biology (78)

Brookhaven and Fake News...

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Climate of fear Anti-science protestors led to the closure of the High Flux Beam Reactor at the Brookhaven National Laboratory in the US 25 years ago using tactics that are widespread today. (Courtesy: iStock/DanielVilleneuve)

Topics: Biology, Cancer, Carl Sagan, Civilization, Climate Change, Philosophy, Physics

I typically don't comment on articles, but this one resonated with my memories of Carl Sagan desperately trying to raise the critical thinking skills of an entire essential nation with "The Demon-Haunted World: Science as a Candle in the Dark." The host of Cosmos would succumb to pneumonia as a consequence of bone marrow disease. I will be the age Carl was when he passed away this year, 62, but not as accomplished as he did in the six decades we all had access to him.

The framework of our current duress was already here in the form of celebrity worship, gossip columns, and talk shows where sensationalism equaled eyeballs, just as the Internet rouses the primitive lizard portion of our brains to be afraid, get angry, and "buy-purchase-consume" products (a friend who's a sound engineer likes to say that a lot).

Underhand tactics by environmental activists led to the closure of a famous physics facility 25 years ago. We can still learn much from the incident, says Robert P Crease.

Fake facts, conspiracy theories, nuclear fear, science denial, baseless charges of corruption, and the shouting down of reputable health officials. All these things happened 25 years ago, long before the days of social media, in a bipartisan, celebrity-driven episode of science denial.  Yet the story offers valuable lessons for what works and what does not (mostly the latter) for anyone wanting to head off such incidents.

The episode in question concerned one of the more valuable scientific facilities in the US, the High Flux Beam Reactor (HFBR) at the Brookhaven National Laboratory. As I mentioned in a previous column and in my book The Leak, the HFBR was a successful research instrument that was used to make medical isotopes and study everything from superconductors to proteins and metals. “Experimentalists saw the reactor as the place to go,” recalls the physicist William Magwood IV, then at the US Department of Energy.

But in 1997, lab scientists discovered a leak of water from a pool located in the same building as the reactor, where its spent fuel was stored. The leak contained tritium, a radioactive isotope of hydrogen that decays with a half-life of about 12 years, releasing low-energy electrons that can be stopped by a few sheets of paper. The total amount of tritium in the leak was about that in typical self-illuminating “EXIT” signs.

The protestors’ tactics are a familiar part of today’s political environment: tell people they are in danger and insist that anyone who says otherwise is lying.

The article goes on to recount the actor Alec Baldwin using his celebrity to put a ten-year-old child on the Montell Williams Show to claim that the tritium and the research facility caused his cancer. It wasn't true, but it was LOUD, drowning out the experts who are used to spirited peer review and erudite discussions of research, not tears and gnashing of teeth.

Montell Williams ended his talk show after announcing that he had multiple sclerosis. Alec Baldwin, though I enjoyed his SNL skits, has other pressing issues.

I have a physicist friend who's using tritium in his research with optical tweezers, separating isotopes to detect and treat cancers, among other applications. I am opting not to give his website as those same elements described in the article about Brookhaven National Labs have metastasized into our current societal mass psychosis. If his research leads to your cancer cure, you can thank him later.

Twenty-five years ago, we weren't as far along in climate disruption as we are now. Twenty-five years ago, CNN was 19 years old, and its clones, Fox and MSNBC, were 3 years old. Five years after the Y2K scare (exquisitely setting us up for election 2000 and 9/11), humanity further siloed itself into warring tribes, first posting on Internet bulletin boards, MySpace. Then, the logical progression was to Facebook, Twitter (now X), and its myriad progeny.

A side note: CERN would go on to discover the Higgs Boson because we, in the spirit of fiscal stewardship, closed the superconducting collider in Waxahachie, Texas, 48 kilometers south of Dallas. Peter Higgs and François Englert owe their 2013 Physics Nobel Prize to Switzerland. U-S-A. U-S-A.

