biology (73)

Polluting the Pristine...


The sea floor near Australia’s Casey station in Antarctica has been found to have levels of pollution comparable to those in Rio de Janeiro’s harbor. Credit: Torsten Blackwood/AFP via Getty

Topics: Antarctica, Biology, Chemistry, Environment, Physics, Research

Antarctica is often described as one of the most pristine places in the world, but it has a dirty secret. Parts of the sea floor near Australia’s Casey research station are as polluted as the harbor in Rio de Janeiro, Brazil, according to a study published in PLoS ONE in August.

The contamination is likely to be widespread across Antarctica’s older research stations, says study co-author Jonathan Stark, a marine ecologist at the Australian Antarctic Division in Hobart. “These contaminants accumulate over long time frames and don’t just go away,” he says.

Stark and his colleagues found high concentrations of hydrocarbons — compounds found in fuels — and heavy metals, such as lead, copper, and zinc. Many of the samples were also loaded with polychlorinated biphenyls, highly carcinogenic chemical compounds that were common before their international ban in 2001.

When the researchers compared some of the samples with data from the World Harbor Project — an international collaboration that tracks large urban waterways — they found that lead, copper, and zinc levels in some cases were similar to those seen in parts of Sydney Harbour and Rio de Janeiro over the past two decades.

Widespread pollution

The problem of pollution is not unique to Casey station, says Ceisha Poirot, manager of policy, environment, and safety at Antarctica New Zealand in Christchurch. “All national programs are dealing with this issue,” she says. At New Zealand’s Scott Base — which is being redeveloped — contamination left from past fuel spills and poor waste management has been detected in soil and marine sediments. More of this historical pollution will emerge as the climate warms, says Poirot. “Things that were once frozen in the soil are now becoming more mobile,” she says.

Most of Antarctica’s contamination is due to historically poor waste management. In the old days, waste was often just dumped a small distance from research stations, says Terence Palmer, a marine scientist at Texas A&M University–Corpus Christi.

Research stations started to get serious about cleaning up their act in 1991. In that year, an international agreement known as the Protocol on Environmental Protection to the Antarctic Treaty, or the Madrid Protocol, was adopted. This designated Antarctica as a “natural reserve, devoted to peace and science,” and directed nations to monitor environmental impacts related to their activities. But much of the damage had already been done — roughly two-thirds of Antarctic research stations were built before 1991.

Antarctic research stations have polluted a pristine wilderness, Gemma Conroy, Nature.

Read more…

Magnetic Chirality...


An RNA-making molecule crystallizes on magnetite, which can bias the process toward a single chiral form. S. FURKAN OZTURK

Topics: Biology, Biotechnology, Chemistry, Magnetism, Materials Science

In 1848, French chemist Louis Pasteur discovered that some molecules essential for life exist in mirror-image forms, much like our left and right hands. Today, we know biology chooses just one of these “chiral” forms: DNA, RNA, and their building blocks are all right-handed, whereas amino acids and proteins are all left-handed. Pasteur, who saw hints of this selectivity, or “homochirality,” thought magnetic fields might somehow explain it, but its origin has remained one of biology’s great mysteries. Now, it turns out Pasteur may have been onto something.

In three new papers, researchers suggest magnetic minerals common on early Earth could have caused key biomolecules to accumulate on their surface in just one mirror image form, setting off positive feedback that continued to favor the same form. “It’s a real breakthrough,” says Jack Szostak, an origin of life chemist at the University of Chicago who was not involved with the new work. “Homochirality is essential to get biology started, and this is [a possible]—and I would say very likely—solution.”

Chemical reactions are typically unbiased, yielding equal amounts of right- and left-handed molecules. But life requires selectivity: Only right-handed DNA, for example, has the correct twist to interact properly with other chiral molecules. To get [life], “you’ve got to break the mirror, or you can’t pull it off,” says Gerald Joyce, an origin of life chemist and president of the Salk Institute for Biological Studies.

Over the past century, researchers have proposed various mechanisms for skewing the first biomolecules, including cosmic rays and polarized light. Both can cause an initial bias favoring either right- or left-handed molecules, but they don’t directly explain how this initial bias was amplified to create the large reservoirs of chiral molecules likely needed to make the first cells. An explanation that creates an initial bias is a good start but “not sufficient,” says Dimitar Sasselov, a physicist at Harvard University and a leader of the new work.

‘Breakthrough’ could explain why life molecules are left- or right-handed, Robert F. Service,

Read more…

Distant Cousins...


The galaxy observed by Webb shows an Einstein ring caused by a phenomenon known as gravitational lensing.  Credit: S. Doyle / J. Spilker

Topics: Astrobiology, Biology, James Webb Space Telescope, Space Exploration

Researchers have detected complex organic molecules in a galaxy more than 12 billion light-years away from Earth—the most distant galaxy in which these molecules are now known to exist. Thanks to the capabilities of the recently launched James Webb Space Telescope and careful analyses from the research team, a new study lends critical insight into the complex chemical interactions that occurred in the first galaxies in the early universe.

