bims-enlima Biomed News
on Engineered living materials
Issue of 2025–05–18
39 papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Adaptations of Gram-Negative and Gram-Positive Probiotic Bacteria in Engineered Living Materials.
  2. Bioinspired nondissipative mechanical energy storage and release in hydrogels via hierarchical sequentially swollen stretched chains.
  3. Design of nondeterministic architected structures via bioinspired distributed agents.
  4. Extreme nonlinearity by layered materials through inverse design.
  5. Bacterial Cells Engineered with Synthetic Genetic Materials for Blind Testing of Random Mutagenesis.
  6. Hybrid Plasmonic Bioresins and dECM-Based Materials for Volumetric Bioprinting of Vascular-Inspired Architectures.
  7. Biocompatible composite hydrogel with on-demand swelling-shrinking properties for 4D bioprinting.
  8. Co-initiating-system dual-mechanism drives the design of printable entangled polymer multinetworks.
  9. Prediction of protein subcellular localization in single cells.
  10. FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data.
  11. Mussel-Inspired Molecular Strategies for Fabricating Functional Materials With Underwater Adhesion and Self-Healing Properties.
  12. 3D Printing of Ultrahigh Filler Content Composites Enabled by Granular Hydrogels.
  13. The Influence of DNA Handles on the Mechanical Response of Single Protein Molecules.
  14. A highly efficient heterologous expression platform to facilitate the production of microbial natural products in Streptomyces.
  15. Hydrogel innovations for 3D organoid culture.
  16. Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis.
  17. Constitutive Promoters Functional in Plant, Fungal, and Bacterial Hosts.
  18. Low-cost robotic manipulation of live microtissues for cancer drug testing.
  19. Protease-Containing Nanobodies for Detecting and Manipulating Intracellular Antigens Using Antiviral Drugs.
  20. Upgraded circular single-stranded DNA regulators for multiple-input multiple-output gene circuits in mammalian cells.
  21. Remote-controlled mechanical and directional motions of photoswitchable DNA condensates.
  22. In Situ Topology Change of Polymer Networks Induces Rapid Hydrogelation and Enables Pathway-Dependent Reinforcement in Double Networks.
  23. Illuminating life processes by vibrational probes.
  24. Exploring Nature's Toolbox: The Role of Biopolymers in Sustainable Materials Science.
  25. Engineered Hydrogels for Organoid Models of Human Nonalcoholic Fatty Liver Disease.
  26. Mechanically and Chemically Defined PEG Hydrogels Improve Reproducibility in Human Cardioid Development.
  27. Reversible Stiffening of Biopolymeric Hybrid Networks by Dynamically Switching Cross-Links In Situ.
  28. Hunting extreme microbes that redefine the limits of life.
  29. Materials Chemistry and Engineering for Drug Delivery.
  30. Can we mimic 3D printing of low molecular weight gels using a rheometer? - a characterisation toolkit for extrusion printed gels.
  31. Structural determinants of soft memory in recurrent biological networks.
  32. Regulating hydrogel mechanical properties with an electric field.
  33. A Continuous Manufacturing Approach for Aligned PVDF Nanofiber Yarns with Enhanced Mechanical and Piezoelectric Properties.
  34. Self-assembling protein nanoparticles for cytosolic delivery of nucleic acids and proteins.
  35. Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase.
  36. Modulating the Curvature of Protein Self-Assembled Spiral Nanotubules.
  37. Photonic Marvels: Exploring the Self-Assembly of Cellulose Nanocrystals for Sustainable Materials and Beyond.
  38. Bacterial effectors mediate kinase reprogramming through mimicry of conserved eukaryotic motifs.
  39. Nanochannels with Varied Outer Surface Charges for Protein Discrimination.
  1. ACS Biomater Sci Eng. 2025 May 13.
    Adaptations of Gram-Negative and Gram-Positive Probiotic Bacteria in Engineered Living Materials.
    Varun Sai Tadimarri, Tanya Amit Tyagi, Cao Nguyen Duong, Sari Rasheed, Rolf Müller, Shrikrishnan Sankaran.
      Encapsulation of microbes in natural or synthetic matrices is a key aspect of engineered living materials, although the influence of such confinement on microbial behavior is poorly understood. A few recent studies have shown that the spatial confinement and mechanical properties of the encapsulating material significantly influence microbial behavior, including growth, metabolism, and gene expression. However, comparative studies within different bacterial species under identical confinement conditions are limited. In this study, Gram-negative Escherichia coli Nissle 1917 and Gram-positive Lactiplantibacillus plantarum WCFS1 were encapsulated in hydrogel matrices, and their growth, metabolic activity, and recombinant gene expression were examined under varying degrees of hydrogel stiffness, achieved by adjusting the polymer concentration and chemical cross-linking. Both bacteria grow from single cells into confined colonies, but more interestingly, in E. coli gels, mechanical properties influenced colony growth, size, and morphology, whereas this did not occur in L. plantarum gels. However, with both bacteria, increased matrix stiffness led to higher levels of recombinant protein production within the colonies. By measuring metabolic heat from the bacterial gels using the isothermal microcalorimetry technique, it was inferred that E. coli adapts to the mechanical restrictions through multiple metabolic transitions and is significantly affected by the different hydrogel properties. Contrastingly, both of these aspects were not observed with L. plantarum. These results revealed that despite both bacteria being gut-adapted probiotics with similar geometries, mechanical confinement affects them considerably differently. The weaker influence of matrix stiffness on L. plantarum is attributed to its slower growth and thicker cell wall, possibly enabling the generation of higher turgor pressures to overcome restrictive forces under confinement. By providing fundamental insights into the interplay between mechanical forces and bacterial physiology, this work advances our understanding of how matrix properties shape bacterial behavior. The implications of these findings will aid the design of engineered living materials for therapeutic applications.
    Keywords:  bacterial physiology; engineered living materials; microbial behavior; spatial confinement
    DOI:  https://doi.org/10.1021/acsbiomaterials.5c00325
  2. Nat Commun. 2025 May 15. 16(1): 4544
    Bioinspired nondissipative mechanical energy storage and release in hydrogels via hierarchical sequentially swollen stretched chains.
    Henri Savolainen, Negar Hosseiniyan, Mario Piedrahita-Bello, Olli Ikkala.
      Nature suggests concepts for materials with efficient mechanical energy storage and release, i.e., resilience, involving small energy dissipation upon mechanical loading and unloading, such as in resilin and elastin. These materials facilitate burst-like movements involving high stiffness and low strain and high reversibility. Synthetic hydrogels that allow highly reversible mechanical energy storage have remained a challenge, despite mimicking biological soft tissues. Here we show a synthetic concept using fixed hydrogel polymer compositions based on sequentially swollen and sequentially photopolymerized gelation steps for hierarchical networks. The sequential swellings facilitate the balance of properties between resilience and dissipation upon controlling of the chain extension. At low hierarchical levels, we show resilience with small hysteresis with increased stiffness and resilient energy storage, whereas at high hierarchical levels, a transition is shown to a dissipative and considerably reinforced state. The generality of this approach is shown using several photopolymerizable monomers.
