Research reveals dual nature of beneficial bacteria UD1022

UD post-doctoral researcher Amanda Rosier is lead author on two papers reporting on the behavior of UD1022, a UD-patented beneficial bacteria that can help protect alfalfa from fungal pathogens.
Photo Credits: Evan Krape and courtesy of Amanda Rosie

Scientific Frontline: Extended "At a Glance" Summary: UD1022 (Beneficial Bacteria)

The Core Concept: UD1022 is a unique, patented strain of Bacillus subtilis, a naturally occurring bacterium that colonizes the surface of plant roots to promote vigorous growth and trigger system-wide resistance against microscopic disease agents.

Key Distinction/Mechanism: While it acts as a highly effective, broad-spectrum antifungal by producing an antibiotic molecule called surfactin and forming protective biofilms, UD1022 exhibits a complex "dual nature." It can inadvertently harm plants by secreting molecules that interrupt the "quorum sensing" (chemical communication) of other beneficial, nitrogen-fixing bacteria like rhizobium, thereby preventing them from colonizing the roots.

Major Frameworks/Components:

• Surfactin Production: An antibiotic molecule synthesized by UD1022 that directly inhibits fungal pathogen growth.
• Biofilm Formation: Thick, sugary coatings produced by the bacteria that help them adhere to plants and suppress specific fungal species.
• Quorum Sensing Interference: The mechanism by which UD1022 silences the chemical signaling molecules of symbiotic bacteria, inhibiting root colonization and nitrogen fixation.
• Rhizosphere Dynamics: The complex, localized ecological interactions between plant roots, soil, and competing microbial communities.

Modified Botox gives long-term pain relief after nerve injury without side effects

A single injection of the elongated Botox could relieve pain for months without risk of paralysis or addiction
Photo Credit: Mufid Majnun

A modified form of Botox could give long-term pain relief to patients with chronic nerve injury pain, according to a new study.

A team of scientists from the Universities of Sheffield, Reading and University College London (UCL) and US-based biopharmaceutical company Neuresta have created a new, elongated botulinum neurotoxin which can alleviate chronic pain without risk of paralysis or addiction. 

Chronic pain is extremely difficult to manage, and currently available drugs are limited by dangerous side effects. Opioids like morphine and fentanyl are the gold standard for short-term pain relief but they cannot effectively treat chronic pain due to the risk of addition, abuse and overdose. 

Findings of the new study, published in the journal Life Science Alliance, show that a single injection of the precisely engineered botulinum neurotoxin provides long-lasting relief in mice models, without adverse effects.

The team, led by Professor Bazbek Davletov, Chair of Biomedical Science, and Research Associate Charlotte Leese from the University of Sheffield, developed a new way of rebuilding Botox by using elements of Clostridium botulinum and created a biopharmaceutical with new properties, without unwanted toxic effects. 

Neutrons for better vaccines against multidrug resistant germs

Dr. Jia-Jheng Kang prepares measurements for the vaccines at the KWS-2 sample site.
Photo Credit: Bernhard Ludewig, FRM II / TUM

Neutrons from the Research Neutron Source Heinz Maier-Leibnitz (FRM II) can be used to explore the structure of biomolecules. The most recent success: the precise analysis of a promising vaccine against multidrug resistant germs.

Bacteria which are resistant to all conventional antibiotics cause more than a million deaths each year. Consequently, researchers around the world are searching for new therapeutic approaches to combat these pathogens. Two years ago, an international team in Grenoble identified an active ingredient suitable for the production of a vaccine against multidrug resistant bacteria Pseudomonas aeruginosa. The vaccine has in the meantime been successfully tested on mice.

"As with many new vaccines, in this case the active ingredient is embedded in liposomes. The exact characterization and understanding of these nanoscopic biomolecules is a key factor in the development and optimization of future vaccines," says Dr. Marco Maccarini, biophysicist at the French National Centre for Scientific Research (CNRS). Together with experts at the TIMC laboratory of the Université Grenoble Alpes (UGA) and at the FRM II he has successfully analyzed the structure of the candidate vaccine against Pseudomonas aeruginosa.

USF geoscientist discovers new phosphorus material after New Port Richey lightning strike

Matthew Pasek
Courtesy of University of South Florida

After lightning struck a tree in a New Port Richey neighborhood, a University of South Florida professor discovered the strike led to the formation of a new phosphorus material. It was found in a rock – the first time in solid form on Earth – and could represent a member of a new mineral group. 