How much further along in cancer research and nuclear energy as an alternative to fossil fuels would we be if, prior to Facebook and the former Twitter, we exercised a little critical thinking and common sense? I'm not talking about tritium, but fission reactors, which we know how to build (fusion, though cleaner and less radioactive, is still far off), but the environmental activists have terrorized anyone from building newer and safer facilities that might have had some positive impact on our warming climate. To paraphrase a famous saying, "Don't let the perfect be the enemy of the good." Our air quality improved during the pandemic, so the logic leads to upgrading public transportation to something matching other countries that rely on it more than we do, or within our borders, the subway systems in New York, New Jersey, Philadelphia, or Washington, DC. You end up doing nothing of any importance. We could replace the fission reactors one by one as fusion comes online.

That is what enrages and disappoints me.

The American reactor that was closed by fake news, Robert P Crease, Physics World

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A Path From Panic...

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PAC1R-expressing dorsal raphe neurons in the mouse brain (red) serve as the projection targets for PACAP parabrachial neurons to mediate panic-like behavioral and physical symptoms. Credit: Salk Institute

Topics: Biology, Medicine, Research, Science

Overwhelming fear, sweaty palms, shortness of breath, rapid heart rate—these are the symptoms of a panic attack, which people with panic disorder have frequently and unexpectedly. Creating a map of the regions, neurons, and connections in the brain that mediate these panic attacks can provide guidance for developing more effective panic disorder therapeutics.

Now, Salk researchers have begun to construct that map by discovering a brain circuit that mediates panic disorder. This circuit consists of specialized neurons that send and receive a neuropeptide—a small protein that sends messages throughout the brain—called PACAP. What's more, they determined that PACAP and the neurons that produce its receptor are possible druggable targets for new panic disorder treatments.

The findings were published in Nature Neuroscience.

"We've been exploring different areas of the brain to understand where panic attacks start," says senior author Sung Han, associate professor at Salk.

"Previously, we thought the amygdala, known as the brain's fear center, was mainly responsible—but even people who have damage to their amygdala can still experience panic attacks, so we knew we needed to look elsewhere. Now, we've found a specific brain circuit outside of the amygdala that is linked to panic attacks and could inspire new panic disorder treatments that differ from currently available panic disorder medications that typically target the brain's serotonin system."

Scientists uncover key brain pathway mediating panic disorder symptoms, Salk Institute.

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The "Tiny Ten"...

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Researchers are working to overcome challenges related to nanoscale optoelectronic interconnects, which use light to transmit signals around an integrated circuit. IMAGE: PROVIDED BY NCNST

Topics: Biology, Materials Science, Nanoengineering, Nanomaterials, Nanotechnology, Quantum Mechanics

The promise of nanotechnology, the engineering of machines and systems at the nanoscale, is anything but tiny. Over the past decade alone, there has been an explosion in research on how to design and build components that solve problems across almost every sector, and nanotechnology innovations have led to huge advancements in our quest to address humanity’s grand challenges, from healthcare to water to food security.

Like any area of scholarship, there are still so many unknowns. And yet, there are more talented scientists and engineers endeavoring to better comprehend and harness the power of nanotechnology than ever before. The future is bright for nanotechnology and its applications.

In celebration of its 20th anniversary, the National Center for Nanoscience and Technology, China (NCNST), a subsidiary of the prestigious Chinese Academy of Sciences, partnered with Science Custom Publishing to survey nanoscience experts from the journal and across the globe about the most knotty and fascinating questions that still need to be answered if we are to advance nanotechnology in society.

The Tiny Ten: Experts weigh in on the top 10 challenges remaining for nanoscience & nanotechnology, Science Magazine

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Anthrobots...

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An Anthrobot is shown, depth colored, with a corona of cilia that provides locomotion for the bot. Credit: Gizem Gumuskaya, Tufts University

Topics: Applied Physics, Biology, Biomimetics, Biotechnology, Research, Robotics

Researchers at Tufts University and Harvard University's Wyss Institute have created tiny biological robots that they call Anthrobots from human tracheal cells that can move across a surface and have been found to encourage the growth of neurons across a region of damage in a lab dish.

