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)
Thursday, June 04, 2026
A user-friendly software suite for DNA structure generation and analysis
Examples that highlight the building of biomolecular assemblies with MDNA: extension of DNA structures (left), using proteins as scaffold to generate DNA structure (centre), and connecting two DNA strands to form a DNA loop (right). (Molecular representations visualized with Mol* Viewer). Image: HIMS.
Computational chemists at the University of Amsterdam’s Van ’t Hoff Institute for Molecular Sciences have developed a comprehensive software suite to create accurate models of DNA in biomolecular assemblies. Called MDNA, the user-friendly molecular modelling toolkit helps biochemists, molecular biologists, bioinformaticians, and biophysicists to visualise and analyse DNA structures and perform accurate simulations.
The development of the MDNA suite, led by associate professor Jocelyne Vreede, has just been presented in in a paper in Nucleic Acids Research. The software is open-source and publicly available through Figshare and Github. It is easily accessible, providing inspiration to any scientist with an interest in DNA. It has been thoroughly tested by students in mathematics, chemistry and biology, some of whom had hardly any programming experience.
Structure generation
MDNA supports molecular simulations by providing atomic resolution structural modelling of double-stranded DNA in diverse shapes and compositions, including DNA-protein assemblies. By facilitating precise structural modelling of DNA at atomic resolution, MDNA contributes to improving the understanding of DNA dynamics and interactions in complex biological systems.
With MDNA, users can easily generate coordinates for the atoms in double-stranded DNA. It represents each base pair as a rigid body, according to the rigid base formalism of the Curves+ code, already a popular tool for analysis and visualisation of three-dimensional nucleic acid conformations. MDNA allows to create DNA coordinates in many different forms on any arbitrary curve in three-dimensional space. Users can create DNA strands or modify and extend existing structures. It comes with a library of sixteen bases that will be expanded in the future.
The Amsterdam researchers collaborated with the group of Helmut Schiessel at TU Dresden (Germany), implementing an energy function to equilibrate the generated structures and ensure that physical properties of DNA, such as stiffness and mobility, are modelled correctly. This does not need to explicitly include all atoms, which enables rapid equilibration within seconds. The energy function also includes constraints that can introduce supercoiling into the DNA.
A single workflow
In addition to generating structures, the software library offers the ability to analyse existing DNA structures, for example from MD simulations. By integrating structure generation and analysis into a single workflow, MDNA facilitates the study of DNA-protein interactions, supporting new insights into DNA dynamics and molecular simulations. To support users at various levels of molecular modelling, MDNA is complemented by tutorials and demos. These resources improve accessibility for novice and experienced users, providing a starting point for educational applications such as workshops or classroom demonstrations.
Researchers at Henan Normal University have developed a new metal-organic framework (MOF) capable of harvesting water directly from the air in extremely dry environments, offering a potential solution for regions facing severe water scarcity.
The study, published in Green Chemical Engineering, focuses on gallate-based MOFs made from low-cost materials including magnesium, cobalt, and nickel. Among them, the magnesium-based material, Mg-gallate, showed the strongest performance, capturing 170 mg of water per gram at just 0.2% relative humidity (RH), one of the highest water uptake capacities reported for porous materials under such ultra-low humidity conditions.
Atmospheric water harvesting is being explored as a sustainable solution to the growing global water crisis, particularly in arid regions where traditional adsorbent materials struggle to function efficiently. Current technologies often lose effectiveness in environments with very low moisture levels, such as deserts.
The researchers found that Mg-gallate combines strong water adsorption capacity with excellent stability. The material remained structurally stable after 28 days in water and maintained strong performance after 20 adsorption-desorption cycles. It also demonstrated high selectivity for water molecules over nitrogen, making it suitable for extracting water directly from air.
In particular, the material's performance is driven by hydrogen-bonding interactions between water molecules and oxygen-containing groups inside the MOF structure, alongside ultramicroporous channel filling effects. The MOF was successfully produced on a gram scale using inexpensive raw materials and standard laboratory methods, highlighting its potential for future large-scale production.
The researchers believe the technology could support atmospheric water harvesting in deserts and other ultra-dry environments, while also offering potential applications in semiconductor dehumidification, electronics protection, natural gas dehydration, and even space-based water recovery systems.
