Real-time, accurate virus detection method could help fight the next pandemic

Scanning electron microscopy image showing carbon nanotubes (purple) effectively trapping Influenza viruses (light purple round objects). These trapped viruses are then analyzed by Raman spectroscopy and machine learning and they can be identified with accuracies >95%.
Credit: Elizabeth Floresgomez and Yin-Ting Yeh.

A method of highly accurate and sensitive virus identification using Raman spectroscopy, a portable virus capture device and machine learning could enable real-time virus detection and identification to help battle future pandemics, according to a team of researchers led by Penn State.

“This virus detection method is label-free and not aimed at any specific virus, thus enabling us to identify potential new strains of viruses,” said Shengxi Huang, assistant professor of electrical engineering and biomedical engineering and co-author of the study that appeared today (June 2) in the Proceedings of the National Academy of Sciences. “It is also rapid, so suitable for fast screening in crowded public spaces. In addition, the rich Raman features together with machine learning analysis enable a deeper understanding of the virus structures.”

Raman spectroscopy detects unique vibrations in molecules by picking up shifts when a laser light beam induces these vibrations. To capture the viruses, a tool known as a microfluidic device would be used to trap viruses between forests of aligned carbon nanotubes.

Microfluidic devices use very small amounts of body fluids on a microchip to do medical and laboratory tests. Such a device could use virus cultures, saliva, nasal washes, or even exhaled breath, including samples gathered on-site during an outbreak. The carbon nanotubes forests would filter out any foreign substance or background molecules from the host or surrounding air that could make it more difficult to get an accurate reading.

Coastal Inundation

Large weather events, such as tropical cyclones and nor’easters, exacerbate coastal flooding.
Credit: Lisa Tossey

Residents on the Mid-Atlantic coast face a dual threat when it comes to coastal flooding, which is one of the most costly, devastating and pervasive natural hazards in the region.

Not only has the Mid-Atlantic experienced increased rates of sea level rise, the area also gets hit with large tropical weather systems, such as hurricanes, as well as battered with non-tropical weather events — midlatitude weather systems such as nor’easters like the one that hit the Delaware coast in mid-May.

These large weather events exacerbate coastal flooding, and when combined with the higher rates of sea level rise, they pose a threat to human life, damage natural and human-built critical infrastructure, erode beaches, and disrupt important ecosystems found along the coast.

John Callahan, climatologist and visiting assistant professor in the University of Delaware’s College of Earth, Ocean and Environment, was the lead author on three papers published in the past year that focused on these large-scale weather events to see just how much coastal areas — particularly the Chesapeake and Delaware Bays — are inundated by tropical and non-tropical weather events. Dan Leathers, professor and Delaware State Climatologist, was a co-author on all of the papers, and Christina Callahan, scientist for the Center for Environmental Monitoring and Analysis (CEMA), was a co-author on two of the papers.

An atomic-scale window into superconductivity paves the way for new quantum materials

Professor Jose Lado.
Photo: Aalto University / Evelin Kask.

Researchers have demonstrated a new technique to measure the quantum excitations in superconducting materials with atomic precision for the first time. Detecting these excitations is an important step towards understanding exotic superconductors, which could help us improve quantum computers and perhaps even pave the way towards room-temperature superconductors.

Superconductors are materials with no electrical resistance whatsoever, commonly requiring extremely low temperatures. They are used in a wide range of domains, from medical applications to a central role in quantum computers. Superconductivity is caused by specially linked pairs of electrons known as Cooper pairs. So far, the occurrence of Cooper pairs has been measured indirectly macroscopically in bulk, but a new technique developed by researchers at Aalto University and Oak Ridge National Laboratories in the US can detect their occurrence with atomic precision.

The experiments were carried out by Wonhee Ko and Petro Maksymovych at Oak Ridge National Laboratory, with the theoretical support of Professor Jose Lado of Aalto University. Electrons can “quantum tunnel” across energy barriers, jumping from one system to another through space in a way that cannot be explained with classical physics. For example, if an electron pairs with another electron right at the point where a metal and superconductor meet, it could form a Cooper pair that enters the superconductor while also “kicking back” another kind of particle into the metal in a process known as Andreev reflection. The researchers looked for these Andreev reflections to detect Cooper pairs.

