Lens-free fluorescence instrument detects deadly microorganisms in drinking water

New approach promises low-cost, real-time water quality monitoring for developing countries, disaster areas and rapid testing needs at events like the Paris Olympics

Peer-Reviewed Publication

Optica

 

image: 

Researchers developed a fluorescence detection system (right) that can provide highly sensitive detection of deadly microorganisms in drinking water, without using any lenses. They are now converting the technology into a lensless dip-in handheld system (left) that could be useful for testing water quality in the traditional natural stone spouts widely used by people in Kathmandu Valley in Nepal (background).

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Credit: Rijan Maharjan, Ashim Dhakal, Phutung Research Institute

WASHINGTON — Researchers have shown that a fluorescence detection system that doesn’t contain any lenses can provide highly sensitive detection of deadly microorganisms in drinking water. With further development, the new approach could provide a low-cost and easy-to-use way to monitor water quality in resource-limited settings such as developing countries or areas affected by disasters. It could also be useful when water safety results are needed quickly, such as for swimming events, a concern highlighted during the Paris Olympics.

“In developing countries, unsafe water sources are responsible for more than one million deaths each year,” said research team leader Ashim Dhakal from the Phutung Research Institute in Nepal. “We hope that our work will facilitate the development of simpler and cost-effective yet highly efficient sensing paradigms for drinking water, saving countless lives around the world.”

Current methods used to assess microbial contamination in water require culturing the water samples and then quantifying harmful bacteria. This can take over 18 hours, making it impractical when immediate confirmation of water safety is needed. This is also a key reason why water surveillance is ineffective in developing countries, where the required skilled human resources, infrastructure and reagents are not readily available.

In Optica, Optica Publishing Group’s journal for high-impact research, researchers from Phutung Research Institute, University of São Paulo in Brazil and University of York in the UK report that their new water monitoring fluorometer can detect fluorescent proteins from bacteria in water down to levels of less than one part per billion, without using any lenses. This sensitivity meets the World Health Organization’s criteria for detecting fecal contamination in drinking water.

“Today’s fluorometers typically use costly lenses that are made of specialty UV-transparent glass and require precise positioning,” said Dhakal. “We show that eliminating the lenses not only reduces the device cost, size and weight but also provides better performance given that we are not aiming for imaging here.” 

Getting rid of the lenses

This research is part of a larger project funded in part by the Optica Foundation Challenge, awarded to Dhakal in 2022 to pilot a portable, low-cost and user-friendly instrument for real-time water quality assessment. During development, the researchers closely examined the fundamentals of optical signal generation in applications like water quality monitoring. They discovered that while optical lenses are commonly used in devices such as cameras, microscopes and telescopes, these optical components often reduce performance for practical situations that don’t require images.

“This was an important finding because lenses account for a significant share of the costs of optical systems and their bulk and weight make it difficult to create practical portable devices,” said Dhakal. “Our analysis revealed that using a light source, detectors and sample sizes that are all as large and as close to each other as possible produces a stronger signal, leading to better performance for water quality monitoring.”

Comparison with a lensed system

Based on their findings, the researchers designed a lensless fluorescence system using large (1-2 mm2) LEDs and detectors, which have recently become available in UV wavelengths. It works by using UV light to excite proteins from harmful microbes and then detecting the resulting fluorescence.

In addition to demonstrating the lensless system’s sensitivity, they also showed that it produced a fluorescence signal that is about double the strength of a lensed system. They found that the performance of the lensed system was limited by its numerical aperture, the use of larger sources and detectors and the finite imaging distance required between the components and the sample.

The researchers are now developing a pocket-sized version of the lensless fluorometers for field testing. They point out that the instrument must be shown to withstand the harsh environments found in multiple scenarios before being widely applied. They are also working to demonstrate that their approach meets the specificity requirements for detecting specific bacterial contamination by incorporating measurement of multiple parameters into the device.

“Our system is already highly useful because the sensitive and accurate measurement of concentration of bacterial proteins that it provides is directly related to efficiency of water treatment, the dose of disinfectants required for disinfection and the likelihood of bacterial proliferation in a recontamination event,” said Dhakal.

Paper: A Maharjan, P Waiba, S. Shrestha, R. Maharjan, A. Martin, K. Li, E. R. Martin, T. F. Krauss, A. Dhakal, “When a lensless fluorometer outperforms a lensed system,” 11, 8 (2024).

