bims-enlima Biomed News
on Engineered living materials
Issue of 2025–05–11
57 papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Cytomimetic calcification in chemically self-regulated prototissues.
  2. Evolution-guided protein design of IscB for persistent epigenome editing in vivo.
  3. Shape-Evolving Structured Liquids.
  4. Programmable Fabrics of Enzyme-Responsive Amphiphiles: A Multiscale Platform for Hierarchical Mesophase Transformations.
  5. Microcapillary Array-Based High Throughput Screening for Protein Biomanufacturability.
  6. Leveraging Protein-Ligand and DNA Interactions to Control Hydrogel Mechanics.
  7. Engineered bacteria can degrade five wastewater pollutants at the same time.
  8. Engineered Bacteria Convert a 3-Bit Binary Code to a 3-Bit Gray Code by Multicellular Artificial-Neural-Network-Type Architecture.
  9. Self-documenting plasmids.
  10. Biomimetic Hydrogels from Mixed Gellan Gum and Tryptophan Zipper Self-Assembling Peptides.
  11. Multiplexing light-inducible recombinases to control cell fate, Boolean logic, and cell patterning in mammalian cells.
  12. Sequence-encoded intermolecular base pairing modulates fluidity in DNA and RNA condensates.
  13. Polymer oxidation: A strategy for the controlled degradation of injectable cryogels.
  14. Biomolecular Actuators for Soft Robots.
  15. Molecular circuits for genomic recording of cellular events.
  16. Frontal polymerization of thermosets to enable vacuum-formed structural electronics.
  17. Design and Characterization of Thioester Networks with Adaptable and Enzymatically Degradable Cross-Links.
  18. Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells.
  19. Architectural control of rod-coil block polypeptide thermoresponsive self-assembly via de novo design of coiled-coil orientation.
  20. Pathways to sustainability: a quantitative comparison of aerobic and anaerobic C1 bioconversion routes.
  21. Microheater hotspot engineering for spatially resolved and repeatable multi-level switching in foundry-processed phase change silicon photonics.
  22. Mechanically Tunable DNA Hydrogels as Prospective Biosensing Modules.
  23. Model-Guided Rational Construction of Escherichia coli Synthetic Consortia for Enhanced 2-Methylbutyric Acid Production.
  24. Covalent Crosslinker-Free Photo-Curing 3D Printing of Liquid Metal Composite Hydrogels Based On SI-photoATRP.
  25. Acoustic holographic assembly of cell-dense tissue constructs.
  26. Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.
  27. An in vivo target mutagenesis system for multiple hosts.
  28. Gelation Dynamics, Formation Mechanism, Functionalization, and 3D Bioprinting of Silk Fibroin Hydrogel Materials for Biomedical Applications.
  29. De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts.
  30. Enhanced biosynthesis of 6-aminocaproic acid in engineered Escherichia coli with artificial protein cage-organized enzymatic cascades.
  31. Unbiased mechanical cloaks.
  32. A Robust and Orthogonal Far-Red Light Sensor for Gene Expression Control in Escherichia coli.
  33. Interspecies interactions in dual, fibrous gels enable control of gel structure and rheology.
  34. Remote Control of Eukaryotic Gene Expression by a Modular Ultrasound-Responsive RNA Toolkit.
  35. Restructuring of Hydrogel Polymer Networks via Ion Storming.
  36. Organic Fouling on Zwitterionic Amphiphilic Copolymers: Implications in Biofouling.
  37. Selective chemical tracking of DNA methylomes in live cells.
  38. In silico identification of gene targets to enhance C12 fatty acid production in Escherichia coli.
  39. Meter-scale heterostructure printing for high-toughness fiber electrodes in intelligent digital apparel.
  40. Visualization of photocuring and 4D printing with real-time phosphorescence.
  41. Coordination of cell envelope biology by Escherichia coli MarA protein potentiates intrinsic antibiotic resistance.
  42. Molecular insights into de novo small-molecule recognition by an intron RNA structure.
  43. The role of mitochondrial mRNA translation in cellular communication.
  44. Beyond CEN.PK - parallel engineering of selected S. cerevisiae strains reveals that superior chassis strains require different engineering approaches for limonene production.
  45. Epigenetics Beyond the Cell: Supracellular Organization of Fate and Form in Morphogenesis.
  46. Daily briefing: How we taste sweetness.
  47. Moving towards sequencing-based metabolomics.
  48. Material Design for Durable Lubricant-Infused Surfaces That Can Reduce Liquid and Solid Fouling.
  49. DNA Organogels Gaining Multifunctions from the Contribution of Molecular Design on Cross-Linker.
  50. Phase separation in mitochondrial fate and mitochondrial diseases.
  51. Biofabrication of microstructured bacterial ecosystems using chaotic bioprinting: advancing in vitro research for microbial engineering.
  52. Control of replication and gene expression by ADP-ribosylation of DNA in Mycobacterium tuberculosis.
  53. Multistage Networks for Glassy Holographic Photopolymers.
  54. Cost-effective urine recycling enabled by a synthetic osteoyeast platform for production of hydroxyapatite.
  55. On-demand Ligate and Release Strategy based on Photoclick Reaction in Tandem with Pd-mediated Deallylation.
  56. The YEATS domain is a selective reader of histone methacrylation.
  57. Naturally ornate RNA-only complexes revealed by cryo-EM.
  1. Nat Commun. 2025 May 03. 16(1): 4138
    Cytomimetic calcification in chemically self-regulated prototissues.
    Rui Sun, Zhuping Yin, Molly M Stevens, Mei Li, Stephen Mann.
      The fabrication of cytomimetic materials capable of orchestrated and adaptive functions remains a significant challenge in bottom-up synthetic biology. Inspired by the cell/matrix integration of living bone, here we covalently tether distributed single populations of alkaline phosphatase-containing inorganic protocells (colloidosomes) onto a crosslinked organic network to establish viscoelastic tissue-like micro-composites. The prototissues are endogenously calcified with site-specific mineralization modalities involving selective intra-protocellular calcification, matrix-specific extra-protocellular calcification or gradient calcification. To mirror the interplay between osteoblasts and osteoclasts, we prepare integrated prototissues comprising a binary population of enzymatically active colloidosomes capable of endogenous calcification and decalcification and utilize chemical inputs to induce structural remodelling. Overall, our methodology opens a route to the chemically self-regulated calcification of homogeneous and gradient tissue-like mineral-matrix composites, advances the development of bottom-up synthetic biology in chemical materials research, and could provide potential opportunities in bioinspired tissue engineering, hydrogel technologies and bone biomimetics.
    DOI:  https://doi.org/10.1038/s41467-025-59251-x
  2. Nat Biotechnol. 2025 May 07.
    Evolution-guided protein design of IscB for persistent epigenome editing in vivo.
    Soumya Kannan, Han Altae-Tran, Shiyou Zhu, Peiyu Xu, Daniel Strebinger, Rachel Oshiro, Guilhem Faure, Lukas Moeller, Julie Pham, Kepler S Mears, Heyuan M Ni, Rhiannon K Macrae, Feng Zhang.
      Naturally existing enzymes have been adapted for a variety of molecular technologies, with enhancements or modifications to the enzymes introduced to improve the desired function; however, it is difficult to engineer variants with enhanced activity while maintaining specificity. Here we engineer the compact Obligate Mobile Element Guided Activity (OMEGA) RNA-guided endonuclease IscB and its guiding RNA (ωRNA) by combining ortholog screening, structure-guided protein domain design and RNA engineering, and deep learning-based structure prediction to generate an improved variant, NovaIscB. We show that the compact NovaIscB achieves up to 40% indel activity (~100-fold improvement over wild-type OgeuIscB) on the human genome with improved specificity relative to existing IscBs. We further show that NovaIscB can be fused with a methyltransferase to create a programmable transcriptional repressor, OMEGAoff, that is compact enough to be packaged in a single adeno-associated virus vector for persistent in vivo gene repression. This study highlights the power of combining natural diversity with protein engineering to design enhanced enzymes for molecular biology applications.
    DOI:  https://doi.org/10.1038/s41587-025-02655-3
  3. Adv Mater. 2025 May 07. e2500804
    Shape-Evolving Structured Liquids.
    Paul Y Kim, Shipei Zhu, Joe Forth, Ganhua Xie, David A King, Brett A Helms, Paul D Ashby, Ahmad K Omar, Thomas P Russell.
      Migration, division, and reconfiguration - functions essential to living systems - are driven by active processes. Developing synthetic mimics is an outstanding challenge. Lipid bilayers that bound natural systems are locally deformed by active species, e.g., microtubules, but the resulting non-equilibrium shapes relax when active species motion ceases, and the shape changes lack immediate control. A fully synthetic system is described, driven by active particles encapsulated by a reconfigurable nanoparticle-surfactant membrane that undergoes shape fluctuations reminiscent of living cells. These shape changes are preserved after particle activity stops. Surfactant concentration tunes the interfacial tension over three orders of magnitude, making on-demand shape evolution possible. Directional migration, division, and reconfiguration across multiple scales are possible, leading to a new class of biomimetic, reconfigurable, and responsive materials, paving the way for autonomous synthetic machines.
    Keywords:  active matter; interfacial assembly; structured liquids
    DOI:  https://doi.org/10.1002/adma.202500804
  4. Biomacromolecules. 2025 May 07.
    Programmable Fabrics of Enzyme-Responsive Amphiphiles: A Multiscale Platform for Hierarchical Mesophase Transformations.
    Nicole Edelstein-Pardo, Shira Kutchinsky, Amit Sitt, Roey J Amir.
      Systems capable of undergoing a controlled cascade of mesophase transitions across hierarchical scales represent a novel class of dynamic materials. Here, we describe an electrospun polymeric fabric composed of enzyme-responsive di- and triblock copolymers that undergoes a hierarchical cascade of four distinct mesophases. Initially, on immersion in water, the macroscale fabric dissolves, forming nanoscale micelles. Enzymatic degradation of the diblock components triggers a transition into a triblock-based hydrogel. Finally, the enzymatic degradation of the hydrogel into hydrophilic polymers leads to complete dissolution. By adjusting the di- and triblock ratios, we can finely tune the fabric's dissolution rate. Moreover, the fibers can encapsulate hydrophobic agents, which are retained within the micelle and hydrogel phases, enabling their controlled release. This cascade of mesophase transitions, from a macroscopic solid to nanoscale assemblies, organized hydrogels, and eventual molecular dissolution, demonstrates sophisticated hierarchical control, unlocking new opportunities for biomedical applications of programmable materials.
