bims-enlima Biomed News
on Engineered living materials
Issue of 2025–09–28
fifty-nine papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Encapsulation-enhanced switchable protein release from engineered probiotic lactobacilli.
  2. Theranostic Probiotic Engineered Living Materials That Dynamically Respond to Inflammation Markers.
  3. Wood-Based Oriented Object Deposition for Programmable Mechanical and 3D Fluidic Control.
  4. Reusable and modular combinatorial libraries for iterative metabolic engineering of Saccharomyces cerevisiae.
  5. Programmable Bio-Derived Noncovalent Glass via Reconfigurable H-Bonding Networks.
  6. Design of facilitated dissociation enables timing of cytokine signalling.
  7. Non-canonical resource allocation in heterotrophically growing Thermoanaerobacter kivui.
  8. Enabling the Fabrication of Complex Soft Iontronics Using Multi-Material 3D Extrusion Printing.
  9. Thermoresponsive Hydrogel with Thermal Memory.
  10. Thioctic Acid-Enabled Melt Processing of Cyclodextrin-Based Polyrotaxane into Functional Supramolecular Networks for Adhesives and Sensors.
  11. Biological and Biologically Inspired Functional Nanostructures: Insights into Structural, Optical, Thermal, and Sensing Applications.
  12. Engineering Bacteria in Hydrogel for Photo-Triggered Metabolic-Regulation AND-Gated Tumor Immunotherapy.
  13. Cell Contractile Force-Mediated Morphogenetic Tissue Engineering via 4D Printed Degradable Hydrogel Scaffolds.
  14. Structural constraint integration in a generative model for the discovery of quantum materials.
  15. Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.
  16. Stimuli-Responsive Hydrogels from Liquid-Liquid Phase Separations of FUS-Derived Peptides.
  17. Processing soft thin films on liquid surface for seamless creation of on-liquid walkable devices.
  18. Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness.
  19. Nanoparticle Superlattices Assembled via Rapid Solvent Destabilization of Macromolecular Ligands.
  20. Mechanical cues guide the formation and patterning of 3D spheroids in fibrous environments.
  21. Trusted Codon Fingerprint: A Streamlined Platform for Deep and Reversible Bacterial Cell Labeling.
  22. Tailoring agarose fluid gels for use in suspension bath bioprinting and culture of spheroid-based bioinks.
  23. RNA-stabilized coat proteins for sensitive and simultaneous imaging of distinct single mRNAs in live cells.
  24. Bioinspired 3D-printing strategies for skeletal tissue regeneration: From natural architectures to clinical applications.
  25. Sequence-Independent RNA Sensing in Living Mammalian Cells.
  26. Virus-like particles as modular interfaces for biomaterial functionalization.
  27. Principles of protein abundance regulation across single cells in a mammalian tissue.
  28. Engineered enzymes can suppress genome-editing errors.
  29. Biomimetic Mineralisation - Nature-inspired Strategy for Promising Hard Tissue Regenerative Materials Development.
  30. Manipulating the delivery and immunogenicity of DNA vaccines through the addition of CB[8] to cationic polymers.
  31. De novo design of hypercompact transcript degraders by engineering substrate-specific toxins and Cas6-CBS system.
  32. Neural CRNs: A Natural Implementation of Learning in Chemical Reaction Networks.
  33. A biocompatible surfactant film for stable microfluidic droplets.
  34. Cell-free recombinase-integrated Boolean output system.
  35. Programmable motion of an enzyme-powered macroscale gel boat: a functional sensing platform.
  36. Versatile Room-Temperature Phosphorescence Silk Fibroin Platforms for Sustainable and Biocompatible Multifunctional Interfaces.
  37. Op-eds connect scientists and communities.
  38. Electrostatic-repulsion-based transfer of van der Waals materials.
  39. From β-Dicarbonyl Chemistry to Dynamic Polymers.
  40. High-resolution, genotype-free mapping of genetic variation with CRI-SPA-Map.
  41. Probiotic-Based Materials as Living Therapeutics.
  42. RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.
  43. A multimodal robotic platform for multi-element electrocatalyst discovery.
  44. De novo design of potent inhibitors of clostridial family toxins.
  45. Programmable Biointerfaces and Adaptive Functionality in Next-Generation Green Nanomaterials.
  46. Accurate prediction of gene deletion phenotypes with Flux Cone Learning.
  47. microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.
  48. BayesCNet: Bayesian inference for cell type-specific regulatory networks leveraging cell type hierarchy in single-cell data.
  49. SCHEPHERD: A universal platform for high-throughput, high-resolution, and programmable control of cell behavior through bioelectric stimulation.
  50. Photothermally Powered 3D Microgels Mechanically Regulate Mesenchymal Stem Cells Under Anisotropic Force.
  51. Megabase-scale human genome rearrangement with programmable bridge recombinases.
  52. mRNA-LNP hydrogels promote skeletal muscle regeneration in situ.
  53. Mechanical control of cell fate decisions in the skin epidermis.
  54. Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.
  55. An open source platform to automate the design, verification, and manufacture of 3D printed microfluidic devices.
  56. Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning.
  57. Engineered basement membrane mimetic hydrogels to study mammary epithelial morphogenesis and invasion.
  58. Uncovering the prevalence, key biogenesis enzymes, and biological significance of archaeal lipoproteins.
  59. Establishing an RNA sensor with high sensitivity and dynamic range utilizing a signal amplifier platform.
  1. J Control Release. 2025 Sep 24. pii: S0168-3659(25)00876-4. [Epub ahead of print] 114264
    Encapsulation-enhanced switchable protein release from engineered probiotic lactobacilli.
    Marc Blanch-Asensio, Varun Sai Tadimarri, Roberto Martinez, Gurvinder Singh Dahiya, Cao Nguyen Duong, Rahmi Lale, Shrikrishnan Sankaran.
      Living microbial therapeutics promise precise, programmable interventions at disease sites, yet most demonstrations of on demand drug release still rely on Escherichia coli, whose rich genetic toolkit is unmatched among probiotics. In particular, genetic parts to regulate in situ protein production are severely lacking in non-model probiotic bacteria like lactobacilli. Here, we equip the probiotic Lactiplantibacillus plantarum with high-performance genetic switches and show how material encapsulation can further enhance their behavior. By integrating cumate or vanillate-responsive operators and repressors with the strongest constitutive promoter in L. plantarum (Ptec), we generated two switches that support micromolar range induction. In rapidly growing culture conditions, acidification-associated leakiness of the switch was observed, which could compromise their applicability for precise on-demand delivery of drugs. Furthermore, such leakiness also limits the duration for which these engineered probiotics can be reliably used. By restricting growth through mild temperature or nutrient limitation, acidification and leakiness were suppressed. Strikingly, immobilizing the engineered cells in core-shell alginate beads (Protein Eluting Alginate with Recombinant Lactobacilli, PEARLs) almost eliminated leakiness, enabling day-scale, reversible control of intracellular reporters and secreted enzymes. This leakiness suppression persisted when two strains carrying orthogonal switches were co-encapsulated and even after miniaturization to submillimeter beads. These results expand the genetic toolbox of probiotic L. plantarum, demonstrate the synergy between genetic circuit design and material encapsulation, and advance lactobacilli toward stimuli-responsive therapeutic platforms.
    Keywords:  Alginate; Engineered living materials; Genetic switch; Probiotic lactobacilli; Protein secretion
    DOI:  https://doi.org/10.1016/j.jconrel.2025.114264
  2. Adv Healthc Mater. 2025 Sep 26. e03809
    Theranostic Probiotic Engineered Living Materials That Dynamically Respond to Inflammation Markers.
    Gokce Altin-Yavuzarslan, Sierra M Brooks, James O Park, Kevin B Reed, McKenna Flynn, Olivia L Lanier, Hongyuan Lu, Hal S Alper, Alshakim Nelson.
      The development of smart, implantable devices localized at the site of inflammation to conditionally and proactively combat active inflammation for inflammatory bowel disease (IBD), has the potential to transform the patient's quality of life compared to conventional treatment modalities. Engineered probiotic organisms can enable dynamic production of therapeutic compounds in response to inflammatory biomarkers. However, delivery and localization of these engineered organisms to the site of inflammation requires their integration into a material or device that sustains their viability and metabolic activity. To this end, a 3D printed engineered living material (ELM) is developed using an engineered probiotic organism (E. coli Nissle 1917) with genetic circuits to sense biomarkers for inflammation and respond with the production of anti-inflammatory compounds. These organisms are incorporated into poly(ethylene glycol) diacrylate (PEGDA) resins for the light-based 3D printing of 3D constructs. The organisms are physically encapsulated within the PEGDA and are fully viable and metabolically active. The 3D printed ELM devices are able to detect clinically relevant amounts of nitric oxide as an inflammatory biomarker and respond with the production of tryptamine or 1-acetyl-3-carboxyl-β-carboline as representative anti-inflammatory agents. Additionally, the ELM devices are efficacious in treating in vitro models of inflammation, including murine macrophages and intestinal epithelial cells. Looking forward, these ELM devices could serve as theranostic modalities for the long-term treatment of inflammatory disorders such as IBD.
    Keywords:  E. coli nissle 1917; engineered living materials; inflammation treatment; probiotic therapy; smart drug delivery; stimuli‐responsive materials; theranostics
    DOI:  https://doi.org/10.1002/adhm.202503809
  3. ACS Appl Mater Interfaces. 2025 Sep 21.
    Wood-Based Oriented Object Deposition for Programmable Mechanical and 3D Fluidic Control.
    Yeonsoo Kim, Donghyeok Kang, Sungchul Shin.
      The aligned fibrous architecture and intrinsic porosity of natural wood offer unique opportunities for constructing mechanically anisotropic and capillary-active structures. However, existing additive manufacturing techniques face challenges in preserving these structural characteristics, which limits the extent to which they can be leveraged in complex functional architectures. Here, we present Wood-based Oriented Object Deposition (WOOD), a 3D printing approach that integrates delignified wood sheets and digital light processing (DLP) to fabricate structures with preserved anisotropy and porosity. Sliced wood layers are impregnated with photocurable monomer, aligned, and selectively photopolymerized, enabling directional control of mechanical and fluidic properties. We further establish processing criteria for hybridizing delignified wood with photocurable monomer, ensuring sufficient light transmission, deep curing, and structural fidelity. Densification improves printing resolution by allowing finer layer stacking and reducing surface artifacts such as stair-stepping. By aligning fiber orientation across layers, we achieve programmable deformation for origami-inspired architectures with integrated flexibility and rigidity. Additionally, vertically laminated structures support 3D fluidic control, enabling pressure-actuated flow switching and spatially resolved pH sensing. WOOD offers a scalable and sustainable platform that unites the structural advantages of natural wood with the precision of additive manufacturing, unlocking possibilities in bioinspired materials, microfluidic devices, and multifunctional composites.
    Keywords:  DLP 3D printing; densification; microfluidic devices; porous and aligned structure; wood-based additive manufacturing
    DOI:  https://doi.org/10.1021/acsami.5c14844
  4. Metab Eng. 2025 Sep 19. pii: S1096-7176(25)00151-X. [Epub ahead of print]93 100-114
    Reusable and modular combinatorial libraries for iterative metabolic engineering of Saccharomyces cerevisiae.
    Philip Tinggaard Thomsen, Peter Gockel, Christina Vasileiou, Ingrid Mohr, Marc Cernuda Pastor, Irina Borodina.
      Efficiently rewiring microbial metabolism for molecule production lies at the core of industrial metabolic engineering. Combinatorial libraries are useful for directing metabolism towards molecule production; however, their construction is labor-intensive, and their use in iterative strain engineering campaigns is often restricted by site-specific genomic integration. Here we present an automation-friendly framework for generating reusable and modular integration-based combinatorial libraries that can be used repeatedly to build high-performing strains. We apply this approach to engineer the production of betacyanins, a commonly used red food colorant extracted from beetroots, in Saccharomyces cerevisiae. Iterative implementation of combinatorial libraries targeting the betacyanin biosynthesis pathway (design space: ∼25,000), precursors (design space: ∼43,000), and cofactors (design space: ∼26,000) consistently improved pigment production by 1.2-5.7-fold per cycle over seven rounds of engineering. Sequencing of high-performing library isolates from each round revealed unique insights into betacyanin and yeast metabolism, e.g. we found strong evidence implicating the S. cerevisiae cytochrome b5 in heterologous red beet pigment production. Altogether, this study demonstrates a framework for combinatorial library engineering well-suited for accelerating the development of high-performing cell factories for industrial fermentation processes.