University of Illinois Urbana-Champaign astronomy and physics professor Joaquin Vieira and graduate student Kedar Phadke collaborated with researchers at Texas A&M University and an international team of scientists to differentiate between infrared signals generated by some of the more massive and larger dust grains in the galaxy and those of the newly observed hydrocarbon molecules.

The study findings are published in the journal Nature.

"This project started when I was in graduate school studying hard-to-detect, very distant galaxies obscured by dust," Vieira said. "Dust grains absorb and re-emit about half of the stellar radiation produced in the universe, making infrared light from distant objects extremely faint or undetectable through ground-based telescopes."

In the new study, the JWST received a boost from what the researchers call "nature's magnifying glass"—a phenomenon called gravitational lensing. "This magnification happens when two galaxies are almost perfectly aligned from the Earth's point of view, and light from the background galaxy is warped and magnified by the foreground galaxy into a ring-like shape, known as an Einstein ring," Vieira said.

Webb Space Telescope detects the universe's most distant complex organic molecules, Lois Yoksoulian, University of Illinois at Urbana-Champaign.

Read more…

Nano Sanitizer...


The disinfectant powder is stirred in bacteria-contaminated water (upper left). The mixture is exposed to sunlight, which rapidly kills all the bacteria (upper right). A magnet collects the metallic powder after disinfection (lower right). The powder is then reloaded into another beaker of contaminated water, and the disinfection process is repeated (lower left). (Image credit: Tong Wu/Stanford University)

Topics: Biology, Chemistry, Environment, Materials Science, Nanotechnology

When exposed to sunlight, a low-cost, recyclable powder can kill thousands of waterborne bacteria per second. Stanford and SLAC scientists say the ultrafast disinfectant could be a revolutionary advance for 2 billion people worldwide without access to safe drinking water.

At least 2 billion people worldwide routinely drink water contaminated with disease-causing microbes.

Now, scientists at Stanford University and SLAC National Accelerator Laboratory have invented a low-cost, recyclable powder that kills thousands of waterborne bacteria per second when exposed to ordinary sunlight. According to the Stanford and SLAC team, the discovery of this ultrafast disinfectant could be a significant advance for nearly 30 percent of the world’s population with no access to safe drinking water. Their results are published in a May 18 study in Nature Water.

“Waterborne diseases are responsible for 2 million deaths annually, the majority in children under the age of 5,” said study co-lead author Tong Wu, a former postdoctoral scholar of materials science and engineering (MSE) at the Stanford School of Engineering. “We believe that our novel technology will facilitate revolutionary changes in water disinfection and inspire more innovations in this exciting interdisciplinary field.”

Conventional water-treatment technologies include chemicals, which can produce toxic byproducts, and ultraviolet light, which takes a relatively long time to disinfect and requires a source of electricity.

The new disinfectant developed at Stanford is a harmless metallic powder that works by absorbing both UV and high-energy visible light from the sun. The powder consists of nano-size flakes of aluminum oxide, molybdenum sulfide, copper, and iron oxide.

“We only used a tiny amount of these materials,” said senior author Yi Cui, the Fortinet Founders Professor of MSE and of Energy Science & Engineering in the Stanford Doerr School of Sustainability. “The materials are low cost and fairly abundant. The key innovation is that, when immersed in water, they all function together.”

New nontoxic powder uses sunlight to quickly disinfect contaminated drinking water, Mark Shwartz, Stanford News.

Read more…

Mice, Men, and Nanoparticles...


Graphical abstract. Credit: Nanomaterials (2023). DOI: 10.3390/nano13081404

Topics: Biology, Environment, Nanomaterials, Nanotechnology

Among the biggest environmental problems of our time, micro- and nanoplastic particles (MNPs) can enter the body in various ways, including through food. And now, for the first time, research conducted at MedUni Vienna has shown how these minute particles manage to breach the blood-brain barrier and, consequently, penetrate the brain. The newly discovered mechanism provides the basis for further research to protect humans and the environment.

Published in the journal Nanomaterials, the study was carried out in an animal model with oral administration of MNPs, in this case, polystyrene, a widely-used plastic found in food packaging. Led by Lukas Kenner (Department of Pathology at MedUni Vienna and Department of Laboratory Animal Pathology at Vetmeduni) and Oldamur Hollóczki (Department of Physical Chemistry, University of Debrecen, Hungary), the research team was able to determine that tiny polystyrene particles could be detected in the brain just two hours after ingestion.

The mechanism that enabled them to breach the blood-brain barrier was previously unknown to medical science. "With the help of computer models, we discovered that a certain surface structure (biomolecular corona) was crucial in enabling plastic particles to pass into the brain," Oldamur Hollóczki explained.

