bims-enlima Biomed News
on Engineered living materials
Issue of 2025–09–14
fifty-one papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Multiscale Engineered Heterogeneous Hydrogel Composites for Digital Light Processing 3D Printing.
  2. Generating structurally and functionally programmable hydrogels by biological membrane hybridization.
  3. Photoswitchable intein for light control of covalent protein binding and cleavage.
  4. Globular proteins as functional-mechanical materials: a multiscale perspective on design, processing, and applications.
  5. Immunization with peptide encapsulated within synthetic spores activates T cell responses and reduces tumor growth.
  6. Proto-SLIPS: Slippery Liquid-Infused Surfaces that Release Highly Water-Soluble Agents.
  7. Nanofibrous supramolecular peptide hydrogels for controlled release of small-molecule drugs and biologics.
  8. Exploring 4D printing of smart materials for regenerative medicine applications.
  9. Computational design of sequence-specific DNA-binding proteins.
  10. Stretch-activated morphing enabled by integrated physical-chemical network engineering.
  11. Sulfone-Bond-Toughened Multifunctional Hydrogels with Ion-Modulated Fluorescence and Mechanical Properties.
  12. Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA.
  13. Sacrificial Biofabrication for Vascularization: Concept, Materials, Technologies, and Applications.
  14. Engineering Noncanonical Cofactors To Expand Cellular Functions.
  15. Engineering robust Saccharomyces cerevisiae cell factory for improving fatty alcohol biosynthesis.
  16. Characterizing Spatiotemporal Microbial Colony Distributions in Printed PEG-DA Hydrogel Films.
  17. Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning.
  18. Stabilizing effect of amino acids on protein and colloidal dispersions.
  19. 3D Surface-Patterned Hyaluronic Acid Hydrogels: Customizable Platforms for Enhanced Chondrogenic Differentiation and Organized Production of a Specific Hyaline Cartilage Extracellular Matrix.
  20. Antibody-bottlebrush prodrug conjugates for targeted cancer therapy.
  21. Dynamic and precise electromagnetic levitation of single cells.
  22. Cellulosic Flexible Electronic Materials: Recent Advances in Structural Design, Functionalization, and Smart Applications.
  23. Kinetic Locking of pH-Sensitive Complexes for Mechanically Responsive Polymer Networks.
  24. Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.
  25. Synergistic borate crosslinking and chain entanglement for mechanically robust and water-rich hydrogels.
  26. Genome-wide mapping of RNA-protein associations through sequencing.
  27. Preventing hypocontractility-induced fibroblast expansion alleviates dilated cardiomyopathy.
  28. Genetic Entanglement Enables Ultrastable Biocontainment in the Mammalian Gut.
  29. All-3D-Printed Multi-Environment Modular Microrobots Powered by Large-Displacement Dielectric Elastomer Microactuators.
  30. Rational assembly of 3D network materials and electronics through tensile buckling.
  31. Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus.
  32. Food production from air: gas precision fermentation with hydrogen-oxidising bacteria.
  33. Giant KASH proteins and ribosomes establish distinct cytoplasmic biophysical properties in vivo.
  34. Amplifying antigen-induced cellular responses with proximity labelling.
  35. DNA Flipping as Facile Mechanism for Transmembrane Signaling in Synthetic Cells.
  36. Concentration-Dependent Nanosheet and Nanotube Networks: Ice-Water Interface Control for Antifreeze Application.
  37. Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
  38. Shear-stress-induced swirling flow in biological systems.
  39. TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples.
  40. Advancing Tomographic Volumetric Printing Via Oxygen Inhibition Control: Improved Accuracy and Large-Volume Capability.
  41. Microbial living materials promote coral larval settlement.
  42. On-Demand Nanoliter Delivering Platform via Electrical-Activated Microdroplet Assembling.
  43. Unravelling the molecular network structure of biohybrid hydrogels.
  44. RNA Sequencing at Single Vesicle Resolution via 3D Printed Embedded Droplet Arrays.
  45. Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci.
  46. Quantifying phage infectivity from characteristics of bacterial population dynamics.
  47. Genetic code expansion and enzymatic modifications as accessible methods for studying site-specific post-translational modifications of alpha-synuclein and tau.
  48. Real-time imaging of protein microenvironment changes in cells with rotor-based fluorescent amino acids.
  49. Matrix directs trophoblast differentiation in a bioprinted organoid model of early placental development.
  50. Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.
  51. Molecular engineering of two-dimensional polyamide interphase layers for anode-free lithium metal batteries.
  1. ACS Appl Mater Interfaces. 2025 Sep 08.
    Multiscale Engineered Heterogeneous Hydrogel Composites for Digital Light Processing 3D Printing.
    Yuang Zhang, Ryan Davis, Saptarshi Biswas, Sarah E Miller, Syed Raza Ur Rehman, Gene T Felix, Akhilesh K Gaharwar.
      Hydrogel-based bioinks are widely adopted in digital light processing (DLP) 3D printing. Modulating their mechanical properties is especially beneficial in biomedical applications, such as directing cell activity toward tissue regeneration and healing. However, in both monolithic and granular hydrogels, the tunability of mechanical properties is limited to parameters such as cross-linking or packing density. Herein, we present a bioink platform with multiscale heterogeneity for DLP printing, fabricated by incorporating microgels within a cross-linked polymer matrix to form a mechanically tunable heterogeneous hydrogel composite. The properties of the separate components as well as their interactions can be efficiently tailored from both chemical and physical perspectives, enabling control across both nano and micro scales. Monodisperse, spherical gelatin methacryloyl (GelMA) microgels with a stiffness that can be tuned through polymer concentration or cross-link density are fabricated by a high-throughput microfluidic device. Microgels that have been precross-linked through chemical or physical methods are then embedded in a continuous GelMA matrix, where they influence the biomechanical and biochemical characteristics of composites through particle density and encapsulation of cells. Modulation of microgel volume and selecting different printing parameters enables tailoring of the composite compressive modulus across a range of 29 to 244 kPa. Using this composite hydrogel platform as a DLP ink allows for the fabrication of complex 3D structures with macroscale heterogeneity, providing the potential to mimic tissue- and organ-level complexity. This study presents a unique approach to designing heterogeneous hydrogel composites with tunable properties at the nano-, micro-, and macro-scales, and introduces a highly modular hydrogel platform for DLP 3D printing.
    Keywords:  biomaterials; digital light processing (DLP) 3D printing; hydrogel composite; microgels; regenerative medicine
    DOI:  https://doi.org/10.1021/acsami.5c09635
  2. Nat Protoc. 2025 Sep 12.
    Generating structurally and functionally programmable hydrogels by biological membrane hybridization.
    Feng Wu, Huan Chen, Jinyao Liu, Yan Pang.
      Hydrogels, as 3D cross-linked hydrophilic networks that exhibit favorable flexibility, cargo loading and release abilities and structure and function designability, are desirable for diverse biomedical applications. For in vivo implementation, however, hydrogels often suffer from swelling-weakened mechanical strength, uncontrollable cargo release and complex composition, inevitably hindering further translation. Despite different reported synthetic approaches, the development of a facile yet universal method capable of fabricating hydrogels with dynamically adjustable structure and function remains difficult. Recently, inspired by biological tissues, we have developed a versatile biological membrane hybridization strategy to generate structurally and functionally programmable hydrogels. Specifically, biological membranes are used as a cross-linker to form a cross-linked network through a supramolecular-covalent cascade reaction route. This protocol demonstrates the construction of two biological membrane-hybridized hydrogels, including liposome-hybridized muscle-mimicking hydrogels with swelling-strengthening mechanical behavior and extracellular vesicle-hybridized skin-mimicking hydrogels with enhanced mechanical strength, lubricity, antibacterial activity and immunoactivity. We describe the detailed preparation procedures and characterize the structures and functions of the obtained hydrogels. We also expand the applicability of this biological membrane hybridization strategy to further tune the structure and function of the biomimetic hydrogels by incorporating a second network. This protocol provides a robust preparative platform to develop dual structure- and function-tunable hydrogels for different biomedical applications. Excluding the synthesis of reactive group-functionalized biological membranes, the fabrication of muscle-mimicking hydrogels takes ~3 d, while the construction of skin-mimicking hydrogels takes ~1 d. The implementation of the protocol requires expertise in polymer modification, hydrogel preparation, nanoscale vesicles, surface functionalization and cell culture.
    DOI:  https://doi.org/10.1038/s41596-025-01247-4
  3. Nat Commun. 2025 Sep 11. 16(1): 8263
    Photoswitchable intein for light control of covalent protein binding and cleavage.
    Mikhail Baloban, Kyrylo Yu Manoilov, Maksim M Karasev, Vladislav V Verkhusha, Daria M Shcherbakova.
      Precise control of covalent protein binding and cleavage in mammalian cells is crucial for manipulating cellular processes but remains challenging due to dark background, poor stability, low efficiency, or requirement of unnatural amino acids in current optogenetic tools. We introduce a photoswitchable intein (PS Intein) engineered by allosterically modulating a small autocatalytic gp41-1 intein with tandem Vivid photoreceptor. PS Intein exhibits superior functionality and low background in cells compared to existing tools. PS Intein-based systems enable light-induced covalent binding, cleavage, and release of proteins for regulating gene expression and cell fate. The high responsiveness and ability to integrate multiple inputs allow for intersectional cell targeting using cancer- and tumor microenvironment-specific promoters. PS Intein tolerates various fusions and insertions, facilitating its application in diverse cellular contexts. This versatile technology offers efficient light-controlled protein manipulation, providing a powerful tool for adding functionalities to proteins and precisely controlling protein networks in living cells.
    DOI:  https://doi.org/10.1038/s41467-025-63595-9
  4. Mater Horiz. 2025 Sep 11.
    Globular proteins as functional-mechanical materials: a multiscale perspective on design, processing, and applications.
    Haonan He, Peng Zhang, Jian Ji.