    Keywords:  Automated strain development; Combinatorial engineering; High-throughput metabolic engineering; Natural products; Saccharomyces cerevisiae
    DOI:  https://doi.org/10.1016/j.ymben.2025.09.006
  5. Angew Chem Int Ed Engl. 2025 Sep 21. e202517982
    Programmable Bio-Derived Noncovalent Glass via Reconfigurable H-Bonding Networks.
    Wei Fan, Ruirui Xing, Peng Zhou, Guizhi Shen, Shuai Cao, Chengqian Yuan, Xuehai Yan.
      Glass has served as a cornerstone of modern civilization due to its exceptional optical transparency and structural integrity. Yet, its static covalent/ionic network fundamentally restricts environmental adaptability, presenting a critical challenge for next-generation sustainable technologies. Here, we report a programmable, bio-derived noncovalent glass (BNG) engineered through multivalent, reconfigurable H-bonding networks composed of natural building blocks (e.g., amino acids, peptides, biomacromolecules) and organic acids with multiple H-bond donors and acceptors. Molecular programming of these networks enables unprecedented four-dimensional control: hydration-tunable mechanical stiffness, amino acid-guided refractive index modulation, humidity/temperature-activated self-healing, and closed-loop aqueous recyclability. This molecularly encoded programmability distinguishes BNG from conventional smart materials, which typically rely on single stimulus-response modes. Critically, the configurability of H-bonding network further endows BNG with versatile processability (e.g., 3D printing, thermal pressing, and mold-casting) for functional architectures. Moreover, the programmable disassembly allows seamless integration into transient electronics as an energy-efficient alternative to energy-intensive glass recycling. By leveraging naturally abundant, metabolically benign building blocks, BNG establishes a sustainable paradigm for adaptive soft electronics and circular packaging-transforming glass from a passive structural medium to a dynamically programmable material.
    Keywords:  H‐bonding networks; Noncovalent glass; Peptide self‐assembly; Programmable; Sustainable
    DOI:  https://doi.org/10.1002/anie.202517982
  6. Nature. 2025 Sep 24.
    Design of facilitated dissociation enables timing of cytokine signalling.
    Adam J Broerman, Christoph Pollmann, Yang Zhao, Mauriz A Lichtenstein, Mark D Jackson, Maxx H Tessmer, Won Hee Ryu, Masato Ogishi, Mohamad H Abedi, Danny D Sahtoe, Aza Allen, Alex Kang, Joshmyn De La Cruz, Evans Brackenbrough, Banumathi Sankaran, Asim K Bera, Daniel M Zuckerman, Stefan Stoll, K Christopher Garcia, Florian Praetorius, Jacob Piehler, David Baker.
      Protein design has focused on the design of ground states, ensuring that they are sufficiently low energy to be highly populated1. Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that are traversed in transitions from one low-lying state to another2,3. This is a challenging task because such states must be sufficiently strained to be poorly populated, but not so strained that they are not populated at all, and because protein design methods have focused on generating near-ideal structures4-7. Here we describe a general approach for designing systems that use an induced-fit power stroke8 to generate a structurally frustrated9 and strained excited state, allosterically driving protein complex dissociation. X-ray crystallography, double electron-electron resonance spectroscopy and kinetic binding measurements show that incorporating excited states enables the design of effector-induced increases in dissociation rates as high as 5,700-fold. We highlight the power of this approach by designing rapid biosensors, kinetically controlled circuits and cytokine mimics that can be dissociated from their receptors within seconds, enabling dissection of the temporal dynamics of interleukin-2 signalling.
    DOI:  https://doi.org/10.1038/s41586-025-09549-z
  7. Nat Commun. 2025 Sep 26. 16(1): 8489
    Non-canonical resource allocation in heterotrophically growing Thermoanaerobacter kivui.
    Franziska Maria Mueller, Albert Leopold Müller, Wenyu Gu, Farshad Abdollah-Nia, Jiawei Sun, Jenna Kim Ahn, Kerwyn Casey Huang, James R Williamson, Alfred Michael Spormann.
      Allocation of resources in the costly proteome reflects trade-offs between cellular functions. For example, proteome composition of Escherichia coli is significantly regulated by growth rate. An increasing anabolic, especially ribosomal, proteome fraction correlates with a decreasing catabolic proteome fraction at faster growth, which then leads to changes in catabolism. Our systems-level studies of the thermophilic acetogen Thermoanaerobacter kivui when growth rate is varied over two orders of magnitude revealed a different strategy: proteome allocation is only partially controlled by growth rate, and metabolic rates are primarily controlled posttranslationally. At slower growth, ribosome numbers are controlled by rRNA concentrations with an excess of ribosomal proteins. Composition of the catabolic proteome is uncoupled from catabolic rates as indicated by flux analysis. This study adds to the understanding of acetogenic Clostridia, which are of interest for biotechnological processes in a carbon-neutral economy, and points to a complex landscape of microbial ecophysiological strategies.
    DOI:  https://doi.org/10.1038/s41467-025-63432-z
  8. Adv Sci (Weinh). 2025 Sep 24. e05172
    Enabling the Fabrication of Complex Soft Iontronics Using Multi-Material 3D Extrusion Printing.
    Trevor J Kalkus, Tamara V Unterreiner, Målin Schmidt, Laura D Wächter, Christina R Schmitt, Ankit Mishra, Christine Selhuber-Unkel.
      Iontronics can improve soft robotics, including wearable devices and environmental sensors, by replacing rigid electronics with viscoelastic materials that mimic biological tissue. Circuit components have been fabricated with soft materials that utilize ionic current, but the process can be tedious and widely applicable manufacturing methods are lacking, hindering the development of complex iontronic circuits for real-world applications. With multi-material 3D printing, this work demonstrates the ability to rapidly iterate ionic diode design and integrate these diodes within complex structures with biomimetic mechanical behavior. Print quality and material properties can be tuned by adjusting the concentration of the ink's components. To emphasize the rapid iteration enabled by 3D printing, a library of the ionic diodes with varying sensitivity to strain is evaluated. The utility of these ionic diodes is demonstrated by integrating them within logic circuits that respond to mechanical cues and demonstrate bio-inspired strain-stiffening behavior. These devices are functional directly from the 3D printer, are extremely flexible, and can be submerged in water without losing functionality. The adaptability afforded by multi-material extrusion printing make it an ideal candidate for enabling the next generation of iontronics capable of advanced computational and mechanical functionality.
    Keywords:  3D printing; ionic diode; iontronics; mixed conductivity; soft robotics; strain‐stiffening
    DOI:  https://doi.org/10.1002/advs.202505172
  9. Adv Mater. 2025 Sep 24. e11341
    Thermoresponsive Hydrogel with Thermal Memory.
    Jiageng Pan, Zican Yang, Hao Ran Chen, Bo Yan, Hong Xiang Li, Yubin Ke, Liang Gao, Guowei Yang.
      Thermal plasticity-the capacity to dynamically reconfigure material properties in response to thermal history-is a hallmark of biological systems that remains elusive in synthetic hydrogels. Inspired by coral symbiont acclimatization, thermally plastic hydrogels (TP-gels) based on polyvinyl butyral are reported, which emulate biological thermal memory through a bioinspired feedback loop: thermoresponsive equilibrium swelling encodes thermal history, while elastic network constraints translate this memory into programmable phase transition thresholds (Tc). By exploiting temperature-dependent polymer-water miscibility, TP-gels achieve multi-stable states through adaptive swelling, enabling reversible opacity transitions with Tc shifts of 3-7 °C per thermal training cycle. Crucially, elasticity-mediated suppression of spinodal decomposition stabilizes metastable states during thermal encoding, preventing premature phase separation. This plasticity is leveraged for cryptographic applications, demonstrating sequential information decryption via thermal trajectory programming-where spatially resolved Tc gradients serve as thermodynamic keys. This work establishes a paradigm for materials with embodied environmental intelligence, bridging the divide between biological adaptability and synthetic systems through thermodynamic metastability engineering.
    Keywords:  phase separation; polyvinyl butyral; thermal acclimation; thermoresponsive hydrogels
    DOI:  https://doi.org/10.1002/adma.202511341
  10. Small. 2025 Sep 24. e09073
    Thioctic Acid-Enabled Melt Processing of Cyclodextrin-Based Polyrotaxane into Functional Supramolecular Networks for Adhesives and Sensors.
    Qinghong Zeng, Bo Qiao, Shijie Ren, Xue Xiao, Longyu Li.
      Cyclodextrin-based polyrotaxanes (CD-PRs), a class of mechanically interlocked materials (MIMs), have attracted attention for their low-cost raw materials, good biocompatibility, mechanical resilience, and dynamic adaptability. However, the extreme insolubility of the unmodified CD-PRs has long prevented scalable fabrication. Herein, a deep-eutectic-solvent (DES)-assisted melt processing strategy is reported in which natural thioctic acid (TA) both dissolves CD-PRs and co-polymerizes into poly(thioctic acid) (PTA) elastomers, forming robust pseudo-sliding-ring networks. By simply tuning the CD-PR loading, two distinct regimes of network reinforcement are demonstrated. Specifically, at low loadings, CD-PRs act as discrete toughening agents, enhancing elastomer toughness and fracture strain with minimal change in elastic modulus, whereas at higher loadings, they contribute as continuous crosslinks, improving both tensile strength and elastic modulus. The versatility of the resultant supramolecular networks is further showcased as two applications: (1) hot-melt adhesives, where the incorporation of CD-PRs enhances adhesion strength by 432% via enhanced cohesive energy, and (2) an ionically conductive elastomer (ICE), which enhances both elastic modulus and toughness to enable reliable underwater/air amphibious Morse Code transmission. This work overcomes the longstanding solubility challenge of cyclodextrin-based polyrotaxanes, reveals their concentration-dependent mechanistic roles, and provides a generalizable, green pathway for processing supramolecular networks from mechanically interlocked polymers.
    Keywords:  cyclodextrin‐based polyrotaxane; deep eutectic solvent; hot melt adhesive; ionically conductive elastomer; pseudo‐sliding ring network
    DOI:  https://doi.org/10.1002/smll.202509073
  11. Adv Mater. 2025 Sep 22. e09281
    Biological and Biologically Inspired Functional Nanostructures: Insights into Structural, Optical, Thermal, and Sensing Applications.
    Chao Hsuan Joseph Sung, Taige Hao, Herry Fang, Andrew Tran Nguyen, Valentina Perricone, Haitao Yu, Wei Huang, Ezra Sarmiento, Adrian Francisco Duran Ornelas, Derek Lublin, Ric Wehling, Sanaz Farajollahi, Atsushi Arakaki, Dhriti Nepal, Nathan Patrick Lord, David Kisailus.
      Biological materials developed over millennia consist of simple biogenic materials, yet exhibit exceptional functional properties. Leveraging design features from these structures with engineered nanomaterial components can lead to bio-inspired structures that demonstrate superior performance over traditional engineering materials. We describe nanoscale based architectures in biological systems, their role in enhancement of structural, optical, thermal and sensing properties, and their subsequent translation to bio-inspired structures. In structurally robust biological materials, we highlight nanoscale design features that enhance strength and stiffness, while retaining toughness. In optically active biological materials, we show how periodic nanostructures manipulate electromagnetic waves resulting in structural coloration as well as antireflective and camouflaging properties. Thermally regulating biological materials utilize nanopores and other nanostructural features to statically or dynamically control temperature. In addition, biological materials that are used in sensing utilize various nanostructures that enhance sensitivity by decreasing activation thresholds for signal transduction. We discuss challenges and opportunities including understanding control mechanisms in the formation of biological materials and leveraging advancements in self-assembly with new additive manufacturing techniques. The continued evaluation of organisms, including those that exhibit multifunctionality, provides not only new design features and pathways, but significant prospects for innovation in this ever-emerging field.