    DOI:  https://doi.org/10.1038/s41467-025-59743-w
  3. Sci Adv. 2025 May 16. 11(20): eadu8260
    Design of nondeterministic architected structures via bioinspired distributed agents.
    Jiakun Liu, Xiaoheng Zhu, Walker Gosrich, Mark Yim, Jordan R Raney.
      Nature manufactures structures via decentralized processes involving groups of agents. This is fundamentally different from traditional manufacturing, where objects are produced via sequences of predefined steps. In this work, we explore the idea of using simulated "swarms" of simple agents to generate new designs for architected materials in a decentralized, bioinspired manner. Individual agents choose their own actions based solely on information in their immediate environment, with no centralized control. The structures that these processes produce are the result of the collective action of the individual agents, rather than a predetermined design. We build an integrated platform for determining "rule-structure-property" relationships, analogous to process-structure-property relationships in materials science. The platform simulates agent behaviors to show how different rules and different environments result in different structures. We then three-dimensional print these and perform finite element analysis to experimentally and numerically characterize mechanical properties, including tensile strength and energy dissipation.
    DOI:  https://doi.org/10.1126/sciadv.adu8260
  4. Sci Adv. 2025 May 16. 11(20): eadr6925
    Extreme nonlinearity by layered materials through inverse design.
    Zhi Zhao, Rahul Dev Kundu, Ole Sigmund, Xiaojia Shelly Zhang.
      Biological materials such as seashell nacre exhibit extreme mechanical properties due to their multilayered microstructures. Collaborative interaction among these layers achieves performance beyond the capacity of a single layer. Inspired by these multilayer biological systems, we architect materials with free-form layered microstructures to program multistage snap-buckling and plateau responses-accomplishments challenging with single-layer materials. The developed inverse design paradigm simultaneously optimizes local microstructures within layers and their interconnections, enabling intricate layer interactions. Each layer plays a synergistic role in collectively achieving high-precision control over the desired extreme nonlinear responses. Through high-fidelity simulations, hybrid fabrication, and tailored experiments, we demonstrate complex responses fundamental to various functionalities, including energy dissipation and wearable devices. We orchestrate multisnapping phenomena from complex interactions between heterogeneous local architectures to encode and store information within architected materials, unlocking data encryption possibilities. These layered architected materials offer transformative advancements across diverse fields, including vibration control, wearables, and information encryption.
    DOI:  https://doi.org/10.1126/sciadv.adr6925
  5. ACS Synth Biol. 2025 May 12.
    Bacterial Cells Engineered with Synthetic Genetic Materials for Blind Testing of Random Mutagenesis.
    Qian Liu, Zhaoguan Wang, Jingsong Cui, Jiawei Li, Changyue Jiang, Gaoxu Tan, Hao Qi.
      Synthetic genetic materials, particularly those in genetically modified organisms (GMOs) deployed into complex environments, necessitate robust postmarket surveillance for continuous monitoring of both the materials and their applications throughout their lifecycle. Here, we introduce novel-coded genomic material for a blind mutation test that evaluates mutagenesis in synthetic genomic sequences without requiring direct sequence comparison. This test utilizes a Genome-Digest, which is embedded within essential genes, establishing mathematical correlation between the nucleotide sequence and codon order. This novel design allows for independent assessment of mutations by decoding the nucleotide sequence, thereby eliminating the need for reference sequences or extensive bioinformatic analysis. Furthermore, the test has the capability to analyze mixed genomic materials from a single sample and can be extended to the pooled testing of multiple samples as well. Building on this framework, we propose the 'Genome-ShockWatch' methodology. In proof-of-concept trials, it successfully detected mutations that exceeded a predefined threshold in long-read sequencing data from a yogurt sample containing Genome-Digest encoded Nissle 1917 E. coli cells and naturally occurring probiotic bacteria. Consequently, the Genome-Digest system provides a robust foundation for the routine surveillance and management of GMOs and related synthetic products, ensuring their safety and efficacy in diverse environmental contexts.
    Keywords:  bioinformatic; biosafety; biotechnology; genetically modified organisms; synthetic biology; synthetic genetic materials
    DOI:  https://doi.org/10.1021/acssynbio.5c00054
  6. ACS Appl Mater Interfaces. 2025 May 16.
    Hybrid Plasmonic Bioresins and dECM-Based Materials for Volumetric Bioprinting of Vascular-Inspired Architectures.
    Uxue Aizarna-Lopetegui, Gabriel Größbacher, Ada Herrero-Ruiz, Aitor Tejo-Otero, Malou Henriksen-Lacey, Riccardo Levato, Dorleta Jimenez de Aberasturi.
      Synergizing nanomaterial technology with advanced 3D printing techniques creates new opportunities for developing smart, stimuli-responsive materials suitable for tissue engineering scaffolds. By incorporation of stimuli-responsive nanoparticles into extracellular matrix mimetics, these composites gain functional elements capable of replicating dynamic biological processes in vitro. Herein, we propose combining hybrid multifunctional inorganic-organic materials with the emerging volumetric bioprinting (VBP) technique. We present two hybrid materials, a light stimuli-responsive polymer-based resin and a biocompatible porcine-derived decellularized extracellular matrix (dECM)-based bioresin, thus expanding the library of materials suitable for VBP. Plasmonic nanoparticles are combined with a thermoresponsive polymeric matrix, formulating the stimuli-responsive plasmonic resin, while a dECM-based bioresin with embedded smooth muscle cells (SMCs) is employed to include the biological component in the system. As proof of concept to demonstrate the versatility of the hybrid materials, we investigated the generation of highly complex structures, including multiwalled channels, using sequential VBP. Overall, this study broadens the range of materials compatible with VBP, thereby enabling the use of smart multicomponent materials in the fabrication of dynamic, stimuli-responsive 3D in vitro models.
    Keywords:  blood vessel tissue models; dECM-based bioinks; plasmonic NPs; stimuli-responsive inks; volumetric bioprinting
    DOI:  https://doi.org/10.1021/acsami.5c03880
  7. Biomater Sci. 2025 May 14.
    Biocompatible composite hydrogel with on-demand swelling-shrinking properties for 4D bioprinting.
    Peter J Jensen, Josh P Graham, Trevor K Busch, Owen Fitz, Sivani Jayanadh, Thomas E Pashuck, Tomas Gonzalez-Fernandez.
      Hydrogels with tunable swelling and shrinking properties are of great interest in biomedical applications, particularly in wound healing, tissue regeneration, and drug delivery. Traditional hydrogels often fail to achieve high swelling without mechanical failure. In contrast, high-swelling hydrogels can absorb large amounts of liquid, expanding their volume by 10-1000 times, due to low crosslink density and the presence of hydrophilic groups. Additionally, some high-swelling hydrogels can also shrink in response to external stimuli, making them promising candidates for applications like on-demand drug delivery and biosensing. An emerging application of high-swelling hydrogels is four-dimensional (4D) printing, where controlled swelling induces structural transformations in a 3D printed construct. However, current hydrogel systems show limited swelling capacity, restricting their ability to undergo significant shape changes. To address these limitations, we developed a high-swelling composite hydrogel, termed SwellMA, by combining gelatin methacryloyl (GelMA) and sodium polyacrylate (SPA). SwellMA exhibits a swelling capacity over 500% of its original area and can increase its original water weight by 100-fold, outperforming existing materials in 4D bioprinting. Furthermore, SwellMA constructs can cyclically swell and shrink on-demand upon changing the ionic strength of the aqueous solution. Additionally, SwellMA demonstrates superior cytocompatibility and cell culture properties than SPA, along with enhanced 3D printing fidelity. These findings demonstrate SwellMA's potential for advanced 4D printing and a broad range of biomedical applications requiring precise and dynamic control over hydrogel swelling and shrinking.
