All life copies DNA unambiguously into proteins. Archaea may be the exception.

An archaea interprets one codon in two different ways, contradicting a 60-year-old doctrine.

University of California - Berkeley

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Methane-producing archaea from the species Methanosarcina acetivorans. The microbes are stained with a fluorescent dye that specifically binds to the membranes of archaea.

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Credit: Alienor Baskevitch/UC Berkeley

The beauty of the DNA code is that organisms interpret it unambiguously. Each three-letter nucleotide sequence, or codon, in a gene codes for a unique amino acid that’s added to a chain of amino acids to make a protein.

But University of California, Berkeley, researchers have now shown that one microorganism can live with a bit of ambiguity in its genetic code, overturning a standard dogma of biology.

The organism, a methane-producing member of a group of microbes called Archaea, interprets one three-letter sequence — normally a stop codon that signals the end of a protein — in two different ways, synthesizing two different proteins seemingly at random, though biased by conditions in the environment. The microbe, Methanosarcina acetivorans, survives just fine with this loosey-goosey translation, proving that life can exist with a slightly imprecise genetic code.

The ambiguity may have arisen to allow the microbes to incorporate an uncommon amino acid, pyrrolysine, into an enzyme needed to digest a specific food — methylamine — that is common in the environment, including the human gut.

“Objectively, ambiguity in the genetic code should be deleterious; you end up generating a random pool of proteins,” said Dipti Nayak, a UC Berkeley assistant professor of molecular and cell biology and senior author of a paper describing the findings published Nov. 6 in the journal Proceedings of the National Academy of Sciences. “But biological systems are more ambiguous than we give them credit to be and that ambiguity is actually a feature — it's not a bug.”

Archaea that eat methylamines, and bacteria that may have acquired that ability too, play an important role in the human body. In the liver, metabolites released by red meat are turned into trimethylamine N-oxide, which is associated with cardiovascular disease. We rely upon these microbes to remove those methylamines before they reach the liver.

The findings have implications for future disease therapies. Some researchers have speculated that introducing some imprecision into the translation machinery might help treat diseases caused by a premature stop codon in important genes, which produces nonfunctional proteins. That includes about 10% of all genetic diseases, including cystic fibrosis and Duchenne muscular dystrophy. Making a stop codon a bit leaky could allow enough of the normal protein to be produced to alleviate symptoms.

The genetic cipher

The DNA in the genome is initially transcribed into RNA, and that genetic code is then read by cellular machinery to produce proteins. The nucleic acids that comprise RNA come in four varieties — adenine (A), cytosine (C), guanine (G) and uracil (U). In most organisms investigated to date, groups of three nucleic acids or codons are either assigned to a single amino acid or a so-called stop codon, which terminates synthesis of that protein. When the RNA gets translated into a string of amino acids, the machinery always abides by this one-to-one association.

Not all organisms decode RNA in the same way, however. Some assign a different amino acid to a given codon, some have more than the standard 20 amino acids per organism, and codons are redundant — several can code for the same amino acid. But uniformly across the tree of life, each codon has only one meaning — no ifs, ands or buts.

“It's essentially like a cipher,” Nayak said. “You're taking something in one language and translating it into another, nucleotides to amino acids.”

Scientists have known for a long time that many members of the Archaea produce pyrrolysine, giving them 21 amino acid options instead of the usual 20 from which to make proteins. It has advantages, Nayak said.

“Now that you have a new amino acid, the world's your oyster,” she said. “You can start playing around with the much larger code. It's like adding one more letter to the alphabet.”

But these organisms were thought to have merely changed the interpretation of the UAG stop codon to code for pyrrolysine instead.

In the new study, Nayak and former graduate student Katie Shalvarjian surveyed the Archaea and found pyrrolysine production in many lineages.

“We found that the machinery required to create pyrrolysine is widespread in the Archaea, especially amongst these methanogenic archaea that consume methylated amines,” said Shalvarjian, now a postdoctoral researcher at Lawrence Livermore National Laboratory.

She was curious, however, how having 21 instead of 20 amino acids affects these organisms and their physiology. While investigating the methanogen’s genetic control of pyrrolysine production, she noticed that the UAG codon was not always interpreted as pyrrolysine (Pyl).