DOI: doi.org/10.1364/OPTICA.527289.

 

About Optica

Optica is an open-access journal dedicated to the rapid dissemination of high-impact peer-reviewed research across the entire spectrum of optics and photonics. Published monthly by Optica Publishing Group, the Journal provides a forum for pioneering research to be swiftly accessed by the international community, whether that research is theoretical or experimental, fundamental or applied. Optica maintains a distinguished editorial board of more than 60 associate editors from around the world and is overseen by Editor-in-Chief Prem Kumar, Northwestern University, USA. For more information, visit Optica.

About Optica Publishing Group

Optica Publishing Group is a division of Optica, Advancing Optics and Photonics Worldwide. It publishes the largest collection of peer-reviewed content in optics and photonics, including 18 prestigious journals, the society’s flagship member magazine, and papers from more than 835 conferences, including 6,500+ associated videos. With over 400,000 journal articles, conference papers and videos to search, discover and access, Optica Publishing Group represents the full range of research in the field from around the globe.

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Journal

Optica

DOI

10.1364/OPTICA.527289 

Article Title

When a lensless fluorometer outperforms a lensed system

Article Publication Date

8-Aug-2024

Disclaimer: AAAS and 

 

Biocides are a useful tool to combat antibiotic resistance but appropriate use is vital, scientists suggest

Applied Microbiology International

A recent review in the journal Sustainable Microbiology discusses how the use of biocides can promote well-being - but must only be used when there are clear benefits.

Biocide use should be restricted to applications where there are tangible benefits but also not unnecessarily restricted where genuine benefits can be demonstrated, the new review suggests.

The article ‘Sustainable application of biocides to promote hygiene and minimise antimicrobial resistance’ by scientists at the University of Manchester, UK, is published in Sustainable Microbiology, an Applied Microbiology International publication.

Contribution to sustainability

“We aimed to present an objective assessment of the potential contribution of microbiocides - widely used non-antibiotic antimicrobials - to sustainability,” explained corresponding author Professor Andrew McBain.

“Having been involved in biocide research since 1999, I am aware of the need for a better understanding of the potential benefits of appropriate biocide use, as well as the generation of data on which to base improved risk assessment.”

Biocidal (microbicidal) products play a critical role in controlling microorganisms in healthcare, industrial, community and home environments but there is concern that their use and misuse might contribute to the evolution of antimicrobial resistance (AMR). 

Microbial control

Benefits of biocides include the control and prevention of infections in clinical settings with associated reductions in antibiotic use, preservation of a range of products and materials, substantial reduction in infection risk for consumers, hygiene in the community, such as in public swimming baths, and microbial control in many facets of industry. 

“Antibiotic resistance is widely understood to be one of humankind’s largest challenges. Biocides are one of a limited number of tools we have to reduce the need for antibiotic use, which most people would agree is a major driver of AMR,” Professor McBain said. 

“Yet at the same time, there is concern that biocides, particularly when used inappropriately, could contribute to AMR. This potential contribution, however, remains poorly understood. Risk assessments are often based on data that we believe do not always best represent the way biocides are used in the real world and should fully consider benefits as well as risks.”

Critical assessment

The review provides a critical assessment of the contribution of biocides to sustainability based on a critical evaluation of the literature, followed by offering views on the future management of biocide use across the globe.

“I would not claim that the work represents a paradigm shift in thinking on the topic, but I do believe that there should be more balanced consideration of risks and benefits in the context of biocides, as well as a push for more realistic data on which to estimate risk,” Professor McBain said.

“More work is needed to develop a reliable basis for appropriate biocide use. This will encompass research in microbiology and biophysics (where we have been developing collaborations), chemistry, formulation, regulation, and education.” 

Joined-up approach

“A joined-up approach with industry stakeholders is required to ensure that effective products are available when needed and that their use is appropriately regulated but not unnecessarily restricted.”

While the review was a team effort, Thomas Willmott drove the writing, and it also formed part of the PhD project of Layali Jadaan. It was supported by microbiologist Gavin Humphreys, and biophysics collaborator Jian Lu. 

“Importantly, I contacted a US-based microbiologist and biocide specialist, John Chapman who helped considerably. John became a friend and mentor after we were introduced in the early 2000s by my late colleague Peter Gilbert,” Professor McBain said.

‘Sustainable application of biocides to promote hygiene and minimise antimicrobial resistance’ is published in Sustainable Microbiology.

