It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Wednesday, July 09, 2025
ZOONOSIS
Large-scale DNA study maps 37,000 years of disease history
A new study maps infectious diseases across millennia and offers new insight into how human-animal interactions permanently transformed our health landscape.
University of Copenhagen - The Faculty of Health and Medical Sciences
A research team led by Eske Willerslev, professor at the University of Copenhagen and the University of Cambridge, has recovered ancient DNA from 214 known human pathogens in prehistoric humans from Eurasia.
The study shows, among other things, that the earliest known evidence of zoonotic diseases – illnesses transmitted from animals to humans, like COVID in recent times – dates back to around 6,500 years ago, with such diseases becoming more widespread approximately 5,000 years ago. It is the largest study to date on the history of infectious diseases and has just been published in the scientific journal Nature.
The researchers analyzed DNA from over 1,300 prehistoric individuals, some up to 37,000 years old. The ancient bones and teeth have provided a unique insight into the development of diseases caused by bacteria, viruses, and parasites.
The results suggest that humans’ close cohabitation with domesticated animals – and large-scale migrations of pastoralist from the Pontic Steppe – played a decisive role in the spread of these diseases.
“We’ve long suspected that the transition to farming and animal husbandry opened the door to a new era of disease – now DNA shows us that it happened at least 6,500 years ago,” says Professor Eske Willerslev. “These infections didn’t just cause illness – they may have contributed to population collapse, migration, and genetic adaptation.”
Could have implications for future vaccines
The findings could be significant for the development of vaccines and for understanding how diseases arise and mutate over time.
“If we understand what happened in the past, it can help us prepare for the future, where many of the newly emerging infectious diseases are predicted to originate from animals,” says Associate Professor Martin Sikora, the study’s first author.
“Mutations that were successful in the past are likely to reappear. This knowledge is important for future vaccines, as it allows us to test whether current vaccines provide sufficient coverage or whether new ones need to be developed due to mutations,” adds Eske Willerslev.
The study was made possible by funding from the Lundbeck Foundation.
In the study, the researchers found 214 pathogens. A remarkable finding is the world’s oldest genetic trace of the plague bacterium Yersinia pestis, identified in a 5,500-year-old sample. The plague is estimated to have killed between one-quarter and one-half of Europe’s population during the Middle Ages.
The plots shown above depict a marked link between a child’s biological age, as determined through DNA methylation age (mAge), and their visual attention for eyes. These factors are also linked to higher scores in the Strength and Difficulties Questionnaire (SDQ) – an indicator of accelerated aging and decreased eye contact as a result of childhood maltreatment.
Credit: Keiko Ochiai from the University of Fukui, Japan Source link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0321952
Childhood maltreatment leaves a lasting impact that goes far beyond physical injuries or fading memories. Scientific evidence has long shown that children who experience abuse and neglect face increased risk of chronic diseases, mental health disorders, and premature death throughout their lives. Beneath these visible signs lies a deeper truth: childhood maltreatment can fundamentally alter a child’s biology, triggering molecular changes that can last for decades.
Recent research is unravelling that childhood maltreatment doesn’t just harm development—it appears to speed up the aging process itself. Despite growing awareness of the lasting impact of childhood maltreatment, the research fraternity has struggled to understand precisely how these early experiences trigger such deep changes, particularly in very young children. A possible reason is that previous studies have relied heavily on inconsistent biological markers or subjective self-reports and also lacked the tools to simultaneously examine both the biological alterations and social behavioral changes that occur in maltreated children.
To address these knowledge gaps, a research team from Japan’s United Graduate School of Child Development—a collaboration between Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and the University of Fukui—conducted a comprehensive study examining both biological aging and social behavior in young children. Their findings, published online in the PLOS One journal on May 30, 2025, provide unprecedented evidence and insights into how childhood maltreatment simultaneously accelerates biological aging and impairs social development. The research team included graduate student Keiko Ochiai, Assistant Professor Shota Nishitani, Associate Professor Takashi X. Fujisawa, and Professor Akemi Tomoda, among others.
The researchers studied 96 Japanese children aged between 4 and 5 years, comparing 36 children who had experienced severe maltreatment with 60 typically developing peers. They measured biological aging by looking at DNA methylation patterns using a novel method called the Pediatric-Buccal-Epigenetic clock, which the team has pioneered in their earlier works. These molecular signatures, captured from genetic material from simple cheek swabs, essentially indicate how fast a child’s body is aging at the cellular level. Additionally, they used eye-tracking technology to monitor the children’s social attention patterns, measuring how long children looked at different elements in carefully selected video footage.
