ome bacteria evolve like clockwork with the seasons

 Like Bill Murray in the movie "Groundhog Day," bacteria species in a Wisconsin lake are in a kind of endless loop that they can't seem to shake. Except in this case, it's more like Groundhog Year.

According to a new study in Nature Microbiology, researchers found that through the course of a year, most individual species of bacteria in Lake Mendota rapidly evolved, apparently in response to dramatically changing seasons. Gene variants would rise and fall over generations, yet hundreds of separate species would return, almost fully, to near copies of what they had been genetically prior to a thousand or so generations of evolutionary pressures. (Individual microbes have lifespans of only a few days -- not whole seasons -- so the scientists' work involved comparing bacterial genomes to examine changes in species over time.) This same seasonal change played out year after year, as if evolution was a movie run back to the beginning each time and played over again, seemingly getting nowhere.

"I was surprised that such a large portion of the bacterial community was undergoing this type of change," said Robin Rohwer, a postdoctoral researcher at The University of Texas at Austin in the lab of co-author Brett Baker. "I was hoping to observe just a couple of cool examples, but there were literally hundreds."

Rohwer led the research, first as a doctoral student working with Trina McMahon at the University of Wisconsin-Madison and then at UT.

Lake Mendota changes greatly from season to season -- during the winter, it's covered in ice, and during the summer, it's covered in algae. Within the same bacterial species, strains that are better adapted to one set of environmental conditions will outcompete other strains for a season, while other strains will get their chance to shine during different seasons.

The team used a one-of-a-kind archive of 471 water samples collected over 20 years from Lake Mendota by McMahon, Rohwer and other UW-Madison researchers as part of National Science Foundation-funded long-term monitoring projects. For each water sample, they assembled a metagenome, all of the genetic sequences from fragments of DNA left behind by bacteria and other organisms. This resulted in the longest metagenome time series ever collected from a natural system.

"This study is a total game changer in our understanding of how microbial communities change over time," Baker said. "This is just the beginning of what these data will tell us about microbial ecology and evolution in nature."

This archive also revealed longer-lasting genetic changes.

In 2012, the lake experienced unusual conditions: The ice cover melted early, the summer was hotter and drier than usual, the flow of water from a river that feeds into the lake dwindled, and algae, which are an important source of organic nitrogen for bacteria, were more scarce than usual. As Rohwer and the team discovered, many of the bacteria in the lake that year experienced a major shift in genes related to nitrogen metabolism, possibly due to the scarcity of algae.

"I thought, out of hundreds of bacteria, I might find one or two with a long-term shift," Rohwer said. "But instead, 1 in 5 had big sequence changes that played out over years. We were only able to dig deep into one species, but some of those other species probably also had major gene changes."

Climate scientists predict more extreme weather events -- like the hot, dry summer experienced at Lake Mendota in 2012 -- for the midwestern U.S. during the coming years.

"Climate change is slowly shifting the seasons and average temperatures, but also causing more abrupt, extreme weather events," Rohwer said. "We don't know exactly how microbes will respond to climate change, but our study suggests they will evolve in response to both these gradual and abrupt changes."

Unlike another famous bacterial evolution experiment at UT, the Long-Term Evolution Experiment, Rohwer and Baker's study involved bacterial evolution under complex and constantly changing conditions in nature. The researchers used the supercomputing resources at the Texas Advanced Computing Center (TACC) to reconstruct bacterial genomes from short sequences of DNA in the water samples. The same work that took a couple of months to complete at TACC would have taken 34 years with a laptop computer, Rohwer estimated, involving over 30,000 genomes from about 2,800 different species.

Source: ScienceDaily

Researchers discover class of anti-malaria antibodies

 A novel class of antibodies that binds to a previously untargeted portion of the malaria parasite could lead to new prevention methods, according to a study from researchers at the National Institutes of Health (NIH) published in Science. The most potent of the new antibodies was found to provide protection against malaria parasites in an animal model. The researchers say antibodies in this class are particularly promising because they bind to regions of the malaria parasite not included in current malaria vaccines, providing a potential new tool for fighting this dangerous disease.