The multicellular robots, ranging in size from the width of a human hair to the point of a sharpened pencil, were made to self-assemble and shown to have a remarkable healing effect on other cells. The discovery is a starting point for the researchers' vision to use patient-derived biobots as new therapeutic tools for regeneration, healing, and treatment of disease.

The work follows from earlier research in the laboratories of Michael Levin, Vannevar Bush, Professor of Biology at Tufts University School of Arts & Sciences, and Josh Bongard at the University of Vermont, in which they created multicellular biological robots from frog embryo cells called Xenobots, capable of navigating passageways, collecting material, recording information, healing themselves from injury, and even replicating for a few cycles on their own.

At the time, researchers did not know if these capabilities were dependent on their being derived from an amphibian embryo or if biobots could be constructed from cells of other species.

In the current study, published in Advanced Science, Levin, along with Ph.D. student Gizem Gumuskaya, discovered that bots can, in fact, be created from adult human cells without any genetic modification, and they are demonstrating some capabilities beyond what was observed with the Xenobots.

The discovery starts to answer a broader question that the lab has posed—what are the rules that govern how cells assemble and work together in the body, and can the cells be taken out of their natural context and recombined into different "body plans" to carry out other functions by design?

Anthrobots: Scientists build tiny biological robots from human tracheal cells, Tufts University

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Quasicrystal Legos...

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A mathematical tool called a fast Fourier transform maps the structure in a way that reveals the 12-fold symmetry of the quasicrystal. The fast Fourier transform of the electron microscope image of the quasicrystal is shown on the left, while the transform of the simulated crystal is shown on the right. Image credit: Mirkin Research Group, Northwestern University, and Glotzer Group, University of Michigan.

Topics: Biology, DNA, Nanoengineering, Nanomaterials, Nanotechnology

ANN ARBOR—Nanoengineers have created a quasicrystal—a scientifically intriguing and technologically promising material structure—from nanoparticles using DNA, the molecule that encodes life.

The team, led by researchers at Northwestern University, the University of Michigan, and the Center for Cooperative Research in Biomaterials in San Sebastian, Spain, reports the results in Nature Materials.

Unlike ordinary crystals, which are defined by a repeating structure, the patterns in quasicrystals don’t repeat. Quasicrystals built from atoms can have exceptional properties—for example, absorbing heat and light differently, exhibiting unusual electronic properties such as conducting electricity without resistance, or their surfaces being very hard or very slippery.

Engineers studying nanoscale assembly often view nanoparticles as a kind of ‘designer atom,’ which provides a new level of control over synthetic materials. One of the challenges is directing particles to assemble into desired structures with useful qualities, and in building this first DNA-assembled quasicrystal, the team entered a new frontier in nanomaterial design.

“The existence of quasicrystals has been a puzzle for decades, and their discovery appropriately was awarded a Nobel Prize,” said Chad Mirkin, the George B. Rathmann Professor of Chemistry at Northwestern University and co-corresponding author of the study. “Although there are now several known examples, discovered in nature or through serendipitous routes, our research demystifies their formation and, more importantly, shows how we can harness the programmable nature of DNA to design and assemble quasicrystals deliberately.”

Nanoparticle quasicrystal constructed with DNA, Kate McAlpine, University of Michigan

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Polluting the Pristine...

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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.

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Magnetic Chirality...

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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, Science.org.

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Distant Cousins...

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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.

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Nano Sanitizer...

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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.

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Mice, Men, and Nanoparticles...

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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, Phys.org

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LNPs...

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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

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Like Mushrooms for Plastics...

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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, Phys.org.

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Wonderful...

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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

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Life Detector...

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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, Phys.org.

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Permafrost Zombies...

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(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

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The Apogee of Evil...

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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

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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

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Cellulose Shoes...

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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

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Nucleocapsid Rhapsody...

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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

Abstract

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

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Soap-Like Properties...

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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

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