“COVID Time” is a real thing, and it’s not good

Credit: xaviandrew

Have you ever noticed that time seems to slow down sometimes? Like when you are waiting in line at a bank or grocery checkout, and it just seems to take forever?

During the peak of the pandemic, and mid-lockdown, many people reported they felt their days dragged on, inducing fatigue and making some tasks almost unbearable during “COVID time.”

An interdisciplinary team of researchers studied this effect of the COVID-19 pandemic, called Blursday, to understand how our perception of time is malleable and influenced by many factors. Blursday was the altered sense of time and difficulty in determining the day of the week during the lockdown.

Dr. Fuat Balci, a UM biologist and part of the research team, notes: “A new lingo emerged during the COVID-19 pandemic to capture the altered psychological state under the extraordinary conditions imposed by the pandemic such as the lockdown and social isolation, including doomscrolling and Blursday.”

The researchers had volunteers answer a questionnaire and perform 15 behavioral tasks, such as estimating how long they had been logged on to the study’s website. They were also asked to guess if a stated time interval was shorter or longer than they experienced to test how the pandemic affected temporal awareness.

Sifting through cellular recycling centers

A cartoon representation of the new method, which allows scientists to isolate the lysosomes (left) of any cell in a mouse to analyze and identify using mass spectrometry (right) all the molecules inside them.
Image credit: Cindy Lin

A new method allows scientists to determine all the molecules present in the lysosomes – the cell’s recycling centers – of mice. This could bring new understanding and treatment of neurodegenerative disorders.

Small but mighty, lysosomes play a surprisingly important role in cells despite their diminutive size. Making up only 1-3% of the cell by volume, these small sacs are the cell’s recycling centers, home to enzymes that break down unneeded molecules into small pieces that can then be reassembled to form new ones. Lysosomal dysfunction can lead to a variety of neurodegenerative or other diseases, but without ways to better study the inner contents of lysosomes, the exact molecules involved in diseases – and therefore new drugs to target them – remain elusive.

A new method, reported in Nature on Sept. 21, allows scientists to determine all the molecules present in the lysosomes of any cell in mice. Studying the contents of these molecular recycling centers could help researchers learn how the improper degradation of cellular materials leads to certain diseases. Led by Stanford University’s Monther Abu-Remaileh, institute scholar at Sarafan ChEM-H, the study’s team also learned more about the cause for a currently untreatable neurodegenerative disease known as Batten disease, information that could lead to new therapies.

Newly Discovered Barrier Prevents Immunity from Reaching Smell-Sensing Cells

Circulating antibody (white) is prevented from accessing olfactory epithelium (green) by a previously unknown blood-olfactory barrier, the BOB.
Credit: Ashley Moseman Lab, Duke University

Duke scientists have identified a previously unknown barrier that separates the bloodstream from smelling cells in the upper airway of mice, likely as a way to protect the brain.

But this barrier also ends up keeping some of the larger molecules of the body’s immune system out, and that may be hindering the effectiveness of vaccines.

It makes sense to have a protective barrier for the olfactory cells lining the nose, because they offer a direct path to the olfactory bulb of the brain, making them effectively extensions of the brain itself, said lead researcher Ashley Moseman, an assistant professor of immunology in the Duke School of Medicine.

However, the new barrier, which his team has dubbed the BOB – the blood-olfactory barrier -- also might be keeping vaccines against respiratory viruses from being more effective by preventing those antibodies from reaching the mucous on the surface of the nose, the first barrier a virus encounters.

The team was trying to understand better how the immune system protects the upper respiratory tract by infecting mice with a virus called vesicular stomatitis virus, or VSV, that is known to penetrate to the central nervous system. Once inhaled, VSV readily infects the olfactory sensing cells and rapidly replicates, reaching the olfactory bulb of the brain within a day. Although it can lead to paralysis and death, it is usually cleared by a T cell response.

Study finds high levels of PFAS in school uniforms

In yet another example of the prevalence of the hazardous chemicals known as PFAS (per- and polyfluoroalkyl substances) in consumer products, industrial products and textiles, researchers have found notably high levels in school uniforms sold in North America.

In a study published in Environmental Science and Technology Letters, scientists at the University of Notre Dame, Indiana University, the University of Toronto and the Green Science Policy Institute analyzed a variety of children’s textiles. Fluorine was detected in 65 percent of samples tested.

But concentrations were highest in school uniforms — and higher in those uniforms labeled as 100 percent cotton as opposed to synthetics.

“What was surprising about this group of samples was the high detection frequency of PFAS in the garments required for children to wear,” said Graham Peaslee, professor of physics at Notre Dame and a co-author of the study. “Children are a vulnerable population when it comes to chemicals of concern, and nobody knows these textiles are being treated with PFAS and other toxic chemicals.”

