Friday, October 09, 2026

 

Fish may look fine in urban waters but their genes tell a different story


Blue damselfish remain abundant along Okinawa’s urbanized coasts, but gene activity reveals physiological stress that conventional environmental monitoring may miss.




Okinawa Institute of Science and Technology (OIST) Graduate University

Juvenile blue damselfish

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Tiny juvenile blue damselfish shelter in coral branches.

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Credit: Emma Gairin





Blue damselfish, with their striking blue hue, are easy to spot, even along Okinawa’s heavily urbanized coastlines. But while abundant, their gene activity reveals a hidden cost to living in human-impacted environments. 

A new Nature Communications study shows that fish living close to human activity can be well fed while simultaneously displaying molecular signs of chronic physiological stress, suggesting a possible “junk food effect.” The research, conducted by scientists at the Okinawa Institute of Science and Technology (OIST), the French National Centre for Scientific Research (CNRS), and the Indiana University School of Medicine, also opens the possibility of using organisms themselves as recorders of environmental conditions, with genome-wide gene activity revealing ecological impacts invisible to conventional environmental monitoring.

Coastal environments worldwide are increasingly under pressure from urbanization, including agricultural, industrial, and residential activity. In Okinawa, less than 40% of the coastline remains natural and unaltered. This is particularly relevant for young coral reef fish, which spend their early lives in calm, shallow waters close to shore. These nursery areas provide relatively safe conditions and abundant food, but their proximity to land also exposes young fish to the impacts of human activity. However, how these conditions affect fish during this important stage of their lives, and into adulthood, remains poorly understood — until now.

“Classic methods of ecological and environmental monitoring involve water sampling, or counting the number of fish species, but this doesn’t really tell us about the health of the fish,” explains first author Emma Gairin, research fellow and former PhD student in the Marine Eco-Eco-Devo Unit at OIST. “To know what the fish is experiencing, looking at gene activity is key.”

But this is easier said than done. For wild animals in the field, scientists have typically focused on the activity of just a few genes at a time. Yet many different factors can affect gene activity, such as temperature and salinity, making it difficult to tell whether differences in gene activity between fish from different environments are really associated with human activity.

Gairin continues: “Our approach was to look at the activity of all genes, not just a few, from fish across multiple different sites to see if we can distinguish any clear environmental signatures.”

The researchers collected blue damselfish (Chrysiptera cyanea), from 18 different sites across Okinawa’s main island, with varying levels of urbanization, ranging from almost pristine reefs in northern Okinawa, to heavily urbanized coastlines in the island’s south.

“Some of the sites we were sampling were really dirty and polluted, but still, there they were,” says Gairin. “But just because they are present, it doesn’t mean that they’re not under stress.

When they analyzed the gene activity of these fish, they found, surprisingly, that many of the genes traditionally used as markers of pollution failed to track urbanization. Their activity was often better explained by factors such as temperature or nutritional status. Only when the researchers looked at gene activity across the genome as a whole did the signature of human activity clearly emerge.

The researchers identified 425 genes in juveniles and 585 genes in adult livers whose activity was associated with urbanization, but not with any of the other environmental factors they measured. These included genes involved in inflammation and immune responses, which were more active in fish from urbanized areas.

The researchers then compared the wild fish with fish raised in the laboratory under different feeding conditions. Adult fish from urbanized areas showed gene activity patterns similar to those of well-fed laboratory fish. Yet these same urban fish also showed increased immune and inflammatory responses, revealing a striking trade-off between nutritional status and physiological stress.

These findings may help answer a long-debated question: why do young reef fish settle in highly urbanized, sometimes visibly degraded coastal areas when cleaner, more natural habitats are available nearby? One possibility is that these environments may be enriched with organic matter, making food abundant and easily accessible.

“We suggest this is a ‘junk food effect’. It’s like teenagers going to a fast food chain: there is plenty to eat, it is cheap, but it may not be good for their health!” says Professor Vincent Laudet, head of OIST’s Marine Eco-Evo-Devo Unit and senior author of the study. “For young fish, an urbanized coastal environment may offer a similar trade-off. There’s plenty of food, but at a physiological cost.”

Overall, the study reveals the potential of using gene activity to better understand environmental conditions and how urbanization affects the organisms living there.