Lichens Adapt to the Substrate on Which They Grow

Aleksandr Paukov, Associate Professor at the Department of Biodiversity and Bioecology at UrFU
Credit: Ural Federal University

Lichens growing on substrates with different chemical properties have a different spectrum of secondary metabolites. This is probably how lichens adapt to unfavorable conditions - low pH of the substrate or toxic elements. Biologists of the Ural Federal University who studied more than 740 species of lichens discovered this new property of these organisms. Samples were collected from rocks and trees (spruce, pine, birch, alder, aspen, poplar) of the Middle Urals. The results were published in the journals Frontiers in Forest and Global Change and Diversity.

According to biologists from the UrFU, secondary metabolites help lichens adapt. These are peculiar "biochemical tools" with which the organism defends itself and survives under stressful conditions. Both animals and plants have primary metabolites, while plants have secondary metabolites only. In other words, to escape, unlike an animal which can escape, a plant produces a certain set of secondary metabolites which endow it with protective properties (taste, smell, color) and allow it to survive in drought, high temperatures, the spread of infections, etc.

In lichens, secondary metabolites accumulate in large amounts. They do not participate in metabolic processes, and the role of many in lichen life is not clear. The patterns of their formation are only beginning to be studied.

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.

How plesiosaurs swam under water

Anna Krahl (front) and Ulrich Witzel used a model made of bone copies and material from the hardware store to reconstruct the muscles. This analog model consists of casts of the front and rear fin, wooden slats, chandelier clamps, eyelets and ropes.
Credit: Ruhr University Bochum

The plesiosaurs are characterized by four uniform fins. Whether they rowed or flew under water could be reconstructed thanks to the combination of paleontological and engineering methods.

Plesiosaurs, which lived around 210 million years ago, have adapted in a unique way to life under water: their front and rear legs have developed into four uniform, wing-like fins in the course of evolution. How they could get on with it in the water, Dr. Anna Krahl worked out in her dissertation supervised at the Ruhr University Bochum and the Rheinische Friedrich-Wilhelms-Universität Bonn. Among other things, by using the finite element method, which is widespread in engineering, it was able to show that the fins had to be twisted in order to advance. Using bones, models and muscle reconstructions, she was able to reconstruct the movement. She reports in the PeerJ journal from 3. June 2022.

Plesiosaurs belong to a group of dinosaurs, the Sauropterygia or paddle lizards, who have adapted to a life in the sea again. They developed in the late Triassic 210 million years ago, lived at the same time as the dinosaurs and died out at the end of the Cretaceous period. Plesiosaurs are characterized by an often extremely elongated neck with a small head - the Elas mosaic animals even have the longest neck of all vertebrates. But there were also large predatory shapes with a rather short neck and huge skulls. In all plesiosaurs, the neck sits on a teardrop-shaped, hydrodynamically well-adapted body with a very shortened tail.

Scientists Show that at Least 44 Percent of Earth’s Land Requires Conservation to Safeguard Biodiversity and Ecosystem Services

Credit Max Melesi on behalf of Koobi Carbon

New research published in the June 3, 2022 journal Science reveals that 44 percent of Earth’s land area – some 64 million square kilometers (24.7 million square miles) requires conservation to safeguard biodiversity.

The team, led by Dr James R. Allan from the University of Amsterdam, used advanced geospatial algorithms to map the optimal areas for conserving terrestrial species and ecosystems across the world. They further used spatially explicit land-use scenarios to quantify how much of this land is at risk from human activities by 2030.

“Our study is the current best estimate of how much land we must conserve to stop the biodiversity crisis - it is essentially a conservation plan for the planet,” said lead author James Allan. “We must act fast, our models show that over 1.3 million square kilometers of this important land – an area larger than South Africa – is likely to have its habitat cleared for human uses by 2030, which would be devastating for wildlife.”