An estimated 20 percent of public schools in the United States require students to wear uniforms —meaning millions of children could be at risk of exposure to the toxic compounds.

Known as “forever chemicals,” PFAS are known to accumulate in the bloodstream and have been linked to an increased risk of several health problems including weakened immune systems, asthma, obesity, and neurodevelopmental and behavioral problems. The National Health and Nutrition Examination Surveys from the Centers for Disease Control and Prevention routinely find PFAS in blood samples of children between the ages of 3 and 11.

No evidence that dehorning black rhinos negatively impacts the species’ reproduction or survival

A sedated black rhino in the process of being dehorned, with a cap over its eye to protect it from the dust
Credit: Piet Beytell, Namibian Ministry of Environment, Forestry and Tourism

There are no statistically significant differences in key factors of population growth - breeding, birth, survival, life span and death - between dehorned or horned black rhinos new research, conducted by the University of Bristol Vet School, Namibian Ministry of Environment, Forestry and Tourism, and Save the Rhino Trust has found.

The black rhino is critically endangered, with poaching one of several threats to the species’ survival. Many reserves across a number of African countries, including Namibia, South Africa, and Zimbabwe, now dehorn their rhinos in an attempt to reduce poaching but few studies have looked at the impacts of dehorning, particularly in black rhinos.

The study aimed to build on existing knowledge of population productivity between dehorned and horned individuals in four sub-populations of black rhino (of the sub-species Diceros bicornis bicornis) in Namibia.

Three of the populations had undergone some level of dehorning at least once while one of the populations had never been dehorned. The measures investigated included: age of females at the birth of their first calf (age at first reproduction or AFR); average time between the birth of calves for each female (inter-calving interval); birth sex ratios, calf survival, life span and cause of death

Octopuses prefer certain arms when hunting and adjust tactics to prey

A California two-spot octopus hunts a shrimp in an experiment, striking with its second arm.
Credit: Wardill Lab, University of Minnesota

Famous for their eight arms, octopuses leverage all of their appendages to move, jet through the water and capture prey. But their movements can look awkward and seemingly unplanned at times, more closely resembling aliens than earthly creatures.

“Normally when you look at an octopus for a short while, nothing is repeatable. They squirm around and just look weird in their exploratory movements,” said Trevor Wardill, an assistant professor in the College of Biological Sciences who studies octopuses and other cephalopods.

For a new study in Current Biology, Wardill and colleagues investigated whether octopuses preferred certain arms over others when hunting, rather than using each arm equally. A better understanding of how they use their arms will aid efforts to develop next-generation, highly-manipulative soft robots.

The research team studied the California two-spot octopus, which live for about two years and grow to the size of tennis balls. Octopus arms are numbered on each side of its body, starting at the center. Researchers dropped different types of prey, including crabs and shrimp, into the tanks and recorded video as the octopuses, who were hiding in ornamental SpongeBob “dens” with one eye facing outward, lunged for the snack. Because crabs move slowly while shrimp can flick their tails to escape quickly, each type of prey potentially requires different hunting tactics.

Mysterious soil virus gene seen for first time

Crystals of the soil virus AMG product (chitosanase) at 400x magnification. Individual crystals were cryo-cooled in liquid nitrogen before being exposed to the powerful SSRL X-rays beams for structure analysis.
Credit: Clyde Smith/SLAC National Accelerator Laboratory

In every handful of soil, there are billions of bacteria, fungi, and viruses, all working to sustain the cycle of life. Understanding how these microorganisms interact with one another helps scientists analyze soil health, soil carbon and nutrient cycling, and even the ways in which dead insects decompose.

Soil viruses contain genes that appear to have some metabolic function, but they are clearly not required for normal viral replication. These genes are called auxiliary metabolic genes (AMGs) and they produce proteins, some of which are enzymes that have a variety of functions. Until now, scientists have wondered whether some AMG proteins play a role in critical soil processes, like carbon cycling. To find out more about soil AMGs, researchers determined the atomic structure of a protein that is expressed by a particular AMG.

Specifically, researchers irradiated fragile crystallized protein samples with high-brightness X-rays generated by the Stanford Synchrotron Radiation Lightsource’s (SSRL) Beam Line 12-2 at the Department of Energy’s (DOE) SLAC National Accelerator Laboratory. The X-rays struck the proteins within the crystal samples, revealing their molecular structures and a bit of the mystery behind their makeup.

AMGs do not, like many viral genes, help a virus replicate. Instead, they encode a variety of proteins, each with their own predicted function. The AMG that was expressed was a putative enzyme that plays a key role in how soils process and cycle carbon in the biosphere.

Scientists find that wolves can show attachment toward humans

The wolf pup Hendrix.
Photo credit: Christina Hansen Wheat/Stockholm University.