    DOI:  https://doi.org/10.1039/d5bm00551e
  8. Nat Commun. 2025 May 13. 16(1): 4407
    Co-initiating-system dual-mechanism drives the design of printable entangled polymer multinetworks.
    An Wei, Qian Wang, Jupen Liu, Yuchan Huang, Haoxiang Li, Zhenhao Zhu, Tao Wang, You Yu.
      Entanglement significantly enhances the mechanical performance and functionality of both natural and synthetic materials. However, developing straightforward, versatile strategies for creating high-performance entangled polymer materials remains a challenge. Here, a co-initiating-system dual-mechanism strategy is designed for fabricating printable entangled polymer multinetworks. This thermal-light dual-initiation process benefits the synthesis of high-molecular-weight polymers and promotes the rapid formation of multinetworks within hydrogels. The resulting long polymer chains enable hydrogels with higher mechanical performance, lower stress relaxation, and activation energy compared to short polymer chain-contained samples. Such a method proves more effective than traditional self-thickening and strengthening techniques for enhancing hydrogel entanglements and is also compatible with additive manufacturing, enabling the design of complex 2D webs with adaptive mechanical performance and capable of detecting and sensing applications. This work provides an effective strategy for designing high-performance entangled polymer materials, which are set to impact numerous fields, from advanced sensing to material science and beyond.
    DOI:  https://doi.org/10.1038/s41467-025-59669-3
  9. Nat Methods. 2025 May 13.
    Prediction of protein subcellular localization in single cells.
    Xinyi Zhang, Yitong Tseo, Yunhao Bai, Fei Chen, Caroline Uhler.
      The subcellular localization of a protein is important for its function, and its mislocalization is linked to numerous diseases. Existing datasets capture limited pairs of proteins and cell lines, and existing protein localization prediction models either miss cell-type specificity or cannot generalize to unseen proteins. Here we present a method for Prediction of Unseen Proteins' Subcellular localization (PUPS). PUPS combines a protein language model and an image inpainting model to utilize both protein sequence and cellular images. We demonstrate that the protein sequence input enables generalization to unseen proteins, and the cellular image input captures single-cell variability, enabling cell-type-specific predictions. Experimental validation shows that PUPS can predict protein localization in newly performed experiments outside the Human Protein Atlas used for training. Collectively, PUPS provides a framework for predicting differential protein localization across cell lines and single cells within a cell line, including changes in protein localization driven by mutations.
    DOI:  https://doi.org/10.1038/s41592-025-02696-1
  10. Nat Methods. 2025 May 12.
    FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data.
    Rohan Patel, Kenneth Pham, Harshini Chandrashekar, Jennifer E Phillips-Cremins.
      Sequential Oligopaints DNA FISH is an imaging technique that measures higher-order genome folding at single-allele resolution via multiplexed, probe-based tracing. Currently there is a paucity of algorithms to identify 3D genome features in sequential Oligopaints data. Here, we present FISHnet, a graph theory method based on optimization of network modularity to detect chromatin domains in pairwise distance matrices. FISHnet sensitively and specifically identifies domains and boundaries in both simulated and real single-allele imaging data and provides statistical tests for the identification of cell-type-specific domains-like folding patterns. Application of FISHnet across multiple published Oligopaints datasets confirms that nested domains consistent with TADs and subTADs are not an emergent property of ensemble Hi-C data but also observable on single alleles. We make FISHnet code freely available to the scientific community, thus enabling future studies aiming to elucidate the role of single-allele folding variation on genome function.
    DOI:  https://doi.org/10.1038/s41592-025-02688-1
  11. Adv Mater. 2025 May 16. e2501542
    Mussel-Inspired Molecular Strategies for Fabricating Functional Materials With Underwater Adhesion and Self-Healing Properties.
    Pan Huang, Hongjian Zhang, Hongbo Zeng.
      The exceptional underwater adhesion and self-healing capabilities of mussels have fascinated researchers for over two decades. Extensive studies have shown that these remarkable properties arise from a series of reversible and dynamic molecular interactions involving mussel foot proteins. Inspired by these molecular interaction strategies, numerous functional materials exhibiting strong underwater adhesion and self-healing performance have been successfully developed. This review systematically explores the nanomechanical mechanisms of mussel-inspired molecular interactions, mainly revealed by direct force measurement techniques such as surface forces apparatus and atomic force microscopy. The development of functional materials, including coacervates, coatings, and hydrogels, with underwater adhesion and self-healing properties, is then summarized. Furthermore, the macroscopic material performances are correlated with the underlying molecular mechanisms, providing valuable insights for the rational design of next-generation mussel-inspired functional materials with enhanced underwater adhesion and self-healing properties.
    Keywords:  force measurements; molecular interactions; mussel‐inspired; self‐healing; underwater adhesion
    DOI:  https://doi.org/10.1002/adma.202501542
  12. Adv Mater. 2025 May 09. e2500782
    3D Printing of Ultrahigh Filler Content Composites Enabled by Granular Hydrogels.
    Chen Cui, Ze-Yong Zhuang, Huai-Ling Gao, Jun Pang, Xiao-Feng Pan, Shu-Hong Yu.
      Ultrahigh filler content composites have exhibited distinctive properties in various areas, such as structural materials, electrical insulation, thermal management, and energy storage devices. However, manufacturing 3D composites with ultrahigh filler content is challenging because excessive fillers have compromised the processing flowability of the composite. Here, using hollow glass microspheres (HGMs) as an example filler, a 3D printing strategy for fabricating particulate composites with ultrahigh HGM content (up to 99.2 wt.%) is reported. By incorporating the highly swollen granular hydrogel as the shear sliding phase between HGMs, the probability of clogging during extrusion of the composite ink with ultrahigh HGM content is substantially reduced. A quantitative phase diagram is developed to optimally choose the ink compositions with the maximum HGM content, as well as printing parameters. The resulting composite with ultrahigh HGM content shows ceramic-foam-like brittle fracture behavior, high wave-transparent properties (0.996), and low thermal conductivity (0.045 W m-1 K-1). Further, a thermal shield with high HGM content on a microcircuit board to validate the localized thermal protection is fabricated. It is believed that incorporating hydrogel matrix into the printing ink will unlock the capabilities of 3D printed ultrahigh filler content composites in creating more intricate structures with advanced functionalities.
    Keywords:  3D printing; clogging behavior; granular hydrogel; ultrahigh filler content composites
    DOI:  https://doi.org/10.1002/adma.202500782
  13. Biomacromolecules. 2025 May 13.
    The Influence of DNA Handles on the Mechanical Response of Single Protein Molecules.