"Water scarcity is one of the most pressing survival challenges facing humanity in the coming decades. What makes Mg-gallate particularly exciting is that it works precisely where other materials give up: at the edge of detectability for humidity," says corresponding author Jianji Wang. "We are not just improving on existing benchmarks by a small margin; at 0.2% relative humidity, this material is operating in territory that was essentially inaccessible before. And because we can synthesise it in gram quantities from inexpensive, commercially available starting materials, there is a genuine path from the laboratory to real-world deployment."
###
Contact the author: Jianji Wang, Henan Normal University, jwang@htu.edu.cn
The publisher KeAiwas established by Elsevier and China Science Publishing & Media Ltd to unfold quality research globally. In 2013, our focus shifted to open access publishing. We now proudly publish more than 200 world-class, open access, English language journals, spanning all scientific disciplines. Many of these are titles we publish in partnership with prestigious societies and academic institutions, such as the National Natural Science Foundation of China (NSFC).
(L-R) The NTU Singapore research team behind the depolymerisation-induced polymer separation (DIPS) process include Dr Liang Yen Nan, Senior Research Fellow, Nanyang Environment and Water Research Institute (NEWRI); Kathirvel Periasamy, PhD student; and Professor Hu Xiao, School of Materials Science and Engineering, Programme Director for Sustainable Chemistry and Materials, NEWRI.
Scientists from Nanyang Technological University, Singapore (NTU Singapore) have developed a new method to recycle mixed plastic packaging without using harmful chemical solvents – an approach that could make one of the world's most difficult waste streams significantly easier to handle.
The research team from NTU Singapore's School of Materials Science and Engineering and Nanyang Environment and Water Research Institute (NEWRI) has introduced a process called depolymerisation-induced polymer separation, or DIPS. The method selectively breaks down one type of plastic in mixed plastic packaging while leaving the other plastics intact, allowing each material to be recovered and reused.
Addressing a global recycling challenge
Mixed plastic packaging, commonly used to wrap snacks, instant noodles and other food products, is designed to be tough and airtight. The packaging is made up of several different plastics bonded tightly together, making it challenging to recycle. Even if recycled, the material is often of low quality and has little commercial value.
As a result, most multilayer packaging ends up in landfills or incinerators, adding to a fast-growing waste burden. Global plastic production is projected to reach 736 million tonnes [1] by 2040.
Lead investigator Professor Hu Xiao, who is also the Programme Director for Sustainable Chemistry and Materials at NEWRI, said: “We’re seeing more mixed plastic packaging used in everyday food products, but recycling it safely and efficiently is still a major challenge. Our team set out to tackle this by developing a practical, scalable way to separate these materials without using harmful solvents."
Study co-author Dr Liang Yen Nan, who is also Senior Research Fellow, NEWRI, said: “One of the biggest hurdles in plastic recycling today is the lack of a viable way to deal with mixed plastics. This project was driven by that challenge, and our goal is to help move the industry closer to a solution that works in the real world.”
A solvent-free, continuous process
The DIPS method uses a technique called reactive extrusion, a solvent-free, continuous industrial process in which an extruder machine – a device commonly used in manufacturing to melt and shape plastics – doubles as a chemical reactor.
During processing of mixed plastic packaging, poly(ethylene terephthalate) (PET) – the plastic commonly used for drink bottles – reacts with glycerol, a cheap and widely available reagent, and is selectively broken down into smaller molecules. This PET-derived material has a different physical and chemical nature from the original plastic, causing it to naturally separate from polypropylene (PP), another common plastic used in packaging.
The separation happens automatically during processing, driven by differences in the materials' polarity (a feature that determines solubility) and viscosity (a material’s resistance to deformation under force).
The entire process runs at room pressure and without any solvents, making it safer and potentially more cost-effective than conventional chemical recycling approaches.
High-quality recycled materials
In laboratory tests, the recovered PP retained mechanical properties close to those of virgin plastic, achieving up to 90 per cent of its original tensile strength (maximum stress a material can sustain before it breaks) under optimal conditions – meaning the recycled material is strong enough for practical reuse.