“The UAG codon is like a fork in the road, where it can be interpreted either as a stop codon or as a pyrrolysine residue,” Shalvarjian said. “We think whether or not a protein exists primarily in its elongated or in its truncated form might form a regulatory cue for the cell.”

Nayak and Shalvarjian looked for sequence or structure dependent cues that might affect interpretation of the UAG codon, but found none.

“The methanogens have not recoded UAG, nor have they added any new factors to make it deterministic,” Nayak said. “They're flip-flopping back and forth between whether they should call this a stop or whether they should keep going by adding this new amino acid. They cannot decide. They just do both and they seem to be fine by making this random choice.”

Preliminary evidence suggests that the supply of pyrrolysine in the cell may be the determining factor. If it’s flooding the cell, it may bias the interpretation of UAG more toward incorporating the amino acid into a protein. There are between 200 and 300 genes in this organism that contain the UAG codon and thus have the ability to produce a protein containing pyrrolysine. With little of the amino acid around, however, UAG is interpreted as a stop codon, yielding a different protein that may or may not be functional, depending on the context.

“This really opens the door to finding interesting ways to control how cells interpret stop codons,” Nayak said.

The work was funded by the Searle Scholars Program, a Rose Hills Innovator Grant, a Beckman Young Investigator Award, an Alfred P. Sloan Research Fellowship, a Simons Foundation Early Career Investigator in Marine Microbial Ecology and Evolution Award, and a Packard Fellowship in Science and Engineering. Nayak is also a Chan-Zuckerberg Biohub-San Francisco investigator.

Other co-authors are Grayson Chadwick and Paloma Pérez of UC Berkeley and Philip Woods and Victoria Orphan of the California Institute of Technology.

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2517473122 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage

 

A new possibility for life: Study suggests ancient skies rained down ingredients

University of Colorado at Boulder

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Nate Reed and Ellie Browne working in the lab.

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Credit: Credit: Patrick Campbell/CU Boulder

Earth’s atmosphere might have contributed to the origin of life more than previously thought.

In a study published Dec. 1 in the Proceedings of the National Academy of Sciences, CU Boulder researchers and collaborators reveal that billions of years ago, the planet’s early sky might have been producing sulfur-containing molecules that were essential ingredients for life. 

The finding challenges a long-held theory that these sulfur molecules emerged only after life had already formed.

“Our study could help us understand the evolution of life at its earliest stages,” said first author Nate Reed, a postdoctoral fellow at NASA, who conducted the work as a postdoctoral researcher in the Department of Chemistry and the Cooperative Institute for Research in Environmental Sciences (CIRES) at CU Boulder. 

Just like carbon, sulfur is an essential element found in all life forms, from single-cell bacteria to humans. It is part of some amino acids, which are the building blocks of protein. 

While the young Earth’s atmosphere contained sulfur elements, scientists had long thought that organic sulfur compounds, or biomolecules like amino acids, emerged later as a product of the living system. 

In previous simulations of early Earth, scientists either failed to detect meaningful amounts of sulfur biomolecules before life existed, or created the molecules only under specialized conditions that were unlikely to be widespread on this planet. 

As a result, when the James Webb Space Telescope detected dimethyl sulfide, an organic sulfur compound produced by marine algae on Earth, on another planet called K2-18b, many thought it was a possible sign of life on other planets. 

But in previous work, Reed and the study’s senior author, Ellie Browne, a chemistry professor and a CIRES fellow, successfully created dimethyl sulfide in their lab using only light and common atmospheric gases. This suggested that this molecule could arise in places void of life. 

This time, Browne, Reed and their team set off to see what early Earth’s sky could have contributed. They shone light on a gas mixture containing methane, carbon dioxide, hydrogen sulfide and nitrogen to simulate Earth’s atmosphere before life emerged. 

Sulfur is a difficult element to work with in the lab, according to Browne. It tends to stick to all equipment, and in the atmosphere, sulfur molecules tend to exist at very low concentrations compared to CO2 and nitrogen. “You have to have equipment that can measure incredibly tiny quantities of the products,” she added.

Using a highly sensitive mass spectrometry instrument that can identify and measure different chemical compounds, Browne’s team found that the early Earth simulation produced a whole suite of sulfur biomolecules, including the amino acids cysteine and taurine, as well as coenzyme M, a compound critical for metabolism. 