    Sabita Sharma, Sadia Rahman, Mattan Ze'ev Becker, Maya Georgia Pelah, Ronen Berkovich, Ionel Popa.
      The mechanical response of proteins to force is governed by their chain stiffness, molecular length, and domain segmentation and can be influenced by unstructured tethers in series with the molecule. Here, we investigate the effect of DNA linkers on the mechanical unfolding of proteins. These tethers are extensively used in single-molecule techniques as spacing handles or calibration standards. We designed two DNA-protein constructs made from covalently cross-linked DNA molecules having 604 bp and 3 kbp in series with eight repeats of bacterial protein L, and compared them with the protein L construct lacking any DNA linker. Using magnetic tweezers, we measured the unfolding dynamics and folding likelihood of protein L connected in series with these DNA linkers. Our findings indicate that stiff DNA linkers do not significantly alter the unfolding kinetics of the tethered protein, while a longer handle slightly increases the force required for refolding. We rationalize our measurements using an energy profile model projected on the pulling end-to-end reaction coordinate. Furthermore, we analyze how the tension is being transmitted along the protein-DNA construct as a function of its size. We conclude that the small differences induced by the presence of DNA linkers in single-molecule measurements are insignificant, given the current instrumental capabilities.
    DOI:  https://doi.org/10.1021/acs.biomac.5c00429
  14. Microb Cell Fact. 2025 May 14. 24(1): 105
    A highly efficient heterologous expression platform to facilitate the production of microbial natural products in Streptomyces.
    Xiuling Wang, Ping Lin, Qiyao Shen, Xueyan Feng, Shouying Xu, Qijun Zhang, Yang Liu, Cailing Ren, Daojing Yong, Qiong Duan, Liujie Huo, Youming Zhang, Gang Li, Jun Fu, Ruijuan Li.
       BACKGROUND: Heterologous expression in Streptomyces provides a platform for mining natural products (NPs) encoded by cryptic biosynthetic gene clusters (BGCs) of bacteria. The BGCs are first engineered in hosts with robust recombineering systems, such as Escherichia coli, followed by expression in optimized heterologous hosts, such as Streptomyces, with defined metabolic backgrounds.
    RESULTS: We developed a highly efficient heterologous expression platform, named Micro-HEP (microbial heterologous expression platform), that uses versatile E. coli strains capable of both modification and conjugation transfer of foreign BGCs and optimized chassis Streptomyces strain for expression. The stability of repeat sequences in these E. coli strains was superior to that of the commonly used conjugative transfer system E. coli ET12567 (pUZ8002). For optimizing expression of foreign BGCs, the chassis strain S. coelicolor A3(2)-2023 was generated by deleting four endogenous BGCs followed by introducing multiple recombinase-mediated cassette exchange (RMCE) sites in the S. coelicolor A3(2) chromosome. Additionally, modular RMCE cassettes (Cre-lox, Vika-vox, Dre-rox, and phiBT1-attP) were constructed for integrating BGCs into the chassis strain. Micro-HEP was tested using BGCs for the anti-fibrotic compound xiamenmycin and griseorhodins. Two to four copies of the xim BGC were integrated by RMCE, with increasing copy number associated with increasing yield of xiamenmycin. The grh BGC was also efficiently expressed, and the new compound griseorhodin H was identified.
    CONCLUSION: We demonstrated that our Micro-HEP system enables the efficient expression of foreign BGCs, facilitating the discovery of new NPs and increasing yields.
    Keywords:  Biosynthetic gene cluster; Chassis strain; Heterologous expression; Integration; Transfer
    DOI:  https://doi.org/10.1186/s12934-025-02722-z
  15. Biomed Mater. 2025 May 13.
    Hydrogel innovations for 3D organoid culture.
    Yicheng Feng, Dongyang He, Xiao An.
      Organoids are functional cell-tissue complexes that mimic structural and functional characteristics of organs in vitro in three dimensions (3D). Mimicking the natural extracellular matrix (ECM) environment is critical for guiding stem cell fate within organoid cultures. Current organoid cultures predominantly utilize animal- or tumor-derived ECMs such as dECMs and Matrigel. However, these materials introduce batch variability and uncertainty in composition, which hinders reproducibility. In contrast, naturally derived and synthetic hydrogels with excellent biocompatibility offer precise and adjustable compositions, along with tunable mechanical properties, thereby providing robust support for organoid development and maturation. We explore innovative hydrogel designs tailored specifically for organoid cultures, emphasizing the influence and meticulous control of functional hydrogels on organoid formation, differentiation, and maturation processes. Furthermore, the review highlights the potential of functionalized hydrogel scaffolds to advance both research and industrial applications in tissue and organ engineering. As research progresses, investigations will further concentrate on improving the adjustable properties, expanding their scope of application, and more biologically compatible gelation strategies of hydrogels.
    Keywords:  biomaterials; hydrogel; matrix; organoid; tissue engineering
    DOI:  https://doi.org/10.1088/1748-605X/add82d
  16. Science. 2025 May 15. 388(6748): eadq7597
    Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesis.
    Ruchao Peng, Xin Xu, Binod Nepal, Yikang Gong, Fenglin Li, Max B Ferretti, Mingyang Zhou, Kristen W Lynch, George M Burslem, Sandhya Kortagere, Ronen Marmorstein, Yi-Wei Chang.
      Influenza viruses replicate and transcribe their genome in the context of a conserved ribonucleoprotein (RNP) complex. By integrating cryo-electron microscopy single-particle analysis and cryo-electron tomography, we define the influenza RNP as a right-handed, antiparallel double helix with the viral RNA encapsidated in the minor groove. Individual nucleoprotein subunits are connected by a flexible tail loop that inserts into a conserved pocket in its neighbor. We visualize the viral polymerase in RNP at different functional states, revealing how it accesses the RNA template while maintaining the double-helical architecture of RNP by strand sliding. Targeting the tail loop binding interface, we identify lead compounds as potential anti-influenza inhibitors. These findings elucidate the molecular determinants underpinning influenza virus replication and highlight a promising target for antiviral development.
    DOI:  https://doi.org/10.1126/science.adq7597
  17. ACS Synth Biol. 2025 May 16.
    Constitutive Promoters Functional in Plant, Fungal, and Bacterial Hosts.
    Viktor V Morozov, Anastasia V Balakireva, Maxim M Perfilov, Tatyana V Chepurnykh, Ilia V Yampolsky, Karen S Sarkisyan, Alexander S Mishin.
      Engineering of orthogonal systems functional across diverse hosts can benefit from employing universal regulatory DNA elements. Here, we screened a number of composite promoters in plant, fungal, and bacterial hosts, identifying variants that drive strong constitutive expression in Nicotiana tabacum, Saccharomyces cerevisiae, Escherichia coli, and Agrobacterium tumefaciens, or only in the eukaryotic subset of these organisms. These promoters can be used in universal vectors to co-optimize for different hosts in directed evolution, engineering of biosynthetic pathways, or other biotechnological tasks that require host switching.
    Keywords:  Synthetic promoter; bacteria; constitutive promoter; plant cells; synthetic terminator; yeast
    DOI:  https://doi.org/10.1021/acssynbio.4c00802
  18. Sci Adv. 2025 May 16. 11(20): eads1631
    Low-cost robotic manipulation of live microtissues for cancer drug testing.
