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  • Designer microbe shows promise for reducing mercury absorption from seafood

    Designer microbe shows promise for reducing mercury absorption from seafood

    UCLA and UCSD scientists inserted DNA-encoding methylmercury detoxification enzymes into the genome of an abundant human gut bacterium. The engineered bacterium detoxified methylmercury in the gut of mice and dramatically reduced the amount that reached other tissues, such as the brain and liver.

    Mice given an oral probiotic containing the engineered microbe and fed a diet high in bluefin tuna had much lower methylmercury levels than expected, suggesting that a probiotic might eventually make it safer for people to consume fish.

    UCLA and UCSD scientists inserted DNA-encoding methylmercury detoxification enzymes into the genome of an abundant human gut bacterium. The engineered bacterium detoxified methylmercury in the gut of mice and dramatically reduced the amount that reached other tissues, such as the brain and liver.

    Mice given an oral probiotic containing the engineered microbe and fed a diet high in bluefin tuna had much lower methylmercury levels than expected, suggesting that a probiotic might eventually make it safer for people to consume fish.

    Researchers performed the tests using pregnant mice and found lower levels of methylmercury in both maternal and fetal tissues, and lower signs of mercury toxicity in the fetal brain.

    An engineered gut microbe can detoxify methylmercury, reducing the amount that passes into the brain and developing fetuses of mice fed a diet rich in fish, UCLA and UC San Diego’s Scripps Institution of Oceanography scientists have discovered.

    “We envision the possibility that people could take a probiotic to offset the risk of consuming too much methylmercury, especially when pregnant,” said UCLA associate professor and director of the UCLA Goodman-Luskin Microbiome Center Elaine Hsiao, who is the senior author of a paper describing the research in the journal Cell Host & Microbe.

    Mercury is a pollutant that enters water from several sources, the largest of which are human activities such as coal burning, artisanal gold mining and smelting, and wastes from consumer products. In the ocean, mercury transforms into a toxic form called methylmercury. It also biomagnifies, meaning that methylmercury concentrations in animal tissues increase up the food chain from algae-eaters to top predators like humans.

    This means that all the methylmercury in something an organism eats goes into its tissues and is passed on to whatever eats it. Organisms near the top of their food chains, like bluefin tuna and humans, acquire all the mercury accumulated by the previous links in the chain. Thus, people who primarily eat food containing high mercury levels are at higher risk of mercury poisoning and birth defects.

    “Despite global efforts to reduce mercury emissions and its accumulation in fish, methylmercury levels in seafood are not expected to decline anytime soon. Fish remains a major and culturally important part of the diet for many people around the world and we hope it continues to be,” said co-senior author and Scripps associate professor of marine biogeochemistry Amina Schartup.

    Researchers modified Bacteroides thetaiotaomicron, a naturally abundant bacterium in the human digestive tract, by inserting DNA-encoding mercury detoxification enzymes from a mercury-resistant soil bacterium. After confirming that the engineered bacteria could clear methylmercury in a test tube, they replaced the natural gut microbiomes of mice with the modified bacteria and orally administered a large amount of methylmercury all at once. The mice had lower levels of methylmercury in their intestines just three hours after, and the level continued to fall for four days, showing that the bacteria helped to effectively eliminate the methylmercury in the intestine.

    They next asked whether the engineered bacteria would be effective at decreasing tissue methylmercury levels when exposure occurs gradually through routine dietary intake. To test this, the researchers fed the mice diets containing bluefin tuna over a period of days and found that not only did the bacteria reduce mercury in the intestine just as well, but less entered the brain and liver, too.

    They then tested pregnant mice and found lower levels of methylmercury in both maternal and fetal tissues, and lower signs of mercury toxicity in the fetal brain.

    “By reducing dietary methylmercury in the intestine, the gut bacteria helped to eliminate it from the body before it could enter the maternal bloodstream and access the developing offspring,” said first author and UCLA research scientist Kristie Yu.

    Co-author and UCLA researcher Franciscus Chandra said that the lowered signs of toxicity in the fetal brain showed that the bacterium works at levels that are biologically meaningful.

    When the team repeated the experiments with salmon, which contains lower levels of methylmercury than in bluefin tuna, the bacterium was also effective.

    Finally, they fed the bacteria as an oral probiotic to mice with intact microbiomes and fed them the same bluefin tuna diet as the mice in the previous experiment. Under these conditions, the engineered bacteria were also remarkably effective at minimizing the amount of methylmercury that entered tissues, suggesting that one day, a probiotic could be developed to reduce the risks of a fish-based diet.

    The researchers were supported by funds from the Eunice Kennedy Shriver National Institute of Child Health and Human Development; the National Institute of Environmental Health Sciences; the National Science Foundation; the Research Corporation of Scientific Advancement; the Simons Foundation; and the Packard Foundation.

    Hsiao and Schartup are working on improving the efficacy of the bacterium and moving closer to translation to humans, an endeavor for which continued federal funding is critical.