When the team scaled their lab results to calculate how much cysteine an entire atmosphere could produce, they found that the early Earth’s sky might have brought cysteine to supply about one octillion—one followed by 27 zeros—cells. Currently, Earth boasts about one nonillion—one followed by 30 zeros—cells.   

“While it’s not as many as what’s present now, that was still a lot of cysteine in an environment without life. It might be enough for a budding global ecosystem, where life is just getting started,” Reed said.

The team said these biomolecules formed in Earth’s atmosphere might have fallen onto the ground or oceans with rain, helping to get life started.

“Life probably required some very specialized conditions to get started, like near volcanoes or hydrothermal vents with complex chemistry,” Browne said. “We used to think life had to start completely from scratch, but our results suggest some of these more complex molecules were already widespread under non-specialized conditions, which might have made it a little easier for life to get going.”

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Journal

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2516779122 

Article Title

An Archean atmosphere rich in sulfur biomolecules

Article Publication Date

1-Dec-2025

THERE WERE NO NARCO BOATS, THEY WERE FISHING BOATS

 

Recognizing the need for more precise community investments to support youth mental health

The complex influence of neighborhood amenities in shaping youth depression and anxiety.

George Mason University

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Parks, libraries, recreation centers, and sidewalks, ideally, would serve to improve the quality of living for residents, but it is not that simple, especially for youth. Research by Melissa Villodas, whose work focuses on understanding how social determinants of health impact the mental health of vulnerable young people, reveals that the relationship between neighborhood amenities and youth mental health is much more complex. 

“The mere presence of neighborhood amenities may not be enough of a protective factor for the mental health of young people from diverse backgrounds, as we recognize that youth from different backgrounds may navigate neighborhood spaces differently due to unfair systems of racism and oppression,” said Villodas, assistant professor of social work at George Mason University. 

With a focus on low-income families, Villodas used national data that captured parent reports of depression and anxiety among their adolescents aged 14-17 to investigate whether the presence of neighborhood amenities was associated with different mental health outcomes. She concluded that neighborhood amenities were linked to mental health in various ways across differing racial and ethnic groups. 

Villodas observed that Hispanic and Black youth had higher rates of anxiety when living in neighborhoods with sidewalks compared to White youth. Villodas outlines theories that suggest it is not necessarily the amenity causing poor mental health, but how youth perceive and interact with it.  

“While neighborhood parks tend to positively influence mental health, our findings suggest external factors may shape youth’s experiences in these spaces. For example, Hispanic youth might be hyper-vigilant in public spaces that traditionally support mental health due to anti-immigration policies and concerns about family members being deported within these spaces. Under these circumstances, access to parks may not function optimally as a protective factor.”  

Youth who identified as multiracial were more likely to experience depression when they reported living in areas with recreation centers, and Hispanic youth showed higher odds of depression in neighborhoods with parks. On the other hand, multiracial youth living in areas with more sidewalks were less likely to experience depression. 

Villodas’s study focuses on understanding how neighborhood amenities relate to the mental health of youth living with limited resources. By honing in on populations with limited financial resources, her work can lead to more targeted and meaningful recommendations for improving youth mental health on the community level. 

“It is important we recognize how the presence of neighborhood amenities may shape youth mental health both for better and for worse. Because of this, our findings can offer a starting point for prioritizing youth-centered design considerations across neighborhood amenities that support the mental health of all youth,” said Villodas. “Community investments in neighborhood amenities can support youth mental health, but require diverse youth voices to achieve equitable outcomes.” 

Exploring associations between neighborhood amenities and mental health: Insights from parent reports of older youth in low-income households was published in December 2025 in Wellbeing, Space & Society. 

About the researcher 

Melissa Villodas is a researcher who believes context matters – this includes both the context of our environments and the context shaped by diverse experiences across sociodemographic factors. Her core research value centers the person-in-environment perspective to more innovatively and effectively improve mental health. 