    Keywords:  biological materials; bio‐inspired materials; nanostructures; structure‐function relationships
    DOI:  https://doi.org/10.1002/adma.202509281
  12. Adv Healthc Mater. 2025 Sep 23. e03275
    Engineering Bacteria in Hydrogel for Photo-Triggered Metabolic-Regulation AND-Gated Tumor Immunotherapy.
    Qiliner Feng, Chen Wang, Si Shi, Junyu Fan, Yurong Chen, Tuanjie Zhang, Zhijun Ruan, Yongzheng Ma, Zifu Li, Jie Liu, Baizhu Chen.
      Tumor cells reprogram the energy metabolism and re-shape the microenvironment to maintain their fast proliferation and metastasis, leading to immunosuppression. Inspired by the design of engineered living materials, in this study, the AND-gated living hydrogel for metabolic-regulation enhanced tumor immunotherapy is constructed. Bacteria are genetically rewired to express lactate oxidase or glucose oxidase as two inputs under the control of thermosensitive promoter and then encapsulated inside the NIR-light controlled hydrogel. Triggered by laser, the engineered living hydrogel weakened the glycolysis and improved the mitochondrial respiration of tumor cells. The regulation of energy metabolism potentiated the antitumor immune responses by stimulating T cells, polarizing tumor associated macrophages to M1 phenotype, inducing the immunogenic cell death and stimulating the cGAS/STING pathway. With "high" inputs of two enzymes, the engineered living hydrogel realized the enhanced tumor immunotherapy as the "high" output. An approach of living hydrogel for metabolic-regulation AND-gated tumor immunotherapy is established.
    Keywords:  AND‐gated; energy metabolism; engineered bacteria; living hydrogel; tumor immunotherapy
    DOI:  https://doi.org/10.1002/adhm.202503275
  13. Adv Sci (Weinh). 2025 Sep 26. e07288
    Cell Contractile Force-Mediated Morphogenetic Tissue Engineering via 4D Printed Degradable Hydrogel Scaffolds.
    Aixiang Ding, Kaelyn L Gasvoda, David S Cleveland, Sriramya Ayyagari, Eben Alsberg.
      Tissue morphogenesis is a critical aspect of tissue development. Recent advances in 4D cell scaffolds have shown promise for modeling morphogenetic processes. While current 4D systems often rely on external stimuli, they frequently overlook the role of intrinsic cell-generated forces, such as cell contractile forces (CCFs), in driving tissue morphogenesis. The paradox between the inherently weak nature of CCFs and the robustness of tissue scaffolds presents a significant challenge in achieving effective shape transformations. In this study, an easily printable, freestanding, cell-laden hydrogel platform is designed to harness CCFs for 4D shape morphing. These hydrogels initially provide mechanical support to maintain structural integrity, followed by rapid degradation that amplifies CCFs through enhanced cell-cell interactions and increased local cell density, thereby inducing tissue morphogenesis. This platform enables the formation of scaffold-free constructs with programmed shape transformations. By modulating the initial printed geometries, complex and large tissue constructs can be generated via controlled global shape transformations. Furthermore, the platform supports 4D tissue engineering by facilitating tissue differentiation coupled with dynamic shape evolution. This CCF-4D system represents an important advancement in biomimetic tissue engineering, offering new avenues for creating dynamic tissue models that partially recapitulate native morphogenesis.
    Keywords:  4D printing; cell scaffold; hydrogel; shape morphing; tissue engineering
    DOI:  https://doi.org/10.1002/advs.202507288
  14. Nat Mater. 2025 Sep 22.
    Structural constraint integration in a generative model for the discovery of quantum materials.
    Ryotaro Okabe, Mouyang Cheng, Abhijatmedhi Chotrattanapituk, Manasi Mandal, Kiran Mak, Denisse Córdova Carrizales, Nguyen Tuan Hung, Xiang Fu, Bowen Han, Yao Wang, Weiwei Xie, Robert J Cava, Tommi S Jaakkola, Yongqiang Cheng, Mingda Li.
      Billions of organic molecules have been computationally generated, yet functional inorganic materials remain scarce due to limited data and structural complexity. Here we introduce Structural Constraint Integration in a GENerative model (SCIGEN), a framework that enforces geometric constraints, such as honeycomb and kagome lattices, within diffusion-based generative models to discover stable quantum materials candidates. SCIGEN enables conditional sampling from the original distribution, preserving output validity while guiding structural motifs. This approach generates ten million inorganic compounds with Archimedean and Lieb lattices, over 10% of which pass multistage stability screening. High-throughput density functional theory calculations on 26,000 candidates shows over 95% convergence and 53% structural stability. A graph neural network classifier detects magnetic ordering in 41% of relaxed structures. Furthermore, we synthesize and characterize two predicted materials, TiPd0.22Bi0.88 and Ti0.5Pd1.5Sb, which display paramagnetic and diamagnetic behaviour, respectively. Our results indicate that SCIGEN provides a scalable path for generating quantum materials guided by lattice geometry.
    DOI:  https://doi.org/10.1038/s41563-025-02355-y
  15. Science. 2025 Sep 25. eadl1988
    Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness.
    Brian D Cosgrove, Lexi R Bounds, Carson Key Taylor, Alan L Su, Anthony J Rizzo, Alejandro Barrera, Tongyu Sun, Alexias Safi, Lingyun Song, Thomas Whitlow, Aleksandra Tata, Nahid Iglesias, Yarui Diao, Purushothama Rao Tata, Brenton D Hoffman, Gregory E Crawford, Charles A Gersbach.
      Epigenetic control of gene expression and cellular phenotype is influenced by changes in the local microenvironment, yet how mechanical cues precisely influence epigenetic state to regulate transcription remains largely unmapped. Here, we combine genome-wide epigenome profiling, epigenome editing, and phenotypic and single-cell RNA-seq CRISPR screening to identify a class of genomic enhancers that responds to the mechanical microenvironment. These "mechanoenhancers" can be preferentially activated on either soft or stiff extracellular matrix contexts and regulate transcription to influence critical cell functions including apoptosis, adhesion, proliferation, and migration. Epigenetic editing of mechanoenhancers reprograms the cellular response to the mechanical microenvironment and modulates the activation of disease-related genes in lung fibroblasts from healthy and fibrotic donors. Epigenetic editing of mechanoenhancers holds potential for precise targeting of mechanically-driven diseases.
    DOI:  https://doi.org/10.1126/science.adl1988
  16. ACS Appl Mater Interfaces. 2025 Sep 24.
    Stimuli-Responsive Hydrogels from Liquid-Liquid Phase Separations of FUS-Derived Peptides.
    Elisabetta Rosa, Mariantonietta Pizzella, Luca Cimmino, Valeria Castelletto, Ian W Hamley, Luigi Vitagliano, Alfonso De Simone, Antonella Accardo.
      Defining soft biomaterials, including stimuli-responsive hydrogels, is essential for advancing applications such as targeted drug delivery, biosensing, and tissue engineering due to their ability to respond to environmental triggers dynamically. In this study, we characterized phase-separating peptides and elucidated the principles governing their self-assembly into hydrogels. Low-complexity aromatic-rich kinked segments (LARKS) were employed as building blocks to generate stimuli-responsive materials. By analyzing the properties of various multi-LARKS peptides, we developed a model informing the rational design of point mutations to modulate the mechanical properties and temperature stability of LARKS-based hydrogels, resulting in stimuli-responsive matrices. Our findings were further supported by demonstrating that these hydrogels effectively act as reservoir matrices capable of releasing drugs efficiently at 40 °C, highlighting their potential for biotechnological and medical applications.
    Keywords:  biomaterials; low-complexity aromatic-rich kinked segments (LARKS); protein liquid–liquid phase separations (LLPS); rheological characterization; stimuli-responsive hydrogels
    DOI:  https://doi.org/10.1021/acsami.5c15249
  17. Sci Adv. 2025 Sep 26. 11(39): eady9840
    Processing soft thin films on liquid surface for seamless creation of on-liquid walkable devices.
    Ziyu Chen, Mengtian Yin, Baoxing Xu.
      Walking on liquid surface is a unique locomotion ability of insects, but engineering on-liquid walkable devices currently requires disjointed, multistage fabrication and delicate deployment. Here, we introduce HydroSpread-a direct processing technology that enables seamless fabrication and patterning of soft films on liquid surface. It leverages the controlled spreading of liquid ink on liquid surface and combines with precise laser engraving supported by rapid heat transfer at the solid-liquid interface. Geometric shapes, including basic forms of straight lines, sharp turns and circles, and complex patterns, were fabricated with exceptional fidelity to design specifications. We propose two heat-driven hydrodynamic locomotion mechanisms, fin-like bending and leg-like buckling. By harnessing these principles, we engineered two walkable devices-HydroFlexor and HydroBuckler-and demonstrated robust on-water locomotion. This work eliminates fragile postfabrication transfers in soft device manufacturing, bridging the gap between soft films and structure fabrication, and establishes a streamlined pathway for designing and deploying functional soft devices directly in liquid environments.
    DOI:  https://doi.org/10.1126/sciadv.ady9840
  18. bioRxiv. 2025 Sep 18. pii: 2025.09.18.677115. [Epub ahead of print]
    Extracellular matrix chemistry tunes bacterial biofilm metabolism and optimizes fitness.
    Jinyang Li, Georgia R Squyres, Kathy Duong, Courtney Reichhardt, Matthew R Parsek, Dianne K Newman.
      Chemically complex extracellular matrices define cellular microenvironments and shape cell behavior. We hypothesized a composition-properties-function relationship in these natural living materials, where interactions among matrix components govern material properties and cellular physiology. Using Pseudomonas aeruginosa biofilms as a model system, we show that electrostatic interactions between the cationic polysaccharide Pel and extracellular DNA (eDNA) regulate retention of pyocyanin (PYO), a redox-active metabolite that supports anaerobic metabolism via extracellular electron transfer (EET). Biofilm-mimetic hydrogels and natural biofilms revealed that altering Pel's charge via pH adjustment or chemical acetylation, or tuning the Pel:eDNA ratio, predictably modulates PYO retention and EET efficiency. Functionally, a lower Pel:eDNA ratio enhances metabolism under oxygen limitation, whereas a higher ratio promotes survival under antibiotic stress. These findings highlight how matrix chemistry encodes tunable material properties that confer biofilm fitness advantages and establish a materials-based framework for understanding extracellular matrices in multicellular communities.
    DOI:  https://doi.org/10.1101/2025.09.18.677115
  19. ACS Nano. 2025 Sep 24.
    Nanoparticle Superlattices Assembled via Rapid Solvent Destabilization of Macromolecular Ligands.
    Matthew Ye, Emmit K Pert, Margaret S Lee, Yun Li, Arisa Nishimura, Rebecca L Li, Steven H Ngo, Wen Yu Huang, Grant M Rotskoff, Robert J Macfarlane.
      Nanoparticle assembly enables bottom-up synthesis of ordered materials with precise control over their nanoscale structure. However, existing methods typically require either complex ligands or long assembly time scales, meaning that scalability and speed of assembly remain key challenges for the development of functional materials. In this work, we demonstrate that polymer brushes can finely tune the chemical potentials between colloidal particles as a simple function of solvent content. Thus, solvent-induced destabilization of particles presents a rapid and scalable method for assembling nanoparticles that allows ordered superlattices to be obtained in gram-scale quantities in minutes. We systematically elucidate how factors like particle concentration, solvent identity, polymer brush architecture, and nanoparticle size affect the crystal quality and crystallographic symmetry of the assemblies. A computational model is presented that describes how these factors affect the chemical interactions between particles, providing insight into crystallographic phase selection in these systems. Finally, we demonstrate the generalizability of this approach to a variety of nanoparticle compositions, including gold, indium tin oxide, and manganese oxide, enabling the formation of multiple crystal symmetries (e.g., FCC, BCC, smectic liquid crystals). Since our method is compatible with polymers prepared via different synthetic routes and bearing different end-group functionalities─including commercially available polymers─it significantly lowers the technical barrier to producing ordered nanocomposite assemblies. Thus, the approach presented here and the fundamental chemical insight into these particles' assembly behavior provide a pathway toward the large-scale production of ordered hybrid materials from a diverse array of colloidal building blocks.