    Ivan Stepanov, Noah R Gottshall, Alireza Ahmadianyazdi, Daksh Sinha, Ethan J Lockhart, Tran N H Nguyen, Sarmad Hassan, Lisa F Horowitz, Raymond S Yeung, Taranjit S Gujral, Albert Folch.
      The scarcity of human biopsies available for drug testing is a paramount challenge for developing therapeutics, disease models, and personalized treatments. Microtechnologies that combine the microscale manipulation of tissues and fluids offer the exciting possibility of miniaturizing both disease models and drug testing workflows on scarce human biopsies. Unfortunately, these technologies presently require microfluidic devices or robotic dispensers that are not widely accessible. We have rapidly prototyped an inexpensive platform based on an off-the-shelf robot that can microfluidically manipulate live microtissues into/out of culture plates without using complicated accessories such as microscopes or pneumatic controllers. The robot integrates complex functions with a simple, cost-effective, and compact construction, allowing placement inside a tissue culture hood for sterile workflows. We demonstrated a proof-of-concept cancer drug evaluation workflow of potential clinical utility using patient tumor biopsies with multiple drugs on 384-well plates. Our user-friendly, low-cost platform promises to make drug testing of microtissues broadly accessible to pharmaceutical, clinical, and biological laboratories.
    DOI:  https://doi.org/10.1126/sciadv.ads1631
  19. ACS Chem Biol. 2025 May 12.
    Protease-Containing Nanobodies for Detecting and Manipulating Intracellular Antigens Using Antiviral Drugs.
    Quan Le, John T Ngo.
      Tools to induce the formation of protein-protein interactions (PPIs) via small molecules are essential for investigating and engineering biological systems. Here we introduce a protease-based strategy for controlling the preservation of otherwise self-cleaving nanobodies. By inserting the hepatitis C virus NS3 cis-protease into the nanobody scaffold, we showed that the antigen-binding ability of these chimeric nanobodies can be controlled in a dose-dependent manner using NS3 inhibitors. We demonstrated the generalizability of this approach by designing and validating drug-controllable nanobodies targeting mCherry (LaM4), eGFP (LaG16), and the ALFA peptide tag. Additionally, we showed that an NS3-containing version of a nanobody targeting the β2-adrenergic receptor can control the endogenous G-protein-mediated signaling activity. Overall, we introduce new chemogenetic components for controlling intracellular PPIs using clinically approved antiviral drugs.
    DOI:  https://doi.org/10.1021/acschembio.5c00176
  20. Sci Adv. 2025 May 16. 11(20): eadv3396
    Upgraded circular single-stranded DNA regulators for multiple-input multiple-output gene circuits in mammalian cells.
    Linlin Tang, Jinghao Wang, Kaiqi Xu, Zhen Li, Jie Song.
      Synthetic gene networks hold promise for genetic diagnostics and gene therapy but face limitations due to insufficient molecular tools. Gene-encoded circular single-stranded DNA (Css DNA) has been developed as a switchable vector to enrich regulatory components beyond protein/RNA-based systems in mammalian cells. However, the previous Css DNA regulator suffered from constrained regulatory sequence flexibility, disability of multiple-input multiple-output (MIMO) signals, and lack of endogenous orthogonal regulation. Here, we address these challenges by engineering a "bridge" design into the Css DNA regulator. These bridges function as sequence-programmable switches to control gene expression, responding to endogenous molecular signals (such as ATP, APE1, and RNase H) and enabling trans-regulation within or between Css DNAs. We exploit the orthogonality of Css DNA regulator to construct the three-input three-output genetic circuits. The upgraded Css DNA-based regulatory strategy represents a versatile and powerful platform for gene regulation and provides a promising avenue for the development of synthetic gene networks.
    DOI:  https://doi.org/10.1126/sciadv.adv3396
  21. Nat Commun. 2025 May 14. 16(1): 4479
    Remote-controlled mechanical and directional motions of photoswitchable DNA condensates.
    Hirotake Udono, Shin-Ichiro M Nomura, Masahiro Takinoue.
      Membrane-free synthetic DNA-based condensates enable programmable control of dynamic behaviors as shown by phase-separated condensates in biological cells. We demonstrate remote-controlled microflow using photocontrollable state transitions of DNA condensates, assembled from multi-branched DNA nanostructures via sticky-end (SE) hybridization. Introducing azobenzene into SEs enables their photoswitchable binding affinity, which underlies photoreversible fluidity of the resulting condensates that transition between gel/liquid/dissociated states in a wavelength-dependent manner. Leveraging base-sequence programmability, spatially coupled orthogonal DNA condensates with divergent photoresponsive capabilities perform multi-modal mechanical actions that depend on azobenzene insertion sites in the SE, including switching flows radially expanding and converging under photoswitching. Localizing photoswitching within a DNA liquid condensate generates two distinct directional motions, whose contrasting morphology, direction, and lifetime are determined by switching frequency. Numerical simulations reveal its regulatory role in weight-adjusting energy-exchanging and energy-dissipative interactions between the photoirradiated and unirradiated domains.
    DOI:  https://doi.org/10.1038/s41467-025-59100-x
  22. ACS Appl Mater Interfaces. 2025 May 16.
    In Situ Topology Change of Polymer Networks Induces Rapid Hydrogelation and Enables Pathway-Dependent Reinforcement in Double Networks.
    Yue Gao, Tianzi Chen, Haijin Chen, Zhanshan Gao, Yin Liu, Qiuhao Luo, Haonan Ye, Haolong Ye, Dongdong Wu.
      The incorporation of deformable network junctions into polymer networks is a new fundamental concept in the design of smart topology-switching materials. However, it is still a nascent field that needs to be amplified by developing new deformable junctions and creating materials with practical properties. Here, we construct a new topology-switching polymer network (TPN) by using conformational transformable peptide coiled-coils as deformable network junctions. The coiled-coil junctions display two distinct branch functionalities at pH 6 and pH 8, respectively. As a consequence, the TPN shows a nearly instantaneous and reversible solution-gel transition when the pH varies between 6 and 8. This transition does not rely on the establishment of interactions between the polymer components that occurs during most hydrogelation processes but only on the reconfiguration of the polymer network triggered by topology change, which may represent a new hydrogel formation mechanism. Moreover, the TPN can be used as the minor network to reinforce the main network in a double network system, but unexpectedly and interestingly, the reinforcement is pathway-dependent and can only be achieved by the in situ topology change of TPN in a double network rather than directly utilizing the TPN with a specific topology to prepare the double network.
    Keywords:  double network; hydrogelation; peptide; polymer network; topology
    DOI:  https://doi.org/10.1021/acsami.5c04361
  23. Nat Methods. 2025 May;22(5): 928-944
    Illuminating life processes by vibrational probes.
    Naixin Qian, Zhilun Zhao, Elsy El Khoury, Xin Gao, Carli Canela, Yihui Shen, Lingyan Shi, Lixue Shi, Fanghao Hu, Lu Wei, Wei Min.
