hypothesis that all complex life forms such as humans, starfish and trees — which feature cells with a nucleus and are called eukaryotes — originated when archaea and bacteria merged to form a hybrid organism. Recent research suggests the first eukaryotes are direct descendants of the so-called Asgard archaea. The latest research, by Ian Rambo (a former doctoral student at UT Austin) and other members of Brett Baker’s lab, sheds light on how viruses, too, might have played a role in this billions-year-old history.

“This study is opening a door to better resolving the origin of eukaryotes and understanding the role of viruses in the ecology and evolution of Asgard archaea,” Rambo said. “There is a hypothesis that viruses may have contributed to the emergence of complex cellular life.”

Ancient microbes may help us find extraterrestrial life forms

Rendering of the process by which ancient microbes captured light with rhodopsin proteins.
Credit: Sohail Wasif/UCR

Using light-capturing proteins in living microbes, scientists have reconstructed what life was like for some of Earth’s earliest organisms. These efforts could help us recognize signs of life on other planets, whose atmospheres may more closely resemble our pre-oxygen planet.

The earliest living things, including bacteria and single-celled organisms called archaea, inhabited a primarily oceanic planet without an ozone layer to protect them from the sun’s radiation. These microbes evolved rhodopsins — proteins with the ability to turn sunlight into energy, using them to power cellular processes.

“On early Earth, energy may have been very scarce. Bacteria and archaea figured out how to use the plentiful energy from the sun without the complex biomolecules required for photosynthesis,” said UC Riverside astrobiologist Edward Schwieterman, who is co-author of a study describing the research.

Rhodopsins are related to rods and cones in human eyes that enable us to distinguish between light and dark and see colors. They are also widely distributed among modern organisms and environments like saltern ponds, which present a rainbow of vibrant colors.

Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts

Artistic rendering of Ca. Thiomargarita magnifica with dime.
Credit: Mangrove photo by Pierre Yves Pascal; Illustration by Susan Brand/Berkeley Lab
Full Size Image

At first glance, the slightly murky waters in the tube look like a scoop of stormwater, complete with leaves, debris, and even lighter threads in the mix. But in the Petri dish, the thin vermicelli-like threads floating delicately above the leaf debris are revealed to be single bacterial cells, visible to the naked eye.

The unusual size is notable because bacteria aren’t usually visible without the assistance of microscope. “It’s 5,000 times bigger than most bacteria. To put it into context, it would be like a human encountering another human as tall as Mount Everest,” said Jean-Marie Volland, a scientist with joint appointments at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National Laboratory (Berkeley Lab) and the Laboratory for Research in Complex Systems (LRC) in Menlo Park, Calif. In the June 24, 2022, issue of the journal Science, Volland and colleagues, including researchers at the JGI and Berkeley Lab, LRC, and at the Université des Antilles, described the morphological and genomic features of this giant filamentous bacterium, along with its life cycle.

Maternal microbiome promotes healthy development of the baby

Bifidobacterium breve 
Credit: Hall Lab, Quadram Institute

A new study has found that a species of gut bacteria, known to have beneficial effects for health in mice and humans, changes the mother’s body during pregnancy and affects the structure of the placenta and nutrient transport - which impacts the growing baby.

The bacteria, Bifidobacterium breve, is widely used as a probiotic so this study could point to ways of combating pregnancy complications and ensuring a healthy start in life across the population.

The research involved scientists from the University of Cambridge, the Quadram Institute, and the University of East Anglia and is published today in the journal Cellular and Molecular Life Sciences.

Microbes in our gut, collectively called the gut microbiome, are known to play a key role in maintaining health by combating infections, and influencing our immune system and metabolism. They achieve these beneficial effects by breaking down food in our diet and releasing active metabolites that influence cells and body processes.

Little is known about how these interactions influence fetal development and the baby’s health pre-birth. To address this, Professor Lindsay Hall from the Quadram Institute and University of East Anglia, and Dr Amanda Sferruzzi-Perri and Dr Jorge Lopez-Tello from the University of Cambridge analysed how supplementation with Bifidobacterium bacteria affected pregnancy in mice.