Using samples from post-industrial mixed packaging waste, the method successfully separated the plastic components and produced significantly better material quality compared to conventional mechanical recycling approaches.
While the recovered PET cannot be directly reused, it contains chemical groups that make it potentially useful for higher-value applications such as specialty materials to replace epoxy used in wind turbine blades or for conversion into a monomer (building block of a polymer).
The researchers believe the DIPS approach can be extended to other mixed plastic combinations and scaled up using commonly used industrial extrusion equipment.
First author Kathirvel Periasamy, a PhD student and Provost Graduate Awardee under NTU’s flagship Interdisciplinary Graduate Programme, said: “Our process attempts to bridge the gap between laboratory research and industrial application. By simplifying separation and eliminating solvents, we aim to make plastic recycling more economically viable and environmentally sustainable."
If mixed plastic waste were efficiently recycled at scale, it could unlock an economic value estimated at more than US$250 billion annually [2].
As a next step, the research team plans to collaborate with industry partners to validate the approach under scaled-up conditions and welcomes interest from potential collaborators.
During the processing of mixed plastic packaging using the depolymerisation-induced polymer separation (DIPS) method, poly(ethylene terephthalate) (PET) and polypropylene (PP) are recovered.
System architecture of the VIBEMed framework, consisting of the multi-agent collaborative framework, three-level self-evolution mechanism and an architecture-level safety sandbox.
Large language models (LLMs) and AI agents have shown strong potential in medical imaging analysis, diagnosis, and treatment planning. However, most current medical AI systems still rely on pre-trained knowledge and fixed workflows. This limitation hinders their ability to learn from long-term clinical feedback, patient outcomes, or previous treatment experience, making it difficult for them to adapt to the complexity of real-world clinical practice.
To address this challenge, a team led by Dr. Lian Zhang from the First Hospital of Hebei Medical University, proposed the concept of "Vibe Medicine" and developed VIBEMed (Versatile Intelligent Behavior-Evolving Medical framework).
"VIBEMed uses multi-agent collaboration to break complex clinical decisions into three specialist roles: the Clinical Diagnostic Agent (CDA) for diagnostic reasoning and hypothesis generation, the Therapeutic Execution Agent (TEA) for treatment planning, and the Clinical Evolution Manager Agent (CEMA) for integrating longitudinal feedback and driving continuous optimization," shares co-corresponding author Lian Zhang.
Unlike conventional single-model approaches, VIBEMed further implements a three-level self-evolution mechanism spanning memory, model, and code, improving the performance of the backbone LLM and system over time. It also employs an architecture-level safety sandbox to constrain model updates and data access, ensuring that continuous evolution remains safe, controllable, and traceable.
The team then validated VIBEMed in complex clinical scenarios. Compared with traditional single-model pipelines. "The framework demonstrated superior performance in complex medical reasoning and treatment planning tasks," says Zhang. "VIBEMed presents an experience-driven medical AI system with strong adaptive capabilities, offering a practical direction for clinical decision-support systems that can learn continuously and evolve safely."
###
Contact the author: Lian Zhang, the First Hospital of Hebei Medical University, lianzhang@hebmu.edu.cn
The publisher KeAiwas established by Elsevier and China Science Publishing & Media Ltd to unfold quality research globally. In 2013, our focus shifted to open access publishing. We now proudly publish more than 200 world-class, open access, English language journals, spanning all scientific disciplines. Many of these are titles we publish in partnership with prestigious societies and academic institutions, such as the National Natural Science Foundation of China (NSFC).
WashU Medicine researchers genetically modified hookworms to produce and deliver a therapeutic antibody inside a host, a proof-of-concept that could lead to long-lasting treatments for chronic disease or exposure to toxins in remote settings.
Hookworms, intestinal parasites that infect hundreds of millions of people in under-resourced tropical regions around the globe, have evolved to survive inside the human gut for years, secreting molecules that enable co-existence with their hosts. Now, researchers at Washington University School of Medicine in St. Louis have harnessed that biological mechanism for potential human benefit, engineering a hookworm to produce and deliver a drug within a living host.
