bims-enlima 2025-01-19 papers

bims-enlima

Biomed News

on Engineered living materials

Issue of 2025–01–19
38 papers selected by
Rahul Kumar, Tallinna Tehnikaülikool

Reversible light-responsive protein hydrogel for on-demand cell encapsulation and release.
Living Dual Heat- and pH-Responsive Textiles.
Orthogonalized human protease control of secreted signals.
Synthetic Lipid Biology.
A cell-free biosensor signal amplification circuit with polymerase strand recycling.
Injectable ionic hydrogel conductors: Advancing material design to transform cardiac pacing.
Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes.
AI-designed proteins tackle century-old problem - making snake antivenoms.
Design of an exclusive obligate symbiosis for organism-based biological containment.
Programing Green Light-Responsive Hydrogels: from Photo-Weakening to Photo-unresponsiveness and Photo-Strengthening.
Morphology remodelling and membrane channel formation in synthetic cells via reconfigurable DNA nanorafts.
3D polycatenated architected materials.
Digital and Tunable Genetically Encoded Tension Sensors Based on Engineered Coiled-Coils.
Programmed shape transformations in cell-laden granular composites.
A compliant metastructure design with reconfigurability up to six degrees of freedom.
Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability.
Two-Level Spatially Localized Proximity Labeling for Cross-Biological-Hierarchy Measurement and Manipulation.
Transforming an ATP-dependent enzyme into a dissipative, self-assembling system.
Nanofibrous Peptide Hydrogels Leveraging Histidine to Modulate pH-Responsive Supramolecular Assembly and Antibody Release.
Temperature-Directed Morphology Transformation Method for Precision-Engineered Polymer Nanostructures.
Single-cell phenotyping of extracellular electron transfer via microdroplet encapsulation.
3D bioprinting: Advancing the future of food production layer by layer.
Silica hydrogels as a carbon-free solid media for the culture of diverse organisms.
Optimizing the value of bioinks and robotics to advance in vivo bioprinting.
Visible-light-switchable Molecular Glues for Reversible Control of Protein Function.
Revealed: the fatty cells that are the 'bubble wrap' of the body.
Vat Photopolymerization Additive Manufacturing of WC-Co Hardmetals Enabled by In Situ Polymerization-Induced Microencapsulation.
Optimized directed evolution of E. coli leucyl-tRNA synthetase adds many noncanonical amino acids into the eukaryotic genetic code including ornithine and Nε-acetyl-methyllysine.
Targeting protein-ligand neosurfaces with a generalizable deep learning tool.
Symmetric Diblock Copolymers Form Versatile and Switchable Ultrasmall Nanoparticles.
Evaluation of Silica and Bioglass Nanomaterials in Pulp-like Living Materials.
Transducing chemical energy through catalysis by an artificial molecular motor.
Nanospiked Cellulose Gauze That Attracts Bacteria with Biomolecules for Reducing Bacterial Load in Burn Wounds.
Construction and Characterization of MoClo-Compatible Vectors for Modular Protein Expression in E. coli.
A data-driven modeling framework for mapping genotypes to synthetic microbial community functions.
Complex Core-Shell Architectures through Spatially Organized Nano-Assemblies.
Morphogenesis of bacterial cables in polymeric environments.
Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System.

Acta Biomater. 2025 Jan 10. pii: S1742-7061(25)00020-0. [Epub ahead of print]

Reversible light-responsive protein hydrogel for on-demand cell encapsulation and release.

Om Prakash Narayan, Jiawei Dong, Miao Huang, Liqiang Chen, Lu Liu, Vivian Nguyen, Abdul Vehab Dozic, Xiangping Liu, Huiliang Wang, Qian Yin, Xin Tang, Juan Guan.