NOTES TO EDITORS

1. Applied Microbiology International (AMI) is the oldest microbiology society in the UK and with more than half of its membership outside the UK, is truly global, serving microbiologists based in universities, private industry and research institutes around the world. AMI provides funding to encourage research and broad participation at its events and to ensure diverse voices are around the table working together to solve the sustainability development goals it has chosen to support. AMI publishes leading industry magazine, The Microbiologist, and in partnership with Oxford University Press, publishes three internationally acclaimed journals. It gives a voice to applied microbiologists around the world, amplifying their collective influence and informing international, evidence-based, decision making. 
2. Oxford University Press (OUP) is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. OUP is the world's largest university press with the widest global presence.
3. OUP publishes more than 500 academic and research journals covering a broad range of subject areas, two-thirds of which are published in collaboration with learned societies and other international organizations. It has been publishing journals for more than a century and, as the world’s largest university press, has more than 500 years of publishing expertise.

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Journal

Sustainable Microbiology

Article Title

Sustainable application of biocides to promote hygiene and minimise antimicrobial resistance

 HARD TO BELIEVE, BUT TRUE...

Study: Flying keeps getting safer

Reflecting a “Moore’s Law of aviation,” commercial flight has become roughly twice as safe each decade since the 1960s; Covid-19 added a wrinkle, however

Massachusetts Institute of Technology

Many airline passengers naturally worry about flying. But on a worldwide basis, commercial air travel keeps getting safer, according to a new study by MIT researchers.  

The risk of a fatality from commercial air travel was 1 per every 13.7 million passenger boardings globally in the 2018-2022 period — a significant improvement from 1 per 7.9 million boardings in 2008-2017 and a far cry from the 1 per every 350,000 boardings that occurred in 1968-1977, the study finds.

“Aviation safety continues to get better,” says Arnold Barnett, an MIT professor and co-author of a new paper detailing the research results.

“You might think there is some irreducible risk level we can’t get below,” adds Barnett, a leading expert in air travel safety and operations. “And yet, the chance of dying during an air journey keeps dropping by about 7 percent annually, and continues to go down by a factor of two every decade.”

To be sure, there are no guarantees of continual improvement; some recent near-collisions on runways in the U.S. have gained headlines in the last year, making it clear that airline safety is always an ongoing task.

Additionally, the Covid-19 pandemic may have caused a sizable — though presumably temporary — new risk stemming from flying. The study analyzes this risk but quantifies it separately from the long-term safety trend, which is based on accidents and deliberate attacks on aviation.

Overall, Barnett compares these long-run gains in air safety to “Moore’s Law,” the observation that innovators keep finding ways to double the computing power of chips roughly every 18 months. In this case, commercial air travel has gotten roughly twice as safe in each decade dating to the late 1960s. 

“Here we have an aerial version of Moore’s Law,” says Barnett, who has helped refine air travel safety statistics for many years. 

In per-boarding terms, passengers are about 39 times safer than they were in the 1968-1977 period. 

The paper, “Airline safety: Still getting better?” appears in the August issue of the Journal of Air Transport Management. The authors are Barnett, who is the George Eastman Professor of Management Science at the MIT Sloan School of Management, and Jan Reig Torra MBA ’24, a former graduate student at MIT Sloan. 

Covid-19 impact

The separate, additional finding about the impact of Covid-19 focuses on cases spread by airline passengers during the pandemic. This is not part of the top-line data, which evaluates airline incidents during normal operations. Still, Barnett thought it would also be valuable to explore the special case of viral transmission during the pandemic.

The study estimates that from June 2020 through February 2021, before vaccines were widely available, there were about 1,200 deaths in the U.S. from Covid-19 associated, directly or indirectly, with its transmission on passenger planes. Most of those fatalities would have involved not passengers but people who got Covid-19 from others who had been infected during air travel. 

In addition, the study estimates that from March 2020 through December 2022, around 4,760 deaths around the globe were linked to the transmission of Covid-19 on airplanes. Those estimates are based on the best available data about transmission rates and daily death rates, and take account of the age distributions of air passengers during the pandemic. Perhaps surprisingly, older Americans do not seem to have flown less during the Covid-19 pandemic, even though their risks of death given infection were far higher than those of younger travelers.

“There’s no simple answer to this,” Barnett says. “But we worked to come up with realistic and conservative estimates, so that people can learn important lessons about what happened. I believe people should at least look at these numbers.” 