    DOI:  https://doi.org/10.1021/acs.biomac.4c01649
  5. ACS Synth Biol. 2025 May 08.
    Microcapillary Array-Based High Throughput Screening for Protein Biomanufacturability.
    Khushank Singhal, Harry E Adamson, Thomas M Baer, Howard M Salis, Melik C Demirel.
      Gene expression is a complex phenomenon involving numerous interlinked variables, and studying these variables to control expression is essential in bioengineering and biomanufacturing. While cloning techniques for achieving plasmid libraries that cover large design spaces exist, multiplex techniques offering cell culture screening at similar scales are still lacking. We introduced a microcapillary array-based platform aimed at high-throughput, multiplex screening of miniature cell cultures through fluorescent reporters. The clone recovery mechanism provides 100× enrichment ratios compared to traditional techniques for establishing phenotype-to-genotype linkages. We conducted experiments to delineate the effects of three key plasmid design features─promoters, 5' untranslated regions, and amino acid sequences─on protein titer. We identified a small set of promoters that maximize protein titer from thousands of promoters with widely varying transcription rates. We established that mRNA half-lives, controlled by 5' untranslated regions, correlate with protein expression. Using dual-reporter imaging, we demonstrate relative analyses of multiple ribosome binding sites in operons. Lastly, we discuss the effect of structural protein hydrophobicity scores on their expression and cell growth profiles. Through multiple experiments with libraries of plasmid constructs, we demonstrate population binning, dual-reporter operon screening, chemical perturbation, and cell growth estimation using brightfield absorbance measurements with the platform.
    Keywords:  biomanufacturing; expression constructs; high-throughput screening; plasmid libraries; protein engineering; proteins
    DOI:  https://doi.org/10.1021/acssynbio.5c00205
  6. J Am Chem Soc. 2025 May 09.
    Leveraging Protein-Ligand and DNA Interactions to Control Hydrogel Mechanics.
    Namrata Ramani, Jeongmin Hwang, Alex J Anderson, Jennifer Delgado, Laura Hernández-López, C Adrian Figg, Peter H Winegar, Chad A Mirkin.
      Biomacromolecules can serve as molecularly precise building blocks for hydrogel materials, dictating material properties that depend on the chemical identity and interactions of the individual components. Herein, we introduce biomolecular hydrogels where ligand-functionalized DNA sequences form the hydrogel backbone and multivalent protein-ligand interactions form supramolecular cross-links. In these hydrogels, we can independently leverage the programmable rigidity of DNA (i.e., single-stranded vs double-stranded DNA) and defined protein-ligand binding affinities spanning >10 orders of magnitude to modulate the gel stiffness, stress relaxation, and shear thinning. We learn that (1) double-stranded networks have stiffness values up to 3 orders of magnitude greater than single-stranded networks and exhibit thermoresponsiveness and (2) the protein-ligand binding affinities and dissociation rate constants determine the network topologies and stress relaxation rates of the hydrogels. Finally, the hydrogels exhibit cytocompatibility and cell-type-specific degradation, where cells can migrate through the gels via interactions between the gels and their ligand-binding receptors. Together, this work demonstrates that varying the local chemical interactions of the hydrogel backbone and the supramolecular binding affinity of dynamic cross-links leads to cytocompatible hydrogels with tunable viscoelastic properties for applications in drug delivery and tissue engineering.
    DOI:  https://doi.org/10.1021/jacs.5c03523
  7. Nature. 2025 May 07.
    Engineered bacteria can degrade five wastewater pollutants at the same time.
      
    Keywords:  Microbiology; Organic chemistry; Synthetic biology
    DOI:  https://doi.org/10.1038/d41586-025-01371-x
  8. ACS Synth Biol. 2025 May 07.
    Engineered Bacteria Convert a 3-Bit Binary Code to a 3-Bit Gray Code by Multicellular Artificial-Neural-Network-Type Architecture.
    Saswata Chakraborty, Sangram Bagh.
      The neuromorphic computing with genetically engineered cells is still in its infancy and shows great promise to solve various complex computational problems. The success of such computing is dependent on the expansion of its capability to build new and versatile computation functions. The conversion of a binary code to a Gray code is a fundamental concept in digital electronics and computer science. In this work, by using genetically engineered E. coli cells, we created a single-layer artificial neural network (ANN) that works as a 3-bit-binary to Gray code converter. The ANN architecture is built by five engineered E. coli populations in a liquid culture, where a binary input in chemical form is given by adding or not adding (1/0) three chemical inputs, and the converted codes are manifested by the appropriate expression of three fluorescent proteins. The work may have significance in biocomputer technology development, bacterial ANN, and synthetic biology.
    Keywords:  Artificial Neural Network; Biocomputer; Cellular Device; Code Converter; Synthetic Biology
    DOI:  https://doi.org/10.1021/acssynbio.5c00145
  9. Trends Biotechnol. 2025 Apr 07. pii: S0167-7799(25)00095-2. [Epub ahead of print]
    Self-documenting plasmids.
    Sarah I Hernandez, Samuel J Peccoud, Casey-Tyler Berezin, Jean Peccoud.
      Plasmids are the workhorse of biotechnology. These small DNA molecules are used to produce recombinant proteins and to engineer living organisms. They can be regarded as the blueprints of many biotechnology products. Therefore, it is critical to ensure that the sequences of these DNA molecules match their intended designs. Yet, plasmid verification remains challenging. To secure the exchange of plasmids in research and development workflows, we have developed self-documenting plasmids that encode information about themselves in their own DNA molecules. Users of self-documenting plasmids can retrieve critical information about the plasmid without prior knowledge of the plasmid identity. The insertion of documentation in the plasmid sequence does not preclude their propagation in bacteria or functional fluorescent protein expression in mammalian cells. This technology simplifies plasmid verification, hardens supply chains, and has the potential to transform the protection of intellectual property (IP) in the life sciences.
    Keywords:  bioinformatics; cryptography; cyberbiosecurity; digital signature; plasmid; reproducibility; sequencing
    DOI:  https://doi.org/10.1016/j.tibtech.2025.03.010
  10. ACS Macro Lett. 2025 May 09. 679-686
    Biomimetic Hydrogels from Mixed Gellan Gum and Tryptophan Zipper Self-Assembling Peptides.
    Riddhesh Doshi, Dhushanthan Mohanathas, Md Shariful Islam, Juanfang Ruan, Richard D Tilley, Kristopher A Kilian.
      Peptide self-assembly has been used to fabricate synthetic hydrogels that emulate many of the chemical and physical properties of natural hydrogels. However, these materials often lack stability for many applications and do not display the native bioactivity found in tissue. Here we demonstrate a hybrid hydrogel system in which self-assembling peptides are integrated with polysaccharides to enhance gelation and provide improved mechanics and bioactivity. A peptide based on the tryptophan zipper (trpzip) motif was mixed with the anionic polysaccharide gellan gum, demonstrating gelation within minutes with increased stiffness compared to that of trpzip alone. The hybrid material maintained viscoelastic character with shear-thinning, self-healing, and stress-relaxation on the order of natural materials like collagen. All hydrogels supported cell adhesion and viability with increased gellan gum content, promoting cell assembly into aggregates. The enhanced gelation kinetics, stability, self-healing, and bioactivity of these materials make them promising candidates as matrices for cell culture and reagents for biofabrication and syringe extrusion for biological delivery.
    DOI:  https://doi.org/10.1021/acsmacrolett.5c00076
  11. Sci Adv. 2025 May 09. 11(19): eadt1971
    Multiplexing light-inducible recombinases to control cell fate, Boolean logic, and cell patterning in mammalian cells.
    Cristina Tous, Ian S Kinstlinger, Maya E L Rice, Jenny Deng, Wilson W Wong.
      Light-inducible regulatory proteins are powerful tools to interrogate fundamental mechanisms driving cellular behavior. In particular, genetically encoded photosensory domains fused to split proteins can tightly modulate protein activity and gene expression. While light-inducible split protein systems have performed well individually, few multichromatic and orthogonal gene regulation systems exist in mammalian cells. The design space for multichromatic circuits is limited by the small number of orthogonally addressable optogenetic switches and the types of effectors that can be actuated by them. We developed a library of red light-inducible recombinases and directed patterned myogenesis in a mesenchymal fibroblast-like cell line. To address the limited number of light-inducible domains (LIDs) responding to unique excitation spectra, we multiplexed light-inducible recombinases with our "Boolean logic and arithmetic through DNA excision" (BLADE) platform. Multiplexed optogenetic tools will be transformative for understanding the role of multiple interacting genes and their spatial context in endogenous signaling networks.
    DOI:  https://doi.org/10.1126/sciadv.adt1971
  12. Nat Commun. 2025 May 07. 16(1): 4258
    Sequence-encoded intermolecular base pairing modulates fluidity in DNA and RNA condensates.
    Sumit Majumder, Sebastian Coupe, Nikta Fakhri, Ankur Jain.
      Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA-based liquids with exquisite programmability in their macroscopic rheological properties. In the presence of multivalent cations, nucleic acids can condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that sequence-specific inter-molecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the inter-molecular hybridization energy, enabling precise sequence-based modulation of condensate properties over several orders of magnitude. Our work offers a robust platform to create bottom-up programmable fluids and may help advance our understanding of liquid-like compartments in cells.
    DOI:  https://doi.org/10.1038/s41467-025-59456-0
  13. Mater Today Bio. 2025 Jun;32 101743
    Polymer oxidation: A strategy for the controlled degradation of injectable cryogels.
    Alexandra Nukovic, Mohammad Hamrangsekachaee, Mahalakshmi Rajkumar, Gwyneth Wong, Emily R Tressler, Sara M Hashmi, Stephen M Hatfield, Sidi A Bencherif.
      Cryogels, an advanced subclass of hydrogels, are widely used in biomedical applications such as tissue engineering, drug delivery, and immunotherapy. Biopolymers, like hyaluronic acid (HA), are key building blocks for cryogel fabrication due to their intrinsic biological properties, biocompatibility, and biodegradability. HA undergoes biodegradation through hydrolysis, enzymatic degradation, and oxidation, but becomes less susceptible to degradation once chemically modified. This modification is necessary for producing HA-based cryogels with unique properties, including an open macroporous network, mechanical resilience, shape memory, and syringe injectability. Endowing cryogels with resorbable features is essential for meeting regulatory requirements and improving treatment outcomes. To this end, HA was oxidized with sodium periodate (HAox) and chemically modified with glycidyl methacrylate (HAoxGM) to create HAoxGM cryogels with controlled degradation. Oxidation of HA increased the susceptibility of the polymer backbone to breakdown through various mechanisms, including oxidative cleavage and alkaline hydrolysis. Compared to their poorly degradable counterparts, HAoxGM cryogels retained their advantageous properties despite reduced compressive strength. HAoxGM cryogels were highly cytocompatible, biocompatible, and tunable in degradation. When injected subcutaneously into mice, the HAoxGM cryogels were biocompatible and resorbed within two weeks. To validate the beneficial effect of controlled biodegradation in a relevant in vivo setting, we demonstrated that the degradation of HAoxGM cryogels accelerates ovalbumin release and enhances its uptake and response by immune cells in mice. This versatile oxidation strategy can be applied to a wide range of polymers, allowing better control over cryogel degradation, and advancing their potential for biomedical applications and clinical translation.