When it comes to showing affection towards people, many dogs are naturals. Now comes word reported in the journal Ecology and Evolution on September 20th that the remarkable ability to show attachment behavior toward human caregivers also exists in wolves.

The findings were made when researchers at Stockholm University, Sweden, tested 10 wolves and 12 dogs in a behavioral test specifically designed to quantify attachment behaviors in canids. During this test 23-week-old wolves spontaneously discriminated between a familiar person and a stranger just as well as dogs did, and showed more proximity seeking and affiliative behaviors towards the familiar person. Additionally, the presence of the familiar person acted as a social stress buffer for the wolves, calming them in a stressful situation. These discoveries build on a slowly accumulating body of evidence contradicting the hypothesis that the abilities necessary to form attachment with humans arose in dogs only after humans domesticated them at least 15,000 years ago.

“We felt that there was a need to thoroughly test this,” says Dr. Christina Hansen Wheat, PhD in Ethology from Stockholm University, Sweden. “Together with earlier studies making important contributions to this question, I think it is now appropriate to entertain the idea that if variation in human-directed attachment behavior exists in wolves, this behavior could have been a potential target for early selective pressures exerted during dog domestication.”

Risk of blood clots remains for almost a year after COVID-19 infection, study suggests

Credit: pixabay

COVID-19 infection increases the risk of potentially life-threatening blood clots for at least 49 weeks, according to a new study of health records of 48 million unvaccinated adults from the first wave of the pandemic.

The findings suggest that the COVID-19 pandemic may have led to an additional 10,500 cases of heart attacks, strokes and other blood clot complications such as deep vein thrombosis in England and Wales in 2020 alone, although the excess risk to individuals remains small and reduces over time.

The research – involving a large team of researchers led by the Universities of Bristol, Cambridge, and Edinburgh, and Swansea University – shows that people with only mild or moderate disease were also affected. The authors suggest that preventive strategies, such as giving high-risk patients medication to lower blood pressure, could help reduce cases of serious clots.

Researchers studied de-identified electronic health records across the whole population of England and Wales from January to December 2020 to compare the risk of blood clots after COVID-19 with the risk at other times. Data were accessed securely and safely via the NHS Digital Trusted Research Environment for England, and the SAIL Databank for Wales.

In the first week after a COVID-19 diagnosis, people were 21 times more likely to have a heart attack or stroke, conditions which are mainly caused by blood clots blocking arteries. This dropped to 3.9 times more likely after 4 weeks.

Scientists Unveil New System for Naming Majority of the World’s Microorganisms

Fluorescent-stained bacteria (pink) and archaea (green) from near-boiling water from Great Boiling Spring in Gerlach, Nevada.
Photo credit: Jeremy Dodsworth.

What’s in a name? For microorganisms, apparently a lot.

Prokaryotes are single-celled microorganisms - bacteria are an example - that are abundant the world over. They exist in the oceans, in soils, in extreme environments like hot springs, and even alongside and inside other organisms including humans.

In short, they’re everywhere, and scientists worldwide are working to both categorize and communicate about them. But here’s the rub: Most don’t have a name.

Less than 0.2% of known prokaryotes have been formally named because current regulations – described in the International Code of Nomenclature of Prokaryotes (ICNP) – require new species to be grown in a lab and freely distributed as pure and viable cultures in collections. Essentially, to name it you have to have multiple physical specimens to prove it.

In an article published in the journal Nature Microbiology, a team of scientists present a new system, the SeqCode, and a corresponding registration portal that could help microbiologists effectively categorize and communicate about the massive number of identified yet uncultivated prokaryotes.

Discovery explains cancer chemotherapy resistance, offers solution

 Experimental DNA fibers with fluorescence (pictured) were used to reveal the speed of DNA replication forks.
Credit: Diego Dibitetto/Smolka Lab

Researchers have uncovered a novel pathway that explains how cancer cells become resistant to chemotherapies, which in turn offers a potential solution for preventing chemo-resistance.

The study, “DNA-PKcs Promotes Fork Reversal and Chemoresistance,” was published Sept. 20 in the journal Molecular Cell.

The research describes for the first time how a type of enzyme – previously known for its roles in DNA repair – prevents DNA damage in cancer cells, making them tolerant to chemotherapy drugs.

“It provides us tools to manipulate and then break chemo-resistance in cancer cells,” said Marcus Smolka, interim director of the Weill Institute for Cell and Molecular Biology and professor of molecular biology and genetics in the College of Agriculture and Life Sciences. Diego Dibitetto, a former postdoctoral researcher in Smolka’s lab who is currently at the University of Bern in Switzerland, is the paper’s first author.