    Keywords:  colloidal crystals; colloidal stability; nanoparticles; polymers; self-assembly
    DOI:  https://doi.org/10.1021/acsnano.5c10677
  20. PNAS Nexus. 2025 Sep;4(9): pgaf263
    Mechanical cues guide the formation and patterning of 3D spheroids in fibrous environments.
    Sharan Sharma, Atharva Agashe, Jennifer C Hill, Keya Ganguly, Puja Sharma, Tara D Richards, Weijian Huang, David J Kaczorowski, Pablo G Sanchez, Rakesh Kapania, Julie A Phillippi, Amrinder S Nain.
      Multicellular spheroids have shown great promise in 3D biology. Many techniques exist to form spheroids, but how cells take mechanical advantage of native fibrous extracellular matrix (ECM) to form spheroids remains unknown. Here, we identify the role of fiber diameter, architecture, and cell contractility on spheroids' spontaneous formation and growth in ECM-mimicking fiber networks. We show that matrix deformability revealed through force measurements on aligned fiber networks promotes spheroid formation independent of fiber diameter. At the same time, larger-diameter crosshatched networks of low deformability abrogate spheroid formation. Thus, designing fiber networks of varying diameters and architectures allows spatial patterning of spheroids and monolayers simultaneously. Forces quantified during spheroid formation revealed the contractile role of Rho-associated protein kinase in spheroid formation and maintenance. Interestingly, we observed spheroid-spheroid and multiple spheroid mergers initiated by cell exchanges to form cellular bridges connecting the two spheroids. Unexpectedly, we found large pericyte spheroids contract rhythmically. Transcriptomic analysis revealed striking changes in cell-cell, cell-matrix, and mechanosensing gene expression profiles concordant with spheroid assembly on fiber networks. Overall, we ascertained that contractility and network deformability work together to spontaneously form and pattern 3D spheroids, potentially connecting in vivo matrix biology with developmental, disease, and regenerative biology.
    Keywords:  ECM nanofibers; cell forces; morphogenesis; pericytes; spheroids
    DOI:  https://doi.org/10.1093/pnasnexus/pgaf263
  21. ACS Synth Biol. 2025 Sep 22.
    Trusted Codon Fingerprint: A Streamlined Platform for Deep and Reversible Bacterial Cell Labeling.
    Zhaoguan Wang, Jingsong Cui, Gaoxu Tan, Gaili Cao, Jie Zhang, Hao Qi.
      The proliferation of artificially engineered cells, driven by advances in synthetic biology, underscores the urgent need to efficiently and precisely tag or identify these synthetic entities, ensuring robust management, oversight, and traceability. Here, we present a platform called trusted codon fingerprint (TCF), which leverages synonymous codon substitutions to integrate identification information into the open reading frames of antibiotic-resistant genes on a plasmid, thereby establishing unique codon fingerprints for target cells. TCF is devised for streamlined and erasable cell labeling with favorable identification capabilities. The dual mechanisms consist of antibiotic selection, which eliminates nearly all incorrectly assembled antibiotic-resistant genes, and error-correcting codes, which accommodate the rest of the minor substitutions. These features eliminate the necessity for a validation step and significantly streamline the process of writing TCF into cells, with cell viability guaranteeing the label's proper functioning. Through evaluating thousands of clones, TCF has achieved 100% writing efficiency and successful identification of the host cell genome via hash function computation using long-read sequencing. Finally, by using a temperature-sensitive plasmid backbone, an Escherichia coli strain engineered through 10-step genome modifications was recorded by TCF in a time- and labor-efficient manner, enabling cyclic writing and erasure of cell labels. Consequently, the TCF labeling system provides a streamlined, erasable, and effective tool, facilitating regulatory compliance and enhancing the flexibility for identity management of engineered strains.
    Keywords:  DNA writing; biotechnology; cell labeling; fingerprint; strain engineering; synthetic biology
    DOI:  https://doi.org/10.1021/acssynbio.5c00263
  22. Biofabrication. 2025 Sep 24.
    Tailoring agarose fluid gels for use in suspension bath bioprinting and culture of spheroid-based bioinks.
    Megan Elin Cooke, Nikolas Di Caprio, Jason P Killgore, Jason A Burdick.
      Suspension bath bioprinting, whereby bioinks are extruded into a yield stress bath with rapid recovery from shearing, has enabled the printing of low viscosity bioinks into constructs with high geometric complexity. This is particularly useful for soft materials, such as bioinks of cells and hydrogel precursors or even those comprised of cells alone (e.g., cell suspensions, cell spheroids). Previous studies have often relied upon external stabilization of the suspension bath (e.g., thermally crosslinking collagen or basement membrane extract) in order to culture soft materials without loss of printed structure. Here, we report a systematic investigation of suspension bath properties that support the printing, fusion, and culture of spheroid-only bioinks without any external stabilization. Specifically, agarose fluid gel suspension baths of varied polymer concentrations and dilutions were produced and characterized morphologically and rheologically. Juvenile bovine chondrocytes were formed into spheroids of ~150 µm in diameter and their fusion was investigated across the suspension baths in hanging drop cultures. Suspension baths of lower polymer concentrations and increased dilution enabled faster spheroid fusion. Further, spheroids were jammed by centrifugation into a paste-like bioink and printed into the agarose fluid gel suspension baths and cultured. The most heavily diluted suspension bath was unable to maintain print fidelity, whereas other formulations supported the printing, fusion, and culture of spheroid inks. These findings help to inform the design of suspension baths for bioprinting and culture without the use of external stabilization.
    Keywords:  Agarose Fluid Gel; Bioinks; Bioprinting; Spheroids; Suspension Bath
    DOI:  https://doi.org/10.1088/1758-5090/ae0aff
  23. Nat Methods. 2025 Sep 22.
    RNA-stabilized coat proteins for sensitive and simultaneous imaging of distinct single mRNAs in live cells.
    Christopher J Kuffner, Alexander M Marzilli, John T Ngo.
      RNA localization and regulation are critical for cellular function, yet many live RNA imaging tools suffer from limited sensitivity due to background emissions from unbound probes. Here we introduce conditionally stable variants of MS2 and PP7 coat proteins (which we name dMCP and dPCP) designed to decrease background in live-cell RNA imaging. Using a protein engineering approach that combines circular permutation and degron masking, we generated dMCP and dPCP variants that rapidly degrade except when bound to cognate RNA ligands. These enhancements enabled the sensitive visualization of single mRNA molecules undergoing differential regulation within various subcompartments of live cells. We further demonstrate dual-color imaging with orthogonal MS2 and PP7 motifs, allowing simultaneous low-background visualization of distinct RNA species within the same cell. Overall, this work provides versatile, low-background probes for RNA imaging, which should have broad utility in the imaging and biotechnological utilization of MS2-containing and PP7-containing RNAs.
    DOI:  https://doi.org/10.1038/s41592-025-02782-4
  24. J Biomater Appl. 2025 Sep 24. 8853282251382716
    Bioinspired 3D-printing strategies for skeletal tissue regeneration: From natural architectures to clinical applications.
    Sahar Jelodari, Payam Baei, Majid Halvaei, Niloofar Hosseinpour, Mohsen Sheykhhasan, Samaneh Hosseini.
      Skeletal tissues possess complicated structures and thereby their regeneration confronts considerable challenges. The final objective of skeletal tissue engineering is the development of efficient engineered substitutes in order to promote tissue regeneration. Numerous efforts have been made to develop functional biomimetic constructs with superior functions and characteristics to create advanced biomaterials for skeletal regeneration. One of the efficient approaches for designing bioinspired materials is mimicking the microstructure and architecture of natural living organisms and applying them in developing biomaterials with relevant functionality. Moreover, bioinspired complex structures which are developed by mimicking natural or synthetic architectures provide a crucial role in tissue engineering. Since the traditional approaches can not fulfill the demands to design intricate biomimetic materials, employing novel technologies may be satisfying. 3D bioprinting is a rapidly evolving technology which offers accurate multi-material and multi-scale manufacturing of biomimetic constructs for the patient-specific tissue regeneration. Numerous attempts such as mimicking the hierarchical structure and function of bone tissue, resembling the zonal architecture of cartilage tissue and imitating the microstructure and mechanical characteristics of natural osteochondral tissue, can suggest clinically desirable candidates for skeletal reconstruction. Here, 3D bioprinting technology for creating bioinspired constructs for use in skeletal tissue regeneration is discussed. We review various types of bioinspired constructs developed by mimicking the endogenous structure and function of skeletal tissues. Next, biomimetic constructs that are designed by imitating other natural and synthetic structures are discussed. Clinical trials utilizing 3D-printed constructs for skeletal tissue regeneration is discussed as the final part of the story. Different strategies such as mimicking strong adhesion to different surfaces, imitating the morphology of different architectures and resembling the hierarchical structure of natural and synthetic structures can expand the opportunity to develop realistic and effective constructs for clinical regeneration of skeletal tissue.
    Keywords:  3D bioprinting; bioinspired constructs; clinical application; hierarchical structures; skeletal tissues
    DOI:  https://doi.org/10.1177/08853282251382716
  25. bioRxiv. 2025 Sep 18. pii: 2025.09.18.677213. [Epub ahead of print]
    Sequence-Independent RNA Sensing in Living Mammalian Cells.
    Natalie S Kolber, K Eerik Kaseniit, Tobias V Lanz, William H Robinson, Xiaojing J Gao.
      Recently, several groups described sensors in living cells that take advantage of adenosine deaminases acting on RNA (ADARs) to link the presence of an RNA (a "target transcript") to the translation of a payload from a second, exogenously introduced mRNA. These sensors share the key mechanism of editing a stop codon opposite a specific sequence motif in the target transcript, where this motif requirement is dictated by ADAR's strong sequence preference. This constrains sensor design and precludes the sensing of short sequences that lack such motifs, often essential for key applications such as sensing viral RNAs and differentiating splice isoforms. Here we address this limitation with modular RNA sensors using adenosine deaminases acting on RNA ("modulADAR"). ModulADAR features two key elements that mirror the modularity of ADARs: regions that hybridize with the target transcript to recruit ADAR's dsRNA-binding domains, and a stem-loop for stop-codon editing by ADAR's catalytic domain. We optimize modulADAR and apply it to detect short subsequences that cannot be sensed by prior-generation sensors. We anticipate that modulADAR will empower broader basic science and therapeutic applications, especially those that will uniquely benefit from programmable RNA detection in living cells.
    DOI:  https://doi.org/10.1101/2025.09.18.677213
  26. Trends Biotechnol. 2025 Sep 23. pii: S0167-7799(25)00354-3. [Epub ahead of print]
    Virus-like particles as modular interfaces for biomaterial functionalization.
    Hasna Maayouf, Rayane Hedna, Alphonse Boché, Thomas Dos Santos, Kaspars Tārs, Isabelle Brigaud, Tatiana Petithory, Franck Carreiras, Carole Arnold, Ambroise Lambert, Laurent Pieuchot.
      Biomaterial surface biofunctionalization refers to the process of modifying a biomaterial's surface to improve its interaction with biological systems. Controlling cell-material interactions is crucial, but current methods using native extracellular matrix (ECM) proteins, typically derived from human or animal tissue, or synthetic peptides are hampered by limitations such as batch variability, high cost, poor surface adsorption, and limited control over peptide presentation. This study introduces a technology that uses virus-like particles (VLPs) displaying biomimetic ECM-derived peptides. We engineered VLPs to present the RGD motif (arginine-glycine-aspartic acid), a well-established sequence that promotes cell adhesion, using either direct genetic fusion or SpyTag/SpyCatcher ligation, with the latter providing a more versatile conjugation strategy. These VLPs effectively functionalized cell-repellent silicone surfaces, significantly enhancing cell adhesion, migration, proliferation, and differentiation, achieving performance comparable with or exceeding that of native ECM proteins or synthetic RGD peptides. Additionally, the VLP/SpyCatcher particle enabled the co-presentation of multiple bioactive peptides, opening avenues for complex tissue engineering strategies. This tunable system represents a powerful tool for directing cell behavior, with significant potential for advancing nanomedicine and biomaterials development.