    Keywords:  Biocompatibility; Cryogel; Degradation; Hydrolysis; Oxidation
    DOI:  https://doi.org/10.1016/j.mtbio.2025.101743
  14. Chem Rev. 2025 May 07.
    Biomolecular Actuators for Soft Robots.
    Michelle C Quan, Danielle J Mai.
      Biomolecules present promising stimuli-responsive mechanisms to revolutionize soft actuators. Proteins, peptides, and nucleic acids foster specific intermolecular interactions, and their boundless sequence design spaces encode precise actuation capabilities. Drawing inspiration from nature, biomolecular actuators harness existing stimuli-responsive properties to meet the needs of diverse applications. This review features biomolecular actuators that respond to a wide variety of stimuli to drive both user-directed and autonomous actuation. We discuss how advances in biomaterial fabrication accelerate prototyping of precise, custom actuators, and we identify biomolecules with untapped actuation potential. Finally, we highlight opportunities for multifunctional and reconfigurable biomolecules to improve the versatility and sustainability of next-generation soft actuators.
    DOI:  https://doi.org/10.1021/acs.chemrev.4c00811
  15. Trends Genet. 2025 May 06. pii: S0168-9525(25)00079-4. [Epub ahead of print]
    Molecular circuits for genomic recording of cellular events.
    Wei Chen, Junhong Choi.
      Advances in precise genome editing are enabling genomic recordings of cellular events. Since the initial demonstration of CRISPR-based genome editing, the field of genomic recording has witnessed key strides in lineage recording, where clonal lineage relationships among cells are indirectly recorded as synthetic mutations. However, methods for directly recording and reconstructing past cellular events are still limited, and their potential for revealing new insights into cell fate decisions has yet to be realized. The field needs new sensing modules and genetic circuit architectures that faithfully encode past cellular states into genomic DNA recordings to achieve such goals. Here we review recently developed strategies to construct diverse sensors and explore how emerging synthetic biology tools may help to build molecular circuits for genomic recording of diverse cellular events.
    Keywords:  CRISPR; genomic recording; molecular circuits; synthetic biology
    DOI:  https://doi.org/10.1016/j.tig.2025.04.004
  16. Nat Commun. 2025 May 05. 16(1): 4165
    Frontal polymerization of thermosets to enable vacuum-formed structural electronics.
    Hayden E Fowler, Mychal S Taylor, Chi Phuong H Nguyen, David A Boese, Esteban Baca, Andrew J Greenlee, Georgia E Kaufman, Michael A Gallegos, Emily F Huntley, Leah N Appelhans, Bryan Kaehr, Samuel C Leguizamon.
      Material design and accessible manufacturing are often at odds with each other, calling for creative solutions to adapt high-performance materials to available processes. This challenge is represented well by in-mold electronics, an innovative approach to the manufacture of 3D circuitry and electronic components that offers game-changing advantages. In-mold electronics relies on vacuum forming processes, which are historically limited to thermoplastics. Extending these methods to include thermosets would enable manufacturing of robust components with desirable properties. Here, we provide a solution to make thermoset materials amenable to vacuum forming. Specifically, an ambient polymerization is used to transition a liquid monomeric solution to an elastomeric gel. These free-standing gels can then be vacuum formed, and the reaction can be completed via frontal polymerization. Thermoset materials produced with this method have properties that provide benefits over traditionally employed thermoplastic substrates and enable 3D device integration into environmentally demanding architectural, automotive, and extraterrestrial structures.
    DOI:  https://doi.org/10.1038/s41467-025-59455-1
  17. Macromolecules. 2025 Apr 22. 58(8): 3872-3885
    Design and Characterization of Thioester Networks with Adaptable and Enzymatically Degradable Cross-Links.
    Shivani Desai, Gautam V Khare, Kristi S Anseth, Kelly M Schultz.
      Viscoelastic properties of the extracellular matrix (ECM) impact cell processes including proliferation, spreading, and migration. During these basic cellular processes, cells remodel the ECM by secreting enzymes and applying cytoskeletal tension to the network. To design cell delivery platforms that mimic physical ECM properties, new designs incorporate viscoelasticity and moieties that enable cell-mediated network remodeling. In this work, we design and characterize networks with two different types of cross-links, covalent adaptable and enzymatically degradable. Our networks consist of 8-arm poly(ethylene glycol) (PEG)-thiol, PEG-thioester norbornene, and a norbornene functionalized matrix metalloproteinase (MMP)-degradable peptide, KKGPQG↓IWGQKK. We characterize three network compositions with a ratio of 1:1, 3:1, and 4:1 adaptable to MMP-degradable cross-links. We characterize network mechanical properties using bulk rheology. Using multiple particle tracking microrheology (MPT), we measure the evolving microstructure of the network during degradation. MPT measures Brownian motion of fluorescently labeled probe particles, which can be used to calculate rheological properties. Our results show that the elastic modulus increases with an increasing ratio of adaptable to MMP-degradable cross-links, and all networks have the same extent of stress relaxation. We then measure degradation of these networks by incubating in l-cysteine, which degrades only the adaptable cross-links by the thioester exchange reaction. We measure complete degradation of all three compositions using bulk rheology. Networks with 4:1 adaptable to MMP-degradable cross-links are the slowest to degrade and networks with 3:1 adaptable to MMP-degradable cross-links are the fastest to degrade. MPT measurements during degradation show networks with 1:1 and 4:1 adaptable to MMP-degradable cross-links rearrange multiple times before complete degradation. In networks with 3:1 adaptable to MMP-degradable cross-links, we measure fewer network rearrangements prior to degradation. Using time-cure superposition (TCS), we measure the network structure at the phase transition. Networks with 1:1 and 4:1 adaptable to MMP-degradable cross-links are elastic and tightly cross-linked and networks with 3:1 adaptable to MMP-degradable cross-links can range from elastic to open networks. The most open network structure, networks with 3:1 adaptable to MMP-degradable cross-links, degrade on the shortest time scale. We also measure ≥70% hMSC viability in each network after 3D encapsulation. In this work, we characterize different compositions of hybrid networks that incorporate both adaptable and enzymatically degradable cross-links. This work can enable design that specifies the mechanical properties and degradation behavior of the material to better mimic aspects of the native ECM.
    DOI:  https://doi.org/10.1021/acs.macromol.5c00487
  18. Nat Commun. 2025 May 09. 16(1): 4328
    Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells.
    Sunfengda Song, Haiyang Xie, Qingwen Wang, Xinyi Sun, Jiasu Xu, Rui Chen, Yuankang Zhu, Lai Jiang, Xianting Ding.
      Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduce the Composition of LLPS proteome Assembly by Proximity labeling-assisted Mass spectrometry (CLAPM). We demonstrate that CLAPM can instantaneously label and monitor the FUS interactome shifts within intracellular droplets undergoing spatiotemporal LLPS. We report 129, 182 and 822 proteins specifically present in the LLPS droplets of HeLa, HEK 293 T and neuronal cells respectively. CLAPM further categorizes spatiotemporal dynamic proteome in droplets for living neuronal cells and identifies 596 LLPS-aboriginal proteins, 226 LLPS-dependent proteins and 58 LLPS-sensitive proteins. For validation, we uncover 11 previously unknown LLPS proteins in vivo. CLAPM provides a versatile tool to decipher proteins involved in LLPS and enables the accurate characterization of dynamic proteome in living cells.
    DOI:  https://doi.org/10.1038/s41467-025-59457-z
  19. J Mater Chem B. 2025 May 06.
    Architectural control of rod-coil block polypeptide thermoresponsive self-assembly via de novo design of coiled-coil orientation.
    Bin Wang, Weiran Xie, Tianren Zhang, Darrin J Pochan, Jeffery G Saven, Kristi L Kiick.
      The architectural control of the self-assembly of a series of block polypeptides comprising a concatenation of an elastin-like peptide and a coiled-coil, bundle-forming peptide (ELP-BFPs), has been demonstrated. Assembly of the polypeptides is controlled by coacervation of the hydrophobic ELP domain, while the type of coiled-coil assembly of the BFP and the specific placement of short histidine tags significantly tunes assembly behavior. Spectrophotometric analysis of self-assembly demonstrated that the transition temperature of assembly can be controlled by the design of the BFP domain and positioning of the His-tags in the constructs. Cryogenic transmission electron microscopy of assembled polypeptides confirmed distinct morphologies including core-shell particles and multilayer vesicles, depending on the parallel or antiparallel bundle architecture of the block polypeptide. The results have applications in materials design and highlight the potential for controlling multi-stimuli responsiveness and morphologies through fine control of the architectural features of the component polypeptide domains.
    DOI:  https://doi.org/10.1039/d4tb02420f
  20. Curr Opin Biotechnol. 2025 May 05. pii: S0958-1669(25)00054-0. [Epub ahead of print]93 103310
    Pathways to sustainability: a quantitative comparison of aerobic and anaerobic C1 bioconversion routes.
    William Gasparrini, Seung H Lee, Benjamin M Woolston.
      One-carbon (C1) substrates are attractive feedstocks for biological upgrading as part of a circular, carbon-negative bioeconomy. Nature has evolved a diverse set of C1-trophs that use a variety of pathways. Additionally, intensive effort has recently been invested in developing synthetic C1 assimilation pathways. This complicated landscape presents the question: "What pathways should be used to produce what products from what C1 substrates?" To guide the selection, we calculate and compare maximal theoretical yields for a range of bioproducts from different C1 feedstocks and pathways. The results highlight emerging opportunities to apply metabolic engineering to specific C1 pathways to improve pathway performance. Since the C1 landscape is dynamic, with new discoveries in the biochemistry of native pathways and new synthetic alternatives rapidly emerging, we present detailed procedures for these yield calculations to enable others to easily adapt them to additional scenarios as a foundation for establishing industrially relevant production strains.