Many anti-cancer drugs work by creating blocks on the DNA of cancer cells as they replicate. During replication, DNA strands entwined in a double helix separate into two individual strands so each strand can be copied, eventually leading to two new double helixes. The junction where this separation and copying occurs is called a replication fork, which unzips down the double helix.

Malaria Spike Linked to Amphibian Die-Off

The Panamanian golden frog is endemic to Panama and is among the species whose populations collapsed following the deadly fungal pathogen "Bd."
Credit: Brian Gratwicke, Wikimedia Common

Dozens of species of frogs, salamanders and other amphibians quietly disappeared from parts of Latin America in the 1980s and 2000s, with little notice from humans, outside of a small group of ecologists. Yet the amphibian decline had direct health consequences for people, according to a study from the University of California, Davis.

The study, published in the journal Environmental Research Letters, links an amphibian die-off in Costa Rica and Panama with a spike in malaria cases in the region. At the spike’s peak, up to 1 person per 1,000 annually contracted malaria that normally would not have had the amphibian die-off not occurred, the study found.

“Stable ecosystems underpin all sorts of aspects of human well-being, including regulating processes important for disease prevention and health,” said lead author Michael Springborn, a professor in the UC Davis Department of Environmental Science and Policy. “If we allow massive ecosystem disruptions to happen, it can substantially impact human health in ways that are difficult to predict ahead of time and hard to control once they’re underway.”

The first look at how rabies affects vampire bat social behavior

Researchers said no previous studies had tried to quantify changes in grooming habits in vampire bats infected with rabies – despite the possibility that they might infect each other through the licking and chewing that constitute the grooming behavior they engage in for up to 5% of their active time in the roost.
Photo credit: Rachel Moon

Vampire bats infected with the rabies virus aren’t likely to act stereotypically “rabid,” according to a new study – instead, infected male bats tended to withdraw socially, scaling back on the common habit of grooming each other before they died of the disease.

The study was the first to observe how rabies affects vampire bat social behavior, and one of only a few research efforts to understand how rabies infection impacts behavior in one of the species most responsible for causing rabies outbreaks in humans and livestock in Latin America. The virus is typically transmitted to other species by direct contact between vampire bats’ infected saliva and the broken skin of the livestock or other animals (and, rarely, humans) they bite to feed on blood.

In the roost, vampire bats might infect each other through the licking and chewing that constitute the grooming behavior they engage in for up to 5% of their active time, said Gerald Carter, senior author of the study and assistant professor of evolution, ecology and organismal biology at The Ohio State University.

Supercomputing and 3D printing capture the aerodynamics of F1 cars

A photo of the 3D color printed McLaren 17D Formula One front wing endplate. The colors visualize the complex flow a fraction of a millimeter away from the wing's surface.
Photo credit: KAUST

In Formula One race car design, the manipulation of airflow around the car is the most important factor in performance. A 1% gain in aerodynamics performance can mean the difference between first place and a forgotten finish, which is why teams employ hundreds of people and spend millions of dollars perfecting this manipulation.

Of special interest is the design of the front wing endplate, which is critical for the drag and lift of the car. Dr. Matteo Parsani, associate professor of applied mathematics and computational science at King Abdullah University of Science and Technology (KAUST), has led a multidisciplinary team of scientists and engineers to simulate and 3D color print the solution of the McLaren 17D Formula One front wing endplate. The work is the result of a massively high-performance computing simulation, with contributing expertise by research scientist Dr. Lisandro Dalcin of the KAUST Extreme Computing Research Center (ECRC), directed by Dr. David Keyes, and also the Advanced Algorithm and Numerical Simulations Lab (AANSLab), and Prototyping and Product Development Core Lab (PCL).

Creating diamonds to shed light on the quantum world

Sandia National Laboratories’ Andy Mounce makes microscopic sensors to try to understand quantum materials at the Center for Integrated Nanotechnologies. He is one of four employees to earn DOE’s Early Career Research Award.
Photo credit: Bret Latter

Diamonds are a scientist’s best friend. That much is at least true for physicist Andy Mounce, whose work with diamond quantum sensors at Sandia National Laboratories has earned him the DOE’s Early Career Research Award.

As a scientist in Sandia’s Center for Integrated Nanotechnologies, he specializes in making microscopic sensors to try to understand the nature of quantum materials and their electrons’ behavior. Mounce is an expert in creating nitrogen-vacancy defects in artificial diamonds, which are extremely sensitive to the electric and magnetic fields at a nanoscale.

“With these quantum sensors we can study basic properties of low dimensional quantum materials, such as superconducting phases, magnetic phases,” he said. “A quantum material can be anything from a nanostructure to a large material that just has electrons that interact with each other very strongly. The distinguishing property of a quantum material, is that their behavior is defined by quantum mechanics, so not your typical copper conductor”.