Study shows how tiny plastic particles manage to breach the blood-brain barrier, Medical University of Vienna,

Read more…



Cancer cells are one of the main targets for expanded mRNA-LNP use. Credit: Iliescu Catalin / Alamy

Topics: Biology, Biotechnology, Cancer, COVID-19, Nanotechnology

Note: This is an advertisement on Nature Portfolio discussing that there may be a silver lining in the pandemic we've all experienced.

Lipid nanoparticles (LNPs) transport small molecules into the body. The most well-known LNP cargo is mRNA, the key constituent of some of the early vaccines against COVID-19. But that is just one application: LNPs can carry many different types of payload and have applications beyond vaccines.

Barbara Mui has been working on LNPs (and their predecessors, liposomes) since she was a Ph.D. student in Pieter Cullis’s group in the 1990s. “In those days, LNPs encapsulated anti-cancer drugs,” says Mui, who is currently a senior scientist at Acuitas. This company developed the LNPs used in the Pfizer-BioNTech mRNA vaccine against SARS-CoV-2. She says it soon became clear that LNPs worked even better as carriers of polynucleotides. “The first one that worked really well was encapsulating small RNAs,” Mui recalls.

But it was mRNA where LNPs proved most effective, primarily because LNPs are comprised of positively charged lipid nanoparticles that encapsulate negatively charged mRNA. Once in the body, LNPs enter cells via endocytosis into endosomes and are released into the cytoplasm. “Without the specially designed chemistry, the LNP and mRNA would be degraded in the endosome,” says Kathryn Whitehead, professor in the departments of chemical engineering and biomedical engineering at Carnegie Mellon University.

LNPs are an ideal delivery system for mRNA. “COVID accelerated the acceptance of LNPs, and people are more interested in them,” says Mui. LNP-mRNA vaccines for other infectious diseases, such as HIV or malaria, or for non-communicable diseases, such as cancer, could be next. And the potential doesn’t end with mRNA; there is even more scope to adapt LNPs to carry different types of cargo. But to realize these potential benefits, researchers first need to overcome challenges and decrease toxicity, increase their ability to escape from the endosomes, increase their thermostability, and work out how to effectively target LNPs to organs across the body.

Another potential application for LNPs is immunotherapy. Genetically modifying lymphocytes such as T cells or NK cells with chimeric antibody receptors (CARs) has proven useful in blood cancers. Often this process involves extracting lymphocytes from the blood of the person receiving the treatment, editing the cells in culture to express CARs, and then reintroducing them into the blood. However, LNPs could make it possible to express the desired CAR in vivo by shuttling CAR mRNA to the target lymphocytes. Mui has been involved in vivo studies showing this process works in mouse T cells (Rurik, J.G. et al. Science 375, 91-96, 2022). And Vita Golubovskaya, VP of research and development at ProMab Biotechnologies, presented preliminary data (available here) at the CAR-TCR Summit in September 2022 regarding LNPs that direct CAR-mRNA to NK cells, which can then kill target cells. “The RNA-LNP is a very exciting and novel technology that can be used for delivering CAR and bi-specific antibodies against cancer,” she says.

Beyond COVID vaccines: what’s next for lipid nanoparticles? Nature Portfolio

Read more…

Like Mushrooms for Plastics...


Credit: VTT Technical Research Centre of Finland

Topics: Biology, Biotechnology, Chemistry, Materials Science, Mechanical Engineering

A research group from VTT Technical Research Center of Finland has unlocked the secret behind the extraordinary mechanical properties and ultra-light weight of certain fungi. The complex architectural design of mushrooms could be mimicked and used to create new materials to replace plastics. The research results were published on February 22, 2023, in Science Advances.

VTT's research shows for the first time the complex structural, chemical, and mechanical features adapted throughout the course of evolution by Hoof mushroom (Fomes fomentarius). These features interplay synergistically to create a completely new class of high-performance materials.

Research findings can be used as a source of inspiration to grow from the bottom up the next generation of mechanically robust and lightweight, sustainable materials for various applications under laboratory conditions. These include impact-resistant implants, sports equipment, body armor, and exoskeletons for aircraft, electronics, or windshield surface coatings.

Mushrooms could help replace plastics in new high-performance ultra-light materials, VTT Technical Research Centre of Finland,

Read more…



Image Source: MedPage Today

Topics: Biology, Biotechnology, Civilization, COVID-19, DNA, Epidemiology

Currently authorized bivalent COVID-19 boosters demonstrated similar protection against symptomatic illness from the XBB/XBB.1.5 Omicron subvariants as from BA.5-related subvariants, according to a CDC study.

From December 2022 to January 2023, the bivalent boosters' vaccine effectiveness (VE) against symptomatic infection was a similar 48% versus XBB/XBB.1.5-related strains and 52% versus BA.5-related sublineages, reported Ruth Link-Gelles, Ph.D., of the CDC's National Center for Immunization and Respiratory Diseases, and colleagues in Morbidity and Mortality Weekly Report (MMWR).