    DOI:  https://doi.org/10.1016/j.copbio.2025.103310
  21. Nat Commun. 2025 May 09. 16(1): 4291
    Microheater hotspot engineering for spatially resolved and repeatable multi-level switching in foundry-processed phase change silicon photonics.
    Hongyi Sun, Chuanyu Lian, Francis Vásquez-Aza, Sadra Rahimi Kari, Yi-Siou Huang, Alessandro Restelli, Steven A Vitale, Ichiro Takeuchi, Juejun Hu, Nathan Youngblood, Georges Pavlidis, Carlos A Ríos Ocampo.
      Nonvolatile photonic integrated circuits employing phase change materials have relied either on optical switching with precise multi-level control but poor scalability or electrical switching with seamless integration and scalability but mostly limited to a binary response. The main limitation of the latter is relying on stochastic nucleation, since its random nature hinders the repeatability of multi-level states. Here, we show engineered waveguide-integrated microheaters to achieve precise spatial control of the temperature profile (i.e., hotspot) and, thus, switch deterministic areas of an embedded phase change material. We experimentally demonstrate this concept using a variety of foundry-processed doped-silicon microheaters on a silicon-on-insulator platform featuring Sb2Se3 or Ge2Sb2Se4Te and achieve 27 cycles with 7 repeatable levels each. We further characterize the microheaters' response using Transient Thermoreflectance Imaging. Our microstructure engineering concept demonstrates the evasive repeatable multi-levels employing a single microheater device, which is necessary for robust and energy-efficient reprogrammable phase change photonics in analog processing and computing.
    DOI:  https://doi.org/10.1038/s41467-025-59399-6
  22. Macromol Rapid Commun. 2025 May 08. e2500149
    Mechanically Tunable DNA Hydrogels as Prospective Biosensing Modules.
    Asya E Can, Abdul W U Ali, Claude Oelschlaeger, Norbert Willenbacher, Iliya D Stoev.
      Sequence-programmable DNA building blocks offer high degree of freedom in designing arbitrarily complex networks of tunable viscoelastic properties. Yet, the deployment of DNA-based functional materials remains limited due to insufficient control over the emerging structures and their mechanics. In an ongoing effort to place structure-property relations in stimuli-responsive DNA materials on a firm foundation, here a systematic rheological study of self-assembling DNA networks is presented, comprised of short DNA nanomotifs, namely trivalent nanostars and bivalent linkers, where the latter differ in their composition on a single base-pair level. Notably, we found through combining conventional bulk rheology with diffusing wave spectroscopy (DWS-based) passive microrheology a relationship between the melting temperature of a DNA hydrogel and its DNA sequence composition. By providing a use case, we demonstrated how the determination of such empirical relations could impact the areas of biosensing and mechanical computing, where control over the system state and target identification are key.
    Keywords:  DNA materials; biosensing; melting temperature; microrheology; sequence‐programmability
    DOI:  https://doi.org/10.1002/marc.202500149
  23. Adv Sci (Weinh). 2025 May 05. e2416272
    Model-Guided Rational Construction of Escherichia coli Synthetic Consortia for Enhanced 2-Methylbutyric Acid Production.
    Yu Liu, Boyuan Xue, Shaojie Wang, Haijia Su.
      Synthetic consortia represent an innovative and effective platform that can significantly alleviate the metabolic burden on host organisms and enable flexible regulation of biosynthetic pathways. However, designing a stable synthetic consortium remains a significant challenge. In this study, a novel citramalate -derived pathway is first developed for 2-methylbutyric acid (2MBA) biosynthesis in an E. coli mono-culture system, achieving a titer of 678.78 ± 49.04 mg L-1. Furthermore, it employs a CulECpy model-guided strategy to design and optimize the division of labor within E. coli synthetic consortia, predicting the optimal pathway allocation for improved 2MBA production. The best-performing consortium, using 2-keto-3-methylvalerate (KMV) as a single node, achieved 1817.03 ± 103.73 mg L-1 of 2MBA, a 28-fold increase over the initial mono-culture strain, with the highest reported yield of 0.091 g/g glucose. This work demonstrates the effectiveness of synthetic consortia and model-guided pathway optimization for improving high-value products, a versatile strategy that can be applied to the production of other valuable metabolites.
    Keywords:  co‐culture; metabolic engineering; metabolic network model; rational construction; synthetic consortia
    DOI:  https://doi.org/10.1002/advs.202416272
  24. Small. 2025 May 03. e2411688
    Covalent Crosslinker-Free Photo-Curing 3D Printing of Liquid Metal Composite Hydrogels Based On SI-photoATRP.
    Ge Yan, Mengjie Zhou, Jun Zhang, Wenjie Zhang, Yanjie He, Xiaoguang Qiao, Ge Shi, Xinchang Pang.
      Photocurable 3D printing (SLA or DLP) materials have garnered considerable attention due to their remarkable efficiency and precision in manufacturing. However, the presence of covalent crosslinking makes the recycling and reuse of printed materials extremely challenging. Here a novel approach to covalent crosslinker-free photo-curing 3D printing (via DLP) of liquid metal (LM) composite hydrogels is reported, leveraging surface-initiated photoinduced atom radical transfer polymerization (SI-photoATRP). The pre-synthesized PHEA-Br macroinitiators are grafted onto the surfaces of LM nanoparticles (LMNPs) by mechanical sonication, stabilizing the LMNPs within the resin solution while simultaneously generating active sites for SI-photoATRP. During the SI-photoATRP process, polymer chains of sufficient length form hydrogen bonds with multiple LMNPs, effectively transforming the LMNPs into crosslinking points. By integrating the aqueous photoATRP system catalyzed by carbon dots, LM@polymer composite hydrogel with complex structures are successfully established through DLP technology. The versatility of the 3D printed hydrogel is investigated by employing HEA, OEGA480, and AAm as the monomers in resin solution, respectively. Notably, all the LM@polymer composite hydrogels can be degraded in aqueous NaOH solution. Furthermore, LM@polymer-based networks exhibit self-repairing capabilities, serve as underwater adhesives, and conduct electricity. This work offers new insights into designing 3D printing materials and sustainable photocurable technology.
    Keywords:  3D Printing; LM hydrogel; SI‐PhotoATRP; functional materials
    DOI:  https://doi.org/10.1002/smll.202411688
  25. Biofabrication. 2025 May 06.
    Acoustic holographic assembly of cell-dense tissue constructs.
    Minghui Shi, Peer Fischer, Kai Melde.
      Tissue engineering aims to develop tissue constructs as models or substitutes for native tissues. For organ-level biological studies and regenerative medicine applications, it is essential to fabricate tissue constructs with physiologically relevant cell densities (on the order of 10 million to 1 billion cells·mL-1, large size (centimeter scale and larger), and a controllable geometry to guide tissue maturation. State-of-the-art biofabrication methods, however, struggle to simultaneously meet all of these demands. The recently proposed acoustic holographic assembly (AHA) method shows promise, as it is compatible with culture media and enables the contactless, label-free, and volumetric assembly of biological cells in a predefined geometry within few minutes. Here we present an AHA biofabrication scheme designated for fabricating cell-dense, centimeter-scale, and arbitrarily-shaped tissue constructs using a compact benchtop instrument compatible with a biolab environment. We demonstrate the assembly of C2C12 myoblasts in gelatin methacryloyl (GelMA) into large and asymmetric branch-shaped constructs, which are rapidly formed with an average cell density of 40 million cells·mL-1and a local density of up to 260 million cells·mL-1. Featuring a high viability of 90.5%±4.3%, the assembled cell constructs are observed to grow within the GelMA hydrogel under perfusion over five days. Further, we show how AHA can --- in a single step --- assemble cells into layered and three-dimensional geometries inside standard cell culture labware. It can therefore help obtain engineered tissue constructs with structural and functional characteristics seen in more complex native tissues.
    Keywords:  Acoustic Holography; Bioassembly; Tissue Engineering
    DOI:  https://doi.org/10.1088/1758-5090/add49e
  26. ACS Synth Biol. 2025 May 06.
    Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.
    Xiaoming Lu, Daniel J Pritko, Megan E Abravanel, Jonah R Huggins, Oluwaferanmi Ogunleye, Tirthankar Biswas, Katia C Ashy, Semaj K Woods, Mariclaire W T Livingston, Mark A Blenner, Marc R Birtwistle.
      Genetically encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), nondestructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are nondestructive, fast, and inexpensive to readout but lack high diversity. We recently proposed a theory for how fluorescent protein combinations may generate a high-diversity barcode library with nondestructive, fast, and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ∼150 barcodes from two-way combinations of 18 fluorescent proteins, 61 of which are tested experimentally. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ∼105 and more) generated from hundreds of spectrally resolvable tandem fluorescent protein probes.
    Keywords:  fluorescent protein; genetically-encoded fluorescence barcodes; nanopore sequencing; single-cell analysis; spectral deconvolution; spectral flow cytometry
    DOI:  https://doi.org/10.1021/acssynbio.4c00807
  27. Trends Biotechnol. 2025 May 08. pii: S0167-7799(25)00132-5. [Epub ahead of print]
    An in vivo target mutagenesis system for multiple hosts.
    Dong Yin, Qingxiao Pang, Yingbo Yuan, Tianyuan Su, Mengmeng Liu, Qian Wang, Jin Hou, Qingsheng Qi.
      In vivo target mutagenesis is a powerful approach to accelerate protein evolution. However, current approaches have been primarily developed in conventional organisms, limiting their capacity to evolve proteins with subtle variations across non-conventional host species. Here, we design an in vivo target mutagenesis system for multiple hosts (ITMU) utilizing the broad host-range plasmid RSF1010 replication element. The ITMU, which is based on a deaminase-helicase fusion and a primase error-prone DNA polymerase I fusion, induces all types of mutation in the target plasmid harboring the RSF1010 replicon, at a mutation rate 1.18 × 105-fold higher than that of the host genome. We show that ITMU-based in vivo continuous evolution is effective in Escherichia coli, Pseudomonas putida, Corynebacterium glutamicum, and Yarrowia lipolytica. This demonstrates that the ITMU is applicable to multiple microbial chassis and provides a viable alternative to in vivo continuous evolution systems.
    Keywords:  in vivo target mutagenesis; multiple hosts; synthetic biology
    DOI:  https://doi.org/10.1016/j.tibtech.2025.04.005
  28. ACS Nano. 2025 May 09.
    Gelation Dynamics, Formation Mechanism, Functionalization, and 3D Bioprinting of Silk Fibroin Hydrogel Materials for Biomedical Applications.