A comprehensive analysis of the data painted a clear yet concerning picture. The team found that children who had experienced maltreatment exhibited significantly accelerated biological aging compared to their typically developing peers. Furthermore, these children spent notably less time looking at eyes when presented with videos of human faces. This reduced attention to eyes—a crucial aspect of social interaction and understanding—suggests there are fundamental differences in how maltreated children process social information. Accelerated biological aging and reduced eye contact were both strongly linked to higher scores on measures of emotional and behavioral difficulties, determined using questionnaire-based tools.
Notably, the researchers found that while accelerated biological aging and reduced eye contact were associated, they appeared to contribute independently to the reported difficulties. This finding highlights that maltreatment may affect children through multiple, distinct biological and social pathways. “Our research sends a powerful message: child maltreatment can leave invisible but measurable marks on a child’s biology and social development. By identifying these early warning signs, we can step in earlier and provide targeted support,” emphasized Ms. Ochiai.
By providing objective measures of the impact of child maltreatment, these findings also underscore an urgent need for early identification and intervention strategies. “Tools such as eye-tracking assessments and stress-related biological testing could help teachers, doctors, and caregivers expedite the identification of children at risk,” remarks Ms. Ochiai. Adding further, she says, “Support programs can then be tailored to improve social skills, reduce emotional stress, and promote healthier development—potentially preventing more serious problems later in life.”
Overall, these findings not only deepen our understanding of how child maltreatment shapes development but also offer practical avenues for offering more proactive support. This, in turn, can hopefully assist in providing vulnerable children with the skills and resilience needed for a healthier future.
Comprehensive path analysis revealed that both DNA methylation age (mAge) and visual attention for eyes independently correlated with higher Strength and Difficulties Questionnaire (SDQ) scores. This suggests that childhood maltreatment leads to difficulties through accelerated aging and decreased eye contact in distinct ways.
Credit
Keiko Ochiai from University of Fukui, Japan Source link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0321952
About University of Fukui, Japan The University of Fukui is a preeminent research institution with robust undergraduate and graduate schools focusing on education, medical and science, engineering, and global and community studies. The university conducts cutting-edge research and strives to nurture human resources capable of contributing to society on the local, national, and global level.
About Graduate Student Keiko Ochiai from University of Fukui, Japan Keiko Ochiai is a graduate student at the United Graduate School of Child Development in Japan, a joint program involving Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and the University of Fukui. She is currently based at the University of Fukui, where she studies how child maltreatment affects children's behavior and emotional development.
Funding information All phases of this study were supported by AMED (20gk0110052), JSPS KAKENHI Scientific Research (A) (19H00617 and 22H00492), Challenging Exploratory Research (Houga) (21K18499), Scientific Research (C) (20K02700), a grant-in-aid for “Creating a Safe and Secure Living Environment in the Changing Public and Private Spheres” from the Japan Science and Technology Corporation (JST)/Research Institute of Science and Technology for Society (RISTEX), a research grant from the Strategic Budget to Realize University Missions, research grants from the University of Fukui (FY 2019 and 2020), a grant-in-aid for translational research from the Life Science Innovation Center, University of Fukui (LSI20305 and LSI22202), and a grant for life cycle medicine from the Faculty of Medical Sciences, University of Fukui.
Behavioral and emotional difficulties in maltreated children: Associations with epigenetic clock changes and visual attention to social cues
AI used to create protein that kills E. coli
Australian scientists have used Artificial Intelligence (AI) to generate a ready-to-use biological protein that can kill antibiotic resistant bacteria like E. coli.
Monash University
In the last year, there has been a surge in proteins developed by AI that will eventually be used in the treatment of everything from snakebites to cancer. What would normally take decades for a scientist to create – a custom-made protein for a particular disease – can now be done in seconds.
This study, published in Nature Communications, provides a new way to combat the growing crisis caused by antibiotic resistant super bugs. By using AI in this way, Australian science has now joined countries like the US and China having developed AI platforms capable of rapidly generating thousands of ready-to-use proteins, paving the way for faster, more affordable drug development and diagnostics that could transform biomedical research and patient care.
The Nature Communications paper is co-led by Dr. Rhys Grinter and Associate Professor Gavin Knott, a Snow Medical Fellow, who lead the new AI Protein Design Program (https://www.monash.edu/discovery-institute/research/ai-protein-design-program) with nodes at the University of Melbourne Bio21 Institute and Monash Biomedicine Discovery Institute.
According to Dr. Grinter and A/Prof. Knott, the AI Protein Design Platform used in this work is the first in Australia that models the work done by David Baker (who won the Nobel Prize in Chemistry last year) developing an end-to-end approach that could create a wide range of proteins. “These proteins are now being developed as pharmaceuticals, vaccines, nanomaterials and tiny sensors, with many other applications yet to be tested” Associate Professor Knott said.