“We have never seen this material occur naturally on Earth – minerals similar to it can be found in meteorites and space, but we've never seen this exact material anywhere,” said geoscientist Matthew Pasek. 

In a recent study published in Communications Earth & Environment, Pasek examines how high-energy events, such as lightning, can cause unique chemical reactions, and in this instance, result in a new material – one that is transitional between space minerals and minerals found on Earth. 

“When lightning strikes a tree, the ground typically explodes out and the surrounding grass dies, forming a scar and sending electric discharge through nearby rock, soil and sand, forming fulgurites, also known as ‘fossilized lightning’,” Pasek said. 

Scientists uncover a key chemical structure in pigment molecule

Photo Credit: NCI

After nearly a century of scientific inquiry, scientists have at last been able to characterize a key component in the substance responsible for giving countless living organisms their color. 

In the study, published online today in the journal Nature Chemistry, an international team of researchers isolated a key molecule involved in the synthesis of melanin, a substance in the human body that produces pigmentation in the hair and skin and protects the cells from being damaged by ultraviolet radiation from the sun. The molecule they studied has many of the physical properties of eumelanin, a type of melanin that typically produces only black and brown pigments. 

Despite what researchers know about melanin, its chemical structure has remained elusive, said Bern Kohler, an Ohio Eminent Scholar and professor of chemistry and biochemistry at The Ohio State University, one of three senior authors on the study.  

“Melanin is literally as plain as the nose on our face and we still don't know exactly what it's made of and how it works,” said Kohler. “It's thought to be a material made of large numbers of interacting components, and so what my collaborators and I are trying to get at is, what are melanin’s underlying chemical units and what are the interactions that give rise to its properties?”

Global study finds some women experience heavier menstrual flow after COVID-19 vaccination

Analyses showed a small increase in the percentage of participants who experienced greater total bleeding quantity following the first COVID-19 vaccine dose compared with an unvaccinated comparison group.
Photo Credit: Obi

A new international study finds that women vaccinated for COVID-19 have a slightly higher risk for a heavier period after vaccination.

The study, led by Oregon Health & Science University reproductive health services researcher Blair Darney, Ph.D., M.P.H., and physician-scientist Alison Edelman, M.D., M.P.H., published in the British Journal of Obstetrics and Gynaecology. These findings build on prior work from the same research team that first identified an association between COVID-19 vaccines and menstrual cycle changes.

While there is a growing body of evidence demonstrating that COVID-19 vaccination is associated with a small increase in cycle length, other disturbances such as bleeding quantity are less well known. This study aimed to estimate the effect of COVID-19 vaccination on menstrual bleeding quantity among individuals with normal menstrual cycles.

“Menstruation is a routine bodily function and a key indicator of overall health, so it’s crucial that we understand the scope of this issue among the global population,” said Edelman, one of the study’s lead authors. “The more we can understand about these reported changes, the more effectively we’re able to counsel individuals about what to expect with a COVID-19 vaccine and how to make an informed decision about getting vaccinated.”

Prior treatments influence immunotherapy response in advanced melanoma

Photo Credit: Ivan Samkov

Research led by scientists at UCLA Jonsson Comprehensive Cancer Center found that responses to a type of immunotherapy called PD-1 checkpoint blockade in patients with advanced melanoma depended on whether or not they had previously received another immunotherapy – CTLA-4 blockade – as well as other factors.

Their findings, based on analysis of seven data sets generated over the past decade, which included results of tumor biopsies from more than 500 patients, are published in Cancer Cell.

“In our large set of data, features that have been used to predict response to anti-PD-1 checkpoint blockade therapy – often called biomarkers –related to the presence of certain immune cell types in the tumor and the genetic profile of the tumors themselves were modified by a patient’s treatment history,” said lead author Katie Campbell, PhD, a postdoctoral fellow in hematology/oncology at UCLA Jonsson Comprehensive Cancer Center.

When a patient is diagnosed with advanced melanoma, they usually are treated with immune therapies like anti-PD-1 blockade and anti-CTLA-4 blockade, in combination or alone. By blocking different proteins that diminish the effectiveness of T cells, these checkpoint inhibitors enhance the body’s immune response to cancer.  

From greenhouse gas to value-added product

Dogukan Apaydin, Dominik Eder, Hannah Rabl, electrochemical cell (from left)
Photo Credit: Dogukan Apaydin / TU Wien

If one converts CO2 into synthesis gas, a valuable starting material for the chemical industry can be obtained. Researchers at TU Wien show how this works even at room temperature and atmospheric pressure.