    Linpeng Fan, Zengxiao Cai, Jian Zhao, Negar Mahmoudi, Yi Wang, Samuel Cheeseman, Lilith Caballero Aguilar, Rui Luís Reis, Subhas C Kundu, David L Kaplan, David R Nisbet, Jing-Liang Li.
      Silk fibroin (SF), derived from silk cocoon fibers (Bombyx mori), is a natural protein polymer known for its biocompatibility, biodegradability, and sustainability. The protein can be processed into various material formats suitable for a range of applications. Among these, SF hydrogels are useful in the biomedical field, such as tissue engineering, due to the tailorable structures and properties achievable through tuning the gelation process. Therefore, the focus of this contribution is to comprehensively review and understand the formation, gelation mechanism, dynamic control, and functionalization of SF hydrogels. Unlike previous reviews, this work delves into understanding the strategies and mechanisms for tuning the gelation dynamics of SF from molecular assembly and crystallization points of view. Further, this review presents functionalization pathways and practical examples, such as for the 3D printing of SF hydrogels, to illustrate how these strategies, mechanisms, and pathways can be implemented in a specific application scenario. With these insights, researchers can gain a deeper understanding of how to manipulate or control the gelation process and the types of functionalization to achieve specific properties and features. This knowledge would further facilitate the development and application of SF hydrogel materials in various fields.
    Keywords:  3D bioprinting; cross-linking; crystallization and functionalization; gelation mechanism and dynamics; injectable hydrogel; self-assembly; silk fibroin hydrogel; silk nanofiber
    DOI:  https://doi.org/10.1021/acsnano.4c18568
  29. Science. 2025 May 08. 388(6747): 665-670
    De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts.
    Kaipeng Hou, Wei Huang, Miao Qi, Thomas H Tugwell, Turki M Alturaifi, Yuda Chen, Xingjie Zhang, Lei Lu, Samuel I Mann, Peng Liu, Yang Yang, William F DeGrado.
      De novo design of protein catalysts with high efficiency and stereoselectivity provides an attractive approach toward the design of environmentally benign catalysts. Here, we design proteins that incorporate histidine-ligated synthetic porphyrin and heme ligands. Four of 10 designed proteins catalyzed cyclopropanation with an enantiomeric ratio greater than 99:1. A second class of proteins were designed to catalyze a silicon-hydrogen insertion and were optimized by directed evolution in whole cells. The evolved proteins incorporated features unlikely to be generated by computational design alone, including a proline in an α helix. Molecular dynamics simulations showed that as the proteins evolved toward higher activity, their conformational ensembles narrowed to favor more productive conformations. Our work demonstrates that efficient de novo protein catalysts are designable and should be useful for manifold chemical processes.
    DOI:  https://doi.org/10.1126/science.adt7268
  30. Bioresour Technol. 2025 May 07. pii: S0960-8524(25)00607-8. [Epub ahead of print] 132641
    Enhanced biosynthesis of 6-aminocaproic acid in engineered Escherichia coli with artificial protein cage-organized enzymatic cascades.
    Ruoshi Luo, Lin Hu, Dan Wang, Kaixing Xiao, Xuemei Liu, Yaqi Kang, Qinhong Wang.
      Microbial synthesis of 6-aminocaproic acid (6-ACA), a key nylon-6 monomer, was the focus of this study. Our previous work on 6-ACA biosynthesis using an artificial iterative carbon-chain-extension cycle showed potential, but the impact of intermediates on metabolism remained unresolved. To address this, a bacterial microcompartment (BMC) was engineered in Escherichia coli to encapsulate 6-ACA synthesis enzymes, effectively controlling the release of intermediate products. This intervention led to a 90.85 % increase in cell growth and a final 6-ACA yield increase from 46.76 mg/L to 1.12 g/L in a 1 L fermentor. The redesigned BMC demonstrated potential in regulating cascade enzymatic catalysis, particularly in managing intermediates that could impact enzyme proteins, cause cytotoxicity, or DNA damage in cells. This work highlights the potential of the redesigned BMC in enhancing production by controlling the effects of intermediates on cellular processes.
    Keywords:  6-aminocaproic acid; Bacterial microcompartment; Compartmentalization; Enzymatic cascade reactions
    DOI:  https://doi.org/10.1016/j.biortech.2025.132641
  31. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2415056122
    Unbiased mechanical cloaks.
    Fernando Vasconcelos Senhora, Emily D Sanders, Glaucio H Paulino.
      The distinction between "reinforcement" and "cloaking" has been overlooked in optimization-based design of devices intended to conceal a defect in an elastic medium. In the former, a so-called "cloak" is severely biased toward one or a few specific elastic disturbances, whereas in the latter, an "unbiased cloak" is effective under any elastic disturbance. We propose a two-stage approach for optimization-based design of elastostatic cloaks that targets true, unbiased cloaks. First, we perform load-case optimization to find a finite set of worst-case design loads. Then we perform topology optimization of the cloak microstructure under these worst-case loads using a judicious choice of the objective function, formulated in terms of energy mismatch. Although a small subset of the infinite load cases that the cloak must handle, these highly nonintuitive, worst-case loads lead to designs that approach perfect and unbiased elastostatic cloaking. In demonstration, we consider elastic media composed of spinodal architected materials, which provides an ideal testbed for exploring elastostatic cloaks in media with varying anisotropy and porosity, without sacrificing manufacturability. To numerically verify the universal nature of our cloaks, we compare the elastic response of the medium containing the cloaked defect to that of the undisturbed medium under many random load cases not considered during design. By using digital light processing additive manufacturing to realize the elastic media containing cloaked defects and analyzing their response experimentally using compression testing with digital image correlation, this study provides a physical demonstration of elastostatic cloaking of a three-dimensional defect in a three-dimensional medium.
    Keywords:  architected materials; elastostatic cloaking; structural optimization
    DOI:  https://doi.org/10.1073/pnas.2415056122
  32. ACS Synth Biol. 2025 May 06.
    A Robust and Orthogonal Far-Red Light Sensor for Gene Expression Control in Escherichia coli.
    Yueyang Sun, Mengran Xu, Baiyang Wang, Chenyang Xia, Zhiming He, Bowen Lu, Jiyun Cui, Qiancheng Liao, Qi Xu, Fei Gan.
      Optogenetics has emerged as a powerful tool for regulating cellular processes due to its noninvasive nature and precise spatiotemporal control. Far-red light (FRL) has increasingly been used in the optogenetic control of mammalian cells due to its low toxicity and high tissue penetration. However, robust and orthogonal FRL sensors are lacking in bacteria. Here, we established an orthogonal FRL sensor in Escherichia coli with a maximum dynamic range exceeding 230-fold based on the RfpA-RfpC-RfpB (RfpABC) signaling system that regulates the far-red light photoacclimation (FaRLiP) in cyanobacteria. We identified a conserved DNA motif in the promoter sequences of the Chl f synthase gene and other genes in the FaRLiP gene clusters, termed the far-red light-regulatory (FLR) motif, which enables the light-responsive activation of gene expression through its interaction with RfpB. Based on the FLR motif, we simplified the FLR-containing promoters and characterized their activation abilities and dynamic ranges, which can be utilized in different synthetic biology scenarios. Additionally, one or two FLR motifs are present at other loci within the FaRLiP gene cluster, providing further FRL-inducible promoter resources. The FRL sensor exhibits effective activation and suppression under low-intensity FRL and white light, respectively, and remains functional in darkness. In conclusion, this study advances the understanding of the regulatory mechanisms of FaRLiP in cyanobacteria and provides robust and orthogonal FRL sensors for synthetic biology applications.
    Keywords:  DNA motif; E. coli; far-red light; far-red light photoacclimation; optogenetics; two-component system
    DOI:  https://doi.org/10.1021/acssynbio.5c00044
  33. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2423293122
    Interspecies interactions in dual, fibrous gels enable control of gel structure and rheology.
    Mauro L Mugnai, Rose Tchuenkam Batoum, Emanuela Del Gado.
      Natural and synthetic multicomponent gels display emergent properties, which implies that they are more than just the sum of their components. This warrants the investigation of the role played by interspecies interactions in shaping gel architecture and rheology. Here, using computer simulations, we investigate the effect of changing the strength of the interactions between two species forming a fibrous double network. Simply changing the strength of interspecies lateral association, we generate two types of gels: one in which the two components demix and another one in which the two species wrap around each other. We show that demixed gels have structure and rheology that are largely unaffected by the strength of attraction between the components. In contrast, architecture and material properties of intertwined gels strongly depend on interspecies "stickiness" and volume exclusion. These results can be used as the basis of a design principle for double networks which are made to emphasize either stability to perturbations or responsiveness to stimuli. Similar ideas could be used to interpret naturally occurring multicomponent gels.
    Keywords:  double-networks; gels; soft materials
    DOI:  https://doi.org/10.1073/pnas.2423293122
  34. Angew Chem Int Ed Engl. 2025 May 08. e202421803
    Remote Control of Eukaryotic Gene Expression by a Modular Ultrasound-Responsive RNA Toolkit.
    Andreas Herrmann, Fahimeh Charbgoo, Aman Ishaqat, Junlin Chen, Fabian Wiertz, Adrian Kuzmanović, Matthias Bartneck, Fabian Kiessling.
      Achieving remote control of biological processes remains a significant challenge in genetics. Although ultrasound has been employed to remotely regulate biological functions by targeting mechanosensitive ion channels, existing systems are constrained by the limited responsiveness of specific channels to specific ultrasound frequencies and their applicabaility to only a few cell types. Sonogenetics has shown promise for promoter control, thereby regulating gene transcription in eukaryotes. Here, we introduce a new modular toolkit for regulating gene expression using ultrasound-responsive RNA carriers capable of releasing small molecule modulators in response to a broad spectrum of ultrasound frequencies. The cells contain engineered mRNA structures encoding riboswitches or aptazymes, which respond specifically to these small molecule modulators finally controlling downstream protein expression by biocompatible ultrasound. This toolkit is versatile, functioning across various eukaryotic systems-from yeast to mammalian cells-and offers control over gene expression by regulating mRNA translation. We demonstrated that this sonogenetic toolkit robustly modulates gene expression, achieving up to a six-fold downregulation of protein levels in response to ultrasound stimulation. By expanding the application of sonogenetics across eukaryots, this RNA-based toolkit might provide a promising platform for remotely controlling protein function in specific tissues through on-demand ultrasound activation in the future.
    Keywords:  Gene expression regulation; RNA; Rolling Circle Transcription; Sonogenetics; Ultrasound-responsive Systems
    DOI:  https://doi.org/10.1002/anie.202421803
  35. Small. 2025 May 07. e2502436
    Restructuring of Hydrogel Polymer Networks via Ion Storming.