      Globular proteins, traditionally regarded as non-structural biomolecules due to the limited load-bearing capacity in their monomeric states, are increasingly recognized as valuable building blocks for functional-mechanical materials. Their inherent bioactivity, chemical versatility, and structural tunability enable the design of materials that combine biological functionality with tailored mechanical performance. This review highlights recent advances in engineering globular proteins-spanning natural systems (serum albumins, enzymes, milk globulins, silk sericin, and soy protein isolates) to recombinant architectures including tandem-repeat proteins-into functional-mechanical platforms. We discuss strategies such as sequence engineering, crosslinking chemistry, hybrid modulation, and hierarchical assembly to enhance the mechanical properties. Diverse material formats including fibers, films, hydrogels, and porous scaffolds are examined, along with processing techniques like wet/electro-spinning, 3D printing, and self-assembly suited to the proteins' thermal and solubility constraints. Emerging applications span tissue engineering, soft electronics, and environmentally adaptive systems. Key challenges such as maintaining functional activity during reinforcement, achieving interfacial stability, and developing scalable, standardized processing methods are critically evaluated. By repositioning globular proteins as dynamic, tunable material platforms, this work aims to inspire new directions in the development of intelligent, biocompatible, and sustainable materials.
    DOI:  https://doi.org/10.1039/d5mh01107h
  5. mBio. 2025 Sep 12. e0225625
    Immunization with peptide encapsulated within synthetic spores activates T cell responses and reduces tumor growth.
    Domenico D'Atri, Elena Tondini, Federico Machinandiarena, Minsuk Kong, Alilin Mia, Devorah Gallardo, Kandice Tanner, Stephen M Hewitt, David J Fitzgerald, Kumaran S Ramamurthi.
      Peptide-based therapeutic immunizations represent safe approaches to elicit antigen-specific T cell responses, but their broad utility remains limited due to poor immunogenicity and short in vivo stability due to rapid degradation and clearance. Here, we employed synthetic bacterial spore-like particles, "SSHELs" (Synthetic Spore Husk-Encased Lipid), made entirely of biocompatible materials, to deliver a model peptide antigen in the absence of additional adjuvants. SSHELs carrying the peptide antigen were internalized by dendritic cells, and SSHEL-delivered peptides were then processed and cross-presented in vitro and in vivo more efficiently than free peptides. Furthermore, SSHEL-delivered peptides elicited effective antigen-specific T cell expansion in a manner that was dependent on particle size and peptide presentation mode (encased peptides were superior to surface-attached peptides). In a mouse melanoma model expressing the antigen ovalbumin, therapeutic immunization reduced tumor size and increased survival. We propose that SSHELs are a self-adjuvanting peptide delivery system that mimics a natural presentation to elicit a robust immune response.IMPORTANCEEffective delivery of antigens to the immune system is essential for activating the adaptive immune system. Synthetic Spore Husk-Encased Lipids (SSHELs) are synthetic bacterial spore-like particles, where the proteinaceous polymerized surface layer of Bacillus subtilis spores is partially reconstituted around a porous silica bead encased in a membrane. The protein surface allows easy covalent modification of the SSHEL surface, and the porous core permits high-capacity cargo loading. Here, we demonstrate that SSHELs act as a self-adjuvanting delivery system that enhances antigen uptake, processing, and MHC-I cross-presentation by dendritic cells. Importantly, we show that both particle size and antigen localization on or within the SSHEL particle profoundly influence the efficiency of T cell priming. These results establish SSHELs as a modular platform for the delivery of peptide antigens.
    Keywords:  Bacillus subtilis; SpoIVA; SpoVM; drug delivery; nanoparticle; spore; sporulation; synthetic biology; tumor
    DOI:  https://doi.org/10.1128/mbio.02256-25
  6. ACS Appl Mater Interfaces. 2025 Sep 09.
    Proto-SLIPS: Slippery Liquid-Infused Surfaces that Release Highly Water-Soluble Agents.
    Fengrui Wang, Jordan T York, Takuma N Kawamura, Douglas H Chang, Sean P Palecek, Helen E Blackwell, David M Lynn.
      Slippery liquid-infused porous surfaces (or "SLIPS") can prevent bacterial surface fouling, but they do not inherently possess the means to kill bacteria or reduce cell loads in surrounding media. Past reports show that the infused liquids in these materials can be leveraged to load and release antimicrobial agents, but these approaches are generally limited to the use of hydrophobic agents that are soluble in the infused oily phases. Here, we report the design of so-called "proto-SLIPS" that address this limitation and permit the release of highly water-soluble (or oil-insoluble) agents. This approach involves the physical patterning of small, dried spots of hydrophilic drugs on the surfaces of hydrophobic porous materials and leads to analogs of conventional SLIPS that contain drug-patterned regions that can dissolve and disperse on exposure to water. We show that proto-SLIPS fabricated by patterning the antibiotic gentamicin on model porous PTFE membranes release drug rapidly, followed by a rapid process of self-healing in which oil from surrounding areas is transported to regions vacated by the drug. This healing process leads to uniform oil-infused surfaces with inherent antibiofouling properties similar to those of conventional SLIPS. The results of microbiological studies demonstrate that gentamicin-patterned proto-SLIPS can kill the common human bacterial pathogen Staphylococcus aureus on the surfaces of hydrogels or in liquid culture media and then transform to substantially reduce further bacterial surface fouling. This approach is modular and has the potential to enable the design of slippery surfaces that can release a wide variety of highly water-soluble and/or oil-soluble agents. In support of this goal, we demonstrate bases for the design of proto-SLIPS that release antifungal peptides, new dual-release coatings that release two agents targeted against different bacterial species, and the integration of concepts from the field of controlled release that provide additional measures of control over drug loading and release. We conclude that this proto-SLIPS strategy presents a new and useful approach to the design of drug-eluting SLIPS, with the potential to improve inherent antibiofouling behaviors and open the door to new applications of liquid-infused coatings in healthcare and other areas.
    Keywords:  antibiofouling; bacteria; controlled release; drug delivery; slippery surfaces
    DOI:  https://doi.org/10.1021/acsami.5c09975
  7. Nat Nanotechnol. 2025 Sep 10.
    Nanofibrous supramolecular peptide hydrogels for controlled release of small-molecule drugs and biologics.
    Brett H Pogostin, Samuel X Wu, Michael J Swierczynski, Christopher Pennington, Si-Yang Li, Dilrasbonu Vohidova, Erin H Seeley, Anushka Agrawal, Chaoyang Tang, Marina H Yu, Arghadip Dey, Sofia Hernandez, Jacob Cabler, Omid Veiseh, Eric L Nuermberger, Zachary T Ball, Jeffrey D Hartgerink, Kevin J McHugh.
      Maintaining safe and potent drug levels in vivo is challenging. Multidomain peptides assemble into supramolecular hydrogels with a well-defined, highly porous nanostructure that makes them attractive for drug delivery. However, their ability to extend release is typically limited by rapid drug diffusion. Here, to overcome this challenge, we present self-assembling boronate ester release (SABER) multidomain peptides capable of engaging in dynamic covalent bonding with payloads containing boronic acids. As examples, we demonstrate that SABER hydrogels can prolong the release of boronic acid-containing small-molecule drugs and boronic acid-modified biologics such as insulin and antibodies. Pharmacokinetic studies reveal that SABER hydrogels extend the therapeutic effect of ganfeborole from days to weeks, preventing Mycobacterium tuberculosis growth compared with oral administration in an infection model. Similarly, SABER hydrogels extended insulin activity, maintaining normoglycemia for 6 days in diabetic mice after a single injection. These results suggest that SABER hydrogels present broad potential for clinical translation.
    DOI:  https://doi.org/10.1038/s41565-025-01981-6
  8. RSC Adv. 2025 Sep 05. 15(39): 32155-32171
    Exploring 4D printing of smart materials for regenerative medicine applications.
    Budur N Alanazi, Hoda A Ahmed, Nuha S Alharbi, Noura A A Ebrahim, Soliman M A Soliman.
      The field of biomaterials has evolved rapidly with the introduction of time as a transformative factor, giving rise to four-dimensional (4D) materials that can dynamically change their structure or function in response to external stimuli. This review presents a comprehensive comparison between traditional three-dimensional (3D) and emerging 4D biomaterials, highlighting the key distinctions in design, adaptability, and functionality. We explore the development of smart biomaterials at the core of 4D systems, including stimuli-responsive polymers, shape-memory materials, and programmable hydrogels. The ability of these materials to undergo controlled transformations under physiological or engineered stimuli offers promising avenues in tissue engineering, drug delivery, regenerative medicine, and soft robotics. By integrating responsiveness and temporal control, 4D biomaterials represent a paradigm shift in biomedical engineering, with the potential to revolutionize patient-specific therapies and next-generation implants. Future challenges and opportunities for clinical translation are also discussed.
    DOI:  https://doi.org/10.1039/d5ra04410c
  9. Nat Struct Mol Biol. 2025 Sep 12.
    Computational design of sequence-specific DNA-binding proteins.
    Cameron J Glasscock, Robert J Pecoraro, Ryan McHugh, Lindsey A Doyle, Wei Chen, Olivier Boivin, Beau Lonnquist, Emily Na, Yuliya Politanska, Hugh K Haddox, David Cox, Christoffer Norn, Brian Coventry, Inna Goreshnik, Dionne Vafeados, Gyu Rie Lee, Raluca Gordân, Barry L Stoddard, Frank DiMaio, David Baker.
      Sequence-specific DNA-binding proteins (DBPs) have critical roles in biology and biotechnology and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. We describe a computational method for the design of small DBPs that recognize short specific target sequences through interactions with bases in the major groove and use this method to generate binders for five distinct DNA targets with mid-nanomolar to high-nanomolar affinities. The individual binding modules have specificity closely matching the computational models at as many as six base-pair positions and higher-order specificity can be achieved by rigidly positioning the binders along the DNA double helix using RFdiffusion. The crystal structure of a designed DBP-target site complex is in close agreement with the design model and the designed DBPs function in both Escherichia coli and mammalian cells to repress and activate transcription of neighboring genes. Our method provides a route to small and, hence, readily deliverable sequence-specific DBPs for gene regulation and editing.
    DOI:  https://doi.org/10.1038/s41594-025-01669-4
  10. Mater Horiz. 2025 Sep 10.
    Stretch-activated morphing enabled by integrated physical-chemical network engineering.
    Zhao Xu, Zi-Yang Fan, Dun-Wen Wei, Rui-Ying Bao, Wei Yang.