Thinking of CO2, terms like climate-damaging or waste product probably quickly come to mind. While CO2 has been that for a long time – a pure waste product – more and more processes are being developed with which the greenhouse gas can be converted into valuable raw materials. Researchers then speak of "value-added chemicals". A new material with which this is possible was developed at TU Wien and recently presented in the journal Communications Chemistry.

Researchers at Dominik Eder's group developed a new material that facilitates the conversion of CO2. These are MOCHAs – organometallic chalcogenolate compounds that serve as catalysts. The result of the electrochemical conversion is synthesis gas, or syngas for short, which is an important raw material for the chemical industry.

Fast light pulse triggers the charge transfer into the water

The study was only made possible by the new laser laboratories in the ZEMOS research building, in which all external interference signals are minimized.
Photo Credit: © RUB, Marquard

With new technology, researchers were able to observe live what happens in the first picosecond when a proton detaches from a dye after light.

In certain molecules, the so-called photoc acids, a proton can be released locally by excitation with light. The solution suddenly changes the pH - a kind of fast switch that is important for many chemical and biological processes. So far, however, it is still unclear what actually happened at the moment of proton release. This is exactly what researchers in the Ruhr Explores Solvation Cluster of Excellence could do RESOLV the Ruhr University Bochum is now experimentally observing using new technology. They saw a tiny quake that only lasted three to five picoseconds before the proton came loose. They report on this in the journal Chemical Sciences.

Scientists Get Closer to Curing Alzheimer's and Parkinson's Diseases

In Russia, the incidence of dementia, Parkinson's disease and Alzheimer's disease will reach the epidemiological threshold of 5%
Image Credit: Gerd Altmann

Prospective compounds for the treatment of neurodegenerative diseases have been synthesized by Russian scientists. The compounds are of great interest for medicinal chemistry, especially for the development of treatments for Alzheimer's and Parkinson's diseases.

According to Timofey Moseev, a member of the group and an employee of the UrFU Chemical Pharmaceutical Center, the researchers managed to test the toxicity of the compounds in vitro on the kidney cells of a healthy human embryo. The researchers used the strategy of nucleophilic hydrogen substitution (a substitution reaction in which the substrate is attacked by a nucleophile, a reagent that carries a pair of unshared electrons). The process does not require metal catalysis, which is particularly important in the production of biologically active compounds, where any metal impurity can significantly distort toxicity and activity data.

To assess the ability of the synthesized molecules to bind to biotargets (proteins that play an important role in a particular disease), the researchers conducted experiments using docking - a molecular modeling technique. Docking allows predicting with a certain probability how a molecule interacts with targeted proteins.

Predatory dinosaurs such as T. rex sported lizard-like lips

A juvenile Edmontosaurus disappears into the enormous, lipped mouth of Tyrannosaurus.
Illustration Credit Dr Mark Witton

A new study suggests that predatory dinosaurs, such as Tyrannosaurus rex, did not have permanently exposed teeth as depicted in films such as Jurassic Park, but instead had scaly, lizard-like lips covering and sealing their mouths.

Researchers and artists have debated whether theropod dinosaurs, the group of two-legged dinosaurs that includes carnivores and top predators like T. rex and Velociraptor, as well as birds, had lipless mouths where perpetually visible upper teeth hung over their lower jaws, similar to the mouth of a crocodile.

However, an international team of researchers challenge some of the best-known depictions, and say these dinosaurs had lips similar to those of lizards and their relative, the tuatara - a rare reptile found only in New Zealand, which are the last survivors of an order of reptiles that thrived in the age of the dinosaurs.

In the most detailed study of this issue yet, the researchers examined the tooth structure, wear patterns and jaw morphology of lipped and lipless reptile groups and found that theropod mouth anatomy and functionality resembles that of lizards more than crocodiles. This implies lizard-like oral tissues, including scaly lips covering their teeth.

Watch nanoparticles grow into crystals

Liquid-phase TEM video of layer-by-layer growth of a crystal with smooth surface from gold concave nanocubes. Surface particles on the growing crystal are tracked (center positions overlaid with yellow dots).

For the first time ever, researchers have watched the mesmerizing process of nanoparticles self-assembling into solid materials. In the stunning new videos, particles rain down, tumble along stairsteps and slide around before finally snapping into place to form a crystal’s signature stacked layers.

Led by Northwestern University and the University of Illinois, Urbana-Champaign, the research team says these new insights could be used to design new materials, including thin films for electronic applications.

