OHSU researchers use AI machine learning to map hidden molecular interactions in bacteria

Andrew Emili, Ph.D., professor of systems biology and oncological sciences, works in his lab at OHSU. Emili is part of a multi-disciplinary research team that uncovered how small molecules within bacteria interact with proteins, revealing a network of molecular connections that could improve drug discovery and cancer research.
Photo Credit: OHSU/Christine Torres Hicks

A new study from Oregon Health & Science University has uncovered how small molecules within bacteria interact with proteins, revealing a network of molecular connections that could improve drug discovery and cancer research.

The work also highlights how methods and principles learned from bacterial model systems can be applied to human cells, providing insights into how diseases like cancer emerge and how they might be treated. The results are published today in the journal Cell.

The multi-disciplinary research team, led by Andrew Emili, Ph.D., professor of systems biology and oncological sciences in the OHSU School of Medicine and OHSU Knight Cancer Institute, alongside Dima Kozakov, Ph.D., professor at Stony Brook University, studied Escherichia coli, or E. coli, a simple model organism, to map how metabolites — small molecules essential for life — interact with key proteins such as enzymes and transcription factors. These interactions control important processes such as cell growth, division and gene expression, but how exactly they influence protein function is not always clear.

A new experimental system to bring quantum technologies closer to students

The expert Raúl Lahoz and a group of students with the new equipment for studying quantum physics.
 Photo Credit: Fundació Catalunya La Pedrera

The world of quantum physics is experiencing a second revolution, which will drive an exponential leap in the progress of computing, the internet, telecommunications, cybersecurity and biomedicine. Quantum technologies are attracting more and more students who want to learn about concepts from the subatomic world — such as quantum entanglement or quantum superposition — to explore the innovative potential of quantum science. In fact, understanding the non-intuitive nature of quantum technology concepts and recognizing their relevance to technological progress is one of the challenges of 2025, declared the International Year of Quantum Science and Technology by UNESCO.

Now, a team from the Faculty of Physics of the University of Barcelona has designed new experimental equipment that makes it possible for students to familiarize themselves with the more complex concepts of quantum physics. The configuration they present —versatile, cost-effective and with multiple ways of application in the classroom — is already operational in the Advanced Quantum Laboratory of the UB’s Faculty of Physics and could also be accessible in less specialized centers.

This innovation is presented in an article in the journal EPJ Quantum Technology, which results from a collaboration between professors Bruno Juliá, from the Department of Quantum Physics and Astrophysics and the UB Institute of Cosmos Sciences (ICCUB); Martí Duocastella, from the Department of Applied Physics and the UB Institute of Nanoscience and Nanotechnology (IN2UB), and José M. Gómez, from the Department of Electronic and Biomedical Engineering. It is based on the result of Raúl Lahoz’s master’s final project, with the participation of experts Lidia Lozano and Adrià Brú.

Child mortality has risen since pandemic, new study shows

Photo Credit: Josue Michel

While child deaths in England fell temporarily during the COVID-19 pandemic, they have now risen to new heights, a new study from researchers at the University of Bristol and based on unique National Child Mortality Database (NCMD) data has found.

The study, published in PLOS Medicine, has shown that children were less likely to die during the pandemic lockdown (April 2020–March 2021) than at any time before or since, with 377 fewer deaths than expected from the previous year.  

The number of deaths in the following year (2021-2022) was similar to before the pandemic, but in 2022−2023, there were 258 more deaths than expected from the pre-pandemic period. 

The aim of the research was to quantify the relative rate, and causes, of childhood deaths in England, before, during, and after national lockdowns for COVID-19 and its social changes.

The researchers identified all those children in England who died between April 2019 and March 2023 and calculated what the rate of death was for each year, for each group of children (e.g., infants or older children) and cause of death.

Eight Psychiatric Disorders Share the Same Genetic Causes

Image Credit: Won Lab

Building off previous groundbreaking research, a new study identifies specific genetic variants that have significant impacts on brain development and are shared across eight different psychiatric disorders. Targeting these variants could pave the way for treatments that address multiple conditions at once.

Psychiatric disorders often overlap and can make diagnosis difficult. Depression and anxiety, for example, can coexist and share symptoms. Schizophrenia and anorexia nervosa. Autism and attention deficit/hyperactivity disorder, too. But, why?

Life experiences, environment, and genetics can all influence psychiatric disorders, but much of it comes down to variations in our genetics. Over the past few years, scientists in the field of psychiatric genetics have found that there are common genetic threads that may be linking and causing coexisting psychiatric disorders.

In 2019, researchers at the Psychiatric Genomics Consortium, Harvard University, and the UNC School of Medicine identified 136 “hot spots” within the genome that are associated with eight psychiatric disorders. Among them, 109 hot spots were shared among multiple disorders, or “pleiotropic”. However, it was not clear at the time how genetic variations within these hot spots differed from those that only have roles in only one disorder.

Better prediction of epidemics

The curve calculated using a “reproduction matrix” (turquoise) reflects the actual infection rate (black) much more accurately than previous models (yellow and blue).
Graphic Credit: Empa

The reproduction number R is often used as an indicator to predict how quickly an infectious disease will spread. Empa researchers have developed a mathematical model that is just as easy to use but enables more accurate predictions than R. Their model is based on a reproduction matrix that takes into account the heterogeneity of society.