Improved overall safety

Overall, to study fatalities during normal airline operations, the researchers used data from the Flight Safety Foundation, the World Bank, and the International Air Transport Association. 

To evaluate air travel risks, experts have used a variety of metrics, including deaths per billion passenger miles, and fatal accidents per 100,000 flight hours. However, Barnett believes deaths per passenger boarding is the most “defensible” and understandable statistic, since it answers a simple question: If you have a boarding pass for a flight, what are your odds of dying? The statistic also includes incidents that might occur in airport terminals. 

Having previously developed this metric, Barnett has now updated his findings multiple times, developing a comprehensive picture of air safety over time:

Commercial air travel fatalities per passenger boarding
1968-1977: 1 per 350,000
1978-1987: 1 per 750,000
1988-1997: 1 per 1.3 million
1998-2007: 1 per 2.7 million
2007-2017: 1 per 7.9 million
2018-2022: 1 per 13.7 million

As Barnett’s numbers show, these gains are not incidental improvements, but instead constitute a long-term trend. While the new paper is focused more on empirical outcomes than finding an explanation for them, Barnett suggests there is a combination of factors at work. These include technological advances, such as collision avoidance systems in planes; extensive training; and rigorous work by organizations such as the U.S. Federal Aviation Agency and the National Transportation Safety Board.

However, there are disparities in air travel safety globally. The study divides the world into three tiers of countries, based on their commercial air safety records. For countries in the third tier, there were 36.5 times as many fatalities per passenger boarding in 2018-2022 than was the case in the top tier. Thus, it is safer to fly in some parts of the world than in others. 

The first tier of countries consists of the United States, the European Union countries, and other European states, including Montenegro, Norway, Switzerland, and the United Kingdom, as well as Australia, Canada, China, Israel, Japan, and New Zealand. 

The second group consists of Bahrain, Bosnia, Brazil, Brunei, Chile, Hong Kong (which has been distinct from mainland China in air safety regulations), India, Jordan, Kuwait, Malaysia, Mexico, the Philippines, Qatar, Singapore, South Africa, South Korea, Taiwan, Thailand, Turkey, and the United Arab Emirates. In each of those two groups of nations, the death risk per boarding over 2018-22 was about 1 per 80 million.

The third group then consists of every other country in the world. Within the top two groups, there were 153 passenger fatalities in the 2018-2022 period, and one major accident, a China Eastern Airlines crash in 2022 that killed 123 passengers. The 30 other fatalities beyond that in the top two tiers stemmed from six other air accidents. 

For countries in the third tier, air travel fatalities per boarding were also cut roughly in half during the 2018-2022 period, although, as Barnett noted, that can be interpreted in two ways: It is good they are improving as rapidly as the leading countries in air safety, but in theory, they might be able to apply lessons learned elsewhere and catch up even more quickly. 

“The remaining countries continue to improve by something like a factor of two, but they’re still behind the top two groups,” Barnett observes.

Overall, Barnett notes, notwithstanding Covid-19, and looking at accident avoidance, especially in countries with the lowest fatality rates, it is remarkable that air safety keeps getting better. Progress is never assured in this area; yet, the leading countries in air safety, including their government officials and airlines, keep finding ways to make flying safer.

“After decades of sharp improvements, it’s really hard to keep improving at the same rate. And yet they do,” Barnett concludes. 

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Written by Peter Dizikes, MIT News

Paper: “Airline Safety: Still Getting Better?”

https://www.sciencedirect.com/science/article/pii/S0969699724001066?dgcid=author#appsec2

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Journal

Journal of Air Transport Management

DOI

10.1016/j.jairtraman.2024.102641 

Article Title

“Airline Safety: Still Getting Better?”

 

When AI aids decisions, when should humans override?

Asking AI to explain its reasons does not always help humans make better decisions

University of Texas at Austin

AUSTIN, Texas -- The $184 billion market for artificial intelligence shows no signs of slowing. A big slice of that market is organizations, from businesses to government agencies, that rely on AI to help make decisions. A 2023 study by IBM found 43% of CEOs are using AI to make strategic decisions.

But relying on AI can be problematic, given its well-documented history of bias, including stereotyping by race and gender. That can lead to flawed recommendations and unfair treatment, when AI considers demographics to discourage granting a bank loan or a job interview to certain people.

One way to mitigate these problems, experts say, is to make AI systems explain themselves. By reviewing an AI’s “explanation” of how they make decisions, human hiring managers or loan officers, for example, can decide whether to override AI recommendations.