      Vibration of chemical bonds can serve as imaging contrast. Vibrational probes, synergized with major advances in chemical bond imaging instruments, have recently flourished and proven valuable in illuminating life processes. Here, we review how the development of vibrational probes with optimal biocompatibility, enhanced sensitivity, multichromatic colors and diverse functionality has extended chemical bond imaging beyond the prevalent label-free paradigm into various novel applications such as imaging metabolites, metabolic imaging, drug imaging, super-multiplex imaging, vibrational profiling and vibrational sensing. These advancements in vibrational probes have greatly facilitated understanding living systems, a new field of vibrational chemical biology.
    DOI:  https://doi.org/10.1038/s41592-025-02689-0
  24. Adv Mater. 2025 May 12. e2507822
    Exploring Nature's Toolbox: The Role of Biopolymers in Sustainable Materials Science.
    Yingying Zhang, Shengjie Ling, Wenshuai Chen, Markus J Buehler, David L Kaplan.
      
    DOI:  https://doi.org/10.1002/adma.202507822
  25. Adv Sci (Weinh). 2025 May 14. e17332
    Engineered Hydrogels for Organoid Models of Human Nonalcoholic Fatty Liver Disease.
    Yueming Liu, Aidan E Gilchrist, Patrik K Johansson, Yuan Guan, Jaydon D Deras, Yu-Chung Liu, Sofia Ceva, Michelle S Huang, Renato S Navarro, Annika Enejder, Gary Peltz, Sarah C Heilshorn.
      Nonalcoholic fatty liver disease (NAFLD) is characterized by increased lipid accumulation and excessive deposition of extracellular matrix (ECM) that results in tissue stiffening. The potential interplay between matrix stiffness and hepatocyte lipid accumulation during NAFLD has not been established. Here, an in vitro NAFLD model is developed using chemically defined, engineered hydrogels and human induced pluripotent stem cell-derived hepatic organoids (HOs). Specifically, dynamic covalent chemistry crosslinking, along with transient small molecule competitors, are used to create dynamic stiffening hydrogels that enable the reproducible culture of HOs. Within matrices that mimic the stiffness of healthy to diseased tissue (≈1-6 kPa), lipid droplet accumulation in HOs is triggered by exposure to an NAFLD-associated free fatty acid. These NAFLD model suggests that higher stiffness microenvironments result in increased hepatic lipid droplet accumulation, increased expression of fibrosis markers, and increased metabolic dysregulation. By targeting the ROCK mechanosignaling pathway, the synergy between matrix stiffness and lipid droplet accumulation is disrupted. The in vitro model of NAFLD has the potential to understand the role of mechanosignaling in disease progression and identify new pathways for therapeutic intervention.
    Keywords:  engineered hydrogels; hepatic organoids; lipid accumulation; matrix stiffening; mechanosignaling
    DOI:  https://doi.org/10.1002/advs.202417332
  26. Adv Healthc Mater. 2025 May 16. e2403997
    Mechanically and Chemically Defined PEG Hydrogels Improve Reproducibility in Human Cardioid Development.
    Yuanhui Song, Michael Seitz, Andrew Kowalczewski, Nhu Y Mai, Era Jain, Huaxiao Yang, Zhen Ma.
      Cardioids are 3D self-organized heart organoids directly derived from induced pluripotent stem cells (hiPSCs) aggregates. The growth and culture of cardioids is either conducted in suspension culture or heavily relies on Matrigel encapsulation. Despite the significant advancements in cardioid technology, reproducibility remains a major challenge, limiting their widespread use in both basic research and translational applications. Here, for the first time, we employed synthetic, matrix metalloproteinase (MMP)-degradable polyethylene glycol (PEG)-based hydrogels to define the effect of mechanical and biochemical cues on cardioid development. Successful cardiac differentiation is demonstrated in all the hydrogel conditions, while cardioid cultured in optimized PEG hydrogel (3 wt.% PEG-2mM RGD) underwent similar morphological development and comparable tissue functions to those cultured in Matrigel. Matrix stiffness and cell adhesion motif play a critical role in cardioid development, nascent chamber formation, contractile physiology, and endothelial cell gene enrichment. More importantly, synthetic hydrogel improved the reproducibility in cardioid properties compared to traditional suspension culture and Matrigel encapsulation. Therefore, PEG-based hydrogel has the potential to be used as an alternative to Matrigel for human cardioid culture in a variety of clinical applications including cell therapy and tissue engineering.
    Keywords:  cardioids; human induced pluripotent stem cells; mechanobiology; organoids; synthetic hydrogel
    DOI:  https://doi.org/10.1002/adhm.202403997
  27. ACS Appl Mater Interfaces. 2025 May 13.
    Reversible Stiffening of Biopolymeric Hybrid Networks by Dynamically Switching Cross-Links In Situ.
    Jana T Reh, Sebastian Voigt, Leonard R Gareis, Ufuk Gürer, Stephan A Sieber, Berna Özkale, Oliver Lieleg.
      Achieving reversible stiffening of biopolymer networks in a controlled manner remains a challenging topic in materials science, especially when trying to assess the following changes in mechanical material properties in real time. To address these challenges, we here utilize a custom-made measurement setup that allows us to manipulate the cross-linking state of alginate-based hydrogels in situ while quantifying the achieved alterations in the viscoelastic response of the biopolymer networks. Interpolymer connections in the biopolymer networks are created by a combination of light-induced, covalent cross-links, ionic cross-links, and DNA-based cross-links, where the latter two can be successfully removed again by employing either chelating agents (e.g., ethylenediaminetetraacetic acid and citrate) or suitable displacement DNA strands. In part, this range of the different cross-linking options mentioned is inter alia made possible by incorporating the glycoprotein mucin into the alginate system, which also allows for a range of different starting (∼0.2-400 Pa), intermediate (∼25 Pa-1.6 kPa), and final stiffnesses (∼4 Pa-1.2 kPa) of the mixed hydrogel matrix. At the same time, the presence of mucins (1-4% (w/v)) in the biopolymer mixture enhances the properties of the cytocompatible hydrogel by improving its antibacterial characteristics. Such well-controllable alginate/mucin networks with dynamically switchable mechanical properties will likely find broad applications in cell cultivation studies or tissue engineering applications.
    Keywords:  antibacterial; biopolymer; hydrogels; reversible cross-links; tunable stiffness
    DOI:  https://doi.org/10.1021/acsami.5c03419
  28. Nature. 2025 May;641(8063): 583-584
    Hunting extreme microbes that redefine the limits of life.
    Andreas Teske.
      
    Keywords:  Evolution; Microbiology; Scientific community
    DOI:  https://doi.org/10.1038/d41586-025-01464-7
  29. Curr Drug Deliv. 2025 ;22(4): 373
    Materials Chemistry and Engineering for Drug Delivery.
    Wing-Fu Lai.
      
    DOI:  https://doi.org/10.2174/156720182204241223164140
  30. Faraday Discuss. 2025 May 14.
    Can we mimic 3D printing of low molecular weight gels using a rheometer? - a characterisation toolkit for extrusion printed gels.
    Rebecca E Ginesi, James Doutch, Emily R Draper.