Malaria is a life-threatening disease caused by Plasmodium parasites, which are spread through the bites of infected mosquitoes. Although malaria is not common in the United States, its global impact is devastating, with 263 million cases and 597,000 deaths estimated by the World Health Organization in 2023. Of the five species of Plasmodium that cause malaria, Plasmodium falciparum is the most common in African countries where the burden of malaria is largest and where young children account for the majority of malaria deaths. Safe and effective countermeasures are critical for reducing the immense burden of this disease.

In recent years, new interventions have been developed against malaria, including vaccines that currently are being rolled out for young children in regions where the disease is prevalent. Anti-malarial monoclonal antibodies (mAbs) are another promising new tool that have been shown to be safe and efficacious against infection with P. falciparum in adults and children in early clinical trials. The anti-malarial mAbs evaluated in trials in malaria-endemic regions target the P. falciparum sporozoite -- the life stage of the parasite that is transmitted from mosquitoes to people. By binding to and neutralizing the sporozoite, the mAbs prevent sporozoites from infecting the liver, where they otherwise develop into blood-stage parasites that infect blood cells and cause disease and death.

The most promising anti-malarial mAbs tested in humans to date bind to a protein on the sporozoite surface called the circumsporozoite protein (PfCSP) at locations near to or containing amino acid repeats in a region called the central repeat region. This portion of PfCSP also is included in the two available malaria vaccines. The researchers in the current study aimed to find mAbs that target new sites on the sporozoite surface.

Led by scientists at NIH's National Institute of Allergy and Infectious Diseases (NIAID), the research team used a novel approach to find new portions -- or epitopes -- on the sporozoite surface where antibodies bind. They isolated human mAbs produced in response to whole sporozoites, rather than to specific parts of the parasite, and then tested the mAbs to see if they could neutralize sporozoites in a mouse model of malaria. One mAb, named MAD21-101, was found to be the most potent, providing protection against P. falciparum infection in mice.

This new mAb binds to an epitope on PfCSP outside of the central repeat region that is conserved -- or similar -- between different strains of P. falciparum. Notably, the epitope, called pGlu-CSP, is exposed only after a specific step in the development of the sporozoite, but it is widely accessible on the sporozoite surface -- a scenario that the researchers say could mean pGlu-CSP would be effective at eliciting a protective immune response if used in a vaccine. As pGlu-CSP is not included in currently used malaria vaccines, mAbs targeting this epitope are unlikely to interfere with the efficacy of these vaccines if the vaccines and mAbs are co-administered. According to the scientists, this could provide an advantage because this new class of antibodies may be suitable to prevent malaria in at-risk infants who have not yet received a malaria vaccine, but may receive one in the future.

Findings from the study will inform future strategies for the prevention of malaria and may facilitate the development of new antibodies and vaccines against the disease, the researchers indicate. The scientists also note that more research is needed to examine the activity and effectiveness of the newly identified antibody class and epitope, according to their paper. The approach used in this study could also aid the development of a new generation of countermeasures against other pathogens, in addition to malaria.

Source: ScienceDaily

Study reveals that sleep prevents unwanted memories from intruding

 The link between poor sleep and mental health problems could be related to deficits in brain regions that keep unwanted thoughts out of mind, according to research from the University of East Anglia (UEA).

Sleep problems play an important role in the onset and maintenance of many mental health problems, but the reason for this link is elusive.

A new study, published in Proceedings of the National Academy of Sciences (PNAS), offers fresh insight into the cognitive and neural mechanisms underlying the connection between sleep and mental health. These findings could support the development of novel treatments and prevention strategies for mental health problems such as depression and anxiety.

Dr Marcus Harrington, a Lecturer in UEA's School of Psychology, is lead author of the paper 'Memory control deficits in the sleep-deprived human brain'. He worked with colleagues at the universities of York, Cambridge, Sussex, and Queen's University (Canada).

Functional neuroimaging was used to reveal for the first time that deficits in memory control after sleep deprivation are related to difficulties in engaging brain regions that support the inhibition of memory retrieval, and that the overnight rejuvenation of these brain regions is associated with rapid eye movement (REM) sleep.

Dr Harrington said: "Memories of unpleasant experiences can intrude into conscious awareness, often in response to reminders.