But new research from Texas McCombs finds that the explanations themselves can be problematic. They may fuel a perception of fairness without being grounded in accuracy or equity.

“What we find is that the process doesn’t lead humans to actually make better quality decisions or fairer decisions,” says Maria De-Arteaga, assistant professor of information, risk, and operations management.

In the study, De-Arteaga and her co-authors — UT postdoctoral research fellow Jakob Schoeffer and Niklas Kühl of the University of Bayreuth, Germany — had an AI system read 134,436 online biographies and predict whether each person was a teacher or professor.

Then, human participants were allowed to read the bios and choose whether to override AI recommendations. There were two types of explanations, and each participant saw one of the two:

• Explanations highlighting task-relevant keywords such as “research” or “schools.”
• Explanations highlighting keywords related to gender, such as “he” or “she.”

The research found that participants were 4.5 percentage points more likely to override AI recommendation when the explanations highlighted gender rather than task-relevance.

A major reason: suspected gender bias. Participants were more likely to think recommendations were unfair when they focused on gender.

Illusion of Accuracy and Fairness

But the participants were not always correct. When it came to identifying professors or teachers, gender-based overrides were no more accurate than task-based overrides. In fact, neither type of explanation improved human accuracy, compared with participants who were not given explanations.

Why didn’t the explanations lead to better decisions? De-Arteaga focuses on the participants who saw task-relevant words and assumed they were free of gender bias.

But research has found the opposite: An algorithm can develop gender bias by learning correlations between seemingly task-relevant words and gender. The explanations don’t reveal that kind of bias. Humans wrongly assume the AI is gender neutral, and they decline to override it.

“There’s this hope that explanations are going to help humans discern whether a recommendation is wrong or biased,” De-Arteaga says. “But there’s a disconnect between what the explanations are doing and what we wish they did.”

Although AI explanations that try to approximate the importance of certain factors can be inherently flawed, De-Arteaga and her co-authors suggest several ways to make their design and deployment more useful to decision-makers.

• Set more concrete and realistic objectives for explanations, based on the decisions to be made, and evaluate whether they accomplish the desired goal.
• Provide more relevant cues in the explanations, such as those related to fairness in the AI system.
• Widen the scope of explanations by giving more insight into how the algorithm works. For example, knowing what data is and is not available to the system may better empower humans to use algorithms well.
• Study the psychological mechanisms at play when humans do or do not decide to override an AI decision. Recommendations should be designed to reflect how humans actually interact with AI, rather than how researchers wish they interacted.

The goal, she says, is to develop tools that help humans successfully complement AI systems — not just offer explanations that build a false sense of trust.

“That’s one of the problems with explanations,” she says. “They can lead you to trust the system more, even if the system is not deserving of your trust.”

“Explanations, Fairness, and Appropriate Reliance in Human-AI Decision Making” is published in Association for Computing Machinery’s Proceedings of the CHI Conference on Human Factors in Computing Systems.

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Journal

Proceedings of the ACM on Human-Computer Interaction

DOI

10.1145/3613904.3642621 

Article Title

Explanations, Fairness, and Appropriate Reliance in Human-AI Decision-Making

 

New study is helping to understand and achieve species elements in the Kunming–Montreal Global Biodiversity Framework

Newcastle University

Experts provide clarity on key terms for urgent species recovery actions to support the implementation of the Global Biodiversity Framework.

The Kunming-Montreal Global Biodiversity Framework (KMGBF) is a landmark agreement ratified in 2022 by Parties to the Convention on Biological Diversity that outlines ambitious goals to combat biodiversity decline.

The Framework states outcomes for species to be achieved by 2050 in Goal A and establishes a range of targets to reduce pressures on biodiversity and halt biodiversity loss by 2030. Target 4 calls for urgent recovery actions for species where the implementation of other targets is insufficient to eliminate extinction risk.

Publishing a review paper in the journal BioScience, experts led by Newcastle University analyse key species elements of Goal A and Target 4, examine their meaning and clarify implementation needs.

The scientists emphasise that achieving the ambitions outlined in Goal A - to halt extinctions, reduce extinction risk, and increase species abundance - will require meaningful progress towards all targets, not just Target 4. Targets 1, 5, 6, 7, and 8 are concerned with reducing pressures, all of which affect species.