    Weicheng Kong, Yuling Lu, Ximin Yuan, Yong He.
      Hydrogel is a 3D network gel with high hydrophilicity, and its mechanical properties are weakened by the disordered polymer network. Although traditional techniques such as directional freezing and salting-out improve the mechanical properties of the hydrogel, the biomedical and chemical engineering applications are limited by the complex processing procedures. In view of this situation, an urgent demand for the non-intrusive in situ hydrogel processing technique is required, and the disordered polymer network resembles a tangled yarn that can be unraveled through the external electric field. It is of interest to elucidate whether there are countless ions at the atomic-scale that can instantly align the disordered polymer networks in the hydrogel. In this study, it is first demonstrated that these ions can move in the hydrogels under the action of the electric field. The rapid ion vibrations break the hydrogen bonds to restructure the networks under the action of the high-frequency electric field, and the soft hydrogel is formed; while that generates the coordination under the action of the low-frequency field, and the tough hydrogel is obtained. This technique integrates the structure and material in the hydrogels, which enhances the mechanical properties of the 3D-printed hydrogel components.
    Keywords:  coordination; electric training; hydrogel; ion storm; mechanical property; training solution
    DOI:  https://doi.org/10.1002/smll.202502436
  36. ACS Appl Mater Interfaces. 2025 May 06.
    Organic Fouling on Zwitterionic Amphiphilic Copolymers: Implications in Biofouling.
    Meng Wang, Murchana Sarma, Samuel J Lounder, Abhishek Narayan Mondal, Lavanya Muthusamy, Goutam Koley, Ayse Asatekin, Debora F Rodrigues.
      Zwitterionic amphiphilic copolymers (ZACs) have shown promise in resisting the attachment of oil emulsions, proteins, and organic biomolecules, suggesting their potential to prevent microbial adhesion as well. However, there is a lack of comprehensive studies exploring the role of ZACs in regulating cell deposition and subsequent biofilm formation on surfaces. Here, we fabricated ZAC coatings including poly(trifluoroethyl methacrylate-random-sulfobetaine methacrylate) (PTFEMA-r-SBMA or PT:SBMA), poly(trifluoroethyl methacrylate-random-2-methacryloyloxyethyl phosphorylcholine) (PTFEMA-r-MPC or PT:MPC), poly(methyl methacrylate-random-sulfobetaine methacrylate) (PMMA-r-SBMA or PM:SBMA), and poly(methyl methacrylate-random-2-methacryloyloxyethyl phosphorylcholine) (PMMA-r-MPC or PM:MPC). These coatings were assessed for their resistance to conditioning with organic molecules, attachment of Gram-positive, Bacillus subtilis TR11 (B. subtilis), and Gram-negative, Escherichia coli K12 (E. coli), bacteria, and subsequent biofilm formation. Surface characterizations highlighted the role of organic molecule conditioning from the media in altering the ZAC-coated surface properties, subsequently influencing bacterial deposition and biofilm growth. Cell deposition results revealed that all ZAC coatings displayed higher resistance to B. subtilis attachment compared to E. coli, indicating that bacterial adhesion to the surfaces depends on the type of bacteria. Among the tested ZAC coatings, PT: SBMA demonstrated the highest potential for resisting adhesion by both types of bacterial cells as well as exhibiting lower surface energy and lower roughness after organic medium conditioning. These findings contribute to enhancing our fundamental understanding of how zwitterionic materials control biofouling.
    Keywords:  Bacillus subtilis TR11; Escherichia coli K12; biofouling; coatings; zwitterionic amphiphilic copolymers (ZACs)
    DOI:  https://doi.org/10.1021/acsami.5c07057
  37. Epigenomics. 2025 May 06. 1-3
    Selective chemical tracking of DNA methylomes in live cells.
    Vaidotas Stankevičius, Liepa Gasiulė, Giedrius Vilkaitis, Saulius Klimašauskas.
      
    Keywords:  DNA methylation; DNMT1; catalysis-dependent DNA labeling; embryonic stem cells; epigenomic tools; methyltransferase reaction engineering; synthetic AdoMet analogs
    DOI:  https://doi.org/10.1080/17501911.2025.2500914
  38. Appl Microbiol Biotechnol. 2025 May 08. 109(1): 116
    In silico identification of gene targets to enhance C12 fatty acid production in Escherichia coli.
    Paul Matthay, Thomas Schalck, Kenneth Simoens, Dorien Kerstens, Bert Sels, Natalie Verstraeten, Kristel Bernaerts, Jan Michiels.
      The global interest in fatty acids is steadily rising due to their wealth of industrial potential ranging from cosmetics to biofuels. Unfortunately, certain fatty acids, such as monounsaturated lauric acid with a carbon atom chain length of twelve (C12 fatty acids), cannot be produced cost and energy-efficiently using conventional methods. Biosynthesis using microorganisms can overcome this drawback. However, rewiring a microbe's metabolome for increased production remains challenging. To overcome this, sophisticated genome-wide metabolic network models have become available. These models predict the effect of genetic perturbations on the metabolism, thereby serving as a guide for metabolic pathways optimization. In this work, we used constraint-based modeling in combination with the algorithm Optknock to identify gene deletions in Escherichia coli that improve C12 fatty acid production. Nine gene targets were identified that, when deleted, were predicted to increase C12 fatty acid titers. Targets play a role in anaplerotic reactions, amino acid synthesis, carbon metabolism, and cofactor-balancing. Subsequently, we constructed the corresponding (combinatorial) deletion mutants to validate the in silico predictions in vivo. Our highest producer (ΔmaeB Δndk ΔpykA) reaches a titer of 6.7 mg/L, corresponding to a 7.5-fold increase in C12 fatty acid production. This study demonstrates that model-guided metabolic engineering is a useful tool to improve C12 fatty acid production. KEY POINTS: •Escherichia coli as a promising biofactory for unsaturated C12 fatty acids. •Optknock to identify non-obvious gene deletions for increased C12 fatty acids. •7.5-fold higher C12 fatty acid production achieved by deleting maeB, ndk, and pykA.
    Keywords:   Escherichia coli ; C12 fatty acids; Lauric acid; Model-guided metabolic engineering; Oleochemicals ; Optknock
    DOI:  https://doi.org/10.1007/s00253-025-13501-6
  39. Nat Commun. 2025 May 09. 16(1): 4320
    Meter-scale heterostructure printing for high-toughness fiber electrodes in intelligent digital apparel.
    Gun-Hee Lee, Yunheum Lee, Hyeonyeob Seo, Kyunghyun Jo, Jinwook Yeo, Semin Kim, Jae-Young Bae, Chul Kim, Carmel Majidi, Jiheong Kang, Seung-Kyun Kang, Seunghwa Ryu, Seongjun Park.
      Intelligent digital apparel, which integrates electronic functionalities into clothing, represents the future of healthcare and ubiquitous control in wearable devices. Realizing such apparel necessitates developing meter-scale conductive fibers with high toughness, conductivity, stable conductance under deformation, and mechanical durability. In this study, we present a heterostructure printing method capable of producing meter-scale (~50 m) biphasic conductive fibers that meet these criteria. Our approach involves encapsulating deformable liquid metal particles (LMPs) within a functionalized thermoplastic polyurethane matrix. This encapsulation induces in situ assembly of LMPs during fiber formation, creating a heterostructure that seamlessly integrates the matrix's durability with the LMPs' superior electrical performance. Unlike rigid conductive materials, deformable LMPs offer stretchability and toughness with a low gauge factor. Through precise twisting using an engineered annealing machine, multiple fiber strands are transformed into robust, electrically stable meter-scale electrodes. This advancement enhances their practicality in various intelligent digital apparel applications, such as stretchable displays, wearable healthcare systems, and digital controls.
    DOI:  https://doi.org/10.1038/s41467-025-59703-4
  40. Nat Commun. 2025 May 05. 16(1): 4173
    Visualization of photocuring and 4D printing with real-time phosphorescence.
    Fan Gu, Mengxing Ji, Lisha Zhang, Tengjiao Zhao, Ruiqing Zhang, Xia Lv, He Tian, Xiang Ma.
      Facile and real-time visualization monitoring of photocuring process is a challenge. Base on the fact that pure organic room-temperature phosphorescence (RTP) is quite sensitive and easy to be regulated via internal rigidity changes of the surrounding environments of phosphore dyes, competitive organic candidates with advantageous RTP are brought into the fields of photocuring and 4D printing materials. Herein, we have put forward a strategy to introduce phosphors into photocuring materials because of the rigidity-increasing liquid-to-solid transformation. Based on this, the obtained luminescent curing films achieve RTP emission with full-color display of blue, green, and orange. Visible real-time monitoring can be realized by observations of phosphorescent changes, thus allowing the recording of curing speed, internal environment, and conversion during the curing process. Moreover, these curing materials successfully complete 4D printing and shape-memory process, demonstrating continuous dynamic deformation in fabricated 2D materials (the fabricated flower-pattern film) and 3D materials (the spaceman and pandas) with vivid RTP emission. Especially, the further regulations of the real-time phosphorescence can realize significant visualization in these 4D printing materials. We believe this discovery with the replacement of phosphors opens a door to further extension in the field of curing materials and more sophisticated morphing in 4D printing.
    DOI:  https://doi.org/10.1038/s41467-025-59502-x
  41. PLoS Genet. 2025 May;21(5): e1011639
    Coordination of cell envelope biology by Escherichia coli MarA protein potentiates intrinsic antibiotic resistance.
    Alexandra E Trigg, Prateek Sharma, David C Grainger.
      The multiple antibiotic resistance activator (MarA) protein is a transcription factor implicated in control of intrinsic antibiotic resistance in enteric bacterial pathogens. In this work, we screened the Escherichia coli genome computationally for MarA binding sites. By incorporating global maps of transcription initiation, and clustering predicted targets according to gene function, we were able to avoid widespread misidentification of MarA sites, which has hindered prior studies. Subsequent genetic and biochemical analyses identified direct activation of genes for lipopolysaccharide (LPS) biosynthesis and repression of a cell wall remodelling endopeptidase. Rewiring of the MarA regulon, by mutating subsets of MarA binding sites, reveals synergistic interactions between regulatory targets of MarA. Specifically, we show that uncoupling LPS production, or cell wall remodelling, from regulation by MarA, renders cells hypersensitive to mutations altering lipid trafficking by the MlaFEDCB system. Together, our findings demonstrate how MarA co-regulates different aspects of cell envelope biology to maximise antibiotic resistance.