  • Artificial intelligence tools make education materials more patient friendly

    Artificial intelligence tools make education materials more patient friendly

    Artificial intelligence (AI) tools significantly improve the readability of online patient education materials (PEMs), making them more accessible, a new study shows.

    Led by researchers at NYU Langone Health, the study focused on the readability of PEMs available on the websites of the American Heart Association (AHA), American Cancer Society (ACS), and American Stroke Association (ASA). According to the researchers, these materials help patients make decisions about their health care but often exceed the recommended reading level of grade 6, making them difficult for many patients to understand.

    For the study, researchers evaluated the capabilities of three large language models (LLMs) — ChatGPT, Gemini, and Claude — to optimize the readability of PEMs without compromising accuracy. These generative AI tools are designed to simplify complex texts by predicting the next word in a sentence based on extensive Internet data. This next-word prediction gives such models the ability to rewrite any article in simpler language as directed.

    Published online April 10 in the Journal of Medical Internet Research, the study involved 60 randomly selected PEMs from the AHA, ACS, and ASA websites. Researchers prompted the LLMs to simplify the reading level of the materials. Results showed that the original readability scores were significantly above the recommended level of grade 6, with mean grade-level scores of 10.7, 10, and 9.6, respectively.

    After optimization by the LLMs, readability scores improved significantly across all three websites. ChatGPT improved readability to a mean grade level of 7.6, Gemini to 6.6, and Claude to 5.6. Word counts were also significantly reduced, making the materials more concise.

    “Our study shows that widely used large language models have the potential to transform patient education materials into more readable content, which is essential for patient empowerment and better health outcomes,” said study senior author Jonah Feldman, MD, medical director of transformation and informatics at NYU Langone.

    “Our findings demonstrate that even expert-composed education materials, which are already patient-directed, can benefit from AI-driven improvements,” said Feldman, who also serves as an assistant professor at NYU Grossman Long Island School of Medicine.

    This study, the researchers say, provides an example of how healthcare organizations can apply AI to make clinical communication more patient friendly. Prior studies demonstrated the capabilities of AI models to create patient-focused explanations of heart test results, to draft responses to electronic advice queries, and to generate human-friendly summaries of complex medical reports.

    “The breadth of possible AI offerings shows how technology can be leveraged to transform the patient experience across health care systems, and not just in the United States,” said study co-author Paul Testa, MD, JD, MPH, chief health informatics officer at NYU Langone.

    “These studies are not just theoretical — after demonstrating their effectiveness, we are actively putting these AI tools into practice,” said Testa, who is also a clinical professor at NYU Grossman School of Medicine.

    According to Testa, the NYU Langone team is already using the same AI tools in a randomized controlled trial that incorporates AI-generated, patient-friendly summaries for hospital discharge instructions, with the goal to evaluate their effectiveness in improving patient comprehension and satisfaction. The researchers hope to show that providing clear and accessible discharge instructions will help ensure better postdischarge care and smoother transitions.

    “Generating real-world evidence through randomized trials is crucial for validating the effectiveness of AI tools in clinical settings,” said study co-author Jonah Zaretsky, MD, associate chief of medicine at NYU Langone Hospital — Brooklyn. “This approach ensures that the AI-generated documentation is not only accurate but also genuinely beneficial for patients and their families,” added Zaretsky, a clinical assistant professor at NYU Grossman School of Medicine.

    The study was self-funded by NYU Langone. Besides Feldman, Testa, and Zaretsky, NYU Langone researchers involved in the study were lead author John Will, and co-authors Mahin Gupta and Aliesha Dowlath.

  • Making magnetic biomaterials

    Making magnetic biomaterials

    What if doctors could guide life-saving treatments through the body using only a magnet?

    An interdisciplinary collaboration at the University of Pittsburgh’s Swanson School of Engineering is bringing that concept closer to reality with the development of silk iron microparticles (SIMPs) — tiny, magnetic, and biodegradable carriers designed to precisely deliver drugs and treatments to sites in the body like aneurysms or tumors.

    Led by Pitt alumna Ande Marini (BioE PhD ’25), now a postdoctoral scholar in cardiothoracic surgery at Stanford University, David Vorp, John A. Swanson Professor of bioengineering, and Justin Weinbaum, research assistant professor of bioengineering, the team’s results, “Chemical Conjugation of Iron Oxide Nanoparticles for the Development of Magnetically Directable Silk Particles”, were published in the February edition of ACS Applied Materials & Interfaces.

    Marini’s team was inspired to develop these particles as part of their lab’s mission to improve treatments for abdominal aortic aneurysms (AAA), which can be life-threatening if left untreated and lead to nearly 10,000 deaths per year. By enabling early stage, noninvasive delivery of regenerative therapies using extracellular vesicles — membrane capsules that can facilitate intercellular communication — they hope to ultimately reduce the need for surgical intervention for AAA.

    “We want to find a way to deliver extracellular vesicles to the site of an abdominal aortic aneurysm in the least invasive way possible.” Vorp said. “We envisioned that we could inject extracellular vesicles onto a carrier and then somehow guide the carrier to the outside of the aortic wall, so we came up with the idea of using magnetic attraction.”