"While such intrusive memories are an occasional and momentary disturbance for most people, they can be recurrent, vivid and upsetting for individuals suffering from mental health disorders such as depression, anxiety and post-traumatic stress disorder.

"Given that memories play a central role in our affective perception of the external world, memory control failures may go a long way towards explaining the relationship between sleep loss and emotional dysregulation.

"A better understanding of the mechanisms that precipitate the occurrence of intrusive memories is vital to improving emotional wellbeing and reducing the global burden of mental illness."

Eighty-five healthy adults attempted to suppress unwanted memories while images of their brain were taken using functional MRI. Half of the participants enjoyed a restful night of sleep in the sleep lab before the task, whereas the other half stayed awake all night.

During memory suppression, the well-rested participants showed more activation in the right dorsolateral prefrontal cortex -- a brain region that controls thoughts, actions, and emotions -- compared to those who stayed awake all night. The rested participants also showed reduced activity in the hippocampus -- a brain region involved in memory retrieval -- during attempts to suppress unwanted memories.

Among the participants who slept in the lab, those who spent more time in REM sleep were better able to engage the right dorsolateral prefrontal cortex during memory suppression, pointing to a role for REM sleep in restoring prefrontal control mechanisms underpinning the ability to prevent unwanted memories from entering conscious thought.

Dr Harrington said: "Taken together, our findings highlight the critical role of sleep in maintaining control over both our memories and ongoing thoughts."

Source:ScienceDaily

Pluto-Charon formation scenario mimics Earth-Moon system

 A NASA postdoctoral researcher at Southwest Research Institute has used advanced models that indicate that the formation of Pluto and Charon may parallel that of the Earth-Moon system. Both systems include a moon that is a large fraction of the size of the main body, unlike other moons in the solar system. The scenario also could support Pluto's active geology and possible subsurface ocean, despite its location at the frozen edge of the solar system.

"We think the Earth-Moon system initiated when a Mars-sized object hit the Earth and led to the formation of our large Moon sometime later," said Dr. Adeene Denton, who led the research, published in Nature Geoscience. "In comparison, Mars has two tiny moons that look like potatoes, while the moons of the giant planets make up a small fraction of their total systems."In 2005, SwRI Vice President Dr. Robin Canup performed simulations that first demonstrated that the Pluto-Charon pair could have originated with a giant collision. However, those simplified early models treated the colliding material as a strengthless fluid. In the last five years, advancements in impact formation models have included material strength properties. Integrating this information into the simulation results in Pluto behaving like it has a rocky core covered in ice, which changes the outcome significantly.

"In previous models, when proto-Charon hit proto-Pluto, you have a massive shearing effect of fluids that looks like two blobs in a lava lamp that bend and swirl around each other," she said. "Adding in structural properties allows friction to distribute the impact momentum, leading to a 'kiss-and-capture' regime."

When Pluto and Charon collide, they stick together in the shape of a snowman. They rotate as one body until Pluto pushes Charon out into a stable orbit.

"Most cosmic collisions are what we call a hit-and-run, when an impactor hits a planet and keeps going," Denton continued. "Or an impactor hits a planet, and they merge, which is called a graze and merge. For the Pluto-Charon system, we have a new paradigm where the two bodies hit and then stick together but do not merge because they are behaving like rock and ice."

Pluto and Charon likely exchanged some material between each other but didn't lose a lot of material to the solar system. Pluto is bigger and started and ended up with much more rock than ice, while Charon is smaller and about 50% rock and 50% ice. The bodies maintain their structural integrity and eventually separate, likely preserving the ancient structures of both bodies, which initially formed in the Kuiper Belt. The interior structures could be quite ancient."And this collision scenario supports the formation of other moons, such as Pluto's four other tiny, lumpy satellites," she said.

This new model tells us how the impact may have happened but not when, which is significant, particularly because Pluto is thought to be geologically active and may have a liquid ocean beneath its icy surface.

"Even if Pluto starts out really cold, which makes more sense from a solar system evolution perspective, the giant impact and the subsequent tidal forces following the separation could result in an ocean down the line," said Denton. "And that has pretty big implications for the Kuiper Belt as a whole, because eight of the 10 largest Kuiper Belt objects are similar to Pluto and Charon.

sources-science daily

Earth's air war: Explaining the delayed rise of plants, animals on land

 If you like the smell of spring roses, the sounds of summer birdsong, and the colors of fall foliage, you have the stabilization of the ozone layer to thank for it. Located in the stratosphere, where it shields the Earth from harmful ultraviolet radiation, the ozone layer plays a key role in preserving the planet's biodiversity.