Rethinking the rabies vaccine

Scientists from La Jolla Institute for Immunology and the Institut Pasteur have shed light on the structure of the rabies virus glycoprotein. 
Credit: Heather Callaway, Ph.D., LJI

Rabies virus kills a shocking 59,000 people each year, many of them children. Some victims, especially kids, don’t realize they’ve been exposed until it is too late. For others, the intense rabies treatment regimen is out of the question: treatment is not widely available and the average $3,800 expense poses unthinkable economic burden for most people around the world.

Rabies vaccines, rather than treatments, are much more affordable and easier to administer. But those vaccines also come with a massive downside:

“Rabies vaccines don’t provide lifelong protection. "You have to get your pets boosted every year to three years,” says LJI Professor Erica Ollmann Saphire, Ph.D. “Right now, rabies vaccines for humans and domestic animals are made from killed virus. But this inactivation process can cause the molecules to become misshapen—so these vaccines aren’t showing the right form to the immune system. If we made a better shaped, better structured vaccine, would immunity last longer?”

Saphire and her team, in collaboration with a team led by Institut Pasteur Professor Hervé Bourhy, DVM, PhD., may have discovered the path to better vaccine design. In a new study, published in Science Advances, the researchers share one of the first high-resolution looks at the rabies virus glycoprotein in its vulnerable “trimeric” form.

A warming climate decreases microbial diversity

Researchers with the Institute for Environmental Genomics at the University of Oklahoma are investigating plant diversity and taking samples for microbial diversity analysis. 
Credit: Institute for Environmental Genomics, University of Oklahoma

Researchers at the University of Oklahoma have found that the warming climate is decreasing microbial diversity, which is essential for soil health. Led by Jizhong Zhou, Ph.D., the director of the Institute for Environmental Genomics at OU, the research team conducted an eight-year experiment that found that climate warming played a predominant role in shaping microbial biodiversity, with significant negative effect. Their findings are published in Nature Microbiology.

“Climate change is a major driver of biodiversity loss from local to global scales, which could further alter ecosystem functioning and services,” Zhou said. “Despite the critical importance of belowground soil biodiversity in maintaining ecosystem functions, how climate change might affect the richness and abundant distribution of soil microbial communities (bacteria, fungi, protists) was unresolved.”

Using a long-term multifactor experimental field site at OU, researchers with the university’s Institute for Environmental Genomics examined the changes of soil microbial communities in response to experimental warming, altered precipitation and clipping (annual biomass removal) on the grassland soil bacterial, fungal and protistan biodiversity since 2009.

How ‘viral dark matter’ may help mitigate climate change

A network-based ecological interaction analysis showed the diversity of RNA viral species was higher than expected in the Arctic and Antarctic.
Photo Credit: Tara Ocean Foundation

A deep dive into the 5,500 marine RNA virus species scientists recently identified has found that several may help drive carbon absorbed from the atmosphere to permanent storage on the ocean floor.

Ahmed Zayed

The analysis also suggests that a small portion of these newly identified species had “stolen” genes from organisms they infected, helping researchers identify their presumed hosts and functions in marine processes.

Beyond mapping a fount of foundational ecological data, the research is leading to a fuller understanding of the outsize role these tiny particles play in the ocean ecosystem.

“The findings are important for model development and predicting what is happening with carbon in the correct direction and at the correct magnitude,” said Ahmed Zayed, a research scientist in microbiology at The Ohio State University and co-first author of the study.

The question of magnitude is a serious consideration when taking into account the vastness of the ocean.

Lead author Matthew Sullivan, professor of microbiology at Ohio State, envisions identifying viruses that, when engineered on a massive scale, could function as controllable “knobs” on a biological pump that affects how carbon in the ocean is stored.

How a harmless environmental bacterium became the dreaded hospital germ Acinetobacter baumannii

A scanning electron micrograph (SEM) of a highly magnified cluster of Gram-negative, non-motile ''en:Acinetobacter baumannii'' bacteria; Mag - 13331x.
Source: CDC

Hospital-acquired infections (HAIs) are often particularly difficult to treat because the pathogens have developed resistance to common antibiotics. The bacterium Acinetobacter baumannii is particularly dreaded in this respect, and research is seeking new therapeutic approaches to combat it. To look for suitable starting points, an international team led by bioinformaticians at Goethe University Frankfurt has compared thousands of genomes of pathogenic and harmless Acinetobacter strains. This has delivered clues about which properties might have made A. baumannii a successful pathogen – and how it might possibly be combated.