      Mechanical stimuli-responsive shape transformations, exemplified by mimosa leaves, are widespread in nature, yet remain challenging to realize through facile fabrication in synthetic morphing materials. Herein, we demonstrate stretch-activated shape-morphing enabled by an elastic-plastic bilayer structure assembled via dynamic crosslinking. Through dioxaborolane metathesis, a dynamic, crosslinked polyolefin elastomer (POEV) with elasticity and a co-crosslinked POE/paraffin wax blend (POE/PW-V) with tunable plasticity are prepared. An elastic-plastic mismatched bilayer is then assembled via dioxaborolane metathesis at the interface. Upon stretching and release, the elastic POEV layer attempts to recover, while the plastic POE/PW-V layer resists recovery, inducing curled deformation of the bilayer strips. The localized bilayer design allows for selective activation and region-specific shape transformation under tensile stress, enabling the creation of customizable morphing geometries. Moreover, the low-entropy conformation fixed during stretching spontaneously reverts to a high-entropy state upon heating-induced melting of PW crystals, thereby restoring the original shape. This thermally induced recovery ensures repeatable stretch activation. This work presents a design strategy that integrates physical and chemical network engineering to develop heterogeneously responsive systems, offering promising potential for soft morphing device applications.
    DOI:  https://doi.org/10.1039/d5mh01289a
  11. ACS Macro Lett. 2025 Sep 09. 1382-1388
    Sulfone-Bond-Toughened Multifunctional Hydrogels with Ion-Modulated Fluorescence and Mechanical Properties.
    Shujing Lei, Meng Huo.
      Sulfone bonding is an emerging dipole-dipole interaction between sulfone groups. Herein, sulfone bonding is used for the first time for engineering tough hydrogels. Sulfone-bond-toughened hydrogels are prepared by copolymerizing acrylamide with a sulfone-functionalized monomer. The integration of sulfone groups establishes cooperative supramolecular interactions between sulfone bonding and hydrogen bonding, endowing the hydrogels with tailorable mechanical properties, thermoresponsiveness, and clustering-induced fluorescence, which are readily modulated by varying the monomer composition. Moreover, the unique ion-responsiveness of sulfone bonding allows ion-responsive engineering of these hydrogel properties. Capitalizing on the ion-modulated fluorescence and thermal-responsive transitions of these hydrogels, we demonstrate their potential for rewritable information display applications. This work provides new insights into noncovalently toughened hydrogels and opens avenues for designing supramolecular networks based on sulfone bonding.
    DOI:  https://doi.org/10.1021/acsmacrolett.5c00511
  12. ACS Synth Biol. 2025 Sep 09.
    Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA.
    Kiara Reyes Gamas, Travis R Seamons, Matthew J Dysart, Lin Fang, James Chappell, Lauren B Stadler, Jonathan J Silberg.
      Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNAs (rRNAs) and perform a trans-splicing reaction that adds a barcode to the rRNAs. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida, the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNAs that store information within user-defined sets of microbes in environmental communities for gene transfer studies.
    Keywords:  RNA; and synthetic biology; barcoding; conjugation; horizontal gene transfer; information storage; ribozyme
    DOI:  https://doi.org/10.1021/acssynbio.5c00313
  13. Adv Mater. 2025 Sep 09. e07747
    Sacrificial Biofabrication for Vascularization: Concept, Materials, Technologies, and Applications.
    Jiezhong Shi, Chunyao Wang, Xuan Mei, Ben Zhang, Junxi Wu, Rylie A Green, Yu Shrike Zhang, Wenmiao Shu.
      Vasculature plays a crucial role in tissue engineering since it is essential for maintaining tissue viability by efficient nutrient and oxygen exchange as well as waste removal. The creation of biomimetic vascular networks is therefore critical for the development of functional tissue constructs. Sacrificial biofabrication has emerged as an effective method for engineering vascular structures by creating temporary templates that are subsequently removed to form well-defined vascular channels. In this review, the concept of sacrificial biofabrication is introduced and defined, with a focus on vascularization. Then, a comprehensive overview of the commonly used sacrificial materials based on different types of external stimuli is provided, and the classification and design principles of surrounding materials are briefly introduced. Additionally, various fabrication technologies employed to process sacrificial materials are summarized, and the diverse applications of sacrificial biofabrication in disease models and regenerative medicine are discussed. Finally, the current challenges are highlighted, and the future perspectives for advancing sacrificial biofabrication are explored to address the demand for vasculature manufacturing.
    Keywords:  3D printing; biomedical engineering; hydrogel; sacrificial biofabrication; vasculature
    DOI:  https://doi.org/10.1002/adma.202507747
  14. ACS Synth Biol. 2025 Sep 09.
    Engineering Noncanonical Cofactors To Expand Cellular Functions.
    Samuel Lim, Scott Banta.
      Synthetic biology often employs heterologous enzymatic reactions to reprogram cell metabolism or otherwise introduce novel functions. However, precise control of a particular metabolic pathway can be difficult to achieve because cofactors are shared with endogenous enzymes from a common pool. Recently, the use of noncanonical cofactors (NCCs) has emerged as a promising approach to bypass this problem by isolating desired reactions without the need for a physical barrier. Metabolic pathways that exclusively utilize NCCs can be insulated from the native machinery of the host cell, allowing them to function independently of the thermodynamic constraints imposed by sharing cofactors. This perspective explores the different types of NCCs and their synthesis methods, advancements in engineering NCC-dependent enzymes, and the potential applications of NCC-utilizing cells across various areas of synthetic biology.
    Keywords:  directed evolution; enzyme engineering; metabolic regulation; noncanonical cofactors
    DOI:  https://doi.org/10.1021/acssynbio.5c00473
  15. Synth Syst Biotechnol. 2025 Dec;10(4): 1414-1420
    Engineering robust Saccharomyces cerevisiae cell factory for improving fatty alcohol biosynthesis.
    Sijia Kong, Wei Yu, Zulin Wu, Ning Gao, Yongjin J Zhou.
      Engineering yeast cell factories is a feasible approach to produce value chemicals from renewable feedstocks. However, during the production process, reprogramming of the internal metabolic pathways of yeast cells and environmental stress always compromises its production performance. Here, we engineered the robust Saccharomyces cerevisiae to enhance the production of fatty alcohols by downregulating the expression of target of rapamycin gene TOR1 and deleting histone deacetylase gene HDA1 in S. cerevisiae. The enhanced cellular robustness resulted in the extended chronological lifespan (CLS) through metabolic balance and stress response regulation, thus increasing the production of fatty alcohols by up to 56 %. This strategy may be used as a general strategy for building effective microbial cell factories.
    Keywords:  Cell performance; Fatty alcohol; Robustness; Yeast
    DOI:  https://doi.org/10.1016/j.synbio.2025.08.003
  16. Biomed Mater. 2025 Sep 12.
    Characterizing Spatiotemporal Microbial Colony Distributions in Printed PEG-DA Hydrogel Films.
    Isaak Thornton, Kathryn Zimlich, Matthew W Fields, James Nolen Wilking.
      Biofilms are surface-attached microbial communities that play vital roles in natural ecosystems and contribute to persistent problems in medicine and industry. These communities exhibit heterogeneous chemical, physical, and physiological properties, which are governed by reciprocal structure-function relationships. Linking structure to function is crucial for understanding biofilm physiology but remains challenging due to the structural complexity of naturally formed biofilms. Bioprinting offers exquisite control over biofilm structure and holds potential for systematically exploring these relationships; however, the microscale colony distributions that emerge within hydrogel-based print resins remain unexplored. To address this, we use light-based bioprinting to create single-layer hydrogel films containing homogeneously dispersed Pseudomonas fluorescens bacteria and characterize the spatiotemporal distribution of colonies that develop within these films. We systematically vary the concentration of bacteria over nearly three orders of magnitude, track colony growth using microscopy, and quantify structural features with image analysis. We observe empirical relationships between initial cell concentration and key structural features: colony size, colony volume, total biovolume, and characteristic gradient length scale. This knowledge can be used to print microbial communities with well-defined features that can be quantitatively measured, is readily applicable to more complex three-dimensional shapes, and provides a tool for advancing our understanding of microbial communities.
    Keywords:  3D Printing; Biofilm; Bioprinting; Hydrogel; Microbial Communities; Photopolymerization; Structure-Function
    DOI:  https://doi.org/10.1088/1748-605X/ae066e
  17. STAR Protoc. 2025 Sep 11. pii: S2666-1667(25)00480-0. [Epub ahead of print]6(3): 104074
    Protocol for single-cell spatial transcriptomic profiling of cultured cells and engineered tissues without embedding or sectioning.
    Haylie R Helms, Luiz E Bertassoni.
      Spatial transcriptomics is a powerful tool for investigating how cellular composition and spatial relationships influence cell behavior. Here, we present a protocol for spatial transcriptomic profiling of 2D engineered tissues and cell cultures that are not compatible with standard embedding and sectioning. We detail steps for sample generation, fixation, and staining to integrate with Visium HD spatial technology. This protocol provides a flexible solution for sample generation for spatial transcriptomic analysis.
    Keywords:  Biotechnology and bioengineering; Cancer; Cell Biology; Cell culture; Cell-based Assays; Gene Expression; Genomics; Microscopy; Sequence analysis; Sequencing; Single Cell; Tissue Engineering
    DOI:  https://doi.org/10.1016/j.xpro.2025.104074
  18. Nature. 2025 Sep 10.
    Stabilizing effect of amino acids on protein and colloidal dispersions.
    Ting Mao, Xufeng Xu, Pamina M Winkler, Cécilia Siri, Ekaterina Poliukhina, Paulo Jacob Silva, Nan Xu, Yu Hu, Karim Al Zahabi, Rémi La Polla, Zhi Luo, Quy Ong, Alfredo Alexander-Katz, Francesco Stellacci.
      Amino acids (AAs) have a long history of being used as stabilizers for biological media1. For example, they are important components in biomedical formulations. The effect of AAs on biological systems is also starting to be appreciated. For example, it is believed that water-stressed cells increase the levels of AAs to prevent protein aggregation2. Several hypotheses have been put forward regarding their function, ranging from water-structuring3 to hydrotropic4 to specific effects such as stabilization against misfolding, yet it is not known whether their stabilizing function is protein specific or a generic colloidal property. Here we deduce that AAs possess a new and broad colloidal property: they stabilize patchy nanoscale colloids by adsorbing onto their surfaces through weak interactions. We demonstrate this general property by careful experimental evaluation of the stabilizing effect of AAs on dispersions of various proteins, plasmid DNA and non-biological nanoparticles. Furthermore, we develop a theoretical framework that captures this phenomenon and experimentally corroborate several new broad theoretical implications that apply beyond AAs. In vivo experiments further demonstrate that the addition of 1 M proline to insulin doubles its bioavailability in blood. Overall, our results indicate that the role of small molecules is as important as that of ionic strength and should always be reported in biophysics experiments.