    Keywords:  RGD peptide; cell-material interactions; extracellular matrix mimetics; surface functionalization; tissue engineering; virus-like particles (VLPs)
    DOI:  https://doi.org/10.1016/j.tibtech.2025.08.017
  27. bioRxiv. 2025 Sep 20. pii: 2025.09.17.676955. [Epub ahead of print]
    Principles of protein abundance regulation across single cells in a mammalian tissue.
    Andrew Leduc, Gergana Shipkovenska, Yanxin Xu, Alexander Franks, Nikolai Slavov.
      Protein synthesis and clearance are major regulatory steps of gene expression, but their in vivo regulatory roles across the cells comprising complex tissues remains unexplored. Here, we systematically quantify protein synthesis and clearance across over 4,200 cells from a primary tissue. Through integration with single-cell transcriptomics, we report the first quantitative analysis of how individual cell types regulate their proteomes across the continuum of gene expression. Our analysis quantifies the relative contributions of RNA abundance, translation, and protein clearance to the abundance variation of thousands of proteins. These results reveal an putative organizing principle: The contributions of both translation and protein clearance are linearly dependent on the cell growth rate. Further, we find that some proteins are primarily regulated by one mechanism (RNA abundance, translation, or clearance) across all cell types while the abundances of other proteins is dominated by different regulatory mechanisms across cell types. Our reliable multimodal measurements enabled quantifying and functionally interpreting molecular variation across single cells from the same cell type. The protein-protein correlations are substantially stronger than the mRNA-mRNA ones, which is mediated by protein clearance regulation. The protein-protein correlations are stronger not only for directly interacting proteins but also between functional sets of proteins. Further, these protein correlations allow identifying cell-type specific functional clusters. These clusters vary across cell types, revealing differences in metabolic processes coordination, partially mediated by protein clearance regulation. Our approach provides a scalable multiplexed framework for quantifying the regulatory processes shaping mammalian tissues and reveals organizing principles determining the relative contributions of translation and protein clearance to the proteomes of primary mammalian cells.
    DOI:  https://doi.org/10.1101/2025.09.17.676955
  28. Nature. 2025 Sep 24.
    Engineered enzymes can suppress genome-editing errors.
      
    Keywords:  Biological techniques; CRISPR-Cas9 genome editing; Genetics
    DOI:  https://doi.org/10.1038/d41586-025-03071-y
  29. Chin J Dent Res. 2025 Sep 26. 28(3): 163-172
    Biomimetic Mineralisation - Nature-inspired Strategy for Promising Hard Tissue Regenerative Materials Development.
    Lin Xue Zhang, Zuo Ying Yuan, Yu Ming Zhao, Yun Fan Zhang.
      Biomineralisation is a remarkable biological process in which living organisms exert precise control over the nucleation and growth of inorganic crystalline phases, resulting in the formation of hierarchically structured biocomposites that exhibit exceptional mechanical and functional properties. Since damage to bone and teeth directly affect everyday life, various biomimetic mineralised materials have been engineered for use in biomedical applications. While bioinspired materials typically demonstrate superior mechanical properties and biological functions, significant disparities remain between biomimetic constructs and their natural counterparts, especially concerning mechanical performance and multiscale structural organisation. This review initially describes the dynamic reciprocity between type I collagen fibrils, amorphous calcium phosphate phases and multifunctional non-collagenous protein within mineralisation microenvironments. Furthermore, it evaluates recent progress in advanced biomaterials based on biomimetic mineralisation strategies and seeks to spark innovative and promising solutions for investigators exploring biomineralisation principles in regenerative medicine and hard tissue reconstruction. Existing problems and future directions are discussed.
    Keywords:  biomineralisation; calcium; calcium phosphate; hard tissue regeneration; noncollagenous proteins
    DOI:  https://doi.org/10.3290/j.cjdr.b6553419
  30. Mol Ther Nucleic Acids. 2025 Sep 09. 36(3): 102585
    Manipulating the delivery and immunogenicity of DNA vaccines through the addition of CB[8] to cationic polymers.
    Hadijatou J Sallah, Benjamin T Cheesman, David J Peeler, Andrew M Howe, Robin J Shattock, Roger Coulston, John S Tregoning.
      Challenges with vaccine reactogenicity, stability, and access have highlighted the need to develop alternative strategies for formulation and delivery. We explored the incorporation of cucurbit[n]urils (CBs), as supramolecular "hosts," into nucleic acid-polymer polyplexes. CBs are small, non-toxic, barrel-shaped molecules that transiently crosslink polymers containing supramolecular "guests," thereby increasing molecular weight (MW) of the complex, a correlate of transfection efficiency. We tested whether the supramolecular interactions of CB[8] impact polyplex function. We generated a library of different CB[8] polyplexes using plasmid DNA (pDNA), varying N/P (the ratio of polymer to plasmid), the length, and guest (phenylalanine [Phe]) group frequency of the polyethylenimine (PEI) polymer backbone. We found that N/P 32 and the 20Phe1 (20kDa PEI with 1 mol% Phe) gave optimal gene expression and that incorporating CB[8] in polyplex formulations improved gene expression, both in vitro and in vivo. Despite increases in gene expression, inclusion of CB[8] in formulations with higher guest-binding capacity led to decreased immunogenicity, possibly as a result of dampened innate immune responses. Our data show that CB[8] polyplexes increase gene delivery and expression but alter inflammatory responses. These findings highlight that rational design of the CB[8] polymer system can enable nucleic acid delivery for both vaccine and therapeutic applications.
    Keywords:  DNA vaccine; MT: Delivery Strategies; cucurbituril; nucleic acid delivery; polymeric nanoparticles; polyplex
    DOI:  https://doi.org/10.1016/j.omtn.2025.102585
  31. Nat Commun. 2025 Sep 26. 16(1): 8446
    De novo design of hypercompact transcript degraders by engineering substrate-specific toxins and Cas6-CBS system.
    Pin-Ru Chen, Pei-Pei Qin, Ya-Nan Wang, Peng-Fu Liu, Xin-Yue Zhang, Tao Qian, Bang-Ce Ye, Bin-Cheng Yin.
      Artificial assembly of small functional proteins provides effective strategies for development of compact RNA degradation systems, which overcome the challenges associated with delivery. Here, we excavate and evolve three small toxin endoribonucleases with simple RNA cleavage motifs (barnase, MqsR, and MaZF), and integrate catalytically dead Cas6 (dCas6) along with its cognate stem-loop RNA (Cas6 binding site, termed CBS) from Escherichia coli (E. coli) to create hypercompact transcript degraders (317 ~ 430 amino acids), named STAR (small toxin- and dEcCas6-CBS-based RNA degraders). We experimentally find that CBS can be fine-tuned for EcCas6 processing but exhibits high conservatism in EcCas6 and dEcCas6 binding, laying a foundation for the design of CBS guides to effectively recruit dEcCas6-toxins. STAR exhibits high-efficiency knockdown of both cytoplasmic and nuclear transcripts in the tested mammalian cells, with significantly reduced off-target activities compared to established CRISPR and RNA interference (RNAi) technologies. Moreover, the small size of STAR enables delivery via a single adeno-associated virus (AAV) for ease of multiplex RNA knockdown, including effective silencing of the oncogenic RNA MYC in human cancer cells. Together, STAR unlocks new territory for employing toxin to design miniature, efficacious and safer RNA degraders.
    DOI:  https://doi.org/10.1038/s41467-025-63166-y
  32. ACS Synth Biol. 2025 Sep 22.
    Neural CRNs: A Natural Implementation of Learning in Chemical Reaction Networks.
    Rajiv Teja Nagipogu, John H Reif.
      Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have primarily relied on emulating discrete-layered neural architectures using steady-state computations of mass action kinetics. Here, we propose an alternative approach where the neural computations are modeled using the continuous-time evolution of molecular concentrations. The analog nature of our framework naturally aligns with chemical kinetics-based computation, resulting in practically viable circuits. We present the advantages of our framework through three key demonstrations: (1) we assemble an end-to-end supervised learning pipeline using only two sequential phases, the minimum required number for supervised learning; (2) we show (through appropriate simplifications) that both linear and nonlinear modeling circuits can be implemented solely using unimolecular and bimolecular reactions, avoiding the complexities of higher-order chemistries; and (3) we show how first-order gradient approximations can be natively incorporated into the framework, enabling nonlinear models to scale linearly rather than combinatorially with input dimensionality. All the circuit constructions are validated through training and inference simulations across various regression and classification tasks. Our work presents a viable pathway toward embedding learning behaviors in synthetic biochemical systems.
    Keywords:  DNA computing; biochemical learning; chemical neural networks; chemical reaction networks; molecular computing; neural CRNs
    DOI:  https://doi.org/10.1021/acssynbio.5c00099
  33. Lab Chip. 2025 Sep 24.
    A biocompatible surfactant film for stable microfluidic droplets.
    Brendan T Deveney, John A Heyman, Raoul G Rosenthal, David A Weitz, Jörg G Werner.
      Droplets serve as practical compartments for the analysis of individual biological species like nucleic acids and single cells due to the small size and ease of production of droplets. However, coalescence among droplets is a persistent challenge that often precludes the application of droplet-based techniques, particularly in cases when droplets are subject to harsh conditions or must remain stable for extended periods of time. Here, we introduce a versatile film-forming surfactant that forms robustly stable droplets. The film is formed at the droplet interface through covalent interactions between a custom polymer in a fluorinated phase and a diol-containing macromolecule in an aqueous phase. The film can stabilize droplets during polymerase chain reaction (PCR) and is biocompatible. The surfactant provides an archetype for new surfactant chemistries employing random copolymers and interfacial association.
    DOI:  https://doi.org/10.1039/d5lc00456j
  34. Cell Syst. 2025 Sep 23. pii: S2405-4712(25)00228-5. [Epub ahead of print] 101395
    Cell-free recombinase-integrated Boolean output system.
    Jingyao Chen, Aviva Borison, Douglas Densmore, Wilson W Wong.
      Cell-free gene expression systems are increasingly important in fundamental research and biomanufacturing, offering a versatile platform for studying gene circuits and biocomputation. We present the cell-free recombinase-integrated Boolean output system (CRIBOS), a site-specific recombinase-based multiplex genetic circuit platform designed for cell-free environments. With CRIBOS, we built over 20 multi-input-multi-output circuits, including 2-input-2-output genetic circuits and a 2-input-4-output decoder. Combined with allosteric transcription factor (aTF)-based sensors, the circuits demonstrate multiplex environmental sensing. Moreover, utilizing paper-based CRIBOS, which demonstrates remarkable portability and stability, we present a biological memory storage logic circuit device that can preserve DNA-based biological information for over 4 months with minimal resources, energy costs, and maintenance requirements. Implementing CRIBOS not only expands the application of multiplex Boolean logic gates from cellular systems to the cell-free environment but also augments their overall versatility, opening new avenues for designing and applying sophisticated genetic circuits. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  Boolean; allosteric transcription factor; biocomputation; cell-free; environmental sensing; genetic circuit; synthetic biology
    DOI:  https://doi.org/10.1016/j.cels.2025.101395
  35. Mater Horiz. 2025 Sep 24.
    Programmable motion of an enzyme-powered macroscale gel boat: a functional sensing platform.
    Vinay Ambekar Ranganath, Indrajit Maity.
      An augmented strategy for constructing intelligent soft robots includes the transfer of biogenic features from nature to man-made artificial systems serving a range of life-like functions. Inspired by living technology, we have customized macroscale hydrogel boats by encoding them with an enzyme-powered engine that can convert chemical information into a mechanical response to create motion at the air-water interface. The engine's non-homogeneous enzyme distribution causes erratic motion along straight lines, random turns, and turns with high or low curvature-like trajectories. Nevertheless, the structural remodeling of the boat as well as the working system's configuration can permit directed, controlled, turning, bi-directional, rotation and run-and-tumble-like motion. Intriguingly, this boat is capable of sensing the precise chirality of amino acids (D-amino acid vs.L-amino acid) from individual isomer samples by translating the chiral information into variations in the boat's speed. Therefore, such miniaturized enzyme-powered boats are anticipated to be an advantage for the upcoming next-generation materials with a broader spectrum of functionalities.