Meanwhile, Pfizer's updated booster demonstrated superior neutralizing antibody activity compared with the company's original product against all the latest Omicron subvariants, including XBB.1, according to Kena Swanson, Ph.D., of Pfizer Vaccine Research and Development in Pearl River, New York and colleagues, writing in the New England Journal of Medicine. Their findings contradict earlier research from other labs that found no significant difference in neutralizing activity with the bivalent over the monovalent vaccine.

According to the latest estimates from the CDC, XBB.1.5 is responsible for 49.1% of new COVID-19 cases in the U.S., while XBB is responsible for another 3.3%.

CDC: Bivalent COVID Vaccines Stop Illness From XBB.1.5

— And Pfizer lab data show better neutralization against the latest variants with the bivalent shot, Ingrid Hein, Staff Writer, MedPage Today

Read more…

Life Detector...


An Orbitrap cell. Credit: Ricardo Arevalo

Topics: Astrobiology, Astronautics, Biology, Laser, NASA, Planetary Science, Space Exploration

As space missions delve deeper into the outer solar system, the need for more compact, resource-conserving, and accurate analytical tools have become increasingly critical—especially as the hunt for extraterrestrial life and habitable planets or moons continues.

A University of Maryland–led team developed a new instrument specifically tailored to the needs of NASA space missions. Their mini laser-sourced analyzer is significantly smaller and more resource efficient than its predecessors—all without compromising the quality of its ability to analyze planetary material samples and potential biological activity onsite. The team's paper on this new device was published in the journal Nature Astronomy on January 16, 2023.

Weighing only about 17 pounds, the instrument is a physically scaled-down combination of two important tools for detecting signs of life and identifying compositions of materials: a pulsed ultraviolet laser that removes small amounts of material from a planetary sample and an Orbitrap analyzer that delivers high-resolution data about the chemistry of the examined materials.

"The Orbitrap was originally built for commercial use," explained Ricardo Arevalo, lead author of the paper and an associate professor of geology at UMD. "You can find them in the labs of pharmaceutical, medical and proteomic industries. The one in my own lab is just under 400 pounds, so they're quite large, and it took us eight years to make a prototype that could be used efficiently in space—significantly smaller and less resource-intensive but still capable of cutting-edge science."

The team's new gadget shrinks down the original Orbitrap while pairing it with laser desorption mass spectrometry (LDMS)—techniques that have yet to be applied in an extraterrestrial planetary environment. The new device boasts the same benefits as its larger predecessors but is streamlined for space exploration and onsite planetary material analysis, according to Arevalo.

Small laser device can help detect signs of life on other planets, University of Maryland,

Read more…

Permafrost Zombies...


(Credit: Tatiana Gasich/Shutterstock)

Topics: Biology, Biosecurity, Climate Change

Thirteen viruses from tens of thousands of years ago have been recovered and reactivated, according to a preprint paper published in BioRxiv. These threats had been idling in the Siberian tundra for approximately 30,000 to 50,000 years before being brought back.

Thanks to climate change, the thawing of the frozen terrain could revive an assortment of ancient pathogens, creating a potential threat that these viral “zombies” could pose.

“Zombie” Viruses

Permafrost — the frigid terrain that stays frozen throughout the year — comprises over 10 percent of our planet’s surface and substantial swaths of the Arctic, a circumpolar area containing Alaska, Scandinavia, and Siberia. But the Arctic’s temperatures are warming almost four times faster than the average worldwide, and the permafrost there is fading fast, freeing all sorts of frozen organisms, including microbes and viruses from thousands of years ago.

An abundance of research has delved into the diversity of microbes that the thawing of the permafrost has freed, but far fewer researchers have described the viruses. In fact, though these threats can sometimes resume their activity following their thaw, scientists have studied this process of viral recovery and reactivation only two other times, in 2014 and in 2015.

'Zombie' Viruses, Up to 50,000 Years Old, Are Awakening, Sam Walters, Discovery Magazine

Read more…

The Apogee of Evil...


Credit: Erik English.

Topics: Biology, Biosecurity, Civilization, COVID-19, Democracy, Existentialism

Weaponizing a pathogen sounds like something out of an archetype Bond villain, minus the wrapped-up plot twists by the time the credits roll, and the obligatory fawning of a stereotypical bikinied woman over the intrepid MI-6 spy. Real life doesn't conclude so cleanly. Before every student became accustomed to active shooter drills, my generation ducked under wooden desks to shield themselves from nuclear fallout. Life has always been precarious, as we have always had a segment of society that would "go there."

On that high note, I will see you on the 29th of November. Happy Thanksgiving!

Pandemics can begin in many ways. A wild animal could infect a hunter, or a farm animal might spread a pathogen to a market worker. Researchers in a lab or in the field could be exposed to viruses and unwittingly pass them to others. Natural spillovers and accidents have been responsible for every historical plague, each of which spread from a single individual to afflict much of humanity. But the devastation from past outbreaks pales in comparison to the catastrophic harm that could be inflicted by malicious individuals intent on causing new pandemics.