    DOI:  https://doi.org/10.1038/s41586-025-09506-w
  19. ACS Appl Mater Interfaces. 2025 Sep 12.
    3D Surface-Patterned Hyaluronic Acid Hydrogels: Customizable Platforms for Enhanced Chondrogenic Differentiation and Organized Production of a Specific Hyaline Cartilage Extracellular Matrix.
    Amrita Natarajan, Anjali Sudha, Derrick Dean, Vineeth M Vijayan.
      Surface patterns and topographies play a pivotal role in directing the stem cell fate and extracellular matrix (ECM) organization. Here, we present a cost-effective, 3D printing-assisted template strategy to generate macroscale surface patterns on hyaluronic acid methacrylate (HAMA) hydrogels. Polylactic acid (PLA) templates with honeycomb, rhombohedral, and triangular geometries were fabricated, and free-radically cross-linked HAMA hydrogels were cast and demolded to yield patterned constructs. Based on the rationale that such patterns can approximate aspects of cartilage zonal organization, we hypothesized that these customizable topographies would enhance the chondrogenic differentiation of human bone marrow-derived mesenchymal stem/stromal cells (hBM-MSCs). A comprehensive evaluation was performed using mechanical testing, swelling analysis, biochemical assays (sGAG, collagen content), metabolic activity (Alamar Blue), immunofluorescence staining, and RT-qPCR for chondrogenic (SOX9, COL2A1, ACAN) and hypertrophic (COL10A1) markers. Honeycomb hydrogels exhibited superior stiffness, swelling resistance, and laminin adsorption compared with rhombohedral, triangular, and nonpatterned controls. hBM-MSCs cultured on honeycomb hydrogels in a chondrogenic medium demonstrated enhanced viability, greater sGAG and collagen deposition normalized to DNA content, and robust upregulation of chondrogenic markers, while limiting hypertrophy and dedifferentiation. Immunostaining further confirmed cartilage-specific ECM organization, with spatial alignment and condensation of MSCs on honeycomb topographies, suggesting the activation of mechanotransduction pathways. This work establishes an innovative design principle linking hydrogel macrogeometry to chondrogenic outcomes, addressing a gap in the field where most studies have focused on micro- and nanoscale cues. Although these hydrogels do not fully replicate all four native cartilage zones, the honeycomb topography promoted alignment, condensation, and stratified ECM deposition, recapitulating key aspects of zonal organization. This 3D-printed template-assisted macropatterning strategy provides a cost-effective, reproducible, and scalable method for fabricating biomimetic scaffolds. These surface patterned hydrogels enable controlled differentiation and spatially organized ECM formation, underscoring their promise for cartilage tissue engineering and personalized repair strategies.
    Keywords:  3D-printed templates; cartilage tissue engineering; chondrogenesis; honeycomb-patterned hydrogels; patterning; surface engineering
    DOI:  https://doi.org/10.1021/acsami.5c16374
  20. Nat Biotechnol. 2025 Sep 09.
    Antibody-bottlebrush prodrug conjugates for targeted cancer therapy.
    Bin Liu, Hung V-T Nguyen, Yivan Jiang, Aiden X Wang, Valerie Lensch, Zehao Sun, Zane H Boyer, Philip A Raftopoulos, Yutong Dai, Piper L MacNicol, Yuyan Wang, Nidhi Jyotsana, Wencong Wang, Sachin Bhagchandani, Sanjana Hemdev, Peyton Shieh, Samantha L Kristufek, Magalie Boucher, Michael Downes, Ronald M Evans, David W C MacMillan, Jeremiah A Johnson.
      Antibody-drug conjugates (ADCs) are effective targeted therapeutics but are limited in their ability to incorporate less-potent payloads, varied drug mechanisms of action, different drug release mechanisms and tunable drug-to-antibody ratios. Here we introduce a technology to overcome these limitations called 'antibody-bottlebrush prodrug conjugates' (ABCs). An ABC consists of an IgG1 monoclonal antibody covalently conjugated to the terminus of a compact bivalent bottlebrush prodrug that has payloads bound through cleavable linkers and polyethylene glycol branches. This design enables the synthesis of ABCs with tunable average drug-to-antibody ratios up to two orders of magnitude greater than those of traditional ADCs. We demonstrate the functional flexibility and manufacturing efficiency of this technology by synthesizing more than 10 different ABCs targeting either HER2 or MUC1 using drugs with potencies spanning several orders of magnitude as well as imaging agents for ABC visualization and photocatalysts for proximity-based labeling of the ABC interactome. ABCs display high target engagement, high cell uptake and improved efficacy in tumor models compared to conventional HER2-targeted ADCs, suggesting promise for clinical translation.
    DOI:  https://doi.org/10.1038/s41587-025-02772-z
  21. Proc Natl Acad Sci U S A. 2025 Sep 16. 122(37): e2512246122
    Dynamic and precise electromagnetic levitation of single cells.
    Malavika Ramarao, Victor Garcia-Gradilla, Mehmet Burcin Unlu, Ronald W Davis, Naside Gozde Durmus.
      The biophysical properties of single cells are crucial for understanding cellular function and behavior in biology and medicine. However, precise manipulation of cells in 3-D microfluidic environments remains challenging, particularly for heterogeneous populations. Here, we present "Electro-LEV," a unique platform integrating electromagnetic and magnetic levitation principles for dynamic 3-D control of cell position during separation. We demonstrated that small current adjustments in electromagnets significantly alter the levitation heights of diverse particles and cell types. By periodically modulating and tracking cell positions along the z-axis, Electro-LEV identified distinct levitation behaviors between single cells and cell clusters, with clusters responding more rapidly to magnetic field changes. Furthermore, we demonstrated that Electro-LEV significantly enhances the purity and efficiency of levitational sorting, achieving 10-fold enrichment of live cells from 50% starting viability samples and 18.8-fold enrichment from 10% starting viability samples. These results establish Electro-LEV as a powerful tool for investigating cellular heterogeneity, differentiating cell sizes and types, and improving cell sorting efficiency. Thus, Electro-LEV is broadly applicable, offering different possibilities for high-resolution cell analysis and label-free cell sorting in various biomedical fields, including but not limited to single-cell sequencing and drug screening.
    Keywords:  electromagnetic levitation; magnetic levitation; real-time control; single cells; sorting
    DOI:  https://doi.org/10.1073/pnas.2512246122
  22. Macromol Rapid Commun. 2025 Sep 08. e00557
    Cellulosic Flexible Electronic Materials: Recent Advances in Structural Design, Functionalization, and Smart Applications.
    Zihao Zheng, Xiaona Li, Geyuan Jiang, Wanke Cheng, Dawei Zhao, Haipeng Yu.
      Rapid advancement of flexible electronics has generated a demand for sustainable materials. Cellulose, a renewable biopolymer, exhibits exceptional mechanical strength, customizable properties, biodegradability, and biocompatibility. These attributes are largely due to its hierarchical nanostructures and modifiable surface chemistry. This paper systematically reviews the molecular and structural properties of cellulose, clarifying the relationships between structure, performance, and application for its multifunctional uses in next-generation devices. Advanced processing techniques-including 3D printing, freeze-drying, and chemical modifications-facilitate the integration of cellulose with conductive polymers and nanomaterials to create multifunctional composites. These innovations are pivotal for breakthroughs in ultra-sensitive flexible sensors, self-powered nanogenerators, high-capacity energy storage systems, and biomimetic electronic skins. The environmental adaptability and tissue compatibility of these composites make them particularly suitable for wearable health monitors and biodegradable electronics. Challenges related to scalability and multifunctional integration are being addressed through molecular engineering and sustainable manufacturing practices approaches like solvent-free 3D printing. By converging nanotechnology with principles of a circular economy, cellulose-based systems are redefining sustainable electronics and bridging human-centered design with eco-intelligent solutions.
    Keywords:  cellulose; flexible electronics; molecular functionalization; smart ionogels; structure design
    DOI:  https://doi.org/10.1002/marc.202500557
  23. J Am Chem Soc. 2025 Sep 08.
    Kinetic Locking of pH-Sensitive Complexes for Mechanically Responsive Polymer Networks.
    Stephen J K O'Neill, Yuen Cheong Tse, Zehuan Huang, Xiaoyi Chen, Jade A McCune, Oren A Scherman.
      Achieving sensitive and reversible responsivity over physiologically relevant pH ranges (4.5-7.5) remains of great interest for the design of next-generation autonomous drug delivery devices. Developing molecular interactions that are responsive within this pH range would enable targeted drug delivery at tumor sites or within inflamed or arthritic joints, where these changes in pH occur. Here, we demonstrate pH-responsive molecular interactions by the kinetic locking of host-guest complexes. Employing these complexes as dynamic crosslinks within polymer networks gives rise to materials with highly pH-responsive mechanical and viscoelastic properties. These systems further exhibit pH-dependent release of cargo, offering a self-responsive approach toward targeted drug delivery.
    DOI:  https://doi.org/10.1021/jacs.5c09897
  24. Nat Methods. 2025 Sep 11.
    Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.
    Heejin Roh, Simon P Shen, Yan Hu, Hui Si Kwok, Allison P Siegenfeld, Ceejay Lee, Marcanthony U Zepeda, Chun-Jie Guo, Shelby A Roseman, Caroline Comenho, Vijay G Sankaran, Jason D Buenrostro, Brian B Liau.
      Genome editing enables sequence-function profiling of endogenous cis-regulatory elements, driving understanding of their mechanisms. However, these approaches lack direct, scalable readouts of chromatin accessibility across long single-molecule chromatin fibers. Here we leverage double-stranded DNA cytidine deaminases to profile chromatin accessibility at endogenous loci of interest through targeted PCR and long-read sequencing, a method we term targeted deaminase-accessible chromatin sequencing (TDAC-seq). With high sequence coverage at targeted loci, TDAC-seq can be integrated with CRISPR perturbations to link genetic edits and their effects on chromatin accessibility on the same single chromatin fiber at single-nucleotide resolution. We employed TDAC-seq to parse CRISPR edits that activate fetal hemoglobin in human CD34+ hematopoietic stem and progenitor cells (HSPCs) during erythroid differentiation as well as in pooled CRISPR and base-editing screens tiling an enhancer controlling the globin locus. We further scaled the method to interrogate 947 variants in a GFI1B-linked enhancer associated with myeloproliferative neoplasm risk in a single pooled CRISPR experiment in CD34+ HSPCs. Together, TDAC-seq enables high-resolution sequence-function mapping of single-molecule chromatin fibers by genome editing.