    DOI:  https://doi.org/10.1039/d5mh00898k
  36. Adv Mater. 2025 Sep 26. e12659
    Versatile Room-Temperature Phosphorescence Silk Fibroin Platforms for Sustainable and Biocompatible Multifunctional Interfaces.
    Tao Wang, Ying-Hao Fu, Jing Wang, Gang Li, Jing Sun, Qi Liu, Yan-Tong Zhao, Zi-Chen Zhang, Zi-Ting Wang, Shu-Jie Wang, Zhao-Zhu Zheng, Yu Wang, Yan-Qing Lu.
      The development of sustainably sourced, biocompatible room-temperature phosphorescence (RTP) materials with rich formats, multimodal tunability, and multifunctional capabilities presents a transformative opportunity for sustainable technologies and biomedical interfaces, yet it remains a significant challenge. Here, RTP silk fibroin systems that feature improved processability, responsiveness, and functionality by multivalently anchoring phosphors to a versatile protein matrix are reported. The RTP silk fibroin can be processed into various fully biodegradable platforms, exhibiting strong RTP emission with a lifetime of up to 233 ms driven by multiple robust phosphor-fibroin interactions. The resulting platforms exhibit multi-responsiveness to UV light, vapor, and temperature, along with diversified functionalities that include recyclability, weldability, morphability, and adhesion. Moreover, their adaptability with diverse micro/nano-processing techniques enables complex RTP patterning and multidimensional information integration. Finally, it is demonstrated that these convergent advantages endow the platforms with multifunctionality and multi-interface compatibility, enabling applications such as smart labels for electronic devices, conformal networks for pharmaceuticals, and scalable textiles for face masks.
    Keywords:  biomedical interface; multifunctionality; phosphorescence; silk fibroin; sustainability
    DOI:  https://doi.org/10.1002/adma.202512659
  37. Science. 2025 Sep 25. 389(6767): 1301
    Op-eds connect scientists and communities.
    Miles J Arnett.
      
    DOI:  https://doi.org/10.1126/science.aea8713
  38. Nature. 2025 Sep;645(8082): 906-914
    Electrostatic-repulsion-based transfer of van der Waals materials.
    Xudong Zheng, Jiangtao Wang, Jianfeng Jiang, Tianyi Zhang, Jiadi Zhu, Tong Dang, Peng Wu, Ang-Yu Lu, Ding-Rui Chen, Tilo H Yang, Xinyuan Zhang, Kenan Zhang, Kyung Yeol Ma, Zhien Wang, Aijia Yao, Haomin Liu, Yi Wan, Ya-Ping Hsieh, Vladimir Bulović, Tomás Palacios, Jing Kong.
      Van der Waals (vdW) materials offer unique opportunities for 3D integration1,2 of planar circuits towards higher-density transistors and energy-efficient computation3-7. Owing to the high thermal budget and special substrate requirement for the synthesis of high-quality vdW materials8-10, an advanced transfer technique is required that can simultaneously meet a broad range of industrial requirements, including high intactness, cleanliness and speed, large scale, low cost and versatility. However, previous efforts based on either etching or etching-free mechanisms typically only improve one or two of the aforementioned aspects11-13 and a comprehensive and systematic solution remains lacking. Here we demonstrate an electrostatic-repulsion-enabled advanced transfer technique that is etching free, high yield, fast, wafer scale, low cost and widely applicable, using ammonia solution compatible with the complementary metal-oxide-semiconductor (CMOS) industry. The high material intactness and interface cleanliness enable superior device performances in 2D field-effect transistors with 100% yield, near-zero hysteresis (7 mV) and near-ideal subthreshold swing (65.9 mV dec-1). The combination with bismuth contact further enables an ultrahigh on-current of 1.3 mA μm-1 under 1 V bias. This advanced transfer approach offers a facile and manufacturing-viable solution for vdW-materials-based electronics, paving the way for advanced 3D integration in the future.
    DOI:  https://doi.org/10.1038/s41586-025-09510-0
  39. Chem Rev. 2025 Sep 23.
    From β-Dicarbonyl Chemistry to Dynamic Polymers.
    Youwei Ma, Christoph Weder, Filip E Du Prez, José Augusto Berrocal.
      The past two decades have witnessed an explosion of the use of dynamic bonds in polymer science. The β-dicarbonyl skeleton has emerged as a most versatile platform motif that has been utilized to synthesize a plethora of dynamic polymers that leverage either reversible metal-ligand coordination or exchangeable dynamic covalent bonds. The high modularity and intrinsic dynamic nature of the structures based on the β-dicarbonyl motif have received considerable interest across diverse fields, in applications that include drug delivery, the development of sustainable polymers, 3D printing, actuators, and many others. This review summarizes the progress on dynamic polymers derived from β-dicarbonyl synthons and focuses on three main topics. The first section provides a comprehensive overview of the prevalent methodologies employed for the preparation of polymers containing β-dicarbonyl moieties. The second part highlights the key features, development, and applications of dynamic polymers based on the β-dicarbonyl chemistry, including metallo-supramolecular polymers and dynamic covalent polymer networks. In the concluding section, we offer our views on the future challenges and prospects pertaining to this class of dynamic polymer systems.
    DOI:  https://doi.org/10.1021/acs.chemrev.5c00307
  40. bioRxiv. 2025 Sep 18. pii: 2025.09.16.676640. [Epub ahead of print]
    High-resolution, genotype-free mapping of genetic variation with CRI-SPA-Map.
    Sheila Lutz, Megan Lawler, Samuel Amidon, Frank W Albert.
      Genetic variation within species shapes phenotypes, but identifying the specific genes and variants that cause phenotypic differences is costly and challenging. Here, we introduce CRI-SPA-Map, a genetic mapping strategy combining CRISPR-Cas9 genome engineering, selective ploidy ablation (SPA), and high-throughput phenotyping for precise genetic mapping with or without genotyping in the yeast Saccharomyces cerevisiae . In CRI-SPA-Map, a donor strain carrying SPA machinery is mated to a genetically different recipient strain harboring a genome-integrated selectable cassette. In the resulting diploid, CRISPR-Cas9 cuts the cassette for replacement with DNA from the homologous donor chromosome. Donor chromosomes are then removed using SPA to yield haploid recombinant strains. To establish CRI-SPA-Map, we mated a W303 SPA strain to 92 strains from the BY4742 yeast knockout collection that carry gene deletion cassettes on the left arm of chromosome XIV and created 1,451 recombinant isolates. Whole-genome sequencing verified that deletion cassette replacement introduced short donor DNA tracts of variable length, resulting in a finely recombined mapping population. Using only the known location of the gene deletions, which marks where donor DNA is introduced, we identified a 6.5 kb-region shaping yeast growth. Further dissection of this region pinpointed two causal variants in two genes, MKT1 and SAL1 . Engineering these variants alone and in combination revealed gene-by-environment interactions at both genes, as well as epistatic interactions between them that were in turn dependent on the environment. CRI-SPA-Map is a cost-effective strategy for creating high-resolution recombinant panels of yeast strains for identifying the genetic basis of phenotypic variation.
    DOI:  https://doi.org/10.1101/2025.09.16.676640
  41. Adv Mater. 2025 Sep 25. e08500
    Probiotic-Based Materials as Living Therapeutics.
    Laura Sabio, Graham J Day, Manuel Salmeron-Sanchez.
      The growing demand for safer, more targeted therapeutics requires the development of advanced biomaterials. Among these, Engineered Living Materials (ELMs)-which integrate synthetic biology with material science-are emerging as promising platforms for biomedical applications. This review focuses on a subclass of ELMs based on genetically engineered probiotics combined with matrices, that are termed Probiotic Living Materials (PLMs) to differentiate them from Living Biotherapeutic Products (LBPs). Recent studies highlight PLM's potential in addressing different health conditions, offering targeted and dynamic therapies. However, PLMs face multiple challenges to be implemented in clinics, including a lack of robust genetic toolkits for probiotic engineering, concerns about biosafety (e.g., horizontal gene transfer or non-desirable biological activity), difficulties in translating preclinical results to humans, and the absence of clear regulatory guidance for clinical use. This review first explores the fundamental features of ELMs, then provides an overview of probiotics, followed by recent advances in the design of engineered PLMs for biomedical applications, particularly in biosensing development, infection treatment, bone repair, wound healing, vaginal imbalances, gut-related conditions, and cancer therapy. Finally, biosafety issues and current gaps in regulatory frameworks to ensure safe and effective use of PLMs, with a particular focus on vulnerable populations, are discussed.
    Keywords:  engineered living materials; probiotics; therapeutics
    DOI:  https://doi.org/10.1002/adma.202508500
  42. Appl Environ Microbiol. 2025 Sep 22. e0092425
    RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.
    Allison N Pearson, Julie M Lynch, Cindy N Ho, Graham A Hudson, Jacob B Roberts, Javier Menasalvas, Aaron A Vilchez, Matthew R Incha, Matthias Schmidt, Aindrila Mukhopadhyay, Adam M Deutschbauer, Mitchell G Thompson, Patrick M Shih, Jay D Keasling.
      Dicarboxylic acids are key components of many polymers and plastics, making them a target for both engineered microbial degradation and sustainable bioproduction. In this study, we generated a comprehensive data set of functional evidence for the genetic basis of dicarboxylic and fatty acid metabolism using randomly barcoded transposon sequencing (RB-TnSeq). We identified four β-proteobacteria that displayed robust growth with dicarboxylic acid sole carbon source and cultured their mutant libraries with dicarboxylic and fatty acids with carbon chain lengths from C3 to C12. The resulting fitness data suggested that dicarboxylic and fatty acid metabolisms are largely distinct, and different sets of β-oxidation genes are required for catabolizing dicarboxylic versus fatty acids of the same carbon chain lengths. In addition, we identified transcriptional regulators and transporters with strong fitness phenotypes related to dicarboxylic acid utilization. In Ralstonia sp. UNC404CL21Col (R. CL21), we deleted two transcriptional repressors to improve its utilization of short-chain dicarboxylic acids. We exploited the diacid-utilizing catabolism of R. CL21 to upcycle a mock mixture of the dicarboxylic acids produced when polyethylene is oxidized. After introducing a heterologous indigoidine production pathway, this engineered Ralstonia produced 0.56 ± 0.02 g/L indigoidine from a mixture of dicarboxylic acids as a carbon source, demonstrating the potential of R. CL21 to upcycle plastic wastes to products derived from tricarboxylic acid (TCA) cycle intermediates.
    IMPORTANCE: Upcycling the carbon in plastic wastes to value-added products is a promising approach to address the plastic waste and climate crises, and dicarboxylic acid metabolism is an important facet of several approaches. Improving our understanding of the genetic basis of this metabolism has the potential to uncover new enzymes and genetic parts for engineered pathways involving dicarboxylic acids. Our data set is the most comprehensive interrogation of dicarboxylic acid catabolism to date, and this work will be of utility to researchers interested in both plastics bioproduction and upcycling applications.
    Keywords:  dicarboxylic acids; functional genomics; plastics upcyling
    DOI:  https://doi.org/10.1128/aem.00924-25
  43. Nature. 2025 Sep 23.
    A multimodal robotic platform for multi-element electrocatalyst discovery.
    Zhen Zhang, Zhichu Ren, Chia-Wei Hsu, Weibin Chen, Zhang-Wei Hong, Chi-Feng Lee, Aubrey Penn, Hongbin Xu, Daniel J Zheng, Shuhan Miao, Yimeng Huang, Yifan Gao, Weiyin Chen, Hugh Smith, Yaoshen Niu, Yunsheng Tian, Ying-Rui Lu, Yu-Cheng Shao, Sipei Li, Hsiao-Tsu Wang, Iwnetim I Abate, Pulkit Agrawal, Yang Shao-Horn, Ju Li.