Thousands of people can now assemble infectious viruses from a genome sequence and commercially available synthetic DNA, and numerous projects aim to find and publicly identify new viruses that could cause pandemics by characterizing their growth, transmission, and immune evasion capabilities in the laboratory. Once these projects succeed, the world will face a significant new threat: If a single terrorist with the necessary skills were to release a new virus equivalent to SARS-CoV-2, which has claimed 20 million lives worldwide, that person would have killed more people than if they were to detonate a nuclear warhead in a dense city. If they were to release numerous such viruses across multiple travel hubs, the resulting pandemics could not plausibly be contained and would spread much faster than even the most rapidly produced biomedical countermeasures. And if one of those viruses spread as easily as the omicron variant—which rapidly infected millions of people within weeks of being identified—but had the lethality of smallpox, which killed about 30 percent of those infected, the subsequent loss of essential workers could trigger the collapse of food, water, and power distribution networks—and with them, societies.

To avoid this future, societies need to rethink how they can delay pandemic proliferation, detect all exponentially growing biological threats, and defend humanity by preventing infections. A comprehensive set of directions detailing how we can build a world free from catastrophic biological threats is required. That roadmap now exists.

How a deliberate pandemic could crush societies and what to do about it, Kevin Esvelt, Bulletin of the Atomic Scientists

Read more…

Syncing Fireflies...

Some fireflies have a mystifying gift for flashing their abdomens in sync. New observations are overturning long-accepted explanations for how the synchronization occurs, at least for some species.

Topics: Biology, Biomimetics, Biotechnology, Computer Modeling, Mathematics

In Japanese folk traditions, they symbolize departing souls or silent, ardent love. Some Indigenous cultures in the Peruvian Andes view them as the eyes of ghosts. And across various Western cultures, fireflies, glow-worms, and other bioluminescent beetles have been linked to a dazzling and at times contradictory array of metaphoric associations: “childhood, crop, doom, elves, fear, habitat change, idyll, love, luck, mortality, prostitution, solstice, stars and fleetingness of words and cognition,” as one 2016 review noted.

Physicists revere fireflies for reasons that might seem every bit as mystical: Of the roughly 2,200 species scattered around the world, a handful has the documented ability to flash in synchrony. In Malaysia and Thailand, firefly-studded mangrove trees can blink on the beat as if strung up with Christmas lights; every summer in Appalachia, waves of eerie concordance ripple across fields and forests. The fireflies’ light shows lure mates and crowds of human sightseers, but they have also helped spark some of the most fundamental attempts to explain synchronization, the alchemy by which elaborate coordination emerges from even very simple individual parts.

Orit Peleg remembers when she first encountered the mystery of synchronous fireflies as an undergraduate studying physics and computer science. The fireflies were presented as an example of how simple systems achieve synchrony in Nonlinear Dynamics and Chaos, a textbook by the mathematician Steven Strogatz that her class was using. Peleg had never even seen a firefly, as they are uncommon in Israel, where she grew up.

“It’s just so beautiful that it somehow stuck in my head for many, many years,” she said. But by the time Peleg began her own lab, applying computational approaches to biology at the University of Colorado and at the Santa Fe Institute, she had learned that although fireflies had inspired a lot of math, quantitative data describing what the insects were actually doing was scant.

How Do Fireflies Flash in Sync? Studies Suggest a New Answer. Joshua Sokol, Quanta Magazine

Read more…

Cellulose Shoes...


Credit: Tom Mannion

Topics: Additive Manufacturing, Biology, Biotechnology, Environment, Genetics, Nanotechnology

For Hermes, the Greek god of speed, these bacterial sneakers would have been just the ticket. Modern Synthesis co-founders Jen Keane, CEO, and Ben Reeve, CTO, are now setting out to make them available to mere mortals, raising a $4.1 million investment to scale up production. Keane, a graduate from Central Saint Martins School of Art and Design in London, and synthetic biologist Reeve, then at Imperial College London, set up Modern Synthesis in 2020 to pursue ‘microbial weaving’.

Their goal is to produce a new class of material, a hybrid/composite that will replace animal- and petrochemical-made sneakers with a biodegradable, yet durable, alternative. The shoe's upper is made by bacteria that naturally produce nanocellulose—Komagataeibacter rhaeticus—and can be further genetically engineered to also self-dye by producing melanin for color.

The process begins with a two-dimensional yarn scaffold shaped by robotics, which the scientists submerge in a fermentation medium containing the cellulose-producing bacteria. The K. rhaeticus ‘weave’ the sneaker upper by depositing the biomaterial on the scaffold. Once the sheets emerge from their microbial baths, they are shaped on shoe lasts following traditional footwear techniques. “It’s more than the sum of its parts,” Reeves says of the biocomposite. “Initially the scaffold helps the bacteria grow, then the microbial yarn reinforces the material: it holds the scaffold together.” Once the shoe is made, it is sterilized and the bacteria are washed out.

