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”.

A new study explains the relationship between diabetes and urinary tract infections

The picture shows large lumps of E. coli (in red) that infects the bladder of a mouse with diabetes.
 Photo: Soumitra Mohanty

Reduced immune systems and recurrent infections are common in type 1 and type 2 diabetes. Now researchers at Karolinska Institutet show that people with diabetes have lower levels of the antimicrobial peptide psoriasis, which is part of the body's immune system, which impacts the leaves' cell barrier with increased risk of urinary tract infection. The study is published in Nature Communications.

Diabetes is due to insulin deficiency or reduced insulin sensitivity. The hormone insulin regulates glucose (sugar) and thus energy to the body's cells. In people with type 1 diabetes, the body has stopped making insulin and in type 2 diabetes, cells have become less sensitive to insulin, which contributes to high blood glucose levels. Diabetes is a common disease that affects health in several ways.

Among other things, the innate immune system determinants and many get recurrent infections, such as urinary tract infections caused by E. colibacteria. In people with diabetes, there is an increased risk that these will lead to general blood poisoning, sepsis, which is based on the urinary tract.