    To create the magnetic particles, the team collaborated with Mostafa Bedewy, associate professor of mechanical engineering & materials science at the Swanson School, and Golnaz Tomaraei (IE PhD ’23), Pitt alumna and Bedewy’s former PhD student. The duo’s expertise in nanomaterials and nanofabrication helped the team create the magnetic nanoparticles, which are roughly one-hundred-thousandth the width of a human hair. At that extremely small scale, nanomaterials can be manipulated to take on unique properties, such as magnetic responsiveness.

    “Our role was to synthesize magnetic nanoparticles with the right properties and bond them to the silk so they’d stay attached during movement,” Bedewy said. “You can think of it like towing cargo — we created the particles to carry drugs, and the nanoparticles are the tow hook.”

    Magnetically directable materials have previously been utilized for a variety of medical applications, but the team’s unique approach was to create the SIMPs by chemically conjugating the magnetic nanoparticles to silk — an FDA approved, biocompatible material — using the chemical compound glutathione.

    “We bridged biomaterials and chemical conjugation to create particles that could be magnetically guided,” Marini said. “By chemically bonding iron oxide nanoparticles to the regenerated silk fibroin, we enhanced their magnetic movability so we can potentially localize them externally to a site of interest in the body. “

    This research opens the door to a wide range of future applications — from targeted cancer therapies to regenerative treatments for cardiovascular disease. With the ability to magnetically guide the particles, the next step is loading them with therapeutic cargo.

    “With this paper, we’re showing that we can create an empty carrier that can be magnetically moved,” Marini said. “The next step is figuring out what kind of cargo we can load — regenerative factors, drugs, or other materials people want to magnetically localize. Whether it’s delivering cancer drugs with fewer side effects or slowing down tissue degradation in aneurysms, this technology has broad potential for regenerative medicine.”

    At the nanoscale, these findings also help Bedewy’s team continue to tailor the particles’ molecular structure and control their drug release rates for enhanced biomedical applications.

    “We’re trying to create a toolbox of treatments, and in materials science, there’s a lot of room for making more tools that can be useful for medical doctors and bioengineers to help create different ways of resolving problems in the body,” Bedewy said. “This is an exciting project where people with very different sets of expertise came together to solve a problem and produce an outcome that could potentially have an immense impact on human lives.”

  • No more copy-pasting: DNA base editing for better Lactobacillus strains

    No more copy-pasting: DNA base editing for better Lactobacillus strains

    A Kobe University team was able to edit the DNA of Lactobacillus strains directly without a template from other organisms. This technique is indistinguishable from natural variation and enabled the researchers to create a strain that doesn’t produce diabetes-aggravating chemicals.

    Humans have improved the microorganisms we rely on for millennia, selecting variants that are better able to produce wine, yogurt, natto and many other products. More recently, direct genetic modification has emerged as a tool to exert more precise and efficient control over the improvement, but also has drawn much public criticism for often using DNA from unrelated organisms in these modifications. Kobe University bioengineer NISHIDA Keiji says, “As a consequence, using such transgenic techniques is not favorable for food products due to legislations being restrictive and social acceptance being low.”

    Nishida and his team have developed a technique that gives even more precise control over the genetic content of a microorganism that does not rely on template DNA from other organisms. He says: “We have invented a DNA base editing technology named ‘Target-AID,’ which is superior to conventional techniques such as ‘CRISPR-Cas9’ in several aspects. For example, CRISPR-Cas9 induces DNA breaks and often causes cell death, while our Target-AID inserts precise point mutations without such breaks.”

    In the journal Applied Microbiology and Biotechnology, Nishida and his team now report that they teamed up with the Kobe University venture Bio Palette Co. Ltd. and successfully applied their technique to industrially important Lactobacillus strains used in manufacturing dairy products and pickles. “We edited individual, targeted locations in the genome at almost 100% efficiency in two major but fairly different Lactobacillus species. This shows that the technique can be readily applied to a wide range of strains,” says Nishida.

    To further showcase the capabilities of their approach, they focused on a gene that is involved in the production of a chemical that aggravates type 2 diabetes. By using Target-AID to mutate that gene, they engineered a Lactobacillus strain that could produce yogurt with less than a tenth of that chemical, making it safer to consume for people with type 2 diabetes. Nishida says: “The bacteria we produced are not subject to regulations concerning genetically modified organisms when used as foods, supplements or medicines. We thus expect that they can be readily commercialized after appropriate safety confirmation.”

    In their paper, the Kobe University team also showed that they could modify multiple genes at once and that they could even use their technique as a novel approach for basic research. For the future, Nishida has a broad outlook, saying, “We think our research will enable probiotic products with various health benefits, such as alleviating the effects on lifestyle-related diseases, strengthening immunity, improving allergic tolerance, and other benefits.”

    This research was funded by the Japan Science and Technology Agency (grants JPMJOP1851 and JPMJGX23B4), the New Energy and Industrial Technology Development Organization, and the Japan Agency for Medical Research and Development (grants 21ek0109448h0002 and 24bk0104169s0201). It was conducted in collaboration with researchers from Bio Palette Co. Ltd.