“What is exciting here is that instead of simply measuring the environment around an animal, we can ask the animal itself what it has experienced,” concludes Laudet. “Genome-wide gene activity integrates the many different environmental influences acting on an organism and can reveal physiological effects that remain invisible when we measure water quality or simply count which species are present. And there is no reason why this approach should be limited to fish or coral reefs. In principle, any animal, in any ecosystem, could become a living sensor of environmental change.”

 

CTHULHU STUDIES

3D structure of DNA may explain how cephalopods evolved complex brains



Study suggests that the 3D "entanglement" of DNA may help drive evolutionary innovation




University of Vienna

Californian two-spot octopus (Octopus bimaculoides). Embryo at the final stage before hatching. The species is named after the two prominent blue eyespots that can help deter predators.

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Californian two-spot octopus (Octopus bimaculoides). Embryo at the final stage before hatching. The species is named after the two prominent blue eyespots that can help deter predators.

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Credit: Natalie Grace Schulz





Octopuses, squid and cuttlefish, collectively known as coleoid cephalopods, have evolved exceptionally large and elaborately structured nervous systems capable of complex behaviours such as problem-solving and rapid camouflage. A new study by scientists at The University of Vienna suggests that the origins of this complexity may lie not just in the genes themselves, but in how the genome is organised in 3D. The researchers found that ancient, extensive reorganisation of the genome altered how DNA is arranged inside the cell. These shifts brought previously distant regions of DNA into contact, changing the way genes are regulated. Understanding this process could change how we think about how new traits emerge during evolution. The findings are currently published in the renowned journal Nature Communications. 

The team studied the 3D structure of the genome across octopus, squid and cuttlefish, combining data on DNA structure with gene activity. "The genome isn't just a sequence of genes. It's folded into a complex three-dimensional structure," said lead author Dr Thea Rogers. "Understanding how that structure evolves is becoming increasingly important for understanding how new forms of biological complexity arise."

"Regulatory entanglement" as a consequence of genome reorganisation

In cephalopods, a large-scale burst of genome reorganisation, which occurred hundreds of millions of years ago, dramatically reshuffled the genome and brought previously distant regions of chromosomes into close proximity.

The researchers found that when regions of DNA are brought into contact, they can begin to interact and influence each other's activity. Over time, these interactions can become embedded, forming increasingly interconnected regulatory networks. 

"Regulatory entanglement" balances innovation and stability in genome evolution 

This process, described by the researchers as "regulatory entanglement", may allow genomes to generate new patterns of gene expression while maintaining essential functions. 

Not all aspects of genome structure appear to respond to genome reorganisation in the same way. The researchers found that large structural units of the genome, known as chromatin domains, remained largely stable over evolutionary time.

In contrast, finer-scale connections known as chromatin loops were far more dynamic. These loops bring distant regions of DNA into contact. They varied widely across species, tissues and developmental stages, and were often found near genes involved in key cephalopod traits, including those linked to the nervous system. This suggests that these more flexible regions may be particularly affected by large-scale changes in DNA organisation.

3D structure of DNA shapes evolutionary processes actively 

Together, these findings challenge the idea that genome architecture is a passive consequence of evolution. Instead, they suggest that the 3D organisation of DNA actively shapes how evolution unfolds. In cephalopods, this may have played a key role in the emergence of their unusually complex nervous systems.

Summary

  • Scientists at the University of Vienna reconstructed the 3D organisation of the genome in octopus, squid and cuttlefish to investigate how genome architecture evolved following an ancient burst of genome reorganisation.
  • The study found that this large-scale reorganisation brought previously distant regions of DNA into contact, creating new networks of regulatory interactions that became embedded over evolutionary time.
  • The researchers describe this process as "regulatory entanglement", whereby new DNA interactions become increasingly interconnected, allowing genomes to generate novel patterns of gene regulation while maintaining essential biological functions.
  • The researchers found that not all aspects of the 3D genome respond to genome reorganisation in the same way. Large chromatin domains remained remarkably stable, whereas finer-scale chromatin loops were far more dynamic.
  • The findings challenge the view of genome architecture as a passive consequence of evolution and instead suggest that the 3D organisation of DNA can actively influence evolutionary change.