    DOI:  https://doi.org/10.1371/journal.pgen.1011639
  42. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2502425122
    Molecular insights into de novo small-molecule recognition by an intron RNA structure.
    Tianshuo Liu, Ling Xu, Kevin Chung, Luke J Sisto, Jimin Hwang, Chengxin Zhang, Michael C Van Zandt, Anna Marie Pyle.
      Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the resulting cocomplexes for guiding optimization. Here, we leveraged high-throughput screening, medicinal chemistry, and structural biology to identify a de novo splicing inhibitor against a large and highly folded fungal group I intron. High-resolution cryoEM structures of the intron in different liganded states not only reveal molecular interactions that rationalize experimental structure-activity relationship but also shed light on a unique strategy whereby RNA-associated metal ions and RNA conformation exhibit exceptional plasticity in response to small-molecule binding. This study reveals general principles that govern RNA-ligand recognition, the interplay between chemical bonding specificity, and dynamic responses within an RNA target.
    Keywords:  RNA-targeting ligands; RNA–ligand recognition; cryoEM; high-throughput screening; splicing inhibitor
    DOI:  https://doi.org/10.1073/pnas.2502425122
  43. J Cell Sci. 2025 May 01. pii: jcs263753. [Epub ahead of print]138(9):
    The role of mitochondrial mRNA translation in cellular communication.
    Eleonora Zilio, Tim Schlegel, Marta Zaninello, Elena I Rugarli.
      Mitochondria are dynamic and heterogeneous organelles that rewire their network and metabolic functions in response to changing cellular needs. To this end, mitochondria integrate a plethora of incoming signals to influence cell fate and survival. A crucial and highly regulated node of cell-mitochondria communication is the translation of nuclear-encoded mitochondrial mRNAs. By controlling and monitoring the spatio-temporal translation of these mRNAs, cells can rapidly adjust mitochondrial function to meet metabolic demands, optimise ATP production and regulate organelle biogenesis and turnover. In this Review, we focus on how RNA-binding proteins that recognise nuclear-encoded mitochondrial mRNAs acutely modulate the rate of translation in response to nutrient availability. We further discuss the relevance of localised translation of these mRNAs for subsets of mitochondria in polarised cells. Finally, we highlight quality control mechanisms that monitor the translation process at the mitochondrial surface and their connections to mitophagy and stress responses. We propose that these processes collectively contribute to mitochondrial specialisation and signalling function.
    Keywords:  Cell signalling; Mitochondria; RNA-binding proteins; Ribosome quality control; Translation; mRNA
    DOI:  https://doi.org/10.1242/jcs.263753
  44. Metab Eng. 2025 May 05. pii: S1096-7176(25)00075-8. [Epub ahead of print]
    Beyond CEN.PK - parallel engineering of selected S. cerevisiae strains reveals that superior chassis strains require different engineering approaches for limonene production.
    Yanmei Zhu, Sasha Yogiswara, Anke Willekens, Agathe Gérardin, Rob Lavigne, Alain Goossens, Vitor B Pinheiro, Zongjie Dai, Kevin J Verstrepen.
      Genetically engineered microbes are increasingly utilized to produce a broad range of high-value compounds. However, most studies start with only a very narrow group of genetically tractable type strains that have not been selected for maximum titers or industrial robustness. In this study, we used high-throughput screening and parallel metabolic engineering to identify and optimize Saccharomyces cerevisiae chassis strains for the production of limonene, a monoterpene with applications in flavors, fragrances, and biofuels. We screened 921 genetically and phenotypically distinct S. cerevisiae strains for limonene tolerance and lipid content to identify optimal chassis strains for precision fermentation of limonene. In parallel, we also evaluated 16 different plant limonene synthases. Our results revealed that two of the selected strains showed approximately a 2-fold increase in titers compared to CEN.PK2-1C, the type strain that is often used as a chassis for limonene production, with the same genetic modifications in the mevalonate pathway. Intriguingly, the most effective engineering strategy proved strain-specific. Metabolic profiling revealed that this difference is likely explained by differences in native mevalonate production. Ultimately, by using strain-specific engineering strategies, we achieved 844 mg/L in a new strain, 40% higher than the titer (605 mg/L) achieved by CEN.PK2-1C. Our findings demonstrate the potential of leveraging genetic diversity in S. cerevisiae for monoterpene bioproduction and highlight the necessity for tailoring metabolic engineering strategies to specific strains.
    Keywords:  Saccharomyces cerevisiae; chassis strain; limonene; mevalonate pathway; microbial cell factory; precision fermentation
    DOI:  https://doi.org/10.1016/j.ymben.2025.04.011
  45. Cold Spring Harb Perspect Biol. 2025 May 05. pii: a041497. [Epub ahead of print]
    Epigenetics Beyond the Cell: Supracellular Organization of Fate and Form in Morphogenesis.
    Rubens Sautchuk, Sichen Yang, Amy Shyer, Alan Rodrigues.
      How biological systems obtain their shape and structure is a fundamental question with many practical implications. Like much of biology, over the last several decades, tissue and organ morphogenesis has focused on uncovering regulatory mechanisms at the cellular and subcellular scales. Such studies have either implicitly or explicitly reified the view that the creation of form is instructed or controlled by a combination of genetic and molecular processes. However, pioneering early twentieth century biological theorists such as Conrad Waddington cautioned against the total subsummation of biology by, for instance, biochemistry and molecular biology. Through the coining of terms such as "epigenotype," it was argued that processes at every scale between genotype and phenotype were necessary to organize morphogenesis. Thus, organizing processes exist that are not reducible merely to the sum of inputs from "genes" and "environment." Here, we argue that uncovering generative epigenetic processes beyond the cell yet within the organism requires a holistically oriented use of physical concepts involving mechanics and material phases. To uncover and clearly articulate such "supracellular" processes, we discuss how relations between mesenchymal cells and extracellular matrix (ECM) serve as a powerful model system. Based on the study of mesenchymal-ECM systems, we suggest that it may not be possible to understand the ultimate functional role of gene products such as signaling molecules without an appreciation of supracellular processes in their own right.
    DOI:  https://doi.org/10.1101/cshperspect.a041497
  46. Nature. 2025 May 08.
    Daily briefing: How we taste sweetness.
    Jacob Smith.
      
    DOI:  https://doi.org/10.1038/d41586-025-01492-3
  47. Trends Genet. 2025 May 06. pii: S0168-9525(25)00081-2. [Epub ahead of print]
    Moving towards sequencing-based metabolomics.
    Alia Clark-ElSayed, Andrew D Ellington, Edward M Marcotte.
      Metabolites are chemically heterogeneous and difficult to quantify in easily read formats. Recently, Tan and Fraser demonstrated that metabolites can be readily quantified by pairing aptamer function with DNA sequencing. This reflects a larger trend of sequencing for assessing biomolecule abundances, further leading to sequencing being a universal analytical tool.
    Keywords:  DNA sequencing; aptamers; high-throughput metabolomics
    DOI:  https://doi.org/10.1016/j.tig.2025.04.006
  48. ACS Nano. 2025 May 07.
    Material Design for Durable Lubricant-Infused Surfaces That Can Reduce Liquid and Solid Fouling.
    Fan-Wei Wang, Jianxing Sun, Anish Tuteja.
      Liquid and solid fouling is a pervasive problem in numerous natural and industrial settings, significantly impacting energy efficiency, greenhouse emissions, operational costs, equipment lifespan, and human health. Inspired by pitcher plants, recently developed lubricant-infused surfaces (LISs) demonstrate resistance to both liquid and solid accretion under diverse environmental conditions, offering a potential solution to combat various foulants such as ice, bacteria, and mineral deposits. However, the commercial viability for most fouling-resistant LISs has thus far been compromised due to the challenges associated with maintaining a stable lubricant layer during operation. This review aims to address this important concern by providing systematic material design guidelines for fabricating durable LISs. We discuss fundamental design principles, methods for evaluating fouling resistance, and strategies to prevent lubricant loss. By presenting a comprehensive design methodology for this important class of materials, this review aims to aid future advancements in the field of antifouling surfaces, potentially impacting a variety of industries ranging from marine engineering to medical device manufacturing.
    Keywords:  Lubricant-infused surface; adhesion; biofouling; fouling; liquid-like polymer brush; lubricant depletion; material design; solid slippery surface; wettability
    DOI:  https://doi.org/10.1021/acsnano.5c03214
  49. ACS Appl Mater Interfaces. 2025 May 06.
    DNA Organogels Gaining Multifunctions from the Contribution of Molecular Design on Cross-Linker.
    Zhongtao Wu, Kang Wang, Huixuan Gan, Xu Zhang, Xue Zhou, Congxia Xie, Jia Chen, Zhen Wang, Yun Liu, Lei Zhang.
      DNA gels have been receiving considerable attention for their good therapeutic and biomedical potential. However, it remains a great challenge for DNA gels to achieve a good combination of high mechanical performance and stimuli responsiveness. In this work, a molecular designing strategy is developed for fabricating a high-performance DNA gel using long sequenced DNA and a tetraphenylethene-containing surfactant. Comprising different structural motifs, the designed surfactant could serve as a contact point for creating a strong and flexible cross-linking network between DNA molecules through noncovalent interactions. The resulting DNA gel gains an impressive adhesion of 7.58 ± 0.49 MPa, which addresses the top level of high-performance DNA gels. Such a DNA gel shows generous adhesion with various materials and good temperature tolerance. The good biosafety and wound-healing promoting effect would also open its potential use in biological and biomedical areas. Additionally, this DNA gel possesses fluorescence for easy detection, achieving a combination of high mechanical performance and stimuli responsiveness. This work presents a design strategy for gaining robust DNA materials with a combination of different physicochemical properties together.
    Keywords:  AIE; DNA material; adhesion; gel; high-performance material
    DOI:  https://doi.org/10.1021/acsami.5c06743
  50. Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2422255122
    Phase separation in mitochondrial fate and mitochondrial diseases.
    Qingyi Chen, Sanqi An, Chuanlong Wang, Yanshuang Zhou, Xingguo Liu, Wenkai Ren.
      Mitochondria are central metabolic organelles that control cell fate and the development of mitochondrial diseases. Traditionally, phase separation directly regulates cell functions by driving RNA, proteins, or other molecules to concentrate into lipid droplets. Recent studies show that phase separation regulates cell functions and diseases through the regulation of subcellular organelles, particularly mitochondria. In fact, phase separation is involved in various mitochondrial activities including nucleoid assembly, autophagy, and mitochondria-related inflammation. Here, we outline the key mechanisms through which phase separation influences mitochondrial activities and the development of mitochondrial diseases. Insights into how phase separation regulates mitochondrial activities and diseases will help us develop interventions for related diseases.