For this study, the AI Protein Design Platform used AI-driven protein design tools that are freely available for scientists everywhere. “It’s important to democratize protein design so that the whole world has the ability to leverage these tools,” said Daniel Fox, the PhD student who performed most of the experimental work for the study. “Using these tools and those we are developing in-house, we can engineer proteins to bind a specific target site or ligand, as inhibitors, agonists or antagonists, or engineered enzymes with improved activity and stability.”
According to Dr Grinter, currently proteins used in the treatment of diseases like cancer or infections are derived from nature and repurposed through rational design or in vitro evolution and selection. “These new methods in deep learning enable efficient de novo design of proteins with specific characteristics and functions, lowering the cost and accelerating the development of novel protein binders and engineered enzymes,” he said.
Since the work of David Baker, new tools and software are being developed, such as Bindcraft and Chai which have been incorporated into an AI Protein Design Platform co-led by Dr. Grinter and A/Prof. Knott..
Professor John Carroll, Director of the Monash Biomedicine Discovery Institute, said the new AI Protein Design Program 'brings Australia “right up to speed in this exciting new modality for designing novel therapeutics and research tools. It is testament to the entrepreneurial spirit of two fabulous young scientists who have worked night and day to build this capability from scratch”.
“The Program, based at Monash University and the University of Melbourne, is run by a team of talented structural biologists and computer scientists who understand the design process from end-to-end. This in-depth knowledge of protein structure and machine learning makes us a highly agile program capable of regularly onboarding cutting edge tools in AI-protein design,” Associate Professor Knott said.
Inhibiting heme piracy by pathogenic Escherichia coli using de novo-1 designed proteins
Article Publication Date
9-Jul-2025
The right mix and planting pattern of trees enhance forest productivity and services
By modelling different planting design strategies and species mixtures, researchers offer insights for sustainable forest management, reforestation, and climate change mitigation in a new paper.
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
Block plantations like these may look efficient, but research shows that more diverse and randomised tree arrangements boost forest productivity and ecosystem health.
A new paper published in Nature Communications reveals how the way tree species are arranged in a forest can help optimise ecosystem functioning and productivity. The study was conducted using empirical field data combined with advanced computer models and simulations by researchers at the German Centre for Integrative Biodiversity Research (iDiv), Leipzig University, Friedrich Schiller University Jena, and the French National Centre for Scientific Research (CNRS).
The researchers simulated virtual forests with multiple arrangements of tree species, such as block and mini-block designs, plantings in single and double lines, and fully random distributions. These simulations incorporated real data from the BEF-China (Biodiversity-Ecosystem Functioning) experiment, including tree growth models (based on field inventories), litterfall collections, and decomposition rate measurements. This data allowed the researchers to model the effect of spatial arrangement on ecosystem functions, such as tree productivity, nitrogen, and carbon cycling.
If a leaf falls in a randomly arranged forest, there are benefits
The researchers found that the way tree species are arranged in a forest—whether clustered or randomly spread out—impacts productivity. This so-called species spatial heterogeneity, which refers to the patterns of species distribution within a forest, such as block or line planting, affects how nutrients cycle through the ecosystem.
The models show that random planting designs increased tree biomass by 11% compared to clustered layouts. A more even spread of tree species helps promote the even distribution of the fallen leaves, boosting nutrients and organic matter recycling, according to the authors.
The rate of carbon decomposition after nine months also increased with greater spatial heterogeneity, rising from 36.5% of carbon being decomposed in block designs to 47.1% in random designs. Notably, line planting — where alternating rows of different tree species are used — provided a middle ground between ecological benefits and ease of forest management, achieving 40.4% of carbon being decomposed after nine months.
Another key factor is the overall diversity and number of species present in a given forest stand, regardless of their arrangement. More diverse forests, with a wide range of species present, showed higher nitrogen and carbon cycling compared to less diverse configurations. This provides a more diverse mix of resources for decomposers and promotes decomposition.
“The combination of experimental analyses and predictive modelling could be used to evaluate different scenarios of forest management. Besides the experimental validation of these findings, an important next step will be to know how general our conclusions are and whether they apply to different types of forests”, explains co-author Benoit Gauzens of iDiv and the University of Jena.
The perks of line planting
From a practical standpoint, the researchers note the balance required between securing ecological benefits and forest management. While random planting designs maximise ecological outcomes—including more biodiversity, enhanced nutrient cycling, and carbon sequestration—line planting offers a manageable compromise, simplifying tasks like thinning and harvesting.