      The 3D printing of hydrogels from low molecular weight gelators (LMWGs) continues to attract notable interest, with many potential applications. One of the main issues with 3D printing is the difficulty characterising these gels after printing. Currently, the understanding of whether these bulk rheological properties are maintained upon printing is limited. To address this, we have developed a series of rheological and scattering methods to characterise these materials before, during, and after printing. We have used rheology and small-angle neutron scattering (SANS) to gain a deeper understanding of the impact printing has on the bulk properties of the hydrogels. We have determined that printing impacts the resulting gel fibril structure, which consequently changes the stiffness and strength of the gel. We hope that through this work, we have provided advances to the field of 3D printing of LMWGs, as well as showing the versatility of this fabrication technique to create gels with different properties.
    DOI:  https://doi.org/10.1039/d4fd00185k
  31. Biophys Rev. 2025 Apr;17(2): 259-269
    Structural determinants of soft memory in recurrent biological networks.
    Maria Sol Vidal-Saez, Jordi Garcia-Ojalvo.
      Recurrent neural networks are frequently studied in terms of their information-processing capabilities. The structural properties of these networks are seldom considered, beyond those emerging from the connectivity tuning necessary for network training. However, real biological networks have non-contingent architectures that have been shaped by evolution over eons, constrained partly by information-processing criteria, but more generally by fitness maximization requirements. Here, we examine the topological properties of existing biological networks, focusing in particular on gene regulatory networks in bacteria. We identify structural features, both local and global, that dictate the ability of recurrent networks to store information on the fly and process complex time-dependent inputs.
    Keywords:  Biological networks; Feedback circuits; Feedforward circuits; Mutual regulation; Reservoir computing
    DOI:  https://doi.org/10.1007/s12551-025-01295-w
  32. Mater Horiz. 2025 May 12.
    Regulating hydrogel mechanical properties with an electric field.
    Hongyi Cai, Max Tepermeister, Chenyun Yuan, Meredith N Silberstein.
      Stimuli-responsive polymeric materials have attracted significant attention due to their ability to change properties in response to various external stimuli. Using an electric field as the stimulus is of particular interest as it possesses the potential for seamless integration of materials with electronic systems. While many materials with electric field responsive actuation have an associated mechanical property change, it is beneficial to develop materials that exhibit mechanical property changes without accompanying significant shape deformation. To address this challenge, here we designed a semi-interpenetrating polymer network (semi-IPN) hydrogel system containing both polyelectrolytes and salt ions, which enables electric field induced changes in mechanical properties while minimizing actuation. We first successfully verified the viability of our design by removing salt ions through a diffusion-only method where we witnessed the stiffness increased to 4.5 times the initial value while still being highly deformable. After this, we applied an electric field to transport the salt ions out of the hydrogel, as shown by both Raman spectroscopy and scanning electron microscopy. We were able to show a time-dependent stiffness increase, the maximum of which was 5 times the original stiffness. We quantified ion transport and water-splitting in the hydrogel by both experiments and simulations. Following this, we showed functional system reversibility by reversing the direction of the current to reinject salt ions into the semi-IPN hydrogel and reducing its stiffness to below the initial value. It's worth noting that our simulations enable us to understand the governing mechanisms behind ion generation and salt transport that leads to mechanical property changes. Finally, we were able to fabricate a spatially variable stiffness haptic interface with our hydrogel, with demonstrated reversibility and cyclability. This research can possibly find applications in soft robotics and haptics and also inspire the development of bio-compatible electronics related devices.
    DOI:  https://doi.org/10.1039/d5mh00308c
  33. ACS Appl Polym Mater. 2025 May 09. 7(9): 5429-5436
    A Continuous Manufacturing Approach for Aligned PVDF Nanofiber Yarns with Enhanced Mechanical and Piezoelectric Properties.
    Adaugo Enuka, Mohamad Keblawi, Emmet Sedar, Vince Beachley.
      Electrospun poly(vinylidene fluoride-co-hexafluoropropylene) (PVDF-HFP) nanofibers possess desirable mechanical and piezoelectric properties, making them promising candidates for smart textiles if they can be assembled into continuous yarns. This study presents a manufacturing approach that enables the production of electrospun PVDF-HFP nanofiber yarns using an automated parallel track system and an adjustable roll-to-roll collector. Results show that this approach has potential for PVDF yarn manufacturing on a commercial scale. Electrospun yarns have previously been fabricated with self-bundling methods, but current technologies are limited by production limitations such as the lack of tight control over assembly parameters and the absence of a postdrawing process. Postdrawing was applied here to individual fibers before yarn spinning to enhance fiber strength by over two times and yarn strength by 39%. The piezoelectrical performance of yarns was enhanced by up to 45% with postdrawing. Continuous PVDF-HFP yarns with specific strength approaching 50,000 N m/kg and a relative β phase content of 97% are promising candidates for piezoelectric nanofiber-based smart textiles, which can be integrated into various wearable devices and intelligent garments.
    DOI:  https://doi.org/10.1021/acsapm.5c00069
  34. Nat Biotechnol. 2025 May 15.
    Self-assembling protein nanoparticles for cytosolic delivery of nucleic acids and proteins.
    Feyisayo Eweje, Vanessa Ibrahim, Aram Shajii, Michelle L Walsh, Kiran Ahmad, Assma Alrefai, Dominie Miyasato, Jessie R Davis, Hyunok Ham, Kaicheng Li, Michael Roehrl, Carolyn A Haller, David R Liu, Jiaxuan Chen, Elliot L Chaikof.
      Intracellular delivery of biomacromolecules is hampered by low efficiency and cytotoxicity. Here we report the development of elastin-based nanoparticles for therapeutic delivery (ENTER), a recombinant elastin-like polypeptide (ELP)-based delivery system for effective cytosolic delivery of biomacromolecules in vitro and in vivo. Through iterative design, we developed fourth-generation ELPs fused to cationic endosomal escape peptides (EEPs) that self-assemble into pH-responsive micellar nanoparticles and enable cytosolic entry of cargo following endocytic uptake. In silico screening of α-helical peptide libraries led to the discovery of an EEP (EEP13) with 48% improved protein delivery efficiency versus a benchmark peptide. Our lead ELP-EEP13 showed similar or superior performance compared to lipid-based transfection reagents in the delivery of mRNA-encoded, DNA-encoded and protein-form Cre recombinase and CRISPR gene editors as well as short interfering RNAs to multiple cell lines and primary cell types. Intranasal administration of ELP-EEP13 combined with Cre protein achieved efficient editing of lung epithelial cells in reporter mice.
    DOI:  https://doi.org/10.1038/s41587-025-02664-2
  35. Science. 2025 May 15. 388(6748): eadt5199
    Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase.
    Isaac P Witte, George D Lampe, Simon Eitzinger, Shannon M Miller, Kiara N Berríos, Amber N McElroy, Rebeca T King, Olivia G Stringham, Diego R Gelsinger, Phuc Leo H Vo, Albert T Chen, Jakub Tolar, Mark J Osborn, Samuel H Sternberg, David R Liu.