  • AI tool grounded in evidence-based medicine outperformed other AI tools — and most doctors- on USMLE exams

    AI tool grounded in evidence-based medicine outperformed other AI tools — and most doctors- on USMLE exams

    A powerful clinical artificial intelligence tool developed by University at Buffalo biomedical informatics researchers has demonstrated remarkable accuracy on all three parts of the United States Medical Licensing Exam (Step exams), according to a paper published today (April 22) in JAMA Network Open.

    Achieving higher scores on the USMLE than most physicians and all other AI tools so far, Semantic Clinical Artificial Intelligence (SCAI, pronounced “Sky”) has the potential to become a critical partner for physicians, says lead author Peter L. Elkin, MD, chair of the Department of Biomedical Informatics in the Jacobs School of Medicine and Biomedical Sciences at UB and a physician with UBMD Internal Medicine.

    Elkin says SCAI is the most accurate clinical AI tool available to date, with the most advanced version scoring 95.2% on Step 3 of the USMLE, while a GPT4 Omni tool scored 90.5% on the same test.

    “As physicians, we are used to using computers as tools,” he explains, “but SCAI is different; it can add to your decision-making and thinking based on its own reasoning.”

    The tool can respond to medical questions posed by clinicians or the public at https://halsted.compbio.buffalo.edu/chat/.

    The researchers tested the model against the USMLE, required for licensing physicians nationwide, which assesses the physician’s ability to apply knowledge, concepts and principles, and to demonstrate fundamental patient-centered skills. Any questions with a visual component were eliminated.

    Elkin explains that most AI tools function by using statistics to find associations in online data that allow them to answer a question. “We call these tools generative artificial intelligence,” he says. “Some have postulated that they are just plagiarizing what’s on the internet because the answers they give you are what others have written.” However, these AI models are now becoming partners in care rather than simple tools for clinicians to utilize in their practice, he says.

    “But SCAI answers more complex questions and performs more complex semantic reasoning,” he says, “We have created knowledge sources that can reason more the way people learn to reason while doing their training in medical school.”

    The team started with a natural language processing software they had previously developed. They added vast amounts of authoritative clinical information gleaned from widely disparate sources ranging from recent medical literature and clinical guidelines to genomic data, drug information, discharge recommendations, patient safety data and more. Any data that might be biased, such as clinical notes, were not included.

    13 million medical facts

    SCAI contains 13 million medical facts, as well as all the possible interactions between those facts. The team used basic clinical facts known as semantic triples (subject-relation-object, such as “Penicillin treats pneumococcal pneumonia”) to create semantic networks. The tool can then represent these semantic networks so that it is possible to draw logical inferences from them.

    “We have taught large language models how to use semantic reasoning,” says Elkin.

    Other techniques that contributed to SCAI include knowledge graphs that are designed to find new links in medical data as well as previously “hidden” patterns, as well as retrieval-augmented generation, which allows the large language model to access and incorporate information from external knowledge databases before responding to a prompt. This reduces “confabulation,” the tendency for AI tools to always respond to a prompt even when it doesn’t have enough information to go on.

    Elkin adds that using formal semantics to inform the large language model provides important context necessary for SCAI to understand and respond more accurately to a particular question.

    ‘It can have a conversation with you’

    “SCAI is different from other large language models because it can have a conversation with you and as a human-computer partnership can add to your decision-making and thinking based on its own reasoning,” Elkin says.

    He concludes: “By adding semantics to large language models, we are providing them with the ability to reason similarly to the way we do when practicing evidence-based medicine.”

    Because it can access such vast amounts of data, SCAI also has the potential to improve patient safety, improve access to care and “democratize specialty care,” Elkin says, by making medical information on specialties and subspecialties accessible to primary care providers and even to patients.

    While the power of SCAI is impressive, Elkin stresses its role will be to augment, not replace, physicians.

    “Artificial intelligence isn’t going to replace doctors,” he says, “but a doctor who uses AI may replace a doctor who does not.”

    In addition to Elkin, UB co-authors from the Department of Biomedical Informatics are Guresh Mehta; Frank LeHouillier; Melissa Resnick, PhD; Crystal Tomlin, PhD; Skyler Resendez, PhD; and Jiaxing Liu.

    Sarah Mullin, PhD, of Roswell Park Comprehensive Cancer Center, and Jonathan R. Nebeker, MD, and Steven H. Brown, MD, both of the Department of Veterans Affairs, also are co-authors.

    The work was funded by grants from the National Institutes of Health and the Department of Veterans Affairs.

  • Our DNA is at risk of hacking, warn scientists

    Our DNA is at risk of hacking, warn scientists

    Next-generation DNA sequencing (NGS) — the same technology which is powering the development of tailor-made medicines, cancer diagnostics, infectious disease tracking, and gene research — could become a prime target for hackers.