    DOI:  https://doi.org/10.1038/s41592-025-02811-2
  25. J Colloid Interface Sci. 2025 Sep 08. pii: S0021-9797(25)02364-1. [Epub ahead of print]702(Pt 2): 138972
    Synergistic borate crosslinking and chain entanglement for mechanically robust and water-rich hydrogels.
    Haidi Wu, Qin Su, Ruigang Zhou, Jun Yan, Yifan Feng, Cheng Guan, Wenwen Su, Dingdong Chen, Longcheng Tang, Xuewu Huang, Jiefeng Gao.
      Hydrogels that simultaneously achieve high water content and mechanical robustness remain a challenge in biomaterials science, as conventional reinforcement strategies tend to conflict with hydration requirements. Herein, we present a chain entanglement-mediated dynamic crosslinking strategy that transcends this limitation in poly(vinyl alcohol) hydrogels through molecular-to-macroscopic hierarchical engineering. By pre-constructing an entangled network in a glycerol organogel and inducing the formation of borate ester bonds via solvent exchange, we establish hydrogels with a dual-reinforcement architecture: borate esterification disrupts crystalline domains and expands the polymeric network to enable good hydration (85.5-93.4 % water content) while synergizing dynamic bond reversibility with macromolecular entanglements for multiscale energy dissipation. The resultant hydrogels achieve skin-matched modulus (370 kPa), high tensile strength (4.3 MPa), toughness (27.2 MJ/m3) and extensibility (1447.9 % fracture strain), surpassing most of the reported water-rich hydrogels. Crucially, the hydrogel maintains stable ionic conductivity and biocompatibility, functioning as a conformal electrode that captures precisely electrocardiogram signals during vigorous physical activities. Therefore, this work provides a facile method for designing hydrogels that reconcile tissue-like functionality with engineered performance, holding implications for their practical applications in biomaterial fields.
    Keywords:  Dynamic crosslinking; Hydrogels; Mechanical properties; Water content
    DOI:  https://doi.org/10.1016/j.jcis.2025.138972
  26. Nat Biotechnol. 2025 Sep 09.
    Genome-wide mapping of RNA-protein associations through sequencing.
    Zhijie Qi, Shuanghong Xue, Junchen Chen, Wenxin Zhao, Kara Johnson, Xingzhao Wen, John Lalith Charles Richard, Pei Lin, Sheng Zhong.
      RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing. We apply PRIM-seq to two human cell lines and construct a human RNA-protein association network (HuRPA), encompassing >350,000 associations involving ~7,000 RNAs and ~11,000 proteins, including 2,610 proteins that each interact with at least 10 distinct RNAs. We experimentally validate the tumorigenesis-associated lincRNA LINC00339, the RNA with the highest number of protein associations in HuRPA, as a protein-associated RNA. We further validate the RNA-associating abilities of chromatin-conformation regulators SMC1A, SMC3 and RAD21, as well as the metabolic enzyme PHGDH. PRIM-seq enables systematic discovery and prioritization of RNA-binding proteins and their targets without gene- or protein-specific reagents.
    DOI:  https://doi.org/10.1038/s41587-025-02780-z
  27. Science. 2025 Sep 11. eadv9157
    Preventing hypocontractility-induced fibroblast expansion alleviates dilated cardiomyopathy.
    Ross C Bretherton, Isabella M Reichardt, Kristin A Zabrecky, Abigail Nagle, Logan R J Bailey, Darrian Bugg, Sasha Smolgovsky, Amy L Gifford, Timothy S McMillen, Alex J Goldstein, Kristina B Kooiker, Galina V Flint, Amy Martinson, Jagdambika Gunaje, Franziska Koser, Elizabeth Plaster, Wolfgang A Linke, Michael Regnier, Farid Moussavi-Harami, Nathan J Sniadecki, Cole A DeForest, Jennifer Davis.
      Cardiomyocyte hypocontractility underlies inherited dilated cardiomyopathy (DCM). Yet, whether fibroblasts modify DCM phenotypes remains unclear despite their regulation of fibrosis, which strongly predicts disease severity. Expression of a hypocontractility-linked sarcomeric variant in mice triggered cardiac fibroblast expansion from the de novo formation of hyperproliferative-mechanosensitized fibroblast states, which occurred prior to eccentric myocyte remodeling. Initially this fibroblast response reorganized fibrillar collagen and stiffened the myocardium albeit without depositing fibrotic tissue. These adaptations coincided with heightened matrix-integrin receptor interactions and diastolic tension sensation at focal adhesions within fibroblasts. Targeted p38 deletion arrested these cardiac fibroblast responses in DCM mice, which prevented cardiomyocyte remodeling and improved contractility. In conclusion, p38-mediated fibroblast responses were essential regulators of DCM severity, marking a potential cellular target for therapeutic intervention.
    DOI:  https://doi.org/10.1126/science.adv9157
  28. ACS Synth Biol. 2025 Sep 07.
    Genetic Entanglement Enables Ultrastable Biocontainment in the Mammalian Gut.
    Gary W Foo, Aathavan S Uruthirapathy, Claire Q Zhang, Izabela Z Batko, David E Heinrichs, David R Edgell.
      Imbalances in the mammalian gut are associated with acute and chronic conditions, and using engineered probiotic strains to deliver synthetic constructs to treat them is a promising strategy. However, high rates of mutational escape and genetic instability in vivo limit the effectiveness of biocontainment circuits needed for safe and effective use. Here, we describe STALEMATE (Sequence enTAngLEd Multi lAyered geneTic buffEring), a dual-layered failsafe biocontainment strategy that entangles genetic sequences to create pseudoessentiality and buffer against mutations. We entangled the colicin E9 immunity protein (Im9) with a thermoregulated meganuclease (TSM) by overlapping the reading frames. Mutations that disrupted this entanglement simultaneously inactivated both biocontainment layers, leading to cell death by the ColE9 nuclease and the elimination of escape mutants. By lengthening the entangled region, refining ColE9 expression, and optimizing the TSM sequence against IS911 insertion, we achieved escape rates below 10-10 as compared to rates of 10-5 with the nonentangled TSM. The STALEMATE system contained plasmids in E. coli Nissle 1917 for over a week in the mouse gastrointestinal tract with nearly undetectable escape rates upon excretion. STALEMATE offers a modular and simple biocontainment approach to buffer against mutational inactivation in the mammalian gut without a requirement for engineered bacteria or exogenous signaling ligands.
    Keywords:  biocontainment; meganuclease; mutational escape; sequence entanglement; temperature-regulated intein; toxin-antitoxin
    DOI:  https://doi.org/10.1021/acssynbio.5c00412
  29. Adv Mater. 2025 Sep 09. e07503
    All-3D-Printed Multi-Environment Modular Microrobots Powered by Large-Displacement Dielectric Elastomer Microactuators.
    Won Jun Song, Yong-Woo Kang, Yun Hyeok Lee, Junhyung Kim, Bastien F G Aymon, Seong-Yu Choi, Yong Eun Cho, Xiao-Yun Yan, Shucong Li, Younghoon Lee, Xuanhe Zhao, Yong-Lae Park, Jeong-Yun Sun.
      Microrobots are expected to push the boundaries of robotics by enabling navigation in confined and cluttered environments due to their sub-centimeter scale. However, most microrobots perform best only in the specific conditions for which they are designed and require complete redesign and fabrication to adapt to new tasks and environments. Here, fully 3D-printed modular microrobots capable of performing a broad range of tasks across diverse environments are introduced. For multi-environment navigation, large-displacement dielectric elastomer microactuators with a soft-stiff hybrid structure are developed, capable of powering microrobots to stride over obstacles on various terrestrial terrain and rapidly propel themselves across aquatic terrain. To further expand their capabilities beyond mere navigation, ten task-specific modules for the microrobots are developed. All modules are fabricated using a digital light processing multimaterial 3D printer capable of simultaneously printing multiple photocurable resins, providing a broadly applicable platform for fabricating mesoscale robotic components. The microrobots navigate across smooth, rough, granular, and aquatic environments, demonstrating tasks such as controlling the movements of nearby robots, interacting with humans to avoid collisions, and collaboratively dragging heavy objects through multi-unit operation. The study addresses key limitations hindering the integration of modular design into microrobots, enabling adaptation to new environments and tasks.
    Keywords:  dielectric elastomer actuators; microrobots; modular design; multimaterial 3D printing
    DOI:  https://doi.org/10.1002/adma.202507503
  30. Sci Adv. 2025 Sep 12. 11(37): eadz0718
    Rational assembly of 3D network materials and electronics through tensile buckling.
    Xiaonan Hu, Zhi Liu, Zhenjia Tang, Shiwei Xu, Zhangming Shen, Yue Xiao, Youzhou Yang, Renheng Bo, Shuheng Wang, Wenbo Pang, Yihui Zhang.
      Bioinspired network designs are widely exploited in biointegrated electronics and tissue engineering because of their high stretchability, imperfection insensitivity, high permeability, and biomimetic J-shaped stress-strain responses. However, the fabrication of three-dimensionally (3D) architected electronic devices with ordered constructions of network microstructures remains challenging. Here, we introduce the tensile buckling of stacked multilayer precursors as a unique route to 3D network materials with regularly distributed 3D microstructures. A data-driven topology optimization framework enables efficient search of the optimal 2D precursor pattern that maximizes out-of-plane dimension of the resulting 3D network material. Computational and experimental results demonstrate rational assembly of optimal multilayer precursor structures into well-architected 3D network materials with an evident interlayer separation. The resulting 3D network materials offer anisotropic, tunable J-shaped stress-strain curves, which can be tailored to reproduce stress-strain responses of biological tissues. Demonstration of reconfigurable volumetric 3D display suggests rich application opportunities in biointegrated electronics and tissue scaffolds.
    DOI:  https://doi.org/10.1126/sciadv.adz0718
  31. Nat Commun. 2025 Sep 10. 16(1): 8254
    Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus.
    Miao Xie, Weixiang Chen, Maria Vonk-de Roy, Andreas Walther.
      Nuclear biomolecular condensates are essential sub-compartments within the cell nucleus and play key roles in transcription and RNA processing. Bottom-up construction of nuclear architectures in synthetic settings is non-trivial but vital for understanding the mechanisms of condensates in real cellular systems. Here, we present a facile and versatile synthetic DNA protonucleus (PN) platform that facilitates localized transcription of branched RNA motifs with kissing loops (KLs) for subsequent condensation into complex condensate architectures. We identify salinity, monomer feeding, and KL-PN interactions as key parameters to control co-transcriptional condensation of these KLs into diverse artificial nuclear patterns, including single and multiple condensates, interface condensates, and biphasic condensates. Over time, KL transcripts co-condense with the PN matrix, with the final architecture determined by their interactions, which can be precisely modulated using a short DNA invader strand that outcompetes these interactions. Our findings deepen the understanding of RNA condensation in nuclear environments and provide strategies for designing functional nucleus-mimetic systems with precise architectural control.