About the University of Vienna: 

For over 650 years the University of Vienna has stood for education, research and innovation. Today, it is ranked among the top 100 and thus the top four per cent of all universities worldwide and is globally connected. With degree programmes covering 188 disciplines, and approximately 11,000 employees, we are one of the largest academic institutions in Europe. Here, people from a broad spectrum of disciplines come together to carry out research at the highest level and develop solutions for current and future challenges. Its students and graduates develop reflected and sustainable solutions to complex challenges using innovative spirit and curiosity.

 

Study links pharmaceutical industry payments to changes in physicians’ prescribing practices



International researchers, including U of T Associate Professor Quinn Grundy find payments and gift relationships often lead physicians to more expensive, less appropriate drugs




University of Toronto






A new Cochrane review led by a team of international researchers including from U of T, has found that marketing strategies used by pharmaceutical companies such as payments for consulting and advisory board membership and free meals offered to physicians, can negatively influence prescribing habits.

The review compiled data from over 93 studies and included observed practices of millions of prescribers who had received either advertising and education, such as sales rep visits, gifts and payments, or free samples from pharmaceutical companies. The researchers found that these gift relationships and marketing tactics led physicians to more often prescribe the drugs a company was promoting. The data also showed that these marketing practices were strongly linked to inappropriate prescribing, meaning physicians were likely prescribing treatments that patients do not necessarily need, or that may cause harm.

Quinn Grundy is an associate professor at the Lawrence Bloomberg Faculty of Nursing and is one of the two Canadian authors involved in the review.  She points out that these marketing tactics employed by pharmaceutical companies are a common practice among physicians globally, with the same multi-national companies marketing their drugs worldwide.

“In the U.S., where companies are required to report payments made to physicians in a public database, just over half of all licensed physicians have accepted a payment, including free meals from a pharmaceutical company,” says Grundy, who is also the Director of the WHO Collaborating Centre for Governance, Accountability, and Transparency in the Pharmaceutical Sector located at the University of Toronto.  “This is important because it shows that companies are focusing their marketing resources on physicians who will deliver the highest return on investment, and prescribe more of their promoted drug, but it also shows that there are a large number of physicians who are choosing not to interact with pharmaceutical companies and remain independent of these influences.”

There were no Canadian studies included in the review, in part because Canada does not have a mechanism in place to track how much or why pharmaceutical companies are paying physicians or nurse practitioners. However, Grundy notes that according to surveys and qualitative research not included in this review, free meals and payments are likely common among Canadian prescribers.

“When physicians accept payments or free meals from the pharmaceutical industry we can see evidence in the data that physicians prescribe more of the promoted drug. This practice can increase the overall costs to our health system, and to patients through higher co-pays and out-of-pocket costs, when they are prescribed a brand name drug even though cost-effective alternatives exist,” says Grundy.

Grundy believes it is imperative that healthcare organizations, professional societies, and health professional schools be more aware of the influence of pharmaceutical industry promotion and address these through policy changes.

“Prescribers need independent, evidence-based sources of information to ensure their own independence in practice and to be trustworthy and accountable to the people they serve,” says Grundy.

Studies included in the review also examined the impact of conflict-of-interest policies or limitations on physician interactions with industry in the practice setting such as within medical schools and teaching hospitals. The review showed that in these instances, conflict-of-interest policies had a mitigating effect where physicians tended to prescribe less overall or prescribed more appropriate treatments. The review authors suggest that more robust conflict-of-interest policies would be an important way forward to reduce the influence of pharma on prescribers.

“These studies show that we can create practice environments that promote and preserve independence and that this is best achieved collectively, within health systems and institutions, rather than leaving it up to individual clinicians,” says Grundy.

While the available research focused on physicians in many health systems, including Canada, physicians are no longer the only prescribers. Other descriptive studies using the Open Payments data in the U.S., and which were not included in this review, found that advanced practice nurses, including nurse practitioners and clinical nurse specialists, are also targets of industry promotion.

“This is not just a problem for medicine, it affects the entire healthcare team,” says Grundy. “We need to create healthcare environments that safeguard the independence and integrity of care.”

 

Global injury crisis highlights urgent need for smarter trauma care 




University of Birmingham






Embargoed copy of the research paper and case study available on request 

A study of almost 9,000 injury patients across Africa and South Asia has found that nearly half were dead or disabled after three months - highlighting the need for smarter, locally tailored trauma-care systems.  

Publishing its findings today (7 Oct) in The Lancet Global Health, the international research group led by University of Birmingham experts, reveal that the biggest influences on survival and recovery are not just the injuries themselves, but how people move through the healthcare system. 