"Your friends have more friends than you do", wrote the US sociologist Scott Feld in 1991. Feld's so-called friendship paradox states that the friends of any given person have more friends on average than the person themselves. This is based on a simple probability calculation: Well-connected people are more likely to appear in other people's social circles. "If you look at any person's circle of friends, it is very likely that this circle contains very well-connected people with an above-average number of friends," explains Empa researcher Ivan Lunati, head of the Computational Engineering laboratory. A similar principle served Lunati and his team as the basis for a new mathematical model that can be used to more accurately predict the development of case numbers during an epidemic.

T cells rise up to fight infections in the gut

An image produced through Xenium analysis of mouse small intestines. Protruding “villi” stick up from the lining of the small intestine. Valley-like “crypts” fill in the gaps.
Image Credit: Reina Lab, La Jolla Institute for Immunology

Your gut is a battleground. The cells that line your small intestine have to balance two seemingly contradictory jobs: absorbing nutrients from food, while keeping a wary eye out for pathogens trying to invade your body.

“This is a surface where pathogens can sneak in,” says La Jolla Institute for Immunology (LJI) Assistant Professor Miguel Reina-Campos, Ph.D. “That’s a massive challenge for the immune system.”

So how do immune cells keep the gut safe? New research led by scientists at LJI, UC San Diego, and the Allen Institute for Immunology shows that pathogen-fighting immune cells called tissue-resident memory CD8 T cells (TRM cells) go through a surprising transformation—and relocation—as they fight infections in the small intestine.

In fact, these cells literally rise up higher in the tissue to fight infections before pathogens can spread to deeper, more vulnerable areas.

Peeing with your peers

 

Male chimps socializing
Photo Credit: Kyoto University, Kumamoto Sanctuary

In Italy, it has been said, there is a proverb for everything.

Chi non piscia in compagnia o è un ladro o è una spia -- "Whoever doesn't pee in the company of others is either a thief or a spy" -- goes one such saying, describing a communal act that in Japanese is known as tsuré-shon.

Social urination can be found represented in artwork across the centuries and around the world, and even today continues to be represented in cultural tropes. Now, researchers in Japan -- observing chimpanzees -- are suggesting that this phenomenon has evolutionary roots even deeper than previously expected.

Despite decades of research into other contagious behaviors such as yawning, contagious urination has never been studied scientifically in any species. To tackle this, a team at Kyoto University conducted 604 hours of direct observation at the University's Kumamoto Sanctuary, documenting 1,328 urination events. The researchers analyzed whether these were aligned in time, triggered by nearby individuals, or influenced by social relationships.

Scientists Have Given a Second Life to Paper Production Waste

Lignosulphonate is a safe waste from pulp and paper industries.
Photo Credit: Rodion Narudinov

Ural Federal University specialists have developed a new method of obtaining growth stimulators for agriculture plants. Waste from pulp and paper industries, lignosulphonate, became the basis for the production of biologically active stimulants of prolonged action for plant crops. Due to the structural features, the obtained samples can be used not only to improve crop growth, but also to remove some toxic substances from wastewater. The results were published in the Journal of Molecular Liquids. 

The Sulfite method is one of the currently used methods for extracting cellulose (the basis of any paper) from wood. In addition to the target product, large-capacity waste is formed in the form of salts lignosulphonic acids or lignosulphonates. These compounds are not toxic, they are biocompatible, water-soluble and relatively cheap.

Lignosulphonate-based nanoparticles have a porous structure and high mass content of carbon atoms that can be absorbed by the soil. Due to this fact, researchers consider them as “sponges” for dyes that can enter wastewater, and even as sorbents for oil. However, there is currently no efficient and cheap way to produce nanomaterials from this class of waste in industry. 

Fluoride in Drinking Water

Photo Credit: Bluewater Sweden

Is Fluoride Safe in Drinking Water?

Do you ever stop to think about what's in your drinking water? While most of us are aware of the importance of clean water, the safety of fluoride in our water supply has been a topic of debate for many years. You might have heard about its benefits for preventing cavities, but also about potential health risks. This article aims to provide a comprehensive overview of the science and expert opinions surrounding fluoride in drinking water, exploring both its benefits and potential drawbacks.

Research Methodology

To ensure accuracy and comprehensiveness, this article draws on a variety of sources, including scientific studies, reports from reputable health organizations (such as the WHO and CDC), news articles, and expert opinions. By examining a wide range of perspectives, we aim to provide a balanced and well-informed analysis of the safety of fluoride in drinking water.

Rice researchers unlock new insights into tellurene, paving the way for next-gen electronics

Shengxi Huang is an associate professor of electrical and computer engineering and materials science and nanoengineering at Rice University, and corresponding author on a study published in Science Advances.
Photo Credit: courtesy of Shengxi Huang/Rice University

To describe how matter works at infinitesimal scales, researchers designate collective behaviors with single concepts ⎯ like calling a group of birds flying in sync a “flock” or “murmuration.” Known as quasiparticles, the phenomena these concepts refer to could be the key to next-generation technologies.

In a recent study published in Science Advances, a team of researchers led by Shengxi Huang, associate professor of electrical and computer engineering and materials science and nanoengineering at Rice, describe how one such type of quasiparticle ⎯ polarons ⎯ behaves in tellurene, a nanomaterial first synthesized in 2017 that is made up of tiny chains of tellurium atoms and has properties useful in sensing, electronic, optical and energy devices.

“Tellurene exhibits dramatic changes in its electronic and optical properties when its thickness is reduced to a few nanometers compared to its bulk form,” said Kunyan Zhang, a Rice doctoral alumna who is a first author on the study. “Specifically, these changes alter how electricity flows and how the material vibrates, which we traced back to the transformation of polarons as tellurene becomes thinner.”