Target 4 should be seen as a target for species that require urgent focused actions. They highlight how the current Monitoring Framework is unable to adequately measure progress towards implementing urgent recovery actions and emphasize that appropriate indicators are needed to measure progress towards Target 4.

The authors discuss the key role of access to information to support attainment of species elements in Goal A, highlighting that Section C of the Framework encourages a whole of government and whole of society approach that will be instrumental for the successful implementation of the Framework.

Capacity building, cooperation, and knowledge exchange will be another key area of development. The experts’ analysis shows that it is critical that all stakeholders, Parties, businesses, and members of civil society identify where they can act and then implement necessary actions.

Study lead author, Professor Philp McGowan, Professor of Conservation Science and Policy at Newcastle University, said: "The new Global Biodiversity Framework has very ambitious Goals and Targets for species and after four years of negotiation by the world's countries, the range of words and phrases it contains may mean different things to different people.

“We have drawn on the negotiations themselves and existing research to suggest what key words and phrases mean in practice, in the hope of helping to achieve the ambition in the Framework."

Study co-author, Dr Alison Hutchinson Research Associate Species Conservation, Newcastle University School of Natural and Environmental Sciences added:

“This paper elaborates on the key terms held within Goal A and Target 4 of the Global Biodiversity Framework to give clarity as to what these concepts may mean in practice.

“Achieving Framework’s ambitions to prevent species extinction and to live in harmony with nature will require recognising and filling knowledge gaps, embracing co-operation across governments and society, and drawing on all available science, resources, and worldviews so that effective and transformative policies and management can be implemented to tackle the biodiversity-loss crisis.”

The review can support Parties updating and implementing their National Biodiversity Strategies and Action Plans, by clarifying the outcomes for species and actions required to address Goal A and Target 4.

--ends--

 

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Journal

BioScience

DOI

10.1093/biosci/biae065 

Method of Research

Systematic review

Article Title

Understanding and achieving species elements in the Kunming–Montreal Global Biodiversity Framework

Article Publication Date

8-Aug-2024

 

Wide genetic diversity in South American indigenous groups highlights diversity gap in genomics research

Cell Press

Amazonians are as genetically different from Andeans as Europeans are from East Asians when it comes to genetic variants that affect the response to certain drugs, according to a commentary published August 8 in the journal Cell. These genetic variations can affect what side effects an individual experiences and influence drug dosage recommendations. Taking the genetic diversity within indigenous groups as an example, the scientists highlight the need to address the diversity gap in genomics research.

Historically, Native American populations have been viewed as a homogeneous group, a bias and oversimplification that researchers argue persists to this day. But the reality is much more complicated. Factors like environment, history, and culture have led to important genetic differences between populations living in the South American Andes and Amazon forests, which are only 150 to 200 miles apart.

“A low-oxygen and dry, high-altitude environment characterizes the Andean region, while the Amazon region is a low-altitude tropical forest. These vastly different environmental stressors can drive genetic changes and biological adaptations,” says corresponding author Eduardo Tarazona-Santos (@tarazona_santos) of Universidade Federal de Minas Gerais, Brazil. “The Andeans and Amazonians also developed distinct languages, social structures, and agricultural practices, which can further contribute to their differentiation through natural selection over time.”

The researchers analyzed the genomic diversity of 294 individuals from 17 indigenous Peruvian groups in the Andes and Amazon regions. They found that certain genetic variations make the Amazonians and Andeans respond to medicine differently. For example, a higher percentage of Amazonians have a variation that makes them respond better to rosuvastatin therapy, often prescribed to lower cholesterol levels and prevent cardiovascular events, but also gives them higher risks of side effects.

Based on clinical guidelines, only 2% of indigenous Andeans require a lower initial dose of rosuvastatin to prevent side effects, compared with 16% of indigenous Amazonians. The findings underscore the need to incorporate genomics research to ensure the effective application of precision medicine.

When it comes to warfarin, a medicine that treats blood clots, dosage is key. Too little warfarin renders the therapy ineffective, while too much can put patients at risk for heavy bleeding. Based on the genetic variations, 69% of indigenous people from the southern Andes region need a lowered warfarin dosage, compared with 93% of indigenous Amazonians.

“These pharmacology-affecting genetic differences observed in the Andeans and Amazonians are even larger than those seen between Europeans and Asians,” says Tarazona-Santos.