In a new study, the team reports the first successful genetic modification of the human hookworm. It was designed to produce an antibody that neutralizes tetrodotoxin, a deadly neurotoxin produced by pufferfish and other marine animals. After colonizing an animal host with the modified hookworms, the parasites produced the antitoxin and secreted it into the bloodstream, partially inactivating the toxin.
The findings demonstrate that this drug production and delivery approach could be a long-term solution to any number of medical needs, from chronic conditions requiring continuous drug treatment to exposure to toxins in remote locations without medical care available.
The findings were published June 3 in Nature Communications.
“The hookworm has spent millions of years perfecting how to assure long-term survival inside a human host and how to get molecules out of its body and into ours,” said senior author Makedonka Mitreva, PhD, the Gordon R. Miller Professor in the John T. Milliken Department of Medicine’s Division of Infectious Diseases at WashU Medicine. “We asked: What if we could add one more molecule to the roughly 1,000 things the worm already secretes, something therapeutically useful to people? This study shows that’s not just a concept. It works.”
A parasite that delivers
Hookworms have already been studied as treatments for inflammatory bowel diseases such as ulcerative colitis, based on evidence that the anti-inflammatory molecules the worms secrete can dampen the immune responses that drive those conditions. Mitreva’s team set out to build on that foundation by engineering the worm to secrete a therapeutic of the researchers’ choosing, rather than relying solely on what the parasite produces naturally.
The appeal of hookworms as a long-term drug production and delivery platform stems from a quirk of their biology. When a person is infected with a controlled number of hookworm larvae, which can be administered orally as a pill or through the skin like a lotion, the worms migrate to the small intestine and take up residence, often for years. Because they cannot multiply inside the host, the number of worms stays fixed, and the infection remains controlled. If the infection ever needs to be cleared, a single dose of an oral anti-parasitic drug eliminates the hookworms within 24 hours.
Although natural hookworm infection may cause only mild digestive symptoms in healthy adults, chronic infection with large number of hookworms can be dangerous for children, pregnant people and malnourished or otherwise vulnerable individuals, leading to anemia, poor growth and development, pregnancy complications and, in extreme untreated cases, heart problems or death. This underscores the importance of keeping the infection strictly controlled for therapeutic use, Mitreva noted, which is possible because of the worms’ inability to reproduce without spending part of their life cycle in soil.
The antibody selected for this proof-of-concept study neutralizes tetrodotoxin, a paralyzing and potentially lethal toxin with no antidote. The work was funded by the U.S. government’s Defense Advanced Research Projects Agency, with an eye toward finding solutions to biological and chemical threats to soldiers in remote locations.
The project presented significant technical hurdles: gene-editing tools that work in other organisms had not been adapted for hookworms, and no one had previously achieved stable genetic modification in the species.
To adapt hookworms for therapeutic use, Mitreva and her team drew on more than two decades of hookworm genomics research conducted at WashU Medicine. This depth of data helped them understand the organism’s biology from the cellular to the genetic level, allowing them to locate a viable site in the genome to insert the new gene carrying instructions for making the new antitoxin. Critically, they had to ensure the insertion wouldn’t disrupt surrounding gene activity and would prompt the worm to secrete the antitoxin out into the host.
The effort was successful: Blood collected from hamsters infected with Mitreva’s genetically modified hookworms partially neutralized tetrodotoxin, whereas blood from animals infected with unmodified worms had no neutralizing capability.
From proof-of-concept to broader platform
Mitreva noted that the level of neutralization achieved in this initial study, while significant, likely represents only a fraction of what the platform can ultimately deliver.
Several components of what she calls a “configurable chassis” are still being optimized to increase the amount of therapeutic protein produced and secreted. Because the worm resides in the gut and a substantial portion of what it secretes remains there, rather than entering the bloodstream, the researchers expect that concentrations of therapeutic molecules in the intestine may be substantially higher than what was detected in circulation in this study, making the platform suitable for gut-directed therapies.
“What we demonstrated here is that the concept works end to end — you can insert a gene, the worm produces the protein, the protein gets out of the worm, and it is functionally active in the host,” Mitreva said. “From that starting point, we can optimize the platform and think carefully about which diseases stand to benefit most from a delivery system that is continuous, targeted and long-lasting. That’s a fundamentally different kind of pharmaceutical biofactory platform, and we think it opens possibilities that are very hard to achieve with any other platform.”