And now we may have a better idea of why that took so long -- more than 2 billion years -- to happen.

According to a new, Yale-led study, Earth's early atmosphere hosted a battle royale between iodine and oxygen -- effectively delaying the creation of a stable ozone layer that would shield complex life from much of the sun's ultraviolet radiation (UVR).The new theory, described in a study in the journal Proceedings of the National Academies of Science, may solve a mystery that has puzzled scientists for hundreds of years.

"The origin and diversification of complex life on Earth remains one of the most profound and enduring questions in natural science," said Jingjun Liu, a doctoral student in Earth and planetary sciences at Yale and first and corresponding author of the new study.

Indeed, scientists have long wondered why land plants did not emerge on Earth until 450 million years ago, even though their progenitors, cyanobacteria, had been in existence for 2.7 billion years. Likewise, there are no fossils for complex land animals or plants before the Cambrian era (541 to 485 million years ago) despite the evidence of much older microfossils.

"The only existing explanation states that this delay is an intrinsic characteristic of evolution -- that an enormous amount of time is required," said Noah Planavsky, a professor of Earth and planetary sciences, faculty member of the Yale Center for Natural Carbon Capture, and senior author of the new study. "Yet that notion fails to explain how and why complex life originated and diversified."

The new study suggests that something beyond the need for time was responsible: the delayed stabilization of Earth's ozone layer, caused by elevated marine iodine concentrations that prevented a protective UVR shield from forming in the atmosphere.

Ozone production depends on atmospheric oxygen and background UVR. It has been widely accepted by scientists that once Earth established a substantial concentration of atmospheric oxygen, the planet formed an ozone layer that allowed for biological evolution to proceed unimpeded.

"We challenge this paradigm by considering how Earth's evolving iodine cycle may have influenced ozone abundance and stability," Liu said.

For the study, a Yale-led research team analyzed multiple lines of independent geological evidence and developed an ocean-atmosphere model to reconstruct the iodine-ozone dynamics for the early Earth. The researchers found that elevated marine iodide content (formed when iodine combines with another element to form a salt) prevailed through most of Earth's history, which would have led to significant inorganic iodine emissions into the atmosphere after the rise of oxygen -- with the potential for disrupting ozone.

The mechanism of ozone destruction by iodine is similar to the process by which chlorofluorocarbons (CFCs) created the "ozone hole" over Antarctica. When CFCs undergo photolysis, they release reactive chlorine, which catalytically destroys ozone in the stratosphere, leading to as much as a 50% depletion over continental Antarctica at the peak of the problem.

"Iodine-driven catalytic cycles for ozone destruction follow a similar process and are kinetically much faster than those involving reactive chlorine," Planavsky said. "Our photochemical calculations indicate that even a moderate increase in marine inorganic iodine emission could result in a whole atmosphere ozone depletion by tens or even hundreds of times relative to modern levels."

Liu noted that at a global scale, unstable and low ozone levels likely persisted from 2.4 billion years ago until roughly half a billion years ago. "During this interval, even under high levels of oxygen production, atmospheric ozone could have been very low and was likely unstable, leading to periodic or persistent high fluxes of solar UVR at Earth's surface," Liu said.

Dalton Hardisty of Michigan State University, James Kasting of Pennsylvania State University, and Mojtaba Fakhraee of Yale are co-authors of the study.

sources-science daily

Dinosaurs roamed the northern hemisphere millions of years earlier than previously thought, according to new analysis of the oldest North American fossils

 How and when did dinosaurs first emerge and spread across the planet more than 200 million years ago? That question has for decades been a source of debate among paleontologists faced with fragmented fossil records. The mainstream view has held that the reptiles emerged on the southern portion of the ancient supercontinent Pangea called Gondwana millions of years before spreading to the northern half named Laurasia.