While there are alternative drugs to warfarin that do not need critical control of dosage, they are ten times more expensive—out of reach for many people in developing countries. Understanding the genetic factors that influence drug dosing is crucial for ensuring the safe and effective use of affordable medicine in resource-limited settings.

Learning from the genetic diversity within indigenous populations, the commentary cautions against conceiving of ethnic groups as a single entity in human genomics study. It also calls for inclusive genomics research that encompasses diverse populations to ensure equitable health care outcomes worldwide.

Tarazona-Santos concludes that including people from diverse socioeconomic and ethnic backgrounds in research groups is very important for human genomics studies like this one. “It makes research and community engagement easier, offering transparency and confidence,” he says. “It makes people more comfortable seeing familiar faces from the same community.”

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Funding information can be found in the paper text.

Cell, Alvim and Silva-Carvalho et al. “The need to diversify genomic studies: insights from Andean highlanders and Amazonians” https://cell.com/cell/fulltext/S0092-8674(24)00769-4

Cell (@CellCellPress), the flagship journal of Cell Press, is a bimonthly journal that publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease mechanisms and therapeutics. Visit http://www.cell.com/cell. To receive Cell Press media alerts, contact press@cell.com.

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Journal

Cell

DOI

10.1016/j.cell.2024.07.009 

Method of Research

Commentary/editorial

Subject of Research

Not applicable

Article Title

The need to diversify genomic studies: insights from Andean highlanders and Amazonians

Article Publication Date

8-Aug-2024

 

Researchers make breakthrough in understanding species abundance

Researchers at the U of A have now added a genetic component to our understanding of species abundance

University of Arkansas

 

image: 

Wade Roberts

view more 

Credit: University Relations

When it comes to predicting the abundance of a species, body size appears to be a fundamental and repeatable predictor, with smaller organisms occurring in greater numbers than larger ones. The caveat, known as Bermann’s Rule, is that in polar regions larger bodied organisms predominate. Other factors that influence species abundance include light availability, food availability, competition and predation.

New findings by a team of researchers in biological sciences at the U of A have now added a genetic component to our understanding of species abundance.

Genome size, the total amount of DNA contained within one copy of a single complete genome, can also be a strong predictor of species abundance. The paper examined diatoms, which are unicellular algae that play an important role in freshwater and marine food webs. They create long-chain fatty acids, like fish oil and other lipids, that serve as energy. The energy molecules that diatoms produce go up the food web from zooplankton to aquatic insects to fish to humans. 

Diatoms also play a critical role in photosynthesis, the process by which carbon dioxide is converted to oxygen. It’s estimated that 20-25 percent of Earth’s oxygen comes from diatoms – more than rainforests and land plants.

The key finding was that temperature and genome size, not body size, had the greatest influence on the maximum population growth rate of the diatoms. Yet body size still mattered in colder latitudes, conserving Bermann’s Rule.

The paper, “Diatom abundance in the polar oceans is predicted by genome size,” was published in PLoS Biology by a trio of authors from the Department of Biological Sciences: Wade Roberts, a postdoctoral researcher in the Alverson Lab; Adam Siepielski, an associate professor; and Andrew Alverson, professor and director of the Alverson Lab.

Roberts noted that the genome size of a diatom is critical to cell function and its ability to adapt to a changing environment. 

“In phytoplankton, cell size is highly correlated to genome size,” Roberts explained. “We’ve known that for a while. But we weren’t sure if cell size was driving genome size or vice versa. We were able to directly test this through a path analysis to determine the directionality. We found that an increase in genome size led to increased cell size. So, we confirmed that size of the genome is driving cell size.”

The genome size of diatoms can vary by 50-fold between species, but most of the difference in genetic material is made up of repeated DNA. DNA codes for the proteins that are the building blocks of life, but it’s unclear how this repetitive DNA is utilized by the cell. It’s estimated that only about 2 percent of the human genome codes for genes.

Overall, the paper’s results advance understanding of species abundance by showing that a single emergent trait fundamental to all life, the size of the genome, can predict species abundance at a global scale.

“Larger organisms are more abundant in polar regions,” Roberts said. “That’s true of mammals and other multi-cellular organisms. But we didn’t know if that was true of phytoplankton. Now we can make predictions about community composition based off temperature. This will help us predict whether larger diatoms will be able to persist in warming waters.”

On a warming planet, this could mean the reduction of larger-celled diatoms and a potential decrease in oxygen output.