    A study, published in IEEE Access, highlights growing concerns over how this powerful sequencing tool — if left unsecured — could be exploited for data breaches, privacy violations, and even future biothreats.

    Led by Dr Nasreen Anjum from the University of Portsmouth’s School of Computing, it is the first comprehensive research study of cyber-biosecurity threats across the entire NGS workflow.

    NGS is a cornerstone of modern biotechnology, enabling rapid and cost-effective DNA and RNA sequencing that supports important advances in cancer research, drug development, agricultural innovation and forensic science.

    The sequencing process within NGS workflow involves a series of complex, interdependent steps — from sample preparation and sequencing to data analysis and interpretation — each involving highly specialised instruments, technologies, software, and connected systems.

    While the steps are essential for generating accurate results, they also open up multiple points of vulnerability. As many DNA datasets are openly accessible online, the study warns it is possible for cybercriminals to misuse the information for surveillance, manipulation, or malicious experimentation.

    Dr Anjum said: “Our work is a wake-up call. Protecting genomic data isn’t just about encryption — it’s about anticipating attacks that don’t yet exist. We need a paradigm shift in how we secure the future of precision medicine.”

    The research was carried out in collaboration with colleagues from the Department of Computer Science at Anglia Ruskin University in Cambridge, the University of Gloucestershire’s Department of Cyber Security and Computing, Narjan University’s Department of Computer Science and Emerging Research Laboratory, and the Department of Microbiology at Shaheed Benazir Bhutto Women University.

    Dr Mahreen-Ul-Hassan, microbiologist and co-author from the Shaheed Benazir Bhutto Women University, said: “Genomic data is one of the most personal forms of data we have. If compromised, the consequences go far beyond a typical data breach.”

    The research team identified new and emerging methods that hackers and those with malicious intent could use to exploit or attack systems, such as synthetic DNA-encoded malware, AI-driven manipulation of genome data, and identity tracing through re-identification techniques. These threats go beyond typical data breaches, posing risks to individual privacy, scientific integrity, and national security.

    Dr Anjun added: “Despite its importance, cyber-biosecurity remains one of the most neglected and poorly understood research disciplines and is leaving a critical gap in global biosecurity. To make sure our DNA information stays safe and is used only for good, we’re urging more research and collaboration to find ways to keep this powerful technology secure.

    “Governments, regulatory bodies, funding agencies, and academic institutions must prioritise this field and invest in dedicated research, education, and policy development before it’s too late.

    “Without coordinated action, genomic data could be exploited for surveillance, discrimination, or even bioterrorism. Current protections are fragmented, and vital collaboration between disciplines is lacking. Key to successful prevention will be interdisciplinary cooperation between computer scientists, bioinformaticians, biotechnologists, and security professionals — groups that rarely work together but must align.

    “Our research lays the foundations for improving biosecurity by providing a single, clear list of all the possible threats in the entire next-generation sequencing process.”

    The paper also recommends practical solutions, including secure sequencing protocols, encrypted storage, and AI-powered anomaly detection, creating a foundation for much stronger cyber-biosecurity.

    The study was funded by the British Council’s UK-Saudi Challenge Fund and a Quality Related Research Grant from the University of Portsmouth.

  • New tool for cutting DNA: Promising prospects for biotechnology

    New tool for cutting DNA: Promising prospects for biotechnology

    An INRS team discovers a new family of enzymes capable of inducing targeted cuts in single-stranded DNA.

    A few years ago, the advent of technology known as CRISPR was a major breakthrough in the scientific world. Developed from a derivative of the immune system of bacteria, CRISPR enables double strands of nucleotides in deoxyribonucleic acid (DNA) to be cut. This makes it possible to specifically modify a targeted gene in plant, animal and human cells. Ultimately, CRISPR became a preferred method in the search for treatments for acquired or hereditary diseases.

    Recently, Professor Frédéric Veyrier at the Institut national de la recherche scientifique (INRS) and his team developed a new genetic tool based on a family of specific enzymes called Ssn that allows targeted cuts to be induced exclusively in single-stranded DNA.

    The results of their work were recently published in the journal Nature Communications. This major breakthrough sheds light on a crucial genetic mechanism that could revolutionize a multitude of biotechnology applications.

    A form of DNA with a key role

    Single-stranded DNA is less common than double-stranded DNA. It is often found in some viruses and plays a key role in certain biological processes, such as cell replication or repair. Single-stranded DNA is also used in many technologies (sequencing, gene editing, molecular diagnostics, nanotechnology).

    To date, no endonuclease — enzyme that cuts DNA — has been described as exclusively targeting a single-stranded DNA sequence, which has constituted a barrier to the development of technologies based on this type of DNA.

    Now, for the first time in a laboratory, Professor Veyrier’s team has identified a family of enzymes capable of cutting a specific sequence in single-stranded DNA: the family of Ssn endonucleases.

    To achieve this, the research team at INRS’s Armand-Frappier Santé Biotechnologie Research Centre first characterized a new family of endonucleases part of the GIY-YIG superfamily called Ssn. More specifically, researchers focused on one of these enzymes in the bacterium Neisseria meningitidis, also known as the meningococcus. The enzyme targeted in the study is crucial to the exchange and alteration of genetic material, which influences evolution.