  The design of biomaterials that can reconfigure on-demand in response to external stimuli is an emerging area in materials research. However, achieving reversible assembly of protein-based biomaterials by light input remains a major challenge. Here, we present the engineering of a new protein material that is capable of switching between liquid and solid state reversibly, controlled by lights of different wavelengths. The materials are created by incorporating a light-responsive mutant Dronpa protein domain into the backbone of Elastin-Like Proteins (termed DELPs). We show that the DELP material can respond to light and undergo multiple cycles of switching between hydrogel and solution, outperforming the conventional irreversible materials. Additionally, the material is biocompatible with long-term cell proliferation in both adherent and suspension cells. Building on the reversible assembly of the material, we demonstrate efficient cell encapsulation and release upon light triggers. The design principle of incorporating a light-responsive protein element into a structural protein matrix, as demonstrated in this work enables, a broad range of other applications that require adaptive materials to intelligently interface with dynamic biological systems and environments. STATEMENT OF SIGNIFICANCE: This work generates a new class of "smart" biomaterials that uniquely switches between liquid and gel states in response to light input. Light input can be precisely delivered in space and time, highly tunable through wavelengths, intensities, and durations of light exposure. In prior research, light-responsive biomaterials are mostly irreversible, limiting their use to only uni-directional applications and the materials cannot be re-used. In contrast, this material robustly displays reversible switching between liquid and gel using a light-responsive crosslinker. Furthermore, the material is biocompatible, programmable, and suitable for broad applications including but not limited to cell encapsulation, controlled release, tissue engineering, and cell/tissue mechanobiology.

Keywords:  Biomaterial; Cell encapsulation; Dronpa; Elastin-like proteins; Light responsive proteins; Protein engineering; Stimuli responsive proteins

DOI:  https://doi.org/10.1016/j.actbio.2025.01.012
ACS Synth Biol. 2025 Jan 16.

Living Dual Heat- and pH-Responsive Textiles.

Dalia Jane Saldanha, Simon James Alexander Rowat, Henry Stephenson, Noémie-Manuelle Dorval Courchesne.

  Smart textiles that integrate multiple environmental sensing capabilities are an emerging frontier in wearable technology. In this study, we developed dual pH- and temperature-responsive textiles by combining engineered bacterial systems with bacterially derived proteins. For temperature sensing, we characterized the properties of a heat sensitive promoter, Phs, in Escherichia coli (E. coli) using enhanced green fluorescent protein as a reporter. Our findings demonstrate that the Phs promoter drives elevated gene expression at temperatures between 37 and 43 °C, maintaining sustained activity for several hours. Moreover, we found that short heat shocks can significantly boost expression levels of the Phs promoter. We successfully integrated E. coli expressing Phs-EGFP cells onto textiles and confirmed their ability to retain heat-responsive behavior after integration. To achieve pH responsiveness, we utilized curli fibers, genetically engineered to incorporate a pH-sensitive fluorescent protein, pHuji. pH-sensing curli fibers are bacterial proteins that have a proven track record of creating stable bioresponsive textile coatings. By embedding Phs-EGFP-expressing bacteria within curli fiber coatings, we created a dual-responsive textile capable of differentiating between acidic and alkaline environments while simultaneously responding to thermal stimuli. These multifunctional textiles exhibited dual environmental response and sensing capabilities. This work establishes a proof-of-concept for creating smart living textiles with modular functionalities, paving the way toward advanced bioresponsive materials.

Keywords:  biosensors; curli fibers; engineered biofilms; heat-inducible promoters; smart textiles

DOI:  https://doi.org/10.1021/acssynbio.4c00808
Nat Chem Biol. 2025 Jan 15.

Orthogonalized human protease control of secreted signals.

Carlos A Aldrete, Connor C Call, Lucas E Sant'Anna, Alexander E Vlahos, Jimin Pei, Qian Cong, Xiaojing J Gao.

Synthetic circuits that regulate protein secretion in human cells could support cell-based therapies by enabling control over local environments. Although protein-level circuits enable such potential clinical applications, featuring orthogonality and compactness, their non-human origin poses a potential immunogenic risk. In this study, we developed Humanized Drug Induced Regulation of Engineered CyTokines (hDIRECT) as a platform to control cytokine activity exclusively using human-derived proteins. We sourced a specific human protease and its FDA-approved inhibitor. We engineered cytokines (IL-2, IL-6 and IL-10) whose activities can be activated and abrogated by proteolytic cleavage. We used species specificity and re-localization strategies to orthogonalize the cytokines and protease from the human context that they would be deployed in. hDIRECT should enable local cytokine activation to support a variety of cell-based therapies, such as muscle regeneration and cancer immunotherapy. Our work offers a proof of concept for the emerging appreciation of humanization in synthetic biology for human health.

DOI: https://doi.org/10.1038/s41589-024-01831-x
Chem Rev. 2025 Jan 13.

Synthetic Lipid Biology.

Po-Hsun Brian Chen, Xiang-Ling