      Programmable gene integration in human cells has the potential to enable mutation-agnostic treatments for loss-of-function genetic diseases and facilitate many applications in the life sciences. CRISPR-associated transposases (CASTs) catalyze RNA-guided DNA integration but thus far demonstrate minimal activity in human cells. Using phage-assisted continuous evolution (PACE), we generated CAST variants with >200-fold average improved integration activity. The evolved CAST system (evoCAST) achieves ~10 to 30% integration efficiencies of kilobase-size DNA cargoes in human cells across 14 tested genomic target sites, including safe harbor loci, sites used for immunotherapy, and genes implicated in loss-of-function diseases, with undetected indels and low levels of off-target integration. Collectively, our findings establish a platform for the laboratory evolution of CASTs and advance a versatile system for programmable gene integration in living systems.
    DOI:  https://doi.org/10.1126/science.adt5199
  36. ACS Appl Mater Interfaces. 2025 May 12.
    Modulating the Curvature of Protein Self-Assembled Spiral Nanotubules.
    Ariel Cohen, Itai Ben-Nun, Raviv Dharan, Tamar Tayri-Wilk, Asaf Shemesh, Avi Ginsburg, Abigail Millgram, Yael Levi-Kalisman, Israel Ringel, Uri Raviv.
      Structural transformations from ribbons to twisted ribbons to helical ribbons are often observed across supramolecular assemblies and macroscopic structures and can be described under a consistent theoretical framework. Conical molecular self-assembled structures, however, are rarely observed, may require more than one subunit, their dimensions are hard to control, and are poorly understood. Cytoskeleton microtubule (MT) is a dynamic protein-polymer that self-assembles from αβ-tubulin heterodimer, providing mechanical support to Eukaryotic cells. Colchicine is a drug known to bind the exchangeable nucleotide site on the β-tubulin subunit and suppress MT assembly. The tetravalent polyamine spermine promotes MT assembly and tubulin spiral structures, including conical tubulin spirals, tubules of conical spirals, and inverted helical tubules. Here we show how colchicine as a single agent suppressed MT and tubulin single ring assembly already at substoichiometric concentrations, whereas in the presence of spermine, the tubulin-colchicine stoichiometry controlled the dimensions and curvature of tubulin spiral assemblies. At a fixed spermine concentration, the concentration of colchicine modulated the radii of the nanotubular structures. The radii of the inverted helical nanotubules and conical spiral nanotubules monotonically decreased with colchicine concentration. We attribute our observation to the increased curvature of the tubulin dimer subunit induced by colchicine.
    Keywords:  SAXS; colchicine; conical spirals; cryo-TEM; helical structures; microtubule; spermine; tubulin
    DOI:  https://doi.org/10.1021/acsami.5c01405
  37. ACS Appl Mater Interfaces. 2025 May 12.
    Photonic Marvels: Exploring the Self-Assembly of Cellulose Nanocrystals for Sustainable Materials and Beyond.
    Saddam Hussain, Sara M AlTowireb, Mohammed Zourob.
      Cellulose nanocrystals (CNCs) are biodegradable, plant-derived colloidal particles that can self-assemble through evaporation-induced self-assembly (EISA) to form photonic films. The ability of CNCs to organize structurally colored films has garnered significant attention as a promising source of sustainable materials. CNCs serve as versatile photonic building blocks for creating biobased colored materials. This review provides a comprehensive overview of the latest advancements in chiral photonic CNC (CPCNC) materials. We delve into the chiral structures of these materials and factors affecting the EISA route, exploring their fundamental principles and bottom-up synthesis techniques. Additionally, various responsive CPCNCs are systematically introduced with a focus on their mechanisms, properties, and potential applications. The review concludes with a discussion of emerging applications, challenges, and future opportunities for CPCNCs. By leveraging the unique properties of CPCNCs within complex responsive polymer networks, we see significant potential for developing innovative physicochemical sensors, structural coatings, and optical devices.
    Keywords:  cellulose nanocrystals; challenges; future optical sensors; latest advancement; self-assembly mechanism; stimuli responsiveness
    DOI:  https://doi.org/10.1021/acsami.5c02679
  38. EMBO Rep. 2025 May 12.
    Bacterial effectors mediate kinase reprogramming through mimicry of conserved eukaryotic motifs.
    Ioanna Panagi, Janina H Muench, Alexi Ronneau, Ines Diaz-Del-Olmo, Agnel Aliyath, Xiu-Jun Yu, Hazel Mak, Enkai Jin, Jingkun Zeng, Diego Esposito, Elliott Jennings, Timesh D Pillay, Regina A Günster, Sarah L Maslen, Katrin Rittinger, Teresa L M Thurston.
      Bacteria have evolved numerous biochemical processes that underpin their biology and pathogenesis. The small, non-enzymatic bacterial (Salmonella) effector SteE mediates kinase reprogramming, whereby the canonical serine/threonine host kinase GSK3 gains tyrosine-directed activity towards neosubstrates, promoting Salmonella virulence. Yet, both the mechanism behind the switch in GSK3's activity and the diversity of this phenomenon remain to be determined. Here we show that kinase reprogramming of GSK3 is mediated by putative homologues from diverse Gram-negative pathogens. Next, we identify both the molecular basis of how SteE targets GSK3 and uncover that the SteE-induced tyrosine activity conferred on GSK3 requires an L/xGxP motif. This motif, found in several CMGC kinases that undergo auto-tyrosine phosphorylation, was previously shown to mediate GSK3 autophosphorylation on a tyrosine. Together, we suggest that the SteE family of intrinsically disordered proteins mediates kinase reprogramming via several short linear motifs that each appear to mimic eukaryotic signalling motifs. With this insight comes the potential for the rationale design of synthetic reprogramming proteins.
    Keywords:   Salmonella ; Host–Pathogen Interactions; Intrinsic Disordered Proteins; Kinase Reprogramming; Short Linear Interaction Motifs
    DOI:  https://doi.org/10.1038/s44319-025-00472-y
  39. Anal Chem. 2025 May 14.
    Nanochannels with Varied Outer Surface Charges for Protein Discrimination.
    Lingxiao Liu, Defang Ding, Cihui Luo, Xugang Wang, Ye Tian, Shao-Chuang Liu, Xiaoding Lou, Yu Huang, Liang Mao, Fan Xia.
      Solid-state nanochannels with probe modification demonstrate effective spontaneous charge modulation and selective ionic current regulation. Outer-surface functionalization of these nanochannels enables tunable ionic current signals before and after analyte detection. To modulate local charge distributions, we designed sensing nanochannels with significant ion rectification properties for protein detection. In this work, we utilized asymmetrically charged sensing nanochannels with DNA probe modifications to generate abundant ionic current information for multianalyte recognition. During protein detection, DNA probes on the outer surfaces of the nanochannels were competitively replaced by proteins, thereby modulating the local charge distribution. This modulation influences the ionic current through ion rectification, generating cross-reactive and differentiated signals for each target. As a result, the sensing nanochannels with asymmetry of the surface charge effectively discriminate 6 proteins using only one kind of probe. Furthermore, this system successfully distinguished proteins across various concentrations and within complex environments. This work represents a significant advancement in the development of differential sensors based on outer-surface-functionalized nanochannels for multianalyte discrimination.
    DOI:  https://doi.org/10.1021/acs.analchem.5c01050
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