But now, a newly described dinosaur whose fossils were uncovered by University of Wisconsin-Madison paleontologists is challenging that narrative, with evidence that the reptiles were present in the northern hemisphere millions of years earlier than previously known.The UW-Madison team has been analyzing the fossil remains since they were first discovered in 2013 in present-day Wyoming, an area that was near the equator on Laurasia. The creature, named Ahvaytum bahndooiveche, is now the oldest known Laurasian dinosaur, and with fossils estimated to be around 230 million years old, it's comparable in age to the earliest known Gondwanan dinosaurs.

UW-Madison scientists and their research partners detail their discovery Jan. 8, 2025, in the Zoological Journal of the Linnean Society.

"We have, with these fossils, the oldest equatorial dinosaur in the world -- it's also North America's oldest dinosaur," says Dave Lovelace, a research scientist at the University of Wisconsin Geology Museum who co-led the work with graduate student Aaron Kufner.

Discovered in a layer of rock known as the Popo Agie Formation, it took years of careful work by Lovelace and his colleagues to analyze the fossils, establish them as a new dinosaur species and determine their estimated age.

While the team doesn't have a complete specimen -- that's an exceedingly rare occurrence for early dinosaurs -- they did find enough fossils, particularly parts of the species' legs, to positively identify Ahvaytum bahndooiveche as a dinosaur, and likely as a very early sauropod relative. Sauropods were a group of herbivorous dinosaurs that included some famously gigantic species like those in the aptly named group of titanosaurs. The distantly related Ahvaytum bahndooiveche lived millions of years earlier and was smaller -- much smaller.

"It was basically the size of a chicken but with a really long tail," says Lovelace. "We think of dinosaurs as these giant behemoths, but they didn't start out that way."

Indeed, the type specimen of Ahvaytum bahndooiveche, which was full-grown but could have been slightly bigger at its maximum age, stood a little over one foot tall and was around three feet long from head to tail. Although scientists haven't found its skull material, which could help illuminate what it ate, other closely related early sauropod-line dinosaurs were eating meat and would likely have been omnivorous.

The researchers found the few known bones of Ahvaytum in a layer of rock just a little bit above those of a newly described amphibian that they also discovered. The evidence suggests that Ahvaytum bahndooiveche lived in Laurasia during or soon after a period of immense climatic change known as the Carnian pluvial episode that has previously been connected to an early period of diversification of dinosaur species.

The climate during that period, lasting from about 234 to 232 million years ago, was much wetter than it had been previously, transforming large, hot stretches of desert into more hospitable habitats for early dinosaurs.

Lovelace and his colleagues performed high-precision radioisotopic dating of rocks in the formation that held Ahvaytum's fossils, which revealed that the dinosaur was present in the northern hemisphere around 230 million years ago. The researchers also found an early dinosaur-like track in slightly older rocks, demonstrating that dinosaurs or their cousins were already in the region a few million years prior to Ahvaytum.

"We're kind of filling in some of this story, and we're showing that the ideas that we've held for so long -- ideas that were supported by the fragmented evidence that we had -- weren't quite right," Lovelace says. "We now have this piece of evidence that shows dinosaurs were here in the northern hemisphere much earlier than we thought."

While the scientific team is confident they've discovered North America's oldest dinosaur, it's also the first dinosaur species to be named in the language of the Eastern Shoshone Tribe, whose ancestral lands include the site where the fossils were found. Eastern Shoshone tribal elders and middle school students were integral to the naming process. Ahvaytum bahndooiveche broadly translates to "long ago dinosaur" in the Shoshone language.Several tribal members also partnered with Lovelace and his UW-Madison colleagues as the researchers sought to evolve their field practices and better respect the land by incorporating the knowledge and perspectives of the Indigenous peoples into their work.

"The continuous relationship developed between Dr. Lovelace, his team, our school district, and our community is one of the most important outcomes of the discovery and naming of Ahvaytum bahndooiveche," says Amanda LeClair-Diaz, a co-author on the paper and a member of the Eastern Shoshone and Northern Arapaho Tribes. LeClair-Diaz is the Indian education coordinator at Fort Washakie school and coordinated the naming process with students and tribal elders -- a process that started under her predecessor, Lynette St. Clair.