Injuries cause an estimated 4.4 million deaths annually worldwide, with 90% occurring in LMICs. This is the first large multi-country study to examine mortality and disability outcomes among hospitalised injury patients across Low- or Middle-Income Countries (LMIC). The study reveals that access to appropriate care, the route patients take to hospital, and the type of services available all play an important role in these outcomes.  

Analysing data from 8,858 patients treated in 19 urban and rural hospitals across Ghana, Pakistan, Rwanda and South Africa, the NIHR-funded Global Health Group on Equitable Access to Quality Health Care for Injured People in Four Low- or Middle-Income Countries (Equi-injury) reveals an enormous and often overlooked global health burden: 

  • 47.6% of patients either died or were left with moderate-to-severe disability within three months of hospital discharge.  

  • 6.1% died in hospital, 9.7% had died within three months, and 40.6% were living with moderate-to-severe disability three months after discharge. 

  • Patients arriving at hospital by ambulance had significantly worse outcomes, with 86% higher odds of death or disability and more than double the odds of mortality within three months compared with those using other forms of transport.  

Lead author Professor Justine Davies, from the University of Birmingham, said: “One of our most surprising findings was that measures often assumed to improve outcomes - such as ambulance transport and rapid transfer to major hospitals which are similar to highly centralised trauma services - were not consistently linked with better recovery or survival. 

“This does not mean that ambulances cause worse outcomes but suggests that investment in ambulance systems alone is unlikely to improve outcomes unless services are coordinated and appropriately resourced.” 

The findings challenge assumptions that healthcare models developed in wealthier countries can simply be copied elsewhere. Instead, the study argues that countries should develop trauma and injury-care systems based on local evidence, resources, and patient needs.  

Corresponding author Dr Leila Ghalichi, from the University of Birmingham, said: “This does not mean ambulances or specialist trauma centres are ineffective. Rather, it suggests that simply investing in expensive emergency systems is not enough.  

“LMICs should be cautious about investing heavily in ambulance services and specialist, centralised, trauma centres without ensuring they are well coordinated, properly staffed, and supported by strong health systems. Better data and further research are needed to understand which trauma-care investments improve patient outcomes.” 

The study notes that stopping first at a nearby hospital for emergency stabilisation may sometimes be beneficial, especially if a specialist hospital is far away. If a major trauma hospital is close by, going directly there may improve outcomes.  

Researchers found no evidence that reaching a hospital more quickly reduced the risk of death. Patients who experienced some delays were less likely to be disabled later - challenging the common belief that faster treatment always leads to better outcomes after injury. 

Age was linked to worse outcomes, but gender, wealth and education had little effect on survival while patients were in hospital. However, once out of hospital wealthier and better-educated patients tended to recover better, suggesting that access to rehabilitation and follow-up care may play an important role. 

Ninety per cent of global injury deaths occur in LMICs and are estimated to account for around 10% of the global burden of disease. Yet trauma care receives far less attention than infectious diseases or chronic conditions in global health policy.  

Country-level differences were striking. Patients in South Africa had the lowest odds of disability but the highest odds of mortality, while patients in Rwanda experienced the lowest odds of mortality. Meanwhile, patients in Pakistan experienced substantially higher odds of the combined outcome of death or disability than those in Ghana. 

The study population reflects the demographics of injury worldwide. Median age was 31 years, 76.8% were male, and road traffic collisions accounted for 50% of all injuries recorded. Orthopaedic injuries were the most common injury type, affecting 39.2% of patients.  

ENDS 

For more information, interview requests, an embargoed copy of the research paper and/or case study please contact Tony Moran, International Communications Manager  t.moran@bham.ac.uk or +44 (0)7827 832312 

‘Mortality and disability after hospitalisation for injuries in low-income and middle-income countries: a cohort study’ - The Equi-Injury Group is published in The Lancet Global Health.

Notes for editors  

  • The University of Birmingham is ranked amongst the world’s top 100 institutions. Its work brings people from across the world to Birmingham, including researchers, teachers and more than 40,000 students from over 150 countries. 

  • England’s first civic university, the University of Birmingham is proud to be rooted in one of the most dynamic and diverse cities in the country. A member of the Russell Group and a founding member of the Universitas 21 global network of research universities, the University of Birmingham has been changing the way the world works for more than a century.