The research was published today (March 30) in the journal Nature Nanotechnology. 

Described by the researchers as an “experimental tour de force,” the study used a newly optimized form of liquid-phase transmission electron microscopy (TEM) to gain unprecedented insights into the self-assembly process. Before this work, researchers used microscopy to watch micron-sized colloids — which are 10 to 100 times larger than nanoparticles — self-assemble into crystals. They also have used X-ray crystallography or electron microscopy to visualize single layers of atoms in a crystalline lattice. But they were unable to watch atoms individually move into place.

“We know that atoms use a similar scheme to assemble into crystals, but we have never seen the actual growth process,” said Northwestern’s Erik Luijten, who led the theoretical and computational work to explain the observations. “Now we see it coming together right in front of our eyes. By viewing nanoparticles, we are watching particles that are larger than atoms, but smaller than colloids. So, we have completed the whole spectrum of length scales. We are filling in the missing length.”

Was plate tectonics occurring when life first formed on Earth?

Plate tectonics melts and mixes rocks to create magmas with specific chemical makeups. Rochester geologists are using that chemical evidence to unlock information about plate tectonic activity on Earth more than 4 billion years ago.
Photo Credit: Tetiana Grypachevska

Zircon crystals and magmas reveal new information about plate tectonic activity on Earth billions of years ago.

Earth is a dynamic and constantly changing planet. From the formation of mountains and oceans to the eruption of volcanoes, the surface of our planet is in a constant state of flux. At the heart of these changes lies the powerful force of plate tectonics—the movements of Earth’s crustal plates. This fundamental process has shaped the current topography of our planet and continues to play a role in its future.

But what was plate tectonic activity like during early Earth? And was the process even occurring during the time when life is thought to have formed?

“The dynamic tectonic nature of the modern Earth is one of the reasons why life exists today,” says Wriju Chowdhury, a postdoctoral research associate in the lab of Dustin Trail, an associate professor of earth and environmental sciences at the University of Rochester. “Exploring the geodynamics and the lithological diversity of the early Earth could lead to revelations of how life first began on our planet.”

AI predicts enzyme function better than leading tools

An Illinois research team created an AI tool to predict an enzyme’s function from its sequence using the campus network and resource group servers. Pictured, from left: Tianhao You, Haiyang (Ocean) Cui, Huimin Zhao and Guangde Jiang.   
Photo Credit: Fred Zwicky

A new artificial intelligence tool can predict the functions of enzymes based on their amino acid sequences, even when the enzymes are unstudied or poorly understood. The researchers said the AI tool, dubbed CLEAN, outperforms the leading state-of-the-art tools in accuracy, reliability and sensitivity. Better understanding of enzymes and their functions would be a boon for research in genomics, chemistry, industrial materials, medicine, pharmaceuticals and more.

“Just like ChatGPT uses data from written language to create predictive text, we are leveraging the language of proteins to predict their activity,” said study leader Huimin Zhao, a University of Illinois Urbana-Champaign professor of chemical and biomolecular engineering. “Almost every researcher, when working with a new protein sequence, wants to know right away what the protein does. In addition, when making chemicals for any application – biology, medicine, industry – this tool will help researchers quickly identify the proper enzymes needed for the synthesis of chemicals and materials.”

The researchers will publish their findings in the journal Science and make CLEAN accessible online March 31.

Allies or enemies of cancer: the dual fate of neutrophils

Neutrophils infiltrating tumors are heterogeneous and different neutrophil types can have opposing effects on cancer progression. The image shows artistic rendering of a lung tumor nodule (in blue) infiltrated by various neutrophil types (shown in green, orange and red) including some (in red) that are expanded by immunotherapy and are required for tumor elimination.
Illustration Credit: © Mate Kiss, Evangelia Bolli and Mikael Pittet

An international team including scientists from the UNIGE and Harvard has discovered a new type of immune cell whose action is essential for the success of immunotherapies.

Why do cancer immunotherapies work so extraordinarily well in a minority of patients, but fail in so many others? By analyzing the role of neutrophils, immune cells whose presence usually signals treatment failure, scientists from the University of Geneva (UNIGE), from Harvard Medical School, and from Ludwig Cancer Center have discovered that there is not just one type of neutrophils, but several. Depending on certain markers on their surface, these cells can either promote the growth of tumors, or fight them and ensure the success of a treatment. By boosting the appropriate factors, neutrophils could become great agents of anti-tumor immunity and reinforce the effects of current immunotherapies. These results can be read in Cell.