Gut inflammatory diseases, including Crohn’s disease and ulcerative colitis, and food allergies are among the conditions Mitreva sees as strong candidates for future development. Diseases requiring small but sustained therapeutic concentrations, where compliance with repeated injections or infusions is a barrier, may also be well-suited to the platform.
Future studies will need to conduct rigorous safety evaluations before human use. Mitreva noted that biocontainment strategies, such as engineering the worms to be unable to produce eggs, are under consideration to protect hosts and their environments as the platform advances.
Singh KS, Bharti S, Rosa BA, Bigham M, Uzoechi SC, Choi YJ, Martin JC, Kemper D, Pavlovic Djuranovic S, Pickering DA, Ryan R, Bracken BK, Bottazzi ME, Carnes E, Ittiprasert W, Moyle M, Brindley PJ, Loukas A, Djuranovic S, Mitreva M. Transgenic hookworm secretes anti-tetrodotoxin human single chain antibody. Nature Communications. June 3, 2026. DOI: 10.1038/s41467-026-73447-9
K.S.S., S.B., B.A.R., M.B., S.C.U., Y.J.C., J.C.M., D.K., S.P.D., D.A.P., R.R., B.K.B., M.E.B., W.I., M.Moyle, P.J.B., A.L., S.D. and M.M. disclose support for the research of this work from the Defense Advanced Research Projects Agency (DARPA) and Naval Information Warfare Center Pacific (NIWC Pacific) [Contract No. N66001-21-C-4013]. E.C.C. discloses support for the research of this work from the Defense Advanced Research Projects Agency (DARPA) [Contract No. N660012314009]. The views, opinions and/or findings expressed are those of the author and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. Distribution Statement “A” (Approved for Public Release, Distribution Unlimited).
About WashU Medicine
WashU Medicine is a global leader in academic medicine, including biomedical research, patient care and educational programs with 3,100 faculty. Its National Institutes of Health (NIH) research funding portfolio is the second largest among U.S. medical schools and has grown 78% since 2016. Together with institutional investment, WashU Medicine commits over $1.6 billion annually to basic and clinical research innovation and training. Its faculty practice is consistently among the top five in the country, with more than 2,550 faculty physicians practicing at 200 locations. WashU Medicine physicians exclusively staff Barnes-Jewish and St. Louis Children’s hospitals — the academic hospitals of BJC HealthCare — and Siteman Cancer Center, a partnership between BJC HealthCare and WashU Medicine and the only National Cancer Institute-designated comprehensive cancer center in Missouri and southern Illinois. WashU Medicine physicians also treat patients at BJC’s community hospitals in our region. With a storied history in MD/PhD training, WashU Medicine recently dedicated $100 million to scholarships and curriculum renewal for its medical students, and is home to top-notch training programs in every medical subspecialty as well as physical therapy, occupational therapy, and audiology and communications sciences.
WashU Medicine researchers genetically modified hookworms to produce and deliver a therapeutic antibody inside a host, a proof-of-concept that could lead to long-lasting treatments for chronic disease or exposure to toxins in remote settings.
Credit
Courtesy of Makedonka Mitreva
Article Title
Transgenic hookworm secretes anti-tetrodotoxin human single chain antibody
Article Publication Date
3-Jun-2026
COI Statement
K.S.S., S.B., B.A.R., M.B., S.C.U., Y.J.C., J.C.M., D.K., S.P.D., D.A.P., R.R., B.K.B., M.E.B., W.I., M.Moyle, P.J.B., A.L., S.D. and M.M. disclose support for the research of this work from the Defense Advanced Research Projects Agency (DARPA) and Naval Information Warfare Center Pacific (NIWC Pacific) [Contract No. N66001-21-C-4013]. E.C.C. discloses support for the research of this work from the Defense Advanced Research Projects Agency (DARPA) [Contract No. N660012314009]. The views, opinions and/or findings expressed are those of the author and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. Distribution Statement “A” (Approved for Public Release, Distribution Unlimited).