    DOI:  https://doi.org/10.1038/s41467-025-63445-8
  32. Trends Biotechnol. 2025 Sep 09. pii: S0167-7799(25)00321-X. [Epub ahead of print]
    Food production from air: gas precision fermentation with hydrogen-oxidising bacteria.
    Margarita Bernal-Cabas, Karan Kumar, Owen Terpstra, Samira van den Bogaard, Aziz B Ammar, Susanna Mäkinen, Lukas Herwig, Marta de Almeida, Petri Tervasmäki, Lars M Blank, Tobias B Alter, Sonja Billerbeck.
      The breach of six planetary boundaries highlights the need for sustainable food production. Aerobic hydrogen-oxidising bacteria (HOBs) convert atmospheric CO2 and green hydrogen (H2) into biomass via gas fermentation, a process already used for food-grade single-cell protein production. This approach enables a supply chain independent of agriculture, requiring minimal land and water, with potential for carbon-neutral production and carbon capture. To expand beyond single-cell protein, HOBs must be engineered into cell factories for precision fermentation. Advances in synthetic biology, metabolic engineering, computational modelling, and bioreactor design have accelerated the development of scalable bioprocesses providing a blueprint for gas-based fermentation. We present a path forward using secreted recombinant milk protein as a case study, highlighting key challenges and opportunities.
    Keywords:  alternative proteins; gas fermentation; hydrogen-oxidising bacteria (HOBs); precision fermentation; single-cell protein; sustainable food production
    DOI:  https://doi.org/10.1016/j.tibtech.2025.08.003
  33. Sci Adv. 2025 Sep 12. 11(37): eadx0952
    Giant KASH proteins and ribosomes establish distinct cytoplasmic biophysical properties in vivo.
    Xiangyi Ding, Hongyan Hao, Daniel Elnatan, Patrick Neo Alinaya, Shilpi Kalra, Abby Kaur, Sweta Kumari, Liam J Holt, G W Gant Luxton, Daniel A Starr.
      Understanding how cells control their biophysical properties during development remains a fundamental challenge. While macromolecular crowding affects multiple cellular processes in single cells, its regulation in living animals remains poorly understood. Using genetically encoded multimeric nanoparticles for in vivo rheology, we found that Caenorhabditis elegans tissues maintain mesoscale properties that differ from those observed across diverse systems, including bacteria, yeast species, and cultured mammalian cells. We identified two conserved mechanisms controlling particle mobility: Ribosome concentration, a known regulator of cytoplasmic crowding, works in concert with a previously unknown function for the giant KASH (Klarsicht/ANC-1/SYNE homology) protein ANC-1 in providing structural constraints through associating with the endoplasmic reticulum. These findings reveal mechanisms by which tissues establish and maintain distinct mesoscale properties, with implications for understanding cellular organization across species.
    DOI:  https://doi.org/10.1126/sciadv.adx0952
  34. Nature. 2025 Sep 10.
    Amplifying antigen-induced cellular responses with proximity labelling.
    Shuojun Li, Yinghui Men, Zihan Wang, Yingcheng Wu, Hao Sun, Mingyang Yin, Xinrui Fan, Guiyun Deng, Zhicheng Yang, Tiange Yang, Yudian Xiao, Hu Zhou, Guangchuan Wang, Jia Fan, Chenqi Xu, Qiang Gao, Shuo Han.
      Antigen-induced clustering of cell surface receptors, including T cell receptors and Fc receptors, represents a widespread mechanism in cell signalling activation1,2. However, most naturally occurring antigens, such as tumour-associated antigens, stimulate limited receptor clustering and on-target responses owing to insufficient density3-5. Here we repurpose proximity labelling6, a method used to biotinylate and identify spatially proximal proteins, to amplify designed probes as synthetic antigen clusters on the cell surface. We develop an in vivo proximity-labelling technology controlled by either red light or ultrasound to covalently tag fluorescein probes at high density near a target antigen. Using T cell receptors as an example, we demonstrate that the amplified fluorescein effectively clusters and directs a fluorescein-binding bispecific T cell engager to induce enhanced T cell activation and cytotoxicity. Noninvasive, tissue-selective labelling in multiple syngeneic mouse tumour models produces potent immune responses that rapidly eradicate treated tumours. Efficient cell lysis further promotes epitope spreading to induce systemic immunity against untreated distal lesions and immune memory against rechallenge. Thus, proximity-labelling chemistry holds promise as a generalized strategy to manipulate antigen-dependent receptor function and cell states.
    DOI:  https://doi.org/10.1038/s41586-025-09518-6
  35. J Am Chem Soc. 2025 Sep 09.
    DNA Flipping as Facile Mechanism for Transmembrane Signaling in Synthetic Cells.
    Lorena Baranda Pellejero, Maria Vonk-de Roy, Doruk Baykal, Livia Lehmann, Andreas Walther.
      Transmembrane signaling is essential for cellular communication, yet reconstituting such mechanisms in synthetic systems remains challenging. Here, we report a simple and robust DNA-based mechanism for transmembrane signaling in synthetic cells using cholesterol-modified single-stranded DNA (Chol-ssDNA). We discovered that anchored Chol-ssDNA spontaneously flips across the membrane of giant unilamellar lipid vesicles (GUVs) in a nucleation-driven, defect-mediated process. This flipping enables internal signal processing through hybridization with encapsulated complementary DNA and activation of downstream processes such as RNA transcription. The phenomenon shows a high transduction efficiency, is generic across DNA sequences and lipid compositions, and can be enhanced by glycerol, which modulates membrane dynamics. Mechanistic insights using fluorescence microscopy, nuclease degradation assays, and membrane permeability assays reveal that flipping is dominated by transient membrane pores. Leveraging this facile translocation process, we demonstrate selective transcriptional activation inside synthetic cells, underscoring the potential of Chol-ssDNA flipping as a programmable tool for synthetic biology and bottom-up synthetic cell design.
    DOI:  https://doi.org/10.1021/jacs.5c09188
  36. ACS Appl Mater Interfaces. 2025 Sep 09.
    Concentration-Dependent Nanosheet and Nanotube Networks: Ice-Water Interface Control for Antifreeze Application.
    Yingjie Bu, Jun Ho Hwang, Nayeong Jeon, Inhye Kim, Eunji Lee.
      Cyclic peptides (CPs) are versatile building blocks whose conformational constraints foster ordered supramolecular architectures with potential in biomedicine, nanoelectronics, and catalysis. Herein, we report the development of biomimetic antifreeze materials by conjugating CPs bearing ice-binding residues to 4-arm polyethylene glycol (PEG) via click chemistry. The concentration-dependent self-assembly of these CP-PEG conjugates induces programmable morphological transitions, forming nanotube networks above the critical aggregation concentration (CAC) and two-dimensional nanosheet networks near the CAC. Strategic incorporation of ice-binding residues (Threonine, Valine, and Serine) systematically enhanced antifreeze activity, with threonine-functionalized nanotubes exhibiting the most pronounced ice recrystallization inhibition. Overall, nanotube assemblies demonstrated superior antifreeze and ice-nucleation inhibition capabilities, whereas nanosheets provided moderate yet significant cryoprotection. Dynamic ice shaping studies revealed distinct morphology-dependent mechanisms: nanotubes induced faceted ice crystals through specific binding, while nanosheets produced rounded crystals via surface interactions. This study establishes that by coupling rational sequence design with controlled self-assembly, these synthetic CP-PEG conjugates can effectively modulate ice-water interfaces through multiple, distinct mechanisms. This offers a highly tunable and robust platform for developing next-generation cryoprotectants and advanced materials for cold-environment applications, overcoming limitations of antifreeze proteins.
    Keywords:  Cyclic peptides; antifreeze; concentration-dependent morphology; ice-binding materials; self-assembly
    DOI:  https://doi.org/10.1021/acsami.5c11154
  37. Nat Biotechnol. 2025 Sep 10.
    Efficient sequence alignment against millions of prokaryotic genomes with LexicMap.
    Wei Shen, John A Lees, Zamin Iqbal.
      The size of microbial sequence databases continues to grow beyond the abilities of existing alignment tools. We introduce LexicMap, a nucleotide sequence alignment tool for efficiently querying moderate-length sequences (>250 bp) such as a gene, plasmid or long read against up to millions of prokaryotic genomes. We construct a small set of probe k-mers, which are selected to efficiently sample the entire database to be indexed such that every 250-bp window of each database genome contains multiple seed k-mers, each with a shared prefix with one of the probes. Storing these seeds in a hierarchical index enables fast and low-memory alignment. We benchmark both accuracy and potential to scale to databases of millions of bacterial genomes, showing that LexicMap achieves comparable accuracy to state-of-the-art methods but with greater speed and lower memory use. Our method supports querying at scale and within minutes, which will be useful for many biological applications across epidemiology, ecology and evolution.
    DOI:  https://doi.org/10.1038/s41587-025-02812-8
  38. Biosystems. 2025 Sep 06. pii: S0303-2647(25)00198-4. [Epub ahead of print]257 105588
    Shear-stress-induced swirling flow in biological systems.
    Ivana Pajic-Lijakovic, Milan Milivojevic, Peter V E McClintock.
      Swirling motion is an essential phenomenon that significantly influences numerous biological processes, such as the mixing of molecular components within living cells, nutrient transport, the structural changes of the cytoskeletons of contractile cells and the rearrangement of multicellular systems caused by collective cell migration. The dynamical relationship between subcellular and supracellular rearrangements enhances cell migration and contributes to tissue homeostasis. However, the basic mechanisms that drive swirling motion in biological contexts remain a matter of ongoing inquiry. Several complex biological systems, including synovial fluid, blood, mucus, cytoskeleton, and epithelial and mesenchymal multicellular systems, are examined in the context of possible swirling motion. Despite their diverse structures and fluid properties, they all exhibited swirling behaviour. Shared characteristics among these systems include: (i) a heterogeneous distribution of density and mechanical stress, (ii) viscoelastic properties, (iii) anisotropic behaviour, and (iv) non-uniform flow patterns. This multifaceted phenomenon is analysed through the integration of experimental findings from the existing literature with modelling considerations, aiming to identify the primary physical factors that contribute to the occurrence of swirling motion such as: lift force and normal stress differences that appear as a consequence of generated shear stress.