    “In studying it, we found that it recognizes a specific sequence that is found in many instances in its genome and plays a key role in the natural transformation of the bacterium. This interaction directly influences the dynamics of the bacterial genome,” explains Professor Veyrier, a specialist in genomic bacteriology and evolution.

    In addition to this fundamental discovery, INRS’s research scientists identified thousands of other similar enzymes. “We demonstrated that they are able to recognize and specifically cut their own single-stranded DNA sequence. Thousands of enzymes therefore have this property with their own specificity,” adds Alex Rivera-Millot, a postdoctoral fellow on Professor Veyrier’s team and co-first author of the study.

    An undeniable asset for health research

    These results, which represent a new tool for DNA recognition and exchange, are significant. They pave the way to many novel applications in biology and medicine. On the one hand, understanding this mechanism could help better control the bacteria in question and the associated infections.

    On the other, the discovery of enzymes specific to single-stranded DNA makes it possible to develop more precise and efficient genetic manipulation tools. This could namely improve methods of gene editing, DNA detection and molecular diagnosis. These enzymes could also be used to detect and manipulate DNA in various medical and industrial applications, such as pathogen detection or genetic manipulation for medical and therapeutic purposes.

    All of these avenues hold significant promise for addressing many health issues. Currently, there is a patent pending for the results of this work.

  • A new tool for parsing the ‘metabolic dialogue’ between microorganisms

    A new tool for parsing the ‘metabolic dialogue’ between microorganisms

    Scientists at the Max Planck Institute for Plant Breeding Research have developed an innovative system — called MetaFlowTrain — that allows the study of metabolic exchange and interactions within microbial communities under different environmental conditions. The study is now published in Nature Communications.

    Microbial communities consist of groups of microorganisms, such as bacteria, fungi, and other microscopic life forms, that coexist in specific environments. Although invisible to the naked eye, these communities are key for nutrient cycling, food web dynamics, and the degradation of pollutants in ecosystems. They are also essential for supporting the health of plants, animals, and humans by enhancing nutrient acquisition, bolstering the immune system, and protecting against harmful pathogens.

    The tiny organisms within microbial communities interact both with their environment and with each other not only via physical contacts — but also through the exchange of metabolites. These so-called exometabolites are small molecules secreted by microorganisms in the environment, such as amino acids, organic acids, alcohols, and secondary metabolites. They play crucial roles in shaping microbial communities, influencing interactions through cooperation and competition. In these highly dynamic systems, it has been challenging for scientists to identify which microorganisms produce specific metabolites and how these metabolites affect other members of the microbial community.

    Stéphane Hacquard and his team work on understanding the interactions between the members of plant-associated microbial communities. They realized that compartmentalizing the microorganisms would allow exclusion of the effects due to physical contact; thus, any remaining phenomena can be attributed solely to the exchange of metabolites and signals.

    The fruit of this realization is the MetaFlowTrain, a purpose-built fluidic system that allows scientists to introduce different microorganisms into special 3D-printed microchambers. These microchambers are surrounded by filters that permit metabolite exchange while preventing microorganism transfer. These microchambers can stand alone or be put in a series (e.g., such as a train with different wagons), each holding different groups of microorganisms. For instance, with bacteria in the first chamber and fungi in the second, scientists can now observe how bacteria affect fungi — and vice versa — by simply switching the chambers.

    The constant flow of fresh medium connecting these chambers allows different stress factors to be introduced to the system and prevents nutrient depletion in the microchambers. This represents a key innovation to identify novel microbial exometabolites with bioactive or signalling properties that shape microbial communities.

    MetaFlowTrain is easy to build and affordable, and holds enormous potential for identifying molecules that mediate microbe-microbe interactions and microbe-host associations. Specifically, scientists can now better ‘eavesdrop’ on the metabolic dialogues that drive cooperation or competition in microbial communities. Further, harnessing the system’s capabilities to discover novel antimicrobials that inhibit destructive plant pathogens presents new opportunities for sustainable agriculture and crop protection. In addition, the system could also be used to identify natural compounds for medicine and other fields.

    “The staggering diversity of molecules produced by microbes is a result of millions of years of evolution. These molecules serve different functions that help these communities to survive, adapt, and thrive in various environments. Understanding the functions and the mode of actions of some of these molecules will drive agricultural innovations,” says Stéphane Hacquard.

  • Further translation of the language of the genome

    Further translation of the language of the genome

    New research has uncovered more about the complexity of human gene regulation by identifying certain sequences of proteins called transcription factors that bind to DNA and regulate the expression of human genes.

    Published today (9 April) in Nature, researchers from the Wellcome Sanger Institute, the University of Cambridge and their collaborators explored how DNA-guided transcription factors interact with each other.

    This research adds to the groundwork of understanding the complex language of the gene regulatory code, and how DNA sequence patterns located close to our genes influence human development and disease risk.