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Journal

PLoS Biology

DOI

10.1371/journal.pbio.3002733 

Method of Research

Computational simulation/modeling

Subject of Research

Not applicable

Article Title

Diatom abundance in the polar oceans is predicted by genome size

Article Publication Date

8-Aug-2024

 

Increasing clinicians’ knowledge about climate change’s impact on health and healthcare sustainability

Physicians at an academic medical center completed surveys about climate change-focused educational modules related to health and sustainability in healthcare offered through an existing biannual quality incentive program

Massachusetts General Hospital

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• Physicians at an academic medical center completed surveys about climate change-focused educational modules related to health and sustainability in healthcare offered through an existing biannual quality incentive program.
• Most respondents thought that the modules were relevant or very relevant to their lives and clinical practices, and that their knowledge on these topics increased after completing the modules.
• Perceptions of the modules’ relevance varied by physicians’ demographics and specialties.

An educational program emphasizing the relationship that climate change has with health and health care environmental sustainability was well-received by physicians, according to a recent survey-based study published in JAMA Network Open and conducted by investigators at Massachusetts General Hospital (MGH), a founding member of the Mass General Brigham healthcare system.

The program provided a foundation about climate change and the impact of fossil fuel-related pollution on health; the healthcare system’s contribution to carbon pollution; and opportunities to address these challenges. To the team’s knowledge, MGH is the first academic medical center to offer incentivized educational programs on climate change and environmental sustainability in healthcare.

“Climate change is a fundamental threat that is recognized by many to be the greatest health crisis humans have ever faced. However, surveys show that the majority of physicians do not feel prepared to address climate change’s impact on health or to take action,” said lead author Wynne Armand, MD, an associate director of the Center for the Environment and Health at MGH and an assistant professor of medicine at Harvard Medical School.

In their study, Armand and her colleagues surveyed the response to climate change–focused educational modules offered at Massachusetts General Hospital, an academic medical center, through an existing biannual physician quality incentive program.

Among a total of 2,559 eligible physicians and psychologists, 2,417 (94.5%) completed the educational modules. Of these participants, 73.1% thought that the modules were relevant or very relevant to their lives, and 65.4% found the modules relevant or very relevant to their clinical practices.

Age did not influence the degree to which physicians thought climate-related education was relevant to their individual lives or practices. Clinicians identifying as female were more likely to consider the education as relevant compared with male clinicians.

As expected, physicians in specialties that specifically treat problems more directly exacerbated by climate change like emergency medicine/urgent care, allergy and primary care were more likely to find the trainings relevant to their practices.

“Our findings indicate that educational strategies should be tailored by specialty to better engage clinicians in learning about climate change’s health effects and ways to mitigate health sector contributions,” said Armand.

Optional comments were provided by 446 (18.5%) of respondents—56.1% were positive, 36.5% were neutral, and 7.4% were negative. Many positive comments supported the importance of the topic and provided suggestions for reducing the carbon footprint of the hospital. Others asked for additional ways to get involved.

Negative comments stated that quality improvement trainings should focus on patient care and that providing climate information to clinicians is inappropriate given their limited influence on hospital-wide policies.

Overall, the survey results indicate that most physicians believe that education on the complex relationships between climate change and health care is important, and they welcome opportunities for action. Importantly, participants felt that their knowledge on these topics increased after completing the modules. Similar efforts across the health care sector may help all those involved to recognize and address the health risks of climate change and take steps to minimize their contribution to the problem.

Authorship: Wynne Armand, Michael Padget, Elizabeth Pinsky, Jason Wasfy, Jonathan Slutzman, and Ann-Christine Duhaime.

Paper cited: Armand W et al. “Clinical Knowledge and Attitudes About Climate Change and Health After a Quality Incentive Program.” JAMA Network Open DOI: 10.1001/jamanetworkopen.2024.26790

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About Massachusetts General Hospital

Massachusetts General Hospital, founded in 1811, is the original and largest teaching hospital of Harvard Medical School. The Mass General Research Institute conducts the largest hospital-based research program in the nation, with annual research operations of more than $1 billion and comprises more than 9,500 researchers working across more than 30 institutes, centers and departments. MGH is a founding member of the Mass General Brigham healthcare system.

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Journal

JAMA Network Open

DOI

10.1001/jamanetworkopen.2024.26790 

Method of Research

Survey

Subject of Research

People

Article Title

Clinical Knowledge and Attitudes About Climate Change and Health After a Quality Incentive Program

Article Publication Date

8-Aug-2024