    Keywords:  Anisotropic structural changes; Low-Reynolds turbulence; Mechanical stress; Swirling motion; Viscoelasticity
    DOI:  https://doi.org/10.1016/j.biosystems.2025.105588
  39. Cell Syst. 2025 Sep 08. pii: S2405-4712(25)00227-3. [Epub ahead of print] 101394
    TissueMosaic: Self-supervised learning of tissue representations enables differential spatial transcriptomics across samples.
    Sandeep Kambhampati, Luca D'Alessio, Fedor Grab, Stephen Fleming, Sophia Liu, Ruth Raichur, Fei Chen, Mehrtash Babadi.
      Spatial transcriptomics allows for the measurement of gene expression within the native tissue context. However, despite technological advancements, computational methods to link cell states with their microenvironment and compare these relationships across samples and conditions remain limited. To address this, we introduce Tissue Motif-Based Spatial Inference across Conditions (TissueMosaic), a self-supervised convolutional neural network designed to discover and represent tissue architectural motifs from multi-sample spatial transcriptomic datasets. TissueMosaic further links these motifs to gene expression, enabling the study of how changes in tissue structure impact cell-intrinsic function. TissueMosaic increases the signal-to-noise ratio of spatial differential expression analysis through a motif enrichment strategy, resulting in more reliable detection of genes that covary with tissue structure changes. Here, we demonstrate that TissueMosaic learns representations that outperform neighborhood cell-type composition baselines and existing methods on downstream tasks. These findings underscore the potential of self-supervised learning to advance spatial transcriptomics discovery.
    Keywords:  Barlow Twins; DINO; SimCLR; case-control analysis; differential expression analysis; representation learning; self-supervised learning; spatial transcriptomics; tissue motifs
    DOI:  https://doi.org/10.1016/j.cels.2025.101394
  40. Adv Mater. 2025 Sep 12. e08729
    Advancing Tomographic Volumetric Printing Via Oxygen Inhibition Control: Improved Accuracy and Large-Volume Capability.
    Yujie Zhang, Katherine Houlahan, Daniel Webber, Nicolas Milliken, Kathleen L Sampson, Hendrick W de Haan, Hao Li, Robynne Vlaming, Liliana Gaburici, Antony Orth, Chantal Paquet.
      Tomographic volumetric additive manufacturing (TVAM) is an emerging 3D printing technology capable of producing complex structures in seconds. However, achieving reliable prints using TVAM requires sufficient light penetration throughout the print volume, which often limits the photoinitiator (PI) concentration that can be used. In (meth)acrylate-based photoresins, this constraint severely restricts achievable print size and quality due to oxygen inhibition. To address this challenge, a chemical strategy is demonstrated to control the oxygen inhibition period without compromising light penetration, using an amine, a thiol, and a phosphine additive as representative examples. Among these, N-methyldiethanolamine (MDEA) emerged as the most promising candidate, effectively reacting with non-reactive peroxy radicals to regenerate propagating radicals and sustain polymerization. Incorporating MDEA into a low-PI photoresin enabled high-resolution and large-volume printing in a custom-built TVAM system, achieving a root-mean-square surface deviation of 0.175 mm (≈2 pixels) and printable structure sizes up to 60 mm. These advances represent a 16-fold increase in print volume relative to the previous TVAM demonstrations and enable high-throughput fabrication of multiple complex parts without sacrificing print quality. This work establishes a scalable approach to overcoming oxygen inhibition in (meth)acrylate TVAM systems, unlocking new possibilities for large-volume, high-resolution additive manufacturing.
    Keywords:  (meth)acrylate photopolymerization; large‐volume printing; oxygen inhibition; print fidelity; tomographic volumetric additive manufacturing
    DOI:  https://doi.org/10.1002/adma.202508729
  41. PNAS Nexus. 2025 Sep;4(9): pgaf268
    Microbial living materials promote coral larval settlement.
    R3D Consortium
      The global decline of coral reefs calls for new strategies to rapidly restock coral populations and maintain ecosystem functions and services. Low recruitment success on degraded reefs hampers coral sexual propagation and leads to reduced genetic diversity and impaired reef resilience. Here, we introduce a Bacterial Reef Ink (Brink) to assist in coral larval settlement. Brink is a photopolymerized living material that can be rapidly applied to restoration substrates and has been formulated to cultivate two settlement-inducing bacterial strains (Cellulophaga lytica and Thalassotalea euphylliae). Settlement assays performed with broadcast spawning (Montipora capitata) and brooding (Pocillopora acuta) Indo-Pacific corals showed that Brink-coated substrates increased settlement >5-fold compared with uncoated control substrates. Brink can be applied as a flat coating or patterned using light-assisted 3D bioprinting, enabling diverse applications in reef restoration and engineering. This approach demonstrates the potential of functional living materials to enhance coral ecosystem engineering and support coral reef rehabilitation.
    Keywords:  bacteria; bioprinting; coral recruitment; coral reef restoration; ecosystem engineering
    DOI:  https://doi.org/10.1093/pnasnexus/pgaf268
  42. Nano Lett. 2025 Sep 10.
    On-Demand Nanoliter Delivering Platform via Electrical-Activated Microdroplet Assembling.
    Jianwei Zhong, Yifu Chang, Minhui Liang, Yinning Zhou, Ye Ai.
      Precise delivery of nanoliter-scale reagents is essential for high-throughput biochemical assays, yet existing platforms often lack real-time control and selective content fusion. Conventional methods rely on passive encapsulation or stochastic pairing, limiting both throughput and biochemical specificity. Here, we introduce an on-demand nanoliter delivery platform that seamlessly integrates electrical sensing, triggered droplet merging, and passive sorting in a single continuous flow. Leveraging impedance-based content detection, the system selectively identifies target droplets and initiates electrocoalescence-based fusion only when specific biochemical criteria are met. Fused nanoliter droplets are then sorted via size-dependent hydrodynamic deflection, enabling energy-free enrichment. Applied to bacterial screening, the system accurately distinguishes metabolically active droplets and could achieve over 6000 events per minute with postfusion purity exceeding 92%. This platform provides a label-free, high-precision solution for programmable nanoliter delivery, offering broad potential for drug discovery, synthetic biology, and single-cell analysis applications.
    Keywords:  Autonomous droplet manipulation; closed-loop droplet control; real-time impedance-controlled fusion; selective droplet pairing
    DOI:  https://doi.org/10.1021/acs.nanolett.5c02928
  43. Mater Today Bio. 2025 Oct;34 102249
    Unravelling the molecular network structure of biohybrid hydrogels.
    Jana Sievers-Liebschner, Ron Dockhorn, Jens Friedrichs, Thomas Kurth, Peter Fratzl, Jens-Uwe Sommer, Carsten Werner, Uwe Freudenberg.
      Glycosaminoglycan-based biohybrid hydrogels represent a powerful class of cell-instructive materials with proven potential in tissue engineering and regenerative medicine. Their biomedical functionality relies on a nanoscale polymer network that standard microscopy techniques cannot resolve. Here, we introduce an advanced analytical approach that integrates transmission electron microscopy, X-ray scattering, and computer simulations to directly and quantitatively characterize the nanoscale molecular network structure of these hydrogels. This method provides detailed insights into network connectivity and inhomogeneities, which are critical factors for understanding their functional properties and the cell-instructive cues they determine. Given that the glycosaminoglycan-based hydrogels facilitate the controlled delivery of soluble growth factors and guide the growth of complex organoid cultures, our approach also illuminates essential aspects of cell-material interactions and remodeling processes. Ultimately, this integrated strategy enables the precise customization of engineered matrices for regenerative therapies and disease/tissue modeling.
    Keywords:  Computer simulation; Glycosaminoglycan; Hydrogel; Nanoscale polymer network; Transmission electron microscopy; X-ray scattering
    DOI:  https://doi.org/10.1016/j.mtbio.2025.102249
  44. ACS Appl Mater Interfaces. 2025 Sep 12.
    RNA Sequencing at Single Vesicle Resolution via 3D Printed Embedded Droplet Arrays.
    Andrew A Brock, Senthilkumar Duraivel, Jinmai Jiang, Jonathan Fischer, Zachary F Greenberg, Mei He, Thomas E Angelini, Thomas D Schmittgen.
      Single-cell RNA sequencing has transformed our understanding of cellular heterogeneity; however, comparable methods for studying individual extracellular vesicles (EVs) remain scarce. To address the heterogeneity of RNA cargo contained within EVs, we developed a platform that 3D prints droplet arrays that generate cDNA for sequencing single EVs. The printing method leverages the interfacial instability between a hydrocarbon-based support material and printed aqueous solutions, driving printed features to break up into controllable, homogeneous droplets of a desired size that become stably trapped in 3D space. We printed picoliter aqueous droplets of EVs, DNA barcoded oligonucleotide beads, and biochemicals and performed a variety of reactions within the organogel support medium including PCR and synthesis of poly(A)+ RNA sequencing compatible cDNA. Printing conditions were optimized to ensure ideal droplet loading of individual barcoded beads and single EVs within each droplet. Following collection of aqueous cDNA material from the organogel, additional biochemical reactions were performed in tubes in order to generate sequencable RNA libraries. Individual CD9, CD63, and CD81 positive EVs contained a wide variety of poly(A)+ RNAs including mRNA, mitochondrial RNA, and noncoding RNAs. Poly(A)+ RNAs of individual 100 nm immunopurified THP-1 EVs were sequenced using the 3D printing method and identified 3689 unique barcodes with at least two corresponding reads of poly(A)+ RNA per EV, and the average amount of poly(A)+ RNA per EV was 3.32. The developed platform resolves EV poly(A)+ RNA heterogeneity with potential implications for biomarker discovery and other clinical applications.
    Keywords:  3D printing; RNA sequencing; cellular heterogeneity; droplet manufacturing; exosomes; extracellular vesicles
    DOI:  https://doi.org/10.1021/acsami.5c09959
  45. Mol Syst Biol. 2025 Sep 10.
    Epigenomic landscape of single vascular cells reflects developmental origin and disease risk loci.
    Chad S Weldy, Soumya Kundu, João Monteiro, Wenduo Gu, Albert J Pedroza, Alex R Dalal, Matthew D Worssam, Daniel Li, Brian Palmisano, Quanyi Zhao, Disha Sharma, Trieu Nguyen, Ramendra Kundu, Michael P Fischbein, Jesse Engreitz, Anshul B Kundaje, Paul P Cheng, Thomas Quertermous.