    Each gene has a regulatory region that contains instructions on when and where the gene is expressed. This information is written in a code that is read by transcription factors, which bind to specific DNA sequences and either increase or decrease the gene’s expression.

    Previous research has explored the ‘language’ of the genome — the regulatory code that controls gene expression. It found that cooperation between multiple transcription factors is a key feature of transcription factor-DNA binding, with DNA actively facilitating interactions between various transcription factors.1 With the regulatory code being far more complex than the genetic code, which explains how DNA sequence determines the structure of proteins, researchers are aiming to understand the regulatory language in more detail, focusing on the ‘words’ and ‘grammar’ — such as the transcription factors — that influence when and where genes are expressed.

    This deeper understanding is crucial for uncovering how cells develop into specific types, how organs form and where they are located in the body during embryonic development, and for understanding what goes wrong in disease.

    The interactions between transcription factors guided by DNA are poorly understood. In a new study, researchers from the Sanger Institute and the University of Cambridge used two novel algorithms to analyse 58,000 pairs of transcription factors from human cells. They did this to identify how and where transcription factors interact with each other to bolster their understanding of the genomic language.2

    The researchers’ results reveal new patterns and preferences in how certain transcription factors interact with each other — also known as ‘motifs’. In this study, the researchers estimate that they identified between 18 and 47 per cent of all human transcription factor pair motifs, greatly adding to their understanding of the regulatory code.

    The team found that certain motifs they identified are present in developmental enhancers — DNA regulatory elements that activate transcription of a gene — that control important stages such as development of fingers. For example, the research notes that certain sequences of transcription factor motifs, or ‘words’ in the language, influence whether or not someone develops polydactyly — too many fingers — or syndactyly — a fusion of fingers.

    The findings also have implications for how scientists will use computational models — such as artificial intelligence — to predict protein structures in the future. Whilst these tools can predict the overall structure, they often cannot look into smaller details, such as how transcription factors interact with each other on DNA. These small interactions can have a big impact on human development, but computational models cannot always predict this. The researchers hope that future models will be able to incorporate the more minute transcription factor details to better predict protein structure and protein-DNA interactions.

    This research marks a step forward in studying the smaller ‘words’ in the language of gene expression. By identifying small but key motifs in the genome, this research will help scientists understand and interpret the mechanisms influenced by transcription factors, particularly in the non-coding regions of the genome. These regions — which make up 99 per cent of the genome — do not code for proteins but still play a significant role in regulation of gene expression, and risk for development of disease.

    Dr Ilya Sokolov, an author of the study at the Wellcome Sanger Institute, said: “By gaining a deeper understanding of how transcription factors interact when guided by DNA, we hope our research will shed light on the molecular basis of the regulatory code, particularly in the context of developmental disorders. These interactions are evolutionarily conserved across mammals and offer several advantages in development, from incorporating positional information to creating sharper gene expression responses. With advanced insights into the regulatory code, we are excited to help drive future research that will improve our understanding of human development and developmental disorders.”

    Professor Jussi Taipale, senior author of the study and Group Leader at the Wellcome Sanger Institute, said: “The human genome’s regulatory code is very complex, far more complex than the genetic code, and this research into transcription factor interactions unlocks deeper insights into the ‘language’ of the genome. Not only does our study provide more information into patterns of human development but it paves the way for future work with computational models that can hopefully incorporate these new data to better understand gene regulation.”

    Notes

    1. Arttu Jolma, Yimeng Yin, Kazuhiro R. Nitta, Kashyap Dave, Alexander Popov, Minna Taipale, Martin Enge, Teemu Kivioja, Ekaterina Morgunova, Jussi Taipale.(2015) ‘DNA-dependent formation of transcription factor pairs alters their binding specificity.’Nature. DOI: 10.1038/nature15518
    2. The researchers expressed a set of human transcription factors — enriched in proteins that are conserved in mammals — in Escherichia coli, combined them into a total of 58,754 transcription factor (TF) pairs and analysed their interactions by CAP-SELEX — consecutive affinity purification evolution of ligands by exponential enrichment. CAP-SELEX is a method which enables the discovery of TF-TF-DNA binding preferences.
  • From bacterial immunity to plant sex

    From bacterial immunity to plant sex

    Could it be that one of only three known markers directly targeting the DNA does not exist outside the realm of microbes? Now, researchers led by Xiaoqi Feng at the Institute of Science and Technology Austria (ISTA) have demonstrated that this marker — N4-methylcytosine (4mC) — is essential for sperm development and maturation in the liverwort Marchantia polymorpha, a key organism in plant evolution. The findings were published in Cell.

    It sometimes takes a living fossil to make some of the most interesting findings about life and evolution. A relative of mosses, the liverwort Marchantia is one of the oldest existing plant forms and probably the oldest lineage of plants to colonize land. In addition to its central function in the plants’ transition from an aquatic to a terrestrial ecosystem, Marchantia still uses an ancestral form of reproduction that is no longer found in most plants. Whereas other plants have evolved sexual reproduction independently of water, Marchantia sperm is released into rainwater drops splashing on the plants’ surface and swims to fertilize the nearby female plants. However, many molecular aspects of Marchantia sperm function have remained in the dark to this day.