Cellulose shoes made by bacteria, Lisa Melton, Nature Biotechnology

Read more…

Nucleocapsid Rhapsody...


Fig. 1. SARS-CoV-2 N is expressed on the surface of live cells early during infection.
(A) Maximum intensity projections of laser confocal microscopy z-stack images of infected Vero cells with wt SARS-CoV-2 (top) or SARS-CoV-2_eGFP, stained live at 24 hpi (MOI = 1). Scale bars, 20 μm. Images are representative of at least three independent experiments with similar results. DAPI, 4′,6-diamidino-2-phenylindole. (B) Flow cytometry analyses of Vero cells inoculated with wt (top) or eGFP-expressing (bottom) SARS-CoV-2 (MOI = 1), stained live at 24 hpi against SARS-CoV-2 S and N proteins. Representative dot plots of flow cytometry analyses showing double staining of surface S, N, and eGFP proteins, indicating the percentage of the gated cell population for each quadrant of the double staining. Data are representative of at least three independent experiments, each performed with triplicate samples. (C and D) Time course of surface S, N, and eGFP protein expression in live infected Vero cells with wt (C) and eGFP reporter (D) SARS-CoV-2 at 8 and 12 hpi (MOI = 1). Representative histogram overlays of surface S, N, and intracellular eGFP proteins of flow cytometry analyses. Data are representative of one experiment of at least two independent experiments performed in triplicate.

Topics: Biology, COVID-19, Research


SARS-CoV-2 nucleocapsid protein (N) induces strong antibody (Ab) and T cell responses. Although considered to be localized in the cytosol, we readily detect N on the surface of live cells. N released by SARS-CoV-2–infected cells or N-expressing transfected cells binds to neighboring cells by electrostatic high-affinity binding to heparan sulfate and heparin, but not other sulfated glycosaminoglycans. N binds with high affinity to 11 human chemokines, including CXCL12β, whose chemotaxis of leukocytes is inhibited by N from SARS-CoV-2, SARS-CoV-1, and MERS-CoV. Anti-N Abs bound to the surface of N-expressing cells activate Fc receptor-expressing cells. Our findings indicate that cell surface N manipulates innate immunity by sequestering chemokines and can be targeted by Fc-expressing innate immune cells. This, in combination with its conserved antigenicity among human CoVs, advances its candidacy for vaccines that induce cross-reactive B and T cell immunity to SARS-CoV-2 variants and other human CoVs, including novel zoonotic strains.

Cell surface SARS-CoV-2 nucleocapsid protein modulates innate and adaptive immunity, Alberto Domingo Lopez-Munoz, Ivan Kosik, Jaroslav Holly, Jonathan W. Yewdell, Science Advances

Read more…

Soap-Like Properties...


1 Soap, shampoo, and worm-like micelles Soaps and shampoos are made from amphiphilic molecules with water-loving (red) and water-hating (blue) parts that arrange themselves to form long tubes known as “worm-like micelles”. Entanglements between the tubes give these materials their pleasant, sticky feel. b The micelles can, however, disentangle themselves, just as entangled long-chain polymer molecules can slide apart too. In polymers, this process can be modeled by imagining the molecule sliding, like a snake, out of an imaginary tube formed by the surrounding spatial constraints. c Worm-like micelles can also morph their architecture by performing reconnections (left), breakages (down), and fusions (right). These operations occur randomly along the backbone, are in thermal equilibrium, and are reversible. (Courtesy: Davide Michieletto)

Topics: Biology, Biotechnology, DNA, Molecules

DNA molecules are not fixed objects – they are constantly getting broken up and glued back together to adopt new shapes. Davide Michieletto explains how this process can be harnessed to create a new generation of “topologically active” materials.

Call me naive, but until a few years ago I had never realized you can actually buy DNA. As a physicist, I’d been familiar with DNA as the “molecule of life” – something that carries genetic information and allows complex organisms, such as you and me, to be created. But I was surprised to find that biotech firms purify DNA from viruses and will ship concentrated solutions in the post. In fact, you can just go online and order DNA, which is exactly what I did. Only there was another surprise in store.

When the DNA solution arrived at my lab in Edinburgh, it came in a tube with about half a milligram of DNA per centimeter cube of water. Keen to experiment with it, I tried to pipette some of the solutions out, but they didn’t run freely into my plastic tube. Instead, it was all gloopy and resisted the suction of my pipette. I rushed over to a colleague in my lab, eagerly announcing my amazing “discovery”. They just looked at me like I was an idiot. Of course, solutions of DNA are gloopy.

I should have known better. It’s easy to idealize DNA as some kind of magic material, but it’s essentially just a long-chain double-helical polymer consisting of four different types of monomers – the nucleotides A, T, C, and G, which stack together into base pairs. And like all polymers at high concentrations, the DNA chains can get entangled. In fact, they get so tied up that a single human cell can have up to 2 m of DNA crammed into an object just 10 μm in size. Scaled up, it’s like storing 20 km of hair-thin wire in a box no bigger than your mobile phone.