      Vascular sites have distinct susceptibility to atherosclerosis and aneurysm, yet the epigenomic and transcriptomic underpinning of vascular site-specific disease risk is largely unknown. Here, we performed single-cell chromatin accessibility (scATACseq) and gene expression profiling (scRNAseq) of mouse vascular tissue from three vascular sites. Through interrogation of epigenomic enhancers and gene regulatory networks, we discovered key regulatory enhancers to not only be cell type, but vascular site-specific. We identified epigenetic markers of embryonic origin including developmental transcription factors such as Tbx20, Hand2, Gata4, and Hoxb family members and discovered transcription factor motif accessibility to be vascular site-specific for smooth muscle, fibroblasts, and endothelial cells. We further integrated genome-wide association data for aortic dimension, and using a deep learning model to predict variant effect on chromatin accessibility, ChromBPNet, we predicted variant effects across cell type and vascular site of origin, revealing genomic regions enriched for specific TF motif footprints-including MEF2A, SMAD3, and HAND2. This work supports a paradigm that cell type and vascular site-specific enhancers govern complex genetic drivers of disease risk.
    Keywords:  Development; Epigenomics; Genomics; Single-Cell Transcriptomics; Vascular Biology
    DOI:  https://doi.org/10.1038/s44320-025-00140-2
  46. Proc Natl Acad Sci U S A. 2025 Sep 16. 122(37): e2513377122
    Quantifying phage infectivity from characteristics of bacterial population dynamics.
    Michael Blazanin, Eli Vasen, Cèlia Vilaró Jolis, William An, Paul E Turner.
      A frequent goal of phage biology is to quantify how well a phage kills a population of host bacteria. Unfortunately, traditional methods to quantify phage success can be time-consuming, limiting the throughput of experiments. Here, we use theory to show how the effects of phages on their hosts can be quantified using bacterial population dynamics measured in a high-throughput microplate reader (automated spectrophotometer). We use mathematical models to simulate bacterial population dynamics where specific phage and bacterial traits are known a priori. We then test common metrics of those dynamics (e.g., growth rate, time and height of peak bacterial density, death rate, extinction time, area under the curve) to determine which best predict: 1) infectivity over the short-term, and 2) phage suppression over the long term. We find that many metrics predict infectivity and are strongly correlated with one another. We also find that metrics can predict phage growth rate, providing an effective way to quantify the combined effects of multiple phage traits. Finally, we show that peak density, time of peak density, and extinction time are the best metrics when comparing across different bacterial hosts or over longer timescales where plasticity or evolution may play a role. In all, we establish a foundation for using bacterial population dynamics to quantify the effects of phages on their bacterial hosts, supporting the design of in vitro empirical experiments using microplate readers.
    Keywords:  methods development; simulations; theory
    DOI:  https://doi.org/10.1073/pnas.2513377122
  47. Protein Sci. 2025 Oct;34(10): e70302
    Genetic code expansion and enzymatic modifications as accessible methods for studying site-specific post-translational modifications of alpha-synuclein and tau.
    Ibrahim G Saleh, Marie Shimogawa, Jennifer Ramirez, Bernard Abakah, Yarra Venkatesh, Honey Priya James, Ming-Hao Li, Sarah A Louie, Marshall G Lougee, Wai-Kit Chia, Christopher Brue, Richard B Cooley, Ryan A Mehl, Tobias Baumgart, Robert H Mach, David Eliezer, Elizabeth Rhoades, E James Petersson.
      Alpha-synuclein (αS) and tau play important roles in the pathology of Parkinson's disease and Alzheimer's disease, respectively, as well as numerous other neurodegenerative diseases. Both proteins are classified as intrinsically disordered proteins (IDPs), as they have no stable structure that underlies their function in healthy tissue, and both proteins are prone to aggregation in disease states. There is substantial interest in understanding the roles that post-translational modifications (PTMs) play in regulating the structural dynamics and function of αS and tau monomers, as well as their propensity to aggregate. While there have been many valuable insights into site-specific effects of PTMs garnered through chemical synthesis and semi-synthesis, these techniques are often outside of the expertise of biochemistry and biophysics laboratories wishing to study αS and tau. Therefore, we have assembled a primer on genetic code expansion and enzymatic modification approaches to installing PTMs into αS and tau site-specifically, including isotopic labeling for NMR and fluorescent labeling for biophysics and microscopy experiments. These methods should be enabling for those wishing to study authentic PTMs in αS or tau as well as the broader field of IDPs and aggregating proteins.
    Keywords:  alpha‐synuclein; genetic code expansion; post‐translational modification; tau
    DOI:  https://doi.org/10.1002/pro.70302
  48. Nat Chem Biol. 2025 Sep 11.
    Real-time imaging of protein microenvironment changes in cells with rotor-based fluorescent amino acids.
    Shudan Yang, Shikai Jin, Mengxi Zhang, Yuda Chen, Yiming Guo, Yu Hu, Peter G Wolynes, Han Xiao.
      Fluorescent protein fusions with environmentally sensitive fluorophores have been widely used to investigate changes in the protein microenvironment. Unfortunately, these techniques often rely on bulky fluorescent proteins or tags to the N terminus or C terminus of the target protein, which can disrupt the behavior of the target protein and may limit their ability to investigate microenvironment changes with high spatial resolution. Here we develop a strategy to visualize microenvironment changes of protein substructures in real time by genetically incorporating environment-sensitive noncanonical amino acids (ncAAs) containing rotor-based fluorophores at specific positions of the target protein. Through computational redesign of aminoacyl-tRNA synthetase, we successfully incorporated these rotor-based ncAAs into several proteins in mammalian cells. Precise placement of these ncAAs at specific sites of proteins enables the detection of microenvironmental changes around individual residues during events such as aggregation, clustering, cluster dissociation and others.
    DOI:  https://doi.org/10.1038/s41589-025-02003-1
  49. Nat Commun. 2025 Sep 12. 16(1): 8267
    Matrix directs trophoblast differentiation in a bioprinted organoid model of early placental development.
    Claire Richards, Hao Chen, Matthew O'Rourke, Ashley Bannister, Grace Owen, Alexander Volkerling, Arnab Ghosh, Catherine A Gorrie, David Gallego-Ortega, Amy L Bottomley, Matthew P Padula, Kristine C McGrath, Louise Cole, Philip M Hansbro, Lana McClements.
      Trophoblast organoids can provide crucial insights into mechanisms of placentation, however their potential is limited by highly variable extracellular matrices unable to reflect in vivo tissues. Here, we present a bioprinted placental organoid model, generated using the first trimester trophoblast cell line, ACH-3P, and a synthetic polyethylene glycol (PEG) matrix. Bioprinted or Matrigel-embedded organoids differentiate spontaneously from cytotrophoblasts into two major subtypes: extravillous trophoblasts (EVTs) and syncytiotrophoblasts (STBs). Bioprinted organoids are driven towards EVT differentiation and show close similarity with early human placenta or primary trophoblast organoids. Inflammation inhibits proliferation and STBs within bioprinted organoids, which aspirin or metformin (0.5 mM) cannot rescue. We reverse the inside-out architecture of ACH-3P organoids by suspension culture with STBs forming on the outer layer of organoids, reflecting placental tissue. Our bioprinted methodology is applicable to trophoblast stem cells. We present a high-throughput, automated, and tuneable trophoblast organoid model that reproducibly mimics the placental microenvironment in health and disease.
    DOI:  https://doi.org/10.1038/s41467-025-62996-0
  50. Nat Biotechnol. 2025 Sep 12.
    Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.
    Ján Burian, Robert E Boer, Yozen Hernandez, Adrian Morales-Amador, Linhai Jiang, Abir Bhattacharjee, Cecilia Panfil, Melinda A Ternei, Sean F Brady.
      Metagenomics provides access to the genetic diversity of uncultured bacteria through analysis of DNA extracted from whole microbial communities. Long-read sequencing is advancing metagenomic discovery by generating larger DNA assemblies than previously possible. However, harnessing the potential of long-read sequencing to access the vast diversity within soil microbiomes is hampered by the challenge of isolating high-quality DNA. Here we introduce a method that can liberate large, high-quality metagenomic DNA fragments from soil bacteria and pair them with optimized nanopore long-read sequencing to generate megabase-sized assemblies. Using this method, we uncover hundreds of complete circular metagenomic genomes from a single soil sample. Through a combination of bioinformatic prediction and chemical synthesis, we convert nonribosomal peptide biosynthetic gene clusters directly into bioactive molecules, identifying antibiotics with rare modes of action and activity against multidrug-resistant pathogens. Our approach advances metagenomic access to the vast genetic diversity of the uncultured bacterial majority and provides a means to convert it to bioactive molecules.
    DOI:  https://doi.org/10.1038/s41587-025-02810-w
  51. Nat Mater. 2025 Sep 08.
    Molecular engineering of two-dimensional polyamide interphase layers for anode-free lithium metal batteries.
    Shuo Wang, Yan Wang, Zhaofeng Ouyang, Shitao Geng, Qianyun Chen, Xiaoju Zhao, Bin Yuan, Xiao Zhang, Shanshan Tang, Qiuchen Xu, Peining Chen, Huisheng Peng, Hao Sun.
      Anode-free lithium (Li) metal batteries are promising candidates for high-performance energy storage applications. Nonetheless, their translation into practical applications has been hindered by the slow kinetics and reversibility of Li plating and stripping on copper foils. Here we report a two-dimensional polyamide (2DPA)/lithiated Nafion (LN) interphase layer for anode-free Li metal batteries. Through molecular engineering, we construct a 2DPA layer with a large conjugated structure and Li-ion adsorption groups that show efficient adsorption, distribution and nucleation of Li ions. 2DPA molecules assembled into two-dimensional sheets are further incorporated with LN to create an ultrathin interphase layer with high-rate, high-capacity Li plating/stripping. These 2DPA/LN layers have higher rate capabilities and maximal energy and power densities compared with alternative polymer interphase layers, enabling the fabrication of an anode-free pouch cell with high performance. Overall, our interphase engineering approach is a promising tool to push the translation of anode-free Li metal batteries based on two-dimensional polymer interphase layers into practical devices, and enable the fabrication of energy storage technologies with high energy and power densities.
    DOI:  https://doi.org/10.1038/s41563-025-02339-y
This page is being maintained by Thomas Krichel. It was last updated on 2025‒09‒14 at 18:24.