New model offers a way to speed up drug discovery

Researchers can screen more than 100 million compounds in a single day — much more than any existing model.
Photo Credit: Myriam Zilles

Huge libraries of drug compounds may hold potential treatments for a variety of diseases, such as cancer or heart disease. Ideally, scientists would like to experimentally test each of these compounds against all possible targets, but doing that kind of screen is prohibitively time-consuming.

In recent years, researchers have begun using computational methods to screen those libraries in hopes of speeding up drug discovery. However, many of those methods also take a long time, as most of them calculate each target protein’s three-dimensional structure from its amino-acid sequence, then use those structures to predict which drug molecules it will interact with.

Researchers at MIT and Tufts University have now devised an alternative computational approach based on a type of artificial intelligence algorithm known as a large language model. These models — one well-known example is ChatGPT — can analyze huge amounts of text and figure out which words (or, in this case, amino acids) are most likely to appear together. The new model, known as ConPLex, can match target proteins with potential drug molecules without having to perform the computationally intensive step of calculating the molecules’ structures.

Researchers warn of future ‘fish wars’ as consequence of climate change

Photo Credit: Sabrina Eickhoff

How climate change could give rise to “fish wars” between nations is the subject of a new research project awarded a £1.1m grant by the US Department of Defense.

The project, entitled “Future Fish Wars: Chasing Ocean Ecosystem Wealth”, is one of 11 to receive a total funding of $18m as part of the US Department of Defense's Minerva Research Initiative, which supports research in social and behavioral sciences on topics relevant to US national security.

The researchers aim to develop new economic theory and approaches to measure the economic value of fisheries in the context of climate change and growing geopolitical ocean conflict.

They say illegal fishing, contested claims to fishing rights and future conflicts are likely outcomes as fish swim for the poles as a result of climate change warming the oceans. 

Over three years, the research team will develop new economic theory for valuing multiple stocks of marine resources, which they will use alongside novel data on conflict and cooperative events to achieve a deeper understanding of future fisheries conflict.

MethaneMapper is poised to solve the problem of underreported methane emissions

A central difficulty in controlling greenhouse gas emissions to slow down climate change is finding them in the first place.

Such is the case with methane, a colorless, odorless gas that is the second most abundant greenhouse gas in the atmosphere today, after carbon dioxide. Although it has a shorter life than carbon dioxide, according to the U.S. Environmental Protection Agency, it’s more than 25 times as potent as CO2 at trapping heat, and is estimated to trap 80 times more heat in the atmosphere than CO2 over 20 years.

 For that reason, curbing methane has become a priority, said UC Santa Barbara researcher Satish Kumar, a doctoral student in the Vision Research Lab of computer scientist B.S. Manjunath.

“Recently, at the 2022 International Climate Summit, methane was actually the highlight because everybody is struggling with it,” he said.

Even with reporting requirements in the U.S., methane’s invisibility means that its emissions are likely going underreported. In some cases, the discrepancies are vast, such as with the Permian Basin, an 86,000-square-mile oil and natural gas extraction field located in Texas and New Mexico that hosts tens of thousands of wells. Independent methane monitoring of the area has revealed that the site emits eight to 10 times more methane than reported by the field’s operators.

Greenhouse gas emissions at ‘an all-time high’, warn scientists

Photo Credit: Chris LeBoutillier

Human-caused global warming has continued to increase at an “unprecedented rate” since the last major assessment of the climate system published two years ago, say 50 leading scientists.

The research, published in the journal Earth System Science Data, found that human-induced warming averaged 1.14°C over the last decade and a record level of greenhouse gases is being emitted each year, equivalent to 54 billion tons of carbon dioxide. The remaining carbon budget - how much carbon dioxide can be emitted to have a better than 50% chance of holding global warming to 1.5°C - has halved over three years  

One of the researchers said the study was a “timely wake-up call” that the pace and scale of climate action has been insufficient, and it comes as climate experts meet in Bonn to prepare the ground for the major COP28 climate conference in the UAE in December, which will include a stock take of progress towards keeping global warming to 1.5°C by 2050.   

Given the speed at which the global climate system is changing, the scientists argue that policymakers, climate negotiators and civil society groups need to have access to up-to-date and robust scientific evidence on which to base decisions.

When Water Temperatures Change, the Molecular Motors of Cephalopods Do Too

Doryteuthis opalescens, otherwise known as market squid, helped UC San Diego researchers discover the animals’ ability to recode RNA in cells to improve their functioning in different water temperatures.
 Credit: UC San Diego/Sea Grant California.