The work has important policy implications since governments are currently negotiating a post-2020 global biodiversity framework under the Convention on Biological Diversity, with new goals and targets for biodiversity which will hopefully come into effect later this year. This will set the conservation agenda for at least the next decade, and governments will have to report progress against these targets on a regular basis.

Tobacco hawkmoths always find the right odor

To collect the nocturnal odor of agave flowers, individual flower umbels on the up to five-meter-high inflorescence are enclosed in foil bags at sunset and connected to a mobile odor collection system.
 Credit: Sonja Bisch-Knaden

A research team at the Max Planck Institute for Chemical Ecology has discovered how tobacco hawkmoths are able to detect odors that are important to them against a complex olfactory background. By looking at the specific activity patterns that the odors triggered in the moths' brains the researcher showed that the sense of smell enables moths not only to perceive the intense floral odors of nectar sources, but also to find the rather unobtrusive smell of their host plants on which the larvae thrive. What is especially amazing is that tobacco hawkmoths can reliably detect the odors of their host plants despite the multitude of background odors emitted by many other plants in the vicinity.

Nocturnal moths, such as tobacco hawkmoths (Manduca sexta), rely primarily on their sense of smell when foraging for flowers that contain nutrient-rich nectar or searching for a host plant on which they lay their eggs. A team of scientists has now turned their attention to the question of how these insects are able to distinguish the odors that are crucial for survival from those that are unimportant in a natural environment full of a wide variety of different odors.

"Our question is based on the fact that the plants that are vital for the tobacco hawkmoth, that is nectar sources and suitable host plants for their offspring, are very sparse in their natural habitat. Apparently, however, these plants are nevertheless found by the moths. We wanted to know whether the olfactory system can also filter out weak odor signals if they provide the moths with clues that lead them to food sources or oviposition sites," says Sonja Bisch-Knaden, lead author of the study. In addition, the researchers were interested in whether female tobacco hawkmoths that have already mated are less receptive to floral odors and more interested in the odors of leaves where they can lay their eggs. This phenomenon has been observed in other moths, such as the moth of the cotton leafworm Spodoptera littoralis.

COVID kidney injury twice as common as diagnosed

A University of Queensland-led study has found millions of COVID-19 patients may have undiagnosed acute kidney injury (AKI).

AKI is a condition where the kidneys suddenly fail to filter waste from the blood, which can lead to serious illness or even death.

Existing data indicates approximately 20 per cent of patients admitted to hospital with COVID-19 develop AKI, rising to roughly 40 per cent for those in intensive care.

But UQ PhD candidate and kidney specialist Dr Marina Wainstein said the true numbers could be double those figures.

“Doctors look at the amount of urine a patient passes and the level of a compound called creatinine in the blood, which rises when the kidneys aren’t working well,” she said.

“However, if that creatinine rise occurs before a patient presents to hospital, we can miss the AKI diagnosis and fail to manage the patient appropriately in those early, critical days of hospitalization.”

Dr Wainstein said when researchers also measured the fall in creatinine levels, which often follows the initial rise, the rate of AKI diagnosis in COVID-19 patients doubled.

Males need not apply

Face of Warramaba flavolineata, one of the two sexual species that crossed to form the parthenogen Warramaba virgo.
Image: Professor Michael Kearney

A unique all-female species of grasshopper that can reproduce without sex provides fascinating insights into evolution; new research led by the University of Melbourne has found.

Published today in Science, the research shows the Australian grasshopper Warramaba virgo (W. virgo) – a parthenogenetic species, meaning it can reproduce asexually by cloning itself – was just as ecologically successful as its counterparts that breed by sex.

Lead author Professor Michael Kearney said the findings were significant because they challenged current evolutionary theory about the advantages of sexual reproduction.

“Most species on earth have two sexes, male and female, that mix their genes when they reproduce. This method of reproduction is thought to increase genetic diversity and ecological success of a species,” Professor Kearney said.

“Parthenogenetic species in theory should be suffering from parasites and a high load of bad mutations. Our study finds no disadvantage to W. virgo compared to other species of grasshoppers that sexually reproduce. In fact, W. virgo has even managed to successfully spread from the west to the east of Australia, unlike its sexual relatives.”