    Keywords:  mitochondrial disease; mitochondrial dynamics; mitophagy; nucleoid assembly; phase separation
    DOI:  https://doi.org/10.1073/pnas.2422255122
  51. Biofabrication. 2025 May 07.
    Biofabrication of microstructured bacterial ecosystems using chaotic bioprinting: advancing in vitro research for microbial engineering.
    Ariel Cantoral Sánchez, Oscar Emmanuel Solís-Pérez, Francisco Javier Javier Flores Loera, Claudia Maribel Luna-Aguirre, Luis Fernando Carmona Ramirez, Ilsa Pamela De Los Santos-Hernández, Nora Greys Greys Zamora Benavides, Mara Neher, Grissel Trujillo-de Santiago, Mario Moisés Álvarez.
      Mixed microbial communities are essential for various ecosystems, with bacteria often exhibiting unique behaviors in structured environments. However, replicating these interactions in vitro remains challenging, as traditional microbiology techniques based on well-mixed cultures fail to capture the spatial organization of natural communities.
Chaotic 3D printing offers a versatile, high-throughput method for fabricating hydrogel constructs with multilayered microstructure in which different bacterial strains can coexist, closely mimicking the partial segregation seen in natural microbial ecosystems. Using a Kenics static mixer (KSM) printing nozzle, we bioprinted a bacterial consortium consisting of Lactobacillus rhamnosus, Bifidobacterium bifidum, and Escherichia coli as a simplified model for human gut microbiota. Chaotic bioprinting enabled the creation of microstructured cocultures with distinct niches, allowing all bacterial strains to coexist (without being scrambled) and reach a population equilibrium.
We characterized the cocultures through fluorescence microscopy, colony counting, and quantitative polymerase chain reactions (qPCR). Our results demonstrate that the microarchitecture of the printed fibers significantly influences bacterial growth dynamics. Stratified arrangements enhanced coculture viability and balance over 72 hours compared to well-mixed and suspension conditions. Chaotic printing also allows the rational arrangement of strict anaerobic bacteria, such as B. bifidum, by positioning them in construct layers that are more susceptible to hypoxia.
Chaotic bioprinting presents a powerful tool for engineering microbial ecosystems with precise spatial control. This approach holds promise for advancing our understanding of microbial interactions and has potential biomedical applications in antibiotic testing, microbiota research, bioremediation, and synthetic biology.&#xD.
    Keywords:  Bioprinting; bacteria; chaotic; coculture; microbial ecosystems; microbiota; structured
    DOI:  https://doi.org/10.1088/1758-5090/add568
  52. EMBO J. 2025 May 08.
    Control of replication and gene expression by ADP-ribosylation of DNA in Mycobacterium tuberculosis.
    Rachel E Butler, Marion Schuller, Ritu Jaiswal, Jayanta Mukhopadhyay, Jim Barber, Suzie Hingley-Wilson, Emily Wasson, Alex Couto Alves, Ivan Ahel, Graham R Stewart.
      Mycobacterium tuberculosis maintains long-term infections characterised by the need to regulate growth and adapt to contrasting in vivo environments. Here we show that M. tuberculosis complex bacteria utilise reversible ADP-ribosylation of single-stranded DNA as a mechanism to coordinate stationary phase growth with transcriptional adaptation. The DNA modification is controlled by DarT, an ADP-ribosyltransferase, which adds ADP-ribose to thymidine, and DarG, which enzymatically removes this base modification. Using darG-knockdown M. bovis BCG, we map the first DNA ADP-ribosylome from any organism. We show that inhibition of replication by DarT is reversible and accompanied by extensive ADP-ribosylation at the origin of replication (OriC). In addition, we observe ADP-ribosylation across the genome and demonstrate that ADP-ribose-thymidine alters the transcriptional activity of M. tuberculosis RNA polymerase. Furthermore, we demonstrate that during stationary phase, DarT-dependent ADP-ribosylation of M. tuberculosis DNA is required to optimally induce expression of the Zur regulon, including the ESX-3 secretion system and multiple alternative ribosome proteins. Thus, ADP-ribosylation of DNA can provide a mechanistic link through every aspect of DNA biology from replication to transcription to translation.
    Keywords:  ADP-ribosylation; ADPr-Seq; DNA Modification; PARP; Transcription Regulation
    DOI:  https://doi.org/10.1038/s44318-025-00451-y
  53. ACS Appl Mater Interfaces. 2025 May 08.
    Multistage Networks for Glassy Holographic Photopolymers.
    Alexander J Osterbaan, Andrew N Sias, Marianela Trujillo-Lemon, Kieran Fung, Jason P Killgore, Robert R McLeod, Christopher N Bowman.
      In the writing of holographic photopolymers, the addition of a third-stage cure to the typical polyurethane matrix and acrylate writing monomer steps is used here to modify the ultimate thermomechanical properties of the final holographic photopolymer. Inclusion of a thermally latent, low-refractive-index epoxide homopolymerization increases the Tg from a value of -22 °C during the writing step to a final Tg of 101 °C after the epoxide cure. Critically, the diffraction grating structure is retained with high fidelity, an index contrast of 0.0057, and a diffraction efficiency of 89% achieved in these materials. Ultimately, the 3-stage design and final glassy nature of these materials promote thermal and dimensional stability of the final holographic material.
    Keywords:  acrylate; diffraction; dual-cure; epoxide; holography; multistage network; optical grating; photopolymer
    DOI:  https://doi.org/10.1021/acsami.5c04731
  54. Nat Commun. 2025 May 06. 16(1): 4216
    Cost-effective urine recycling enabled by a synthetic osteoyeast platform for production of hydroxyapatite.
    Isaak E Müller, Alex Y W Lin, Yusuke Otani, Xinyi Zhang, Zong-Yen Wu, David Kisailus, Nigel J Mouncey, Jeremy S Guest, Behzad Rad, Peter Ercius, Yasuo Yoshikuni.
      Recycling human urine offers a sustainable solution to environmental challenges posed by conventional wastewater treatment. While it is possible to recover nutrients like nitrogen and phosphorus from urine, the low economic value of these products limits large-scale adoption. Here, we show that engineered yeast can convert urine into hydroxyapatite (HAp), a high-value biomaterial widely used in bone and dental applications. Inspired by the biological mechanisms of bone-forming cells, we develop a synthetic yeast platform osteoyeast, which uses enzymes to break down urea and increase the pH of the surrounding environment. This triggers the yeast vacuoles to accumulate calcium and phosphate as amorphous calcium phosphate, which is then secreted in vesicles and crystallized into HAp. We achieve HAp production at titers exceeding 1 g/L directly from urine. Techno-economic analysis demonstrates that this process offers clear economic and environmental advantages, making it a compelling strategy for high-value resource recovery from human waste.
    DOI:  https://doi.org/10.1038/s41467-025-59416-8
  55. Angew Chem Int Ed Engl. 2025 May 03. e202425479
    On-demand Ligate and Release Strategy based on Photoclick Reaction in Tandem with Pd-mediated Deallylation.
    Boon Shing Loh, Hanqing Pang, Soh Wah Yong, Cheng Weng, Wee Han Ang.
      The development of chemoselective tools that can conjugate, modify and decouple chemical groups from biomacromolecules has enabled the study of biological processes at increasing levels of fidelity. Until recently, these tools can either couple chemical entities to biomacromolecules or decouple them, but not both. A method that can perform these functions in distinct steps on demand would be highly useful. To that end, we devised a new-to-nature strategy by bringing together and modifying two biocompatible transformations. In this new strategy, ligation is accomplished via the photoclick reaction between an allenyl motif with 9,10-phenanthrenequinone which installs an allyl group at the site of conjugation. This allyl group can then be selectively utilized as a handle for phenolic release via Pd-mediated deallylation. As a proof of concept, we demonstrated its utility in the selective labelling and delabelling of model protein scaffolds and cellular matrix. This multifunctional method paves the way for controllable "ligate and release" strategy that enables on-demand visualization of biological entities but with an in-built release mechanism to restore their original state.
    Keywords:  Bioorthogonal chemistry; Deallylation; Labelling; Ligate-and-Release; Photoclick reaction
    DOI:  https://doi.org/10.1002/anie.202425479
  56. Structure. 2025 Apr 30. pii: S0969-2126(25)00144-3. [Epub ahead of print]
    The YEATS domain is a selective reader of histone methacrylation.
    Dustin C Becht, Jiabao Song, Karthik Selvam, Kejun Yin, Weizhi Bai, Yingming Zhao, Ronghu Wu, Y George Zheng, Tatiana G Kutateladze.
      Metabolically regulated lysine acylation modifications in proteins play a major role in epigenetic processes and cellular homeostasis. A new type of histone acylation, lysine methacrylation, has recently been identified but remains poorly characterized. Here, we show that lysine methacrylation can be generated through metabolism of sodium methacrylate and enzymatically removed in cells, and that the YEATS domain but not bromodomain recognizes this modification. Structural and biochemical analyses reveal the π-π-π-stacking mechanism for binding of the YEATS domain of ENL to methacrylated histone H3K18 (H3K18mc). Using mass spectrometry proteomics, we demonstrate that methacrylate induces global methacrylation of a set of proteins that differs from the set of methacrylated proteins associated with valine metabolism. These findings suggest that high levels of methacrylate may potentially perturb cellular functions of these proteins by altering protein methacrylation profiles.
    Keywords:  PTM; YEATS; acetylation; bromodomain; epigenetic; methacrylation
    DOI:  https://doi.org/10.1016/j.str.2025.04.010
  57. Nature. 2025 May 06.
    Naturally ornate RNA-only complexes revealed by cryo-EM.
    Rachael C Kretsch, Yuan Wu, Svetlana A Shabalina, Hyunbin Lee, Grace Nye, Eugene V Koonin, Alex Gao, Wah Chiu, Rhiju Das.
      Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures1-4. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryogenic electron microscopy at resolutions of 2.9-3.1 Å. Without precedent among previously characterized natural RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Ornate, Large (ROOL), and Ornate Large Extremophilic (OLE) RNAs form homo-oligomeric complexes whose stoichiometries are retained at concentrations lower than expected in the cell. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, empty except for a disordered loop. Extensive intra- and intermolecular A-minor interactions, kissing loops, an unusual A-A helix, and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.
    DOI:  https://doi.org/10.1038/s41586-025-09073-0
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