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Journal

Wellbeing Space and Society

DOI

10.1016/j.wss.2025.100317 

Article Publication Date

1-Dec-2025

 

Losing sleep over money: Rice study reveals how financial stress follows workers to bed

New research shows that financial worries shape bedtime behaviors, sleep quality

Rice University

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Long before the alarm sounds, many Americans lose quality rest to the quiet worries that surface after dark — whether about bills, the next paycheck or job stability. New research from Rice University shows those bedtime stress moments aren’t just uncomfortable; they’re part of a measurable pathway connecting economic stress to poor sleep. Although not the focus of this specific study, when poor sleep turns into daytime fatigue, it could possibly create a vicious cycle: Stress from work keeps people up at night, and a lack of quality sleep makes the next workday even harder to face.

Financial stress can follow people into the night, influencing the thoughts and habits that shape sleep quality.

“Stress before bed captures a type of cognitive and emotional activation at bedtime that prevents people from unwinding and obtaining good-quality sleep,” said study author Rebecca Brossoit, assistant professor of psychological sciences at Rice.

Published in the Journal of Business and Psychology, the study identifies “stress-before-bed behaviors” as a key mechanism linking financial worry and job insecurity to declining sleep quality. These behaviors can include lying awake feeling tense, replaying work problems or mentally planning tomorrow — habits that quietly erode sleep long before the workday begins.

As part of a larger Department of Defense (DoD) funded study, the research team collected data from full-time Army and Air National Guard service members across nine months. Participants reported their financial stress at the start of the study, their bedtime stress behaviors four months later and their sleep health five months after that. The team collected both self-reported sleep data and objective sleep measurements using wrist-worn actigraph devices. They found a clear sequence: Economic stress predicted elevated stress at bedtime, which in turn predicted more insomnia symptoms, lower sleep satisfaction and greater sleep-related daytime impairments.

“Economic stress is pervasive and it is prevalent, and it’s happening at the same time that our society isn’t getting enough sleep or good-quality sleep,” Brossoit said.

The study also highlights how financial stress affects people across income levels. While income matters, the internal experience of financial vulnerability — worrying about affording basic needs, job security or relying heavily on a paycheck — can disrupt sleep even among workers who appear financially stable. At the same time, other research has shown that inadequate sleep affects attention, memory and mood, which can influence workplace performance.

Graduate student Destiny Castro works alongside assistant professor Rebecca Brossoit, who mentored her through the analysis for the study.

As economic uncertainty continues to affect households nationwide, including lingering strain from the recent government shutdown, Brossoit said the findings offer guidance for workplaces, policymakers and individuals. She noted that organizations directly shape many of the stressors employees face.

“Organizations have a responsibility to mitigate or target some of those stressors,” she said. Competitive pay, benefits, supervisor support, career development opportunities, financial planning resources and schedule flexibility are among the strategies that can help reduce financial strain and support employee well-being.

She added that broader policies — including paid leave, access to affordable food and health care, stable housing and public education campaigns focused on financial literacy and sleep hygiene — can lessen the economic pressures that show up at bedtime.

For individuals, Brossoit emphasized that small steps can help break the stress-sleep cycle. “Practicing healthy sleep hygiene behaviors can help people unwind and obtain good-quality sleep,” she said. Creating consistent sleep routines, keeping phones out of reach at night, limiting screen time before bed and building a relaxing evening wind-down process can all support better rest.

For graduate student Destiny Castro, the project marked her first publication and her first opportunity to lead major data analysis. “Working on this project helped me understand how research can directly improve people’s lives,” she said. “Sleep affects every part of our health.”

Destiny Castro and professor Rebecca Brossoit collaborated on a new study examining how financial stress affects sleep health.

Brossoit said collaborating with Castro was one of the most rewarding parts of the study and she hopes the research encourages a wider understanding of how economic stress influences health. “If we want people to thrive — at work, at home and in their communities — supporting both economic stability and healthy sleep is essential,” she said.

Other co-authors on the paper included Tori Crain at Portland State University, Leslie Hammer at Oregon Health & Science University and Todd Bodner at Portland State University.

The research was supported by the DoD (W81XWH-16–1-0720). The content in this press release is solely the responsibility of the authors and does not necessarily represent the official views of funding organizations and institutions.

 

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Journal

Journal of Business and Psychology

DOI

10.1007/s10869-025-10075-y 

Method of Research

Survey

Article Title

Losing Sleep Over Money: The Impact of Economic Stressors on Stress Before Bed Behaviors and Worker Sleep