Cephalopods are a large family of marine animals that includes octopuses, cuttlefish and squid. They live in every ocean, from warm, shallow tropical waters to near-freezing, abyssal depths. More remarkably, report two scientists at University of California San Diego in a new study, at least some cephalopods possess the ability to recode protein motors within cells to adapt “on the fly” to different water temperatures.    

Writing in the June 8, 2023 edition of Cell, first author Kavita J. Rangan, PhD, a postdoctoral researcher in the lab of senior author Samara L. Reck-Peterson, PhD, a professor in the departments of Cellular and Molecular Medicine at UC San Diego School of Medicine and Cell and Developmental Biology at UC San Diego and an Investigator of the Howard Hughes Medical Institute, describe how opalescent inshore squid (Doryteuthis opalescens) employ RNA recoding to change amino acids at the protein level, improving the function of molecular motors that carry out diverse functions within cells in colder waters.

RNA recoding allows organisms to edit genetic information from the genomic blueprint to create new proteins. The process is rare in humans but is common in soft-bodied cephalopods, such as D. opalescens, which makes seasonal spawning migrations along the coast of San Diego. 

Is “second-guessing” a hard-wired behavior? Mouse study offers clues

U of U Health scientists have found that genes bias decision-making, even decisions that seem irrational.
Illustration Credit: Cornelia Stacher-Hörndli, PhD.

Have you ever made a decision that, in hindsight, seemed irrational? A new study with mice, which could have implications for people, suggests that some decisions are, to a certain extent, beyond their control. Rather, the mice are hard-wired to make them.

“This research is telling us that animals are constrained in the decisions they make,” said Christopher Gregg, PhD, a neurobiologist at University of Utah Health and senior author of the study that was recently published in iScience. “Their genetics push them down one path or another.”

Gregg and his research team started investigating decision-making after noticing mice repeatedly making what appeared to be an irrational decision. After finding a stash of hidden seeds, rather than staying put to eat them, mice kept returning to a location that had food in it the day before. Only on this day, the original location was empty.

“It was as if the mice were second-guessing whether the first location really had no food,” Gregg said. “Like they thought they had missed something.”

Long Covid can impact fatigue and quality of life worse than some cancers

Photo Credit: engin akyurt

Fatigue is the symptom that most significantly impacts the daily lives of long Covid patients, and can affect quality of life more than some cancers, finds a new study led by researchers at UCL and the University of Exeter.

The research, published in BMJ Open and funded by the National Institute for Health and Care Research (NIHR), examines the impact of long Covid on the lives of over 3,750 patients who were referred to a long Covid clinic and used a digital app as part of their NHS treatment for the condition.

Patients were asked to complete questionnaires on the app about how long Covid was affecting them – considering the impact of long Covid on their day-to-day activities, levels of fatigue, depression, anxiety, breathlessness, brain fog, and their quality of life.

The researchers found that many long Covid patients were seriously ill and on average had fatigue scores worse or similar to people with cancer-related anemia or severe kidney disease. Their health-related quality of life scores were also lower than those of people with advanced metastatic cancers, like stage IV lung cancer.

Overall, the team found that the impact of long Covid on the daily activities of patients was worse than that of stroke patients and was comparable to that of patients with Parkinson’s Disease.

COVID-19 can cause brain cells to ‘fuse’

Fused neurons in yellow, expressing Spike S fusogen from the SARS-CoV-2 virus and the human receptor hACE2.
Image Credit: Courtesy of University of Queensland

Researchers at The University of Queensland have discovered viruses such as SARS-CoV-2 can cause brain cells to fuse, initiating malfunctions that lead to chronic neurological symptoms.

Professor Massimo Hilliard and Dr Ramon Martinez-Marmol from the Queensland Brain Institute have explored how viruses alter the function of the nervous system.

SARS-CoV-2, the virus that causes COVID-19, has been detected in the brains of people with ‘long COVID’ months after their initial infection.

“We discovered COVID-19 causes neurons to undergo a cell fusion process, which has not been seen before,” Professor Hilliard said.

“After neuronal infection with SARS-CoV-2, the spike S protein becomes present in neurons, and once neurons fuse, they don’t die.”