Each year, over 670,000 people in Europe fall ill through pathogenic bacteria that exhibit antibiotic resistance, and 33,000 die of the diseases they cause. Especially feared are pathogens that are resistant to several antibiotics at the same time. Among them is the bacterium Acinetobacter baumannii, which is today dreaded above all as a “hospital superbug": up to five percent of all hospital-acquired bacterial infections are caused by this germ alone.

A. baumannii is right at the top of a list of candidates for which, according to the World Health Organization (WHO), new therapies must be developed. This is because the pathogen – due to a flexible genome – easily acquires new antibiotic resistance. At the same time, infections are not only occurring more and more outside the hospital environment but also leading to increasingly severe progression. However, a prerequisite for the development of new therapeutic approaches is that we understand which properties make A. baumannii and its human pathogenic relatives, grouped in what is known as the Acinetobacter calcoaceticus-baumannii (ACB) complex, a pathogen.

Researchers from Goethe University Frankfurt develop new biobattery for hydrogen storage

Model of a potential bacterial hydrogen storage system: during the day, electricity is generated with the help of a photovoltaic unit, which then powers the hydrolysis of water. The bacteria bind the hydrogen produced in this way to CO2, resulting in the formation of formic acid. This reaction is fully reversible, and the direction of the reaction is steered solely by the concentration of the starting materials and end products. During the night, the hydrogen concentration in the bioreactor decreases and the bacteria begin to release the hydrogen from the formic acid again. This hydrogen can then be used as an energy source.
Credit: Goethe University

A team of microbiologists from Goethe University Frankfurt has succeeded in using bacteria for the controlled storage and release of hydrogen. This is an important step in the search for carbon-neutral energy sources in the interest of climate protection. The corresponding paper has now been published in the renowned scientific journal Joule.

The fight against climate change is making the search for carbon-neutral energy sources increasingly urgent. Green hydrogen, which is produced from water with the help of renewable energies such as wind or solar power, is one of the solutions on which hopes are pinned. However, transporting and storing the highly explosive gas is difficult, and researchers worldwide are looking for chemical and biological solutions. A team of microbiologists from Goethe University Frankfurt has found an enzyme in bacteria that live in the absence of air and bind hydrogen directly to CO2, in this way producing formic acid. The process is completely reversible – a basic requirement for hydrogen storage. These acetogenic bacteria, which are found, for example, in the deep sea, feed on carbon dioxide, which they metabolize to formic acid with the aid of hydrogen. Normally, however, this formic acid is just an intermediate product of their metabolism and further digested into acetic acid and ethanol. But the team led by Professor Volker Müller, head of the Department of Molecular Microbiology and Bioenergetics, has adapted the bacteria in such a way that it is possible not only to stop this process at the formic acid stage but also to reverse it. The basic principle has already been patented since 2013.

Models predict that planned phosphorus reductions will make Lake Erie more toxic

Photo by Aerial Associates Photography, Inc. (Zachary Haslick) via NOAA cc 2.0

Reducing levels of the nutrient phosphorus to control harmful algal blooms in places like Lake Erie is actually advantageous to toxic cyanobacteria strains, which can lead to an increase in toxins in the water, according to a new modeling study.

Researchers from Technische Universität Berlin (TU Berlin) detail their findings in a paper published online May 26 in the interdisciplinary journal Science. Two University of Michigan scientists are among the co-authors.

“The big advance here was to integrate our understanding of the microbiology of the blooms into predictive models,” said U-M environmental microbiologist and study co-author Gregory Dick. “The results suggest that biologically informed models are able to reproduce emergent properties of blooms that are not predicted by traditional models.”

Cyanobacteria, also known as blue-green algae, can produce toxins and deplete lakes of oxygen when they die. Phosphorus is an important nutrient for these algae, and efforts are underway worldwide to reduce phosphorus levels and inhibit the growth of cyanobacteria.