    The group of Xiaoqi Feng at the Institute of Science and Technology Austria (ISTA) uses this unique plant as a model to uncover yet unknown molecular principles that shed new light on the evolution of sexual reproduction. And their latest findings are no less than groundbreaking. “Our study provides conclusive evidence for a new DNA marker in plants or animals with a very important function: It is essential for sexual reproduction in Marchantia, specifically affecting sperm development in male plants,” says Feng. The findings could have applications in biotechnology, opening up perspectives for regulating gene expression without altering the underlying DNA sequence.

    A long search beyond the realm of microbes

    N4-methylcytosine (4mC) is a form of immunity in bacteria, camouflaging their genome from enzymes that degrade foreign sequences by adding a methyl chemical group to target locations. It is one of the three known DNA markers: 4mC, 5mC, and 6mA. Since these chemical markers only ‘mask’ the underlying genetic code without mutating it, they are called “epigenetic markers,” based on the Greek prefix epi, meaning ‘over,’ ‘outside of,’ or ‘around.’ While 4mC and 5mC are chemical modifications of the cytosine nucleotide — one of the building blocks of DNA — 6mA is the only one to target the adenine nucleotide. Since it was never conclusively documented in plants or animals, 4mC has interested the scientific community for a long time.

    The levels are “crazy” — but needed for agile sperm

    In their quest to decipher the molecular mechanisms of sperm function in Marchantia, Feng and her team distinguished two waves of extensive DNA methylation during sperm development. These two waves literally cover the sperm’s genome. They showed that the first wave corresponded to 5mC, a DNA modification already known in animals and plants that targets and silences so-called “jumping genes.” However, 5mC alone could not explain the second wave of extensive methylation, which targets short sequences of two nucleotides scattered all over coding genes, the so-called CG (cytosine-guanine) dinucleotides. In addition, the team showed that genes with a sequence similarity to N4-cytosine methyltransferases, the enzymes that catalyze 4mC methylation in bacteria, were expressed in the same window of the plant’s sperm development. Could the team just have stumbled upon the enzymes for 4mC outside of microbes?

    Motivated by this discovery, they used myriad quantitative techniques to show that 4mC was indeed the culprit. They found that 4mC alone was responsible for a whopping fifteen percent of methylated cytosines in the mature Marchantia sperm as opposed to less than one percent in bacteria. “Having used a battery of conclusive experimental approaches, we can safely say we are sure of our results,” says Feng. “The levels of 4mC we detected in Marchantia sperm are crazy to think of.” Thus, the team demonstrated that the extensive 5mC and 4mC methylation waves were orchestrated during the plant’s sperm development. In addition, they showed that these “crazy” levels of 4mC had key functions in the Marchantia sperm. Without 4mC, the plant’s sperm can no longer compete for fertilization: its swimming becomes slower and less directional, its fertility is drastically decreased, and even in the rare cases of successful fertilization, the plant embryo’s early development is affected.

    Horizontal gene transfer

    Another form of DNA methylation, 6mA, was erroneously reported by other researchers in several organisms before its detection was traced to bacterial contamination. This has left a bad taste in scientists’ mouths and led to increased scrutiny in the DNA methylation field. “It is very important to use multiple independent methods for the detection of DNA methylation, and we wanted to make absolutely sure that our claims were sound. But in a way, the high level of 4mC was helpful for our confidence. After all, no bacterium carries this much methylation,” says Feng. But how did 4mC arise in Marchantia in the first place? The answer lies in transferring genetic material between different species outside of sexual reproduction, an evolutionary phenomenon called horizontal gene transfer, or HGT.

    HGT has been reported to happen frequently — on an evolutionary scale — between bacteria and plants. This is most probably how 4mC reached Marchantia. HGT events from soil bacteria to plants have contributed to the plant’s transition from an aquatic to a terrestrial environment. “This might be one of nature’s ad-hoc events that boosted evolution. The horizontal transfer of genetic material from bacteria to Marchantia turned out quite useful for the plants, so the trait was kept and selected for,” explains Feng.

    More 4mC waiting to be discovered?

    The liverwort is the only plant group where 4mC has been conclusively documented to date. “However, our findings are probably not a coincidence,” says Feng. In fact, early developmental stages in mammals usually include extensive methylation reprogramming, completely erasing and re-establishing the DNA epigenetic modifications. “So, we might need to look at a specific window of development in other plants and animals. 4mC might also be there, waiting to be discovered.”

    The present study sheds light on a fundamental function of sexual reproduction that evolved in nature and could find applications in biotechnology. By dissecting the precise function of the 4mC epigenetic modification in Marchantia, this molecular mechanism could potentially be used as a tool for epigenetic genome editing, i.e., methods that target gene expression without altering the DNA sequence.

    The present study was started at the Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK, before Xiaoqi Feng joined the Institute of Science and Technology Austria (ISTA) faculty.