"Typically, the research process in communities, especially Indigenous communities, has been one sided, with the researchers fully benefiting from studies," says LeClair-Diaz. "The work we have done with Dr. Lovelace breaks this cycle and creates an opportunity for reciprocity in the research process."

sources-science daily

System to auto-detect new variants will inform better response to future infectious disease outbreaks

 Researchers have come up with a new way to identify more infectious variants of viruses or bacteria that start spreading in humans -- including those causing flu, COVID, whooping cough and tuberculosis.

The new approach uses samples from infected humans to allow real-time monitoring of pathogens circulating in human populations, and enable vaccine-evading bugs to be quickly and automatically identified. This could inform the development of vaccines that are more effective in preventing disease.

The approach can also quickly detect emerging variants with resistance to antibiotics. This could inform the choice of treatment for people who become infected -- and try to limit the spread of the disease.

It uses genetic sequencing data to provide information on the genetic changes underlying the emergence of new variants. This is important to help understand why different variants spread differently in human populations.

There are very few systems in place to keep watch for emerging variants of infectious diseases, apart from the established COVID and influenza surveillance programmes. The technique is a major advance on the existing approach to these diseases, which has relied on groups of experts to decide when a circulating bacteria or virus has changed enough to be designated a new variant.By creating 'family trees', the new approach identifies new variants automatically based on how much a pathogen has changed genetically, and how easily it spreads in the human population -- removing the need to convene experts to do this.

It can be used for a broad range of viruses and bacteria and only a small number of samples, taken from infected people, are needed to reveal the variants circulating in a population. This makes it particularly valuable for resource-poor settings.

The report is published today in the journal Nature.

"Our new method provides a way to show, surprisingly quickly, whether there are new transmissible variants of pathogens circulating in populations -- and it can be used for a huge range of bacteria and viruses," said Dr Noémie Lefrancq, first author of the report, who carried out the work at the University of Cambridge's Department of Genetics.

Lefrancq, who is now based at ETH Zurich, added: "We can even use it to start predicting how new variants are going to take over, which means decisions can quickly be made about how to respond."

"Our method provides a completely objective way of spotting new strains of disease-causing bugs, by analysing their genetics and how they're spreading in the population. This means we can rapidly and effectively spot the emergence of new highly transmissible strains," said Professor Julian Parkhill, a researcher in the University of Cambridge's Department of Veterinary Medicine who was involved in the study.

Testing the technique

The researchers used their new technique to analyse samples of Bordetella pertussis, the bacteria that causes whooping cough. Many countries are currently experiencing their worst whooping cough outbreaks of the last 25 years. It immediately identified three new variants circulating in the population that had been previously undetected.

"The novel method proves very timely for the agent of whooping cough, which warrants reinforced surveillance, given its current comeback in many countries and the worrying emergence of antimicrobial resistant lineages," said Professor Sylvain Brisse, Head of the National Reference Center for whooping cough at Institut Pasteur, who provided bioresources and expertise on Bordetella pertussis genomic analyses and epidemiology.

In a second test, they analysed samples of Mycobacterium tuberculosis, the bacteria that causes Tuberculosis. It showed that two variants with resistance to antibiotics are spreading.

"The approach will quickly show which variants of a pathogen are most worrying in terms of the potential to make people ill. This means a vaccine can be specifically targeted against these variants, to make it as effective as possible," said Professor Henrik Salje in the University of Cambridge's Department of Genetics, senior author of the report.

He added: "If we see a rapid expansion of an antibiotic-resistant variant, then we could change the antibiotic that's being prescribed to people infected by it, to try and limit the spread of that variant."

The researchers say this work is an important piece in the larger jigsaw of any public health response to infectious disease.

A constant threat

Bacteria and viruses that cause disease are constantly evolving to be better and faster at spreading between us. During the COVID pandemic, this led to the emergence of new strains: the original Wuhan strain spread rapidly but was later overtaken by other variants, including Omicron, which evolved from the original and were better at spreading. Underlying this evolution are changes in the genetic make-up of the pathogens.

Pathogens evolve through genetic changes that make them better at spreading. Scientists are particularly worried about genetic changes that allow pathogens to evade our immune system and cause disease despite us being vaccinated against them.

"This work has the potential to become an integral part of infectious disease surveillance systems around the world, and the insights it provides could completely change the way governments respond," said Salje.

sources-science daily