      One of the goals of 'AI for Science' is to discover customized materials through real-world experiments. Pioneering advances have been achieved in computational predictions and the automation of materials synthesis1-7. Yet, most materials experimentation remains constrained to using unimodal active learning (AL) approaches, relying on a single data stream. The potential of AI to interpret experimental complexity remains largely untapped8,9. Here we present Copilot for Real-world Experimental Scientists (CRESt), a platform that integrates large multimodal models (LMMs, incorporating chemical compositions, text embeddings, and microstructural images) with Knowledge-Assisted Bayesian Optimization (KABO) and robotic automation. CRESt employs knowledge-embedding-based search space reduction and adaptive exploration-exploitation strategy to accelerate materials design, high-throughput synthesis and characterization, and electrochemical performance optimization. CRESt allows monitoring with cameras and vision-language-model-driven hypothesis generation to diagnose and correct experimental anomalies. Applied to electrochemical formate oxidation, CRESt explored over 900 catalyst chemistries and 3500 electrochemical tests within 3 months, identifying a state-of-the-art catalyst in the octonary chemical space (Pd-Pt-Cu-Au-Ir-Ce-Nb-Cr) which exhibits a 9.3-fold improvement in cost-specific performance.
    DOI:  https://doi.org/10.1038/s41586-025-09640-5
  44. Proc Natl Acad Sci U S A. 2025 Sep 30. 122(39): e2509329122
    De novo design of potent inhibitors of clostridial family toxins.
    Robert J Ragotte, Huazhu Liang, John Tam, Sean Miletic, Jacob M Berman, Roger Palou, Connor Weidle, Zhijie Li, Matthias Glögl, Greg L Beilhartz, Kenneth D Carr, Andrew J Borst, Brian Coventry, Xinru Wang, John L Rubinstein, Mike Tyers, Daniel Schramek, Roman A Melnyk, David Baker.
      Clostridioides difficile remains a leading cause of hospital-acquired infections, with its primary virulence factor, toxin B (TcdB), responsible for severe colitis and recurrent disease. The closely related toxin, TcsL, from Paeniclostridium sordellii, causes a rarer but often fatal toxic shock syndrome, particularly in gynecological and obstetric contexts. We report the de novo design of small protein minibinders that directly neutralize TcdB and TcsL by preventing their entry into host cells. Using deep learning and Rosetta-based approaches, we generated high-affinity minibinders that protect cells from intoxication with picomolar potency and, in the case of TcsL, prolonged survival following lethal toxin challenge in mice. The designed proteins against TcdB demonstrate exceptional stability in proteolytic and acidic environments, making them well-suited for oral delivery-a valuable feature for treating C. difficile infections localized to the gastrointestinal tract. For TcsL, potent inhibitors were identified from 48 initial designs and 48 optimized designs, highlighting the potential of computational design for rapidly developing countermeasures against life-threatening bacterial toxins.
    Keywords:  C. difficile; cryo-EM; protein design; tcdb; tcsl
    DOI:  https://doi.org/10.1073/pnas.2509329122
  45. ACS Synth Biol. 2025 Sep 25.
    Programmable Biointerfaces and Adaptive Functionality in Next-Generation Green Nanomaterials.
    Navid Rabiee.
      Recent advances in green nanomaterials have primarily focused on mitigating toxicity through passive approaches, yet emerging technologies suggest a transformative paradigm shift toward programmable nanomaterials with dynamic biointerfaces. This Review explores how convergent innovations in synthetic biology, DNA nanotechnology, artificial intelligence, and advanced manufacturing are creating unprecedented opportunities for developing nanomaterials with context-responsive functionality. Integration of cell-free synthetic biology enables nanomaterials with genetic-circuit-driven responses to biological cues, allowing expression of bioactive compounds precisely when and where needed. DNA nanotechnology provides molecular-level programmability through stimuli-responsive structures that can perform logical operations based on complex biological inputs. Advanced machine learning approaches are revolutionizing predictive design by identifying nonintuitive correlations between green synthesis parameters and programmable functionalities. Metabolic engineering approaches utilizing engineered microbial systems offer unprecedented control over nanomaterial synthesis with reduced batch-to-batch variability, while 4D bioprinting enables macroscale assemblies with nanoscale programmable elements distributed in precise spatiotemporal arrangements. These converging technologies are enabling the development of autonomous theranostic systems with closed-loop functionality, capable of sensing biological parameters, processing this information through molecular computing, and adjusting therapeutic activity accordingly. This evolution represents a fundamental reconceptualization of biocompatibility from a static property to a dynamic, programmable characteristic, potentially yielding nanomaterials that behave more like sophisticated biological entities than traditional therapeutic agents. While significant challenges remain in stability, sensitivity, and manufacturing scalability, this emerging paradigm promises transformative advances in precision nanomedicine through self-regulating, patient-responsive therapeutic systems.
    Keywords:  Adaptive Functionality; Autonomous Theranostic Systems; Green Nanomaterials; Programmable Biointerfaces
    DOI:  https://doi.org/10.1021/acssynbio.5c00620
  46. Nat Commun. 2025 Sep 26. 16(1): 8492
    Accurate prediction of gene deletion phenotypes with Flux Cone Learning.
    Charlotte Merzbacher, Oisin Mac Aodha, Diego A Oyarzún.
      Understanding the impact of gene deletions is crucial for biological discovery, biomedicine, and biotechnology. Due to the complexity of genome-wide deletion screens, there is growing interest in computational methods that leverage existing screening data for predictive modeling. Here, we present Flux Cone Learning, a general framework designed to predict the effects of metabolic gene deletions on cellular phenotypes. Using Monte Carlo sampling and supervised learning, our approach identifies correlations between the geometry of the metabolic space and experimental fitness scores from deletion screens. Flux Cone Learning delivers best-in-class accuracy for prediction of metabolic gene essentiality in organisms of varied complexity (Escherichia coli, Saccharomyces cerevisiae, Chinese Hamster Ovary cells), outperforming the gold standard predictions of Flux Balance Analysis. We demonstrate the versatility of our approach by training a predictor of small molecule production using data from a large deletion screen. Flux Cone Learning can be applied to many organisms and phenotypes, without the need to encode cellular objectives as an optimization task. Our work offers a broadly applicable tool for phenotypic prediction and lays the groundwork for building metabolic foundation models across the kingdom of life.
    DOI:  https://doi.org/10.1038/s41467-025-63436-9
  47. Genome Biol. 2025 Sep 22. 26(1): 292
    microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.
    Haris Zafeiropoulos, Ermis Ioannis Michail Delopoulos, Andi Erega, Aline Schneider, Annelies Geirnaert, John Morris, Karoline Faust.
      Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 annotated representative genomes. microbetag can be applied to custom (metagenome-assembled) genomes via its stand-alone version. MGG, a Cytoscape app designed to support microbetag, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.
    Keywords:  Data integration; Enrichment analysis; Microbial associations; Pathway complementarity; Phenotypic traits; Seed set
    DOI:  https://doi.org/10.1186/s13059-025-03769-2
  48. bioRxiv. 2025 Sep 17. pii: 2025.09.11.675686. [Epub ahead of print]
    BayesCNet: Bayesian inference for cell type-specific regulatory networks leveraging cell type hierarchy in single-cell data.
    Fengdi Zhao, Arkaprava Roy, Weijia Jin, Leeana Peters, Todd Brusko, Qing Lu, Karyn Esser, Ramon Sun, Li Chen.
      Understanding gene regulatory networks (GRNs) is essential for deciphering biological processes and disease mechanisms. Single-cell multiome technologies now enable joint profiling of chromatin accessibility and gene expression, offering an powerful means to infer cell type-specific GRNs. However, existing methods analyze each cell type independently or aggregate data into pseudo-bulk profiles, limiting their ability to resolve rare populations and capture cellular heterogeneity. We introduce BayesCNet, a Bayesian hierarchical model that jointly infers enhancer-gene linkages across all cell types while leveraging their hierarchical relationships for information sharing. Through extensive simulations, BayesCNet consistently outperforms state-of-the-art methods, with the largest improvements in rare cell types. When applied to real datasets, BayesCNet identifies enhancer-gene linkages with higher accuracy validated by promoter-capture Hi-C data, and reconstructs cell type-specific GRNs that highlight key regulators, demonstrating its power to resolve gene regulatory programs across diverse cell types.
    DOI:  https://doi.org/10.1101/2025.09.11.675686
  49. bioRxiv. 2025 Sep 16. pii: 2025.09.16.674226. [Epub ahead of print]
    SCHEPHERD: A universal platform for high-throughput, high-resolution, and programmable control of cell behavior through bioelectric stimulation.
    Yubin Lin, Jeremy S Yodh, Celeste Rodriguez, Paul Kreymborg, Daniel J Cohen.
      Spanning frogs, fish, and humans, direct-current (DC) bioelectric cues play critical roles beyond neuro-muscular function, such as modulating morphogenesis, immune response, and healing through electrotaxis-electrically directed cell migration. Harnessing this potential requires new tools. However, standardized, accessible, and reproducible infrastructure capable of DC stimulation remains a challenge. We present SCHEPHERD: a universal, electrobioreactor integrating 8 stimulation channels and modular inserts to enable most electrotaxis assays in one device (cells, monolayers, and 3D spheroids), while enabling powerful, new capabilities. SCHEPHERD revealed through parameter sweeps that DC fields act like a 'steering wheel and gas pedal' for cell migration. We then used live confocal imaging to observe electrically reprogrammed F-actin dynamics. Finally, our multi-polar inserts generated complex spatial electrical patterns that reorganize engineered tissue dynamics. By significantly improving accessibility through modularity and an open-source, graphically programmed stimulator, we hope SCHEPHERD can help broaden the community studying these important DC bioelectric phenomena.
    DOI:  https://doi.org/10.1101/2025.09.16.674226
  50. Adv Mater. 2025 Sep 24. e06769
    Photothermally Powered 3D Microgels Mechanically Regulate Mesenchymal Stem Cells Under Anisotropic Force.
    Chen Wang, Nergishan İyisan, Philipp Harder, Valentin H K Fell, Viktorija Kozina, Hendrik Dietz, Olivia M Merkel, Berna Özkale.
      Exogenous forces significantly influence mammalian cell behavior, yet current strategies fail to resolve signaling processes between individual cells under conditions that accurately mimic the native microenvironment. This work presents a new cell culture technology capable of applying spatially patterned exogenous forces on individual cells within multicellular clusters encased in three-dimensional (3D) hydrogel matrices. Photothermally powered 3D microgels containing stem cells and integrated force generators are engineered to investigate intercellular communication under anisotropic forces with excellent spatial resolution (≈1 µm). Varying force patterns, such as uniform compression versus spatially heterogeneous tension, are achieved in 3D by relying on the synergistic effect of plasmonic gold nanorods and thermally responsive co-polymers under light actuation. The microgels generate 17-34 nN force locally, which activates mechanically sensitive ion channels in encapsulated cells stimulated with isotropically applied compression and spatially heterogeneous tension in 3D in a selective manner. Spatially patterned exogenous forces trigger F-actin remodeling, nuclear translocation of Yes-associated protein (YAP) and Runt-related transcription factor 2 (RUNX2) in encapsulated cells following cyclic stimulation. Sustained application of exogenous forces over three days is sufficient to regulate stem cell fate toward osteogenesis. This technology allows combinatorial studies of biomolecular and biophysical cues in 3D, making it suitable for applications in mechanobiology and bioengineering.
    Keywords:  differentiation; mechanical stimulation; mechanotransduction; nanorobotic microgels; photothermal actuation; spatially patterned forces; stem cells
    DOI:  https://doi.org/10.1002/adma.202506769
  51. Science. 2025 Sep 25. eadz0276
    Megabase-scale human genome rearrangement with programmable bridge recombinases.
    Nicholas T Perry, Liam J Bartie, Dhruva Katrekar, Gabriel A Gonzalez, Matthew G Durrant, James J Pai, Alison Fanton, Juliana Q Martins, Masahiro Hiraizumi, Chiara Ricci-Tam, Hiroshi Nishimasu, Silvana Konermann, Patrick D Hsu.