Monitoring the "journey" of microplastics through the intestine of a living organism

Drosophila melanogaster 
Credit: Universitat Autònoma de Barcelona

A UAB research team has managed to track the behavior of microplastics during their "journey" through the intestinal tract of a living organism and illustrate what happens along the way. The study, carried out on Drosophila melanogaster using electron microscopy equipment developed by the researchers themselves, represents a significant step towards a more precise analysis of the health risks of being exposed to these pollutants.

The behavior of micro and nanoplastics (MNPLs) inside the organism is a question impossible to answer at present in humans, and in vitro models are not useful. Hence, there is a need to look for models that allow us to answer this question. Furthermore, there are limitations in the current methodologies for detecting and quantifying their presence in different human biological samples, which prevents an accurate assessment of the health risk of exposure.

In this context, researchers from the Mutagenesis Research Group of the Universitat Autònoma de Barcelona (UAB) have managed to monitor the tracking of MNPLs in their "journey" from the environment to the interior of a living organism. They have done it by developing tools based on electron microscopy and in larvae of the Drosophila melanogaster fly, a model organism widely used to study biological phenomena and processes.

“Natural Immunity” from Omicron is Weak and Limited

The new study shows that infection with Omicron does not protect against other variants of COVID-19. In this photo, clear zones on the purple background show the SARS-CoV-2 virus escaping from neutralizing antibodies in patient blood samples.
Credit: Gladstone Institutes

In unvaccinated people, infection with the Omicron variant of SARS-CoV-2 provides little long-term immunity against other variants, according to a new study by researchers at Gladstone Institutes and UC San Francisco (UCSF), published today in the journal Nature.

In experiments using mice and blood samples from donors who were infected with Omicron, the team found that the Omicron variant induces only a weak immune response. In vaccinated individuals, this response—while weak—helped strengthen overall protection against a variety of COVID-19 strains. In those without prior vaccination, however, the immune response failed to confer broad, robust protection against other strains.

“In the unvaccinated population, an infection with Omicron might be roughly equivalent to getting one shot of a vaccine,” says Melanie Ott, MD, PhD, director of the Gladstone Institute of Virology and co-senior author of the new work. “It confers a little bit of protection against COVID-19, but it’s not very broad.”

Soil Microbes Use Different Pathways to Metabolize Carbon

Credit: Victor O. Leshyk/Northern Arizona University

Much of what scientists think about soil metabolism may be wrong. New evidence from Northern Arizona University suggests that microbes in different soils use different biochemical pathways to process nutrients, respire and grow. The study, published in Plant and Soil, upends long-held assumptions in the field of soil ecology and calls for more investigation and higher-resolution methods to be applied to what has been a black box for the field.

“As ecologists, we generally don’t think about soil metabolism in terms of pathways,” said Paul Dijkstra, research professor of biology in the Center for Ecosystem Science and Society at NAU and lead author of the study. “But we now have evidence that metabolism differs from soil to soil. We’re the first to see that.”

“We’ve learned that biochemistry—more specifically, the metabolic pathways the soil microbiota chooses—matters, and it matters a lot,” said co-author Michaela Dippold, a professor of bio-geosphere interactions at University of Tübingen in Germany. “Our field urgently needs to develop experimental approaches that quantify maintenance energy demand and underlying respiration in a robust way. It’s a challenge to which future soil ecology research will have to respond.”

Meet the forest microbes that can survive megafires

The image highlights the diversity in colors and morphologies of microbes obtained from Soberanes Fire-burned soil.
Credit: Jenna Maddox/UCR

New UC Riverside research shows fungi and bacteria able to survive redwood tanoak forest megafires are microbial “cousins” that often increase in abundance after feeling the flames.

Fires of unprecedented size and intensity, called megafires, are becoming increasingly common. In the West, climate change is causing rising temperatures and earlier snow melting, extending the dry season when forests are most vulnerable to burning.

Though some ecosystems are adapted for less intense fires, little is known about how plants or their associated soil microbiomes respond to megafires, particularly in California’s charismatic redwood tanoak forests.

“It’s not likely plants can recover from megafires without beneficial fungi that supply roots with nutrients, or bacteria that transform extra carbon and nitrogen in post-fire soil,” said Sydney Glassman, UCR mycologist and lead study author. “Understanding the microbes is key to any restoration effort.”

The UCR team is contributing to this understanding with a paper in the journal Molecular Ecology.