Groundbreaking findings bring hope for faster and better recovery after stroke

Marcela Pekna och Milos Pekny, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg.
Photo Credits: Milos Pekny, Ylva Pekny

An effective treatment for most stroke victims — even those who, today, are unable to gain access to care within the first few hours. This is the goal of an experimental method that has been tested with great success in an international study headed by the University of Gothenburg.

The work now published in the Journal of Clinical Investigation is a multicenter study in which researchers at the Universities of Gothenburg and Cologne implemented parallel testing of an experimental stroke treatment on mice. The study was conducted in collaboration with researchers at the Czech Academy of Sciences.

By giving mice a molecule, the complement peptide C3a, in nasal drops, the scientists saw them recover motor function faster and better after stroke compared with mice that had received nasal drops with placebo. These results confirm and extend a previous study at the University of Gothenburg and the current study design further strengthens their credibility.

“We see the same positive effects in experiments done in Sweden and in Germany, which makes the results much more robust,” says Marcela Pekna, Professor of Neuroimmunology at Sahlgrenska Academy, University of Gothenburg, who led the study.

Elusive planets play “hide and seek” with CHEOPS

Artist's impression of CHEOPS.
Illustration Credit: ESA / ATG medialab

With the help of the CHEOPS space telescope an international team of European astronomers managed to clearly identify the existence of four new exoplanets. The four mini-Neptunes are smaller and cooler, and more difficult to find than the so-called Hot Jupiter exoplanets which have been found in abundance. Two of the four resulting papers are led by researchers from the University of Bern and the University of Geneva who are also members of the National Centre of Competence in Research (NCCR) PlanetS.

CHEOPS is a joint mission by the European Space Agency (ESA) and Switzerland, under the leadership of the University of Bern in collaboration with the University of Geneva. Since its launch in December 2019, the extremely precise measurements of CHEOPS have contributed to several key discoveries in the field of exoplanets.

NCCR PlanetS members Dr. Solène Ulmer-Moll of the Universities of Bern and Geneva, and Dr. Hugh Osborn of the University of Bern, exploited the unique synergy of CHEOPS and the NASA satellite TESS, in order to detect a series of elusive exoplanets. The planets, called TOI 5678 b and HIP 9618 c respectively, are the size of Neptune or slightly smaller with 4.9 and 3.4 Earth radii. The respective papers have just been published in the journals Astronomy & Astrophysics and Monthly Notices of the Royal Astronomical Society. Publishing in the same journals, two other members of the international team, Amy Tuson from the University of Cambridge (UK) and Dr. Zoltán Garai from the "ELTE Gothard Astrophysical Observatory (Hungary), used the same technique to identify two similar planets in other systems.

Designing the right tools to hunt for elusive axion particles

Inside the newly constructed CCM200 detector, showing the 200 photo-multiplier tube light sensors (circles) and the interior walls coated with a special material to convert the argon scintillation light into visible light that can be detected by the photo-multiplier tubes and then recorded by the data acquisition system. An outer veto region rejects events coming from the outside such as cosmic rays.
Photo Credit: Los Alamos National Laboratory

Since axions were first predicted by theory nearly half a century ago, researchers have hunted for proof of the elusive particle, which may exist outside the visible universe, in the dark sector. But how does one find particles that can’t be seen? The first physics results from the Coherent CAPTAIN-Mills experiment at Los Alamos — just described in a publication in the journal Physical Review D — suggest that liquid-argon, accelerator-based experimentation, designed initially to look for similarly hypothetical particles such as sterile neutrinos, may also be an ideal set-up for seeking out stealthy axions.

“The confirmation of dark sector particles would have a profound impact on the understanding of the Standard Model of particle physics, as well as the origin and evolution of the universe,” said physicist Richard Van de Water. “A big focus of the physics community is exploring ways to detect and confirm these particles. The Coherent CAPTAIN-Mills experiment couples existing predictions of dark matter particles such as axions with high-intensity particle accelerators capable of producing this hard-to-find dark matter.”

New research could improve performance of artificial intelligence and quantum computers

A University of Minnesota Twin Cities-led team has developed a more energy-efficient, tunable superconducting diode — a promising component for future electronic devices — that could help scale up quantum computers for industry and improve artificial intelligence systems.
Photo Credit: Olivia Hultgren.

A University of Minnesota Twin Cities-led team has developed a new superconducting diode, a key component in electronic devices, that could help scale up quantum computers for industry use and improve the performance of artificial intelligence systems. 

The paper is published in Nature Communications, a peer-reviewed scientific journal that covers the natural sciences and engineering. 