Looking ahead, researchers envision extending these computer-based findings by conducting long-term field experiments to validate the study’s results in real-world contexts. Such trials would further investigate the interaction between tree species diversity, spatial arrangement, and ecosystem function, helping develop new approaches to reforestation and sustainable forestry.
“This study is an important example of how basic research can inform management applications under field conditions: we can leverage biodiversity in forests if we arrange it in the right way,” says Nico Eisenhauer, professor at Leipzig University and group head at iDiv. “Moreover, we see how local interactions between trees, their microclimate, and soil biodiversity can scale up to enhance multiple ecosystem services in forests”, he concludes.
New research into the anatomy of blue sharks (Prionace glauca) reveals a unique nanostructure in their skin that produces their iconic blue colouration, but intriguingly, also suggests a potential capacity for colour change.
“Blue is one of the rarest colours in the animal kingdom, and animals have developed a variety of unique strategies through evolution to produce it, making these processes especially fascinating,” says Dr Viktoriia Kamska, a post-doctoral researcher in the lab of Professor Mason Dean at City University of Hong Kong.
The team revealed that the secret to the shark’s colour lies in the pulp cavities of the tooth-like scales — known as dermal denticles— that armour the shark’s skin. The key features of this colour-producing mechanism inside the pulp cavity are guanine crystals, which act as blue reflectors, alongside melanin-containing vesicles called melanosomes, which act as absorbers of other wavelengths. “These components are packed into separate cells, reminiscent of bags filled with mirrors and bags with black absorbers, but kept in close association so they work together,” explains Dr. Kamska. As a result, a pigment (melanin) collaborates with a structured material (guanine platelets of specific thickness and spacing) to enhance colour saturation.
“When you combine these materials together, you also create a powerful ability to produce and change colour,” says Professor Dean. “What’s fascinating is that we can observe tiny changes in the cells containing the crystals and see and model how they influence the colour of the whole organism.”
This anatomical breakthrough was made possible using a mixture of fine-scale dissection, optical microscopy, electron microscopy, spectroscopy, and a suite of other imaging techniques to characterise the form, function, and architectural arrangements of the colour-producing nanostructures. “We started looking at colour at the organismal level, on the scale of metres and centimetres, but structural colour is achieved at the nanometer scale, so we have to use a range of different approaches,” says Professor Dean.
Identifying the likely nanoscale culprits behind the shark’s blue colour was only part of the equation. Dr Kamska and her collaborators also used computational simulations to confirm which architectural parameters of these nanostructures are responsible for producing the specific wavelengths of the observed spectral appearance. “It’s challenging to manually manipulate structures at such a small scale, so these simulations are incredibly useful for understanding what colour palette is available,” says Dr Kamska.
The discovery also reveals that the shark’s trademark colour is potentially mutable through tiny changes in the relative distances between layers of guanine crystals within the denticle pulp cavities. Whereas narrower spaces between layers create the iconic blues, increasing this space shifts the colour into greens and golds.
Dr Kamska and her team have demonstrated that this structural mechanism of colour change could be driven by environmental factors that affect guanine platelet spacing. “In this way, very fine scale alterations resulting from something as simple as humidity or water pressure changes could alter body colour, that then shape how the animal camouflages or counter-shades in its natural environment,” says Professor Dean.
For example, the deeper a shark swims, the more pressure that their skin is subjected to, and the tighter the guanine crystals would likely be pushed together - which should darken the shark’s colour to better suit its surroundings. “The next step is to see how this mechanism really functions in sharks living in their natural environment,” says Dr Kamska.
While this research provides important new insights into shark anatomy and evolution, it also has a strong potential for bio-inspired engineering applications. “Not only do these denticles provide sharks with hydrodynamic and antifouling benefits, but we’ve now found that they also have a role in producing and maybe changing colour too,” says Professor Dean. “Such a multi-functional structural design —a marine surface combining features for high-speed hydrodynamics and camouflaging optics— as far as we know, hasn't been seen before.”
Therefore, this discovery could have implications for improving environmental sustainability within the manufacturing industry. “A major benefit of structural colouration over chemical colouration is that it reduces the toxicity of materials and reduces environmental pollution,” says Dr Kamska. “Structural colour is a tool that could help a lot, especially in marine environments, where dynamic blue camouflage would be useful.”
“As nanofabrication tools get better, this creates a playground to study how structures lead to new functions,” says Professor Dean. “We know a lot about how other fishes make colours, but sharks and rays diverged from bony fishes hundreds of millions of years ago – so this represents a completely different evolutionary path for making colour.”
This research, funded by Hong Kong’s University Grants Committee, General Research Fund, is being presented at the Society for Experimental Biology Annual Conference in Antwerp, Belgium on the 9th July 2025.