      Bridge recombinases are naturally occurring RNA-guided DNA recombinases that we previously demonstrated can programmably insert, excise, and invert DNA in vitro and in Escherichia coli. In this study, we report the discovery and engineering of the bridge recombinase ortholog ISCro4 for universal rearrangements of the human genome. We defined strategies for the optimal application of bridge systems, leveraging mechanistic insights to improve their targeting specificity. Through rational engineering of the ISCro4 bridge RNA and deep mutational scanning of its recombinase, we achieved up to 20% insertion efficiency into the human genome and genome-wide specificity as high as 82%. We further demonstrated intrachromosomal inversion and excision, mobilizing up to 0.93 megabases of DNA. Lastly, we provided proof-of-concept for plasmid-based excision of disease-relevant gene regulatory regions or repeat expansions.
    DOI:  https://doi.org/10.1126/science.adz0276
  52. J Control Release. 2025 Sep 23. pii: S0168-3659(25)00870-3. [Epub ahead of print] 114258
    mRNA-LNP hydrogels promote skeletal muscle regeneration in situ.
    Zhenghua Li, Jiacai Wu, Zhen Liu, Yixuan Huang, Yongqi Lin, Boping Zhou, Bin Li.
      Skeletal muscle has an innate capacity for self-regeneration, but may permanently lose its structure and function following extensive injury. Herein, we develop injectable biocomposite hydrogels embedded with mRNA-loaded lipid nanoparticles for skeletal muscle regeneration. Through construction and screening of a combinatorial library of aromatic ring-based ionizable lipids with varying aliphatic chain lengths and substitution patterns, we identify a lead lipid featuring two n-dodecane chains tethered to the meta position of benzenedimethanamine for efficient mRNA delivery. Embedding the top-performing mRNA nanoformulations in thermosensitive polyethylene-polypropylene glycol hydrogel scaffolds allows mRNA release and subsequent mRNA translation in situ. The implantation of hydrogel networks carrying lipid nanoparticles-encapsulated therapeutic mRNA encoding human nicotinamide phosphoribosyltransferase NAMPT into injury sites promotes substantial vascularized and innervated muscle formation, accompanied by reduced fibrosis in a rat model of volumetric muscle loss, which provides a potential therapeutic option for muscle regeneration.
    Keywords:  Injectable thermosensitive hydrogel; Lipid nanoparticle; Muscle regeneration; Nicotinamide phosphoribosyltransferase; mRNA delivery
    DOI:  https://doi.org/10.1016/j.jconrel.2025.114258
  53. Nat Commun. 2025 Sep 26. 16(1): 8440
    Mechanical control of cell fate decisions in the skin epidermis.
    Preeti Sahu, Sara Monteiro-Ferreira, Sara Canato, Raquel Maia Soares, Adriana Sánchez-Danés, Edouard Hannezo.
      Homeostasis relies on a precise balance of fate choices between renewal and differentiation. Although progress has been done to characterize the dynamics of single-cell fate choices, their underlying mechanistic basis often remains unclear. Concentrating on skin epidermis as a paradigm for multilayered tissues with complex fate choices, we develop a 3D vertex-based model with proliferation in the basal layer, showing that mechanical competition for space naturally gives rise to homeostasis and neutral drift dynamics that are seen experimentally. We then explore the effect of introducing mechanical heterogeneities between cellular subpopulations. We uncover that relatively small tension heterogeneities, reflected by distinct morphological changes in single-cell shapes, can be sufficient to heavily tilt cellular dynamics towards exponential growth. We thus derive a master relationship between cell shape and long-term clonal dynamics, which we validated during basal cell carcinoma initiation in mouse epidermis. Altogether, we propose a theoretical framework to link mechanical forces, quantitative cellular morphologies and cellular fate outcomes in complex tissues.
    DOI:  https://doi.org/10.1038/s41467-025-62882-9
  54. bioRxiv. 2025 Sep 20. pii: 2025.09.19.676866. [Epub ahead of print]
    Mapping transcriptional responses to cellular perturbation dictionaries with RNA fingerprinting.
    Isabella N Grabski, Junsuk Lee, John Blair, Carol Dalgarno, Isabella Mascio, Alexandra Bradu, David A Knowles, Rahul Satija.
      Single-cell perturbation dictionaries provide systematic measurements of how cells respond to genetic and chemical perturbations, and create the opportunity to assign causal interpretations to observational data. Here, we introduce RNA fingerprinting, a statistical framework that maps transcriptional responses from new experiments onto reference perturbation dictionaries. RNA fingerprinting learns denoised perturbation "fingerprints" from single-cell data, then probabilistically assigns query cells to one or more candidate perturbations while accounting for uncertainty. We benchmark our method across ground-truth datasets, demonstrating accurate assignments at single-cell resolution, scalability to genome-wide screens, and the ability to resolve combinatorial perturbations. We demonstrate its broad utility across diverse biological settings: identifying context-specific regulators of p53 under ribosomal stress, characterizing drug mechanisms of action and dose-dependent off-target effects, and uncovering cytokine-driven B cell heterogeneity during secondary influenza infection in vivo. Together, these results establish RNA fingerprinting as a versatile framework for interpreting single-cell datasets by linking cellular states to the underlying perturbations which generated them.
    DOI:  https://doi.org/10.1101/2025.09.19.676866
  55. Sci Rep. 2025 Sep 26. 15(1): 33077
    An open source platform to automate the design, verification, and manufacture of 3D printed microfluidic devices.
    Brady Goenner, Scott Temple, Sebastian Zapata, Daniel Wakeham, Ashton Snelgrove, Pierre-Emmanuel Gaillardon, Gregory P Nordin, Bruce K Gale.
      Microfluidic devices, including lab-on-a-chip devices, have many advantages over conventional laboratory techniques. Although common in some applications, there are several barriers to wider adoption, including the high initial cost to fabricate a design and the labor-intensive process of development. This work seeks to address those barriers by combining 3D printing and computer aided design tools. Building on existing open-source software from electronic design automation (EDA), we present a design, verification, and manufacturing toolchain for 3D design for microfluidic devices. The process starts with a list of components and connections then, automatically lays out a microfluidic device using a library of components, simulates the device, and produces a 3D CAD file that is used for DLP 3D printing process. The automated design and fabrication process was demonstrated by automatically designing and fabricating a calcium quantification assay. This toolchain automatically generated a microfluidic chip that meters each reagent with an error of less than 2.24% as verified by Xyce simulation of the chip. Physical chips were printed and found to perform with errors less than 9.2% on average compared to the assay performed by hand. The demonstration showed the ability of the toolchain to automatically generate a functional microfluidic chip for use with real assays using previously developed EDA tools.
    DOI:  https://doi.org/10.1038/s41598-025-15976-9
  56. Cell Syst. 2025 Sep 24. pii: S2405-4712(25)00225-X. [Epub ahead of print] 101392
    Accelerated design of Escherichia coli reduced genomes using a whole-cell model and machine learning.
    Ioana M Gherman, Kieren Sharma, Joshua Rees-Garbutt, Wei Pang, Zahraa S Abdallah, Thomas E Gorochowski, Claire S Grierson, Lucia Marucci.
      Whole-cell models (WCMs) are multi-scale computational models that aim to simulate the function of all genes and processes within a cell. This approach is promising for designing genomes tailored for specific tasks. However, a limitation of WCMs is their long runtime. Here, we show how machine learning (ML) surrogates can be used to address this limitation by training them on WCM data to accurately predict cell division. Our ML surrogate achieves a 95% reduction in computational time compared with the original WCM. We then show that the surrogate and a genome-design algorithm can generate an in silico-reduced E. coli cell, where 40% of the genes included in the WCM were removed. The reduced genome is validated using the WCM and interpreted biologically using Gene Ontology analysis. This approach illustrates how the holistic understanding gained from a WCM can be leveraged for synthetic biology tasks while reducing runtime. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  gene essentiality; genome design; genome reduction; machine learning surrogate; synthetic biology; whole-cell modeling
    DOI:  https://doi.org/10.1016/j.cels.2025.101392
  57. Sci Adv. 2025 Sep 26. 11(39): eadx2110
    Engineered basement membrane mimetic hydrogels to study mammary epithelial morphogenesis and invasion.
    Jane A Baude, Megan D Li, Sabrina M Jackson, Abhishek Sharma, Daniella I Walter, Ryan S Stowers.
      Reconstituted basement membrane products, like Matrigel, suffer from variability and xenogenic contaminants, hindering three-dimensional cell culture models. To overcome these challenges, we developed engineered basement membranes (eBMs) using peptide-conjugated alginate hydrogels with independently tunable mechanics. Ile-Lys-Val-Ala-Val (IKVAV)-modified eBMs, with fast stress relaxation and low stiffness, supported normal mammary acinus formation. Both increased stiffness and slow relaxation were required to induce invasion in IKVAV-modified eBMs, differing from the invasive phenotype observed in Arg-Gly-Asp (RGD)-modified eBMs regardless of the mechanical properties. Mechanistic studies revealed the balance of β1 and β4 integrin signaling, hemidesmosome formation, and laminin production were influenced by eBM properties. Inhibiting focal adhesion kinase or hemidesmosome signaling disrupted acinus formation in IKVAV-modified eBMs. This defined, xenogenic-free eBM system offers a modular platform for tissue engineering and disease modeling.
    DOI:  https://doi.org/10.1126/sciadv.adx2110
  58. Nat Commun. 2025 Sep 25. 16(1): 8411
    Uncovering the prevalence, key biogenesis enzymes, and biological significance of archaeal lipoproteins.
    Yirui Hong, Kira S Makarova, Andy A Garcia, Rachel Xu, Friedhelm Pfeiffer, Paula V Welander, Mechthild Pohlschroder.
      Lipid-anchored proteins are integral components of cell surfaces. In bacteria, lipidation of proteins with a conserved lipobox motif ([L/V/I]-3 [A/S/T/V/I]-2 [G/A/S]-1 [C]+1) is catalyzed by prolipoprotein diacylglyceryl transferase (Lgt). Although lipobox-containing proteins, or lipoproteins, are predicted to be abundant in several archaeal species, no archaeal homologs of Lgt have been identified, suggesting distinct lipidation enzymes evolved in archaea to accommodate their unique membrane lipids. Here, we predicted lipoprotein presence for all major archaeal lineages and revealed a high prevalence of lipoproteins across the domain Archaea. Using comparative genomics, we identified a comprehensive set of candidates for archaeal lipoprotein biogenesis components (Ali). Genetic and biochemical characterization in the archaeon Haloferax volcanii confirmed that two paralogous genes, aliA and aliB, are important for lipoprotein lipidation. Moreover, deletion of both genes led to a complete absence of diphytanylglyceryl thioether from lipoprotein extracts, revealing the chemical nature of lipid anchors in Hfx. volcanii lipoproteins. Disruption of AliA- and AliB-mediated lipoprotein lipidation caused severe growth defects, decreased motility, and cell-shape alterations, underscoring the importance of lipoproteins in archaeal cell physiology. Notably, AliA and AliB exhibit distinct, non-redundant enzymatic activities with potential substrate selectivity, uncovering a new layer of regulation in prokaryotic lipoprotein lipidation.
    DOI:  https://doi.org/10.1038/s41467-025-63625-6
  59. bioRxiv. 2025 Sep 17. pii: 2025.09.17.675666. [Epub ahead of print]
    Establishing an RNA sensor with high sensitivity and dynamic range utilizing a signal amplifier platform.
    Ha Eun Lim, James Chappell, Laura Segatori.
      Precise control of gene expression in a cell-state-specific manner is essential for effective therapeutic interventions in complex and dynamic disease microenvironments. Traditional targeting strategies that rely on surface markers or cell type-specific promoters often assume static cellular identities, limiting effectiveness in contexts such as cancer and inflammation, where cell states are highly heterogeneous and dynamic. RNA sensors, such as RADAR (RNA sensing using Adenosine Deaminases Acting on RNA), provide a modular, programmable, and non-integrating platform for classifying cell states. However, it is also characterized by low sensitivity and dynamic range, which limits its applications in detecting low-abundance transcripts. In this work, we integrate RADAR sensors with a signal amplification circuit to enhance sensitivity and dynamic range. We demonstrate that this combined RADAR-amplifier platform enables real-time monitoring of subtle changes in the abundance of endogenous transcripts under physiological conditions. Our results demonstrate the utility of this platform for fundamental biological studies and the development of precision therapeutic strategies.
    Abstract Figure:
    DOI:  https://doi.org/10.1101/2025.09.17.675666
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