A diode allows current to flow one way but not the other in an electrical circuit. It essentially serves as half of a transistor — which is the main element in computer chips. Diodes are typically made with semiconductors, substances with electrical properties that form the base for most electronics and computers, but researchers are interested in making them with superconductors, which additionally have the ability to transfer energy without losing any power along the way.

Compared to other superconducting diodes, the researchers’ device is more energy efficient, can process multiple electrical signals at a time, and contains a series of gates to control the flow of energy, a feature that has never before been integrated into a superconducting diode.

What made the brightest cosmic explosion of all time so exceptional?

The afterglow of the Brightest of All Time gamma-ray burst, captured by the Neil Gehrels Swift Observatory’s X-Ray Telescope.
Image Credit: NASA/Swift/A. Beardmore (University of Leicester)

Last year, telescopes registered the brightest known cosmic explosion of all recorded time. Astrophysicists can now explain what made it so dazzling.

Few cosmic explosions have attracted as much attention from space scientists as the one recorded on October 22 last year and aptly named the Brightest of All Time (BOAT). The event, produced by the collapse of a highly massive star and the subsequent birth of a black hole, was witnessed as an immensely bright flash of gamma rays followed by a slow-fading afterglow of light across frequencies.

Since picking up the BOAT signal simultaneously on their giant telescopes, astrophysicists the world over have been scrambling to account for the brightness of the gamma-ray burst (GRB) and the curiously slow fade of its afterglow.

Now an international team that includes Dr Hendrik Van Eerten from the Department of Physics at the University of Bath has formulated an explanation: the initial burst (known as GRB 221009A) was angled directly at Earth and it also dragged along an unusually large amount of stellar material in its wake.

The team’s findings are published today in the prestigious journal Science Advances. Dr Brendan O’Connor, a newly graduated doctoral student at the University of Maryland and George Washington University in Washington, DC is the study’s lead author.

New Dino, ‘Iani,’ Was Face of a Changing Planet

Illustration Credit: Jorge Gonzalez
(CC BY-NC 4.0)

A newly discovered plant-eating dinosaur may have been a species’ “last gasp” during a period when Earth’s warming climate forced massive changes to global dinosaur populations.

The specimen, named Iani smithi after Janus, the two-faced Roman god of change, was an early ornithopod, a group of dinosaurs that ultimately gave rise to the more commonly known duckbill dinosaurs such as Parasaurolophus and Edmontosaurus. Researchers recovered most of the juvenile dinosaur’s skeleton – including skull, vertebrae and limbs – from Utah’s Cedar Mountain Formation.

Iani smithi lived in what is now Utah during the mid-Cretaceous, approximately 99 million years ago. The dinosaur’s most striking feature is its powerful jaw, with teeth designed for chewing through tough plant material.

The mid-Cretaceous was a time of big changes, which had big effects on dinosaur populations. Increased atmospheric carbon dioxide during this time caused the Earth to warm and sea levels to rise, corralling dinosaurs on smaller and smaller landmasses. It was so warm that rainforests thrived at the poles. Flowering plant life took over coastal areas and supplanted normal food sources for herbivores.

Parker Solar Probe flies into the fast solar wind and finds its source

Artist’s concept of the Parker Solar Probe spacecraft approaching the sun. Launched in 2018, the probe is increasing our ability to forecast major space-weather events that impact life on Earth.
Illustration Credit: NASA

NASA’s Parker Solar Probe has flown close enough to the sun to detect the fine structure of the solar wind close to where it is generated at the sun’s surface, revealing details that are lost as the wind exits the corona as a uniform blast of charged particles.

It’s like seeing jets of water emanating from a showerhead through the blast of water hitting you in the face.

In a paper to be published in the journal Nature, a team of scientists led by Stuart D. Bale, a professor of physics at the University of California, Berkeley, and James Drake of the University of Maryland-College Park, report that the Parker Solar Probe has detected streams of high-energy particles that match the supergranulation flows within coronal holes, which suggests that these are the regions where the so-called “fast” solar wind originates.

Coronal holes are areas where magnetic field lines emerge from the surface without looping back inward, thus forming open field lines that expand outward and fill most of the space around the sun. These holes are usually at the poles during the sun’s quiet periods, so the fast solar wind they generate doesn’t hit Earth. But when the sun becomes active every 11 years as its magnetic field flips, these holes appear all over the surface, generating bursts of solar wind aimed directly at Earth.