Make or break: building soft materials with DNA, Davide Michieletto is a Royal Society university research fellow in the School of Physics and Astronomy, University of Edinburgh, UK

Read more…

Zombie Apocalypse...


A nurse prepares a COVID-19 vaccine in Guwahati, India, on 10 April. A new subvariant named BA.2.75 that was first detected in India has surfaced in many other countries. ANUPAM NATH/AP IMAGES

Topics: Biology, COVID-19, DNA, Economics, Environment, Evolution, Existentialism

Ed Rybicki, a virologist at the University of Cape Town in South Africa, concentrated his article in Scientific American on the viruses dominating the news cycle in the early 2000s: Ebola, Marburg, and HIV. Not comforting, but he said, "HIV, which is thought to have first emerged in humans in the 1930s, is another kind of virus, known as a retrovirus." Not mentioned, but the H1N1 comes from the 1918 Flu Pandemic, and a friend in Texas lost his girlfriend to it also in the early 2000s. Retro means "a process that reverses the normal flow of information in cells" and relates to a bridge between the first forms of life on this planet. In an e-brief, I wrote my first year at JSNN, an article in Nature: Education posits that viruses are not ‘alive’ because they don’t have metabolic processes, one of the four criteria for life (“organized, metabolism, genetic code, and reproduction”). The last part is important: they cannot reproduce asexually (unicellular division), or sexually with genders, spermatozoa, and an incubation period before birthing a copy. In other words, they aren't "alive," but they aren't dead either. They manage to replicate themselves by invading a host. Usually us.

It DOES mention three possible mechanisms as to origins: The Progressive Hypothesis, i.e., “bits and pieces” of a genome gained the ability to move in and out of cells (retroviruses like HIV given as an example); The Regressive Hypothesis, meaning the viruses evolved from some common ancestor to their current state (reductio ad absurdum), lastly The Virus-First Hypothesis, which puts any anthropocentric notions away and their hypothesis that viruses existed before mortals as “self-replicating units.”

I am as ready for this pandemic to be over as anyone else. However, this read from AAAS didn't give me hope that a societal "all-clear" will be uttered, or that we'll overcome our shared arrogance and stupidity:

In the short history of the COVID-19 pandemic, 2021 was the year of the new variants. Alpha, Beta, Gamma, and Delta each had a couple of months in the Sun.

But this was the year of Omicron, which swept the globe late in 2021 and has continued to dominate, with subvariants—given more prosaic names such as BA.1, BA.2, and BA.2.12.1—appearing in rapid succession. Two closely related subvariants named BA.4 and BA.5 are now driving infections around the world, but new candidates, including one named BA.2.75, are knocking on the door.

Omicron’s lasting dominance has evolutionary biologists wondering what comes next. Some think it’s a sign that SARS-CoV-2’s initial frenzy of evolution is over and it, like other coronaviruses that have been with humanity much longer, is settling into a pattern of gradual evolution. “I think a good guess is that either BA.2 or BA.5 will spawn additional descendants with more mutations and that one or more of those subvariants will spread and will be the next thing,” says Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Research Center.

But others believe a new variant different enough from Omicron and all other variants to deserve the next Greek letter designation, Pi, may already be developing, perhaps in a chronically infected patient. And even if Omicron is not replaced, its dominance is no cause for complacency, says Maria Van Kerkhove, technical lead for COVID-19 at the World Health Organization. “It’s bad enough as it is,” she says. “If we can’t get people to act [without] a new Greek name, that’s a problem.”

As Omicron rages on, scientists have no idea what comes next, Kai Kupferschmidt, American Association for the Advancement of Science

Read more…

Microbots and Chemo..


Credit: Gao Wang

Topics: Biology, Cancer, Chemotherapy, Robotics

Chemotherapy disrupts cancer cells’ ability to reproduce by frustrating cell division and damaging the cells’ DNA. In response to the pharmaceutical onslaught, cancer cells acquire mutations that reduce the therapy’s effectiveness. Compounding the challenge of fighting cancer: Under chemical and other stresses, mutation rates increase.

A team led by Princeton University’s Robert Austin and Chongqing University’s Liyu Liu has developed a novel approach to study—and potentially thwart—cancer cells’ adaptation to chemotherapy. Their cancer cell analogs are wheeled, cylindrical robots about 65 mm in diameter and 60 mm in height (see photo above). Fifty of the robots roll independently of each other over a square table, whose 4.2 × 4.2 m2 surface is covered by 2.7 million LEDs (see photo below). Light from the LEDs serves as the robots’ food. Once a robot has “eaten” the light beneath it, the corresponding LEDs are dimmed until they recover a fixed time later.

The bottom surface of each robot is equipped with four semiconductor-based sensors that can detect the intensities and spatial gradients of the three colors of light emitted by the light table: red, green, and blue (RGB). Each robot’s six-byte genome analog determines how sensitive it is to the three colors. The sensitivity, in turn, determines how readily the robot moves in response to the colors’ intensities and spatial gradients.

Evolving robots could optimize chemotherapy, Charles Day, Physics Today

Read more…

Breadbaskets and War...


Image Source: Hub Pages

Topics: Biology, Civics, Civil Rights, Climate Change, Democracy, Existentialism, Politics

The cornucopia’s history lies in Greek mythology. There are a lot of different stories it might have originated from, but the most common one tells the story of the lightning god, Zeus. As an infant, Zeus was in great danger from his father, Cronus. Zeus was taken to the island of Crete and cared for and nursed by a goat named Amalthea. One day, he accidentally broke off one of her horns, and in order to repay her, he used his powers to ensure that the horn would be a symbol of eternal nourishment, which is where we get the idea that the cornucopia represents abundance.

The History Behind the “Horn of Plenty”, Winnie Lam, Daily Nexus


Russia’s war highlights the fragility of the global food supply — sustained investment is needed to feed the world in a changing climate.

Six boxes of wheat seed sit in our cold store. This is the first time in a decade that my team has not been able to send to Ukraine the improved germplasm we’ve developed as part of the Global Wheat Program at the International Maize and Wheat Improvement Center in Texcoco, Mexico. International postal and courier services are suspended. The seed had boosted productivity year on year in the country, which is now being devastated by war.

Our work builds on the legacy of Norman Borlaug, who catalyzed the Green Revolution and staved off famine in South Asia in the 1970s. Thanks to him, I see how a grain of wheat can affect the world.

Among the horrifying humanitarian consequences of Russia’s invasion of Ukraine are deeply troubling short-, medium- and long-term disruptions to the global food supply. Ukraine and Russia contribute nearly one-third of all wheat exports (as well as almost one-third of the world’s barley and one-fifth of its corn, providing an estimated 11% of the world’s calories). Lebanon, for instance, gets 80% of its wheat from Ukraine alone.

Broken bread — avert global wheat crisis caused by invasion of Ukraine, Alison Bentley, Nature

Read more…

Fantastic Plastic...


Plastic fantastic: this perovskite-based device can be reconfigured and could play an important role in artificial intelligence systems. (Courtesy: Purdue University/Rebecca McElhoe)

Topics: Artificial Intelligence, Biology, Computer Science, Materials Science

Researchers in the US have developed a perovskite-based device that could be used to create a high-plasticity architecture for artificial intelligence. The team, led by Shriram Ramanathan at Purdue University, has shown that the material’s electronic properties can be easily reconfigured, allowing the devices to function like artificial neurons and other components. Their results could lead to more flexible artificial-intelligence hardware that could learn much like the brain.

Artificial intelligence systems can be trained to perform a task such as voice recognition using real-world data. Today this is usually done in software, which can adapt when additional training data are provided. However, machine learning systems that are based on hardware are much more efficient and researchers have already created electronic circuits that behave like artificial neurons and synapses.

However, unlike the circuits in our brains, these electronics are not able to reconfigure themselves when presented with new training information. What is needed is a system with high plasticity, which can alter its architecture to respond efficiently to new information.

Device can transform into four components for artificial intelligence systems, Sam Jarman, Physics World

Read more…

RNA and Covid-19...


NIST researcher Megan Cleveland uses a PCR machine to amplify DNA sequences by copying them numerous times through a series of chemical reactions.
Credit: M. Cleveland/NIST

Topics: Biology, Biotechnology, COVID-19, Diversity in Science, NIST, Research, Women in Science

Scientists track and monitor the circulation of SARS-CoV-2, the virus that causes COVID-19, using methods based on a laboratory technique called polymerase chain reaction (PCR). Also used as the “gold standard” test to diagnose COVID-19 in individuals, PCR amplifies pieces of DNA by copying them numerous times through a series of chemical reactions. The number of cycles it takes to amplify DNA sequences of interest so that they are detectable by the PCR machine, known as the cycle threshold (Ct), is what researchers and medical professionals look at to detect the virus.

However, not all labs get the same Ct values (sometimes also called “Cq” values). In efforts to make the results more comparable between labs, the National Institute of Standards and Technology (NIST) contributed to a multiorganizational study that looked at anchoring these Ct values to a reference sample with known amounts of the virus.

Researchers published their findings in the journal PLOS One.

SARS-CoV-2 is an RNA virus: Its genetic material is single-stranded instead of double-stranded like DNA and contains some different molecular building blocks, namely uracil in place of thymine. But the PCR test only works with DNA, and labs first must convert the RNA to DNA to screen for COVID-19. For the test, RNA is isolated from a patient’s sample and combined with other ingredients, including short DNA sequences are known as primers, to transform the RNA into DNA.

RNA Reference Materials Are Useful for Standardizing COVID-19 Tests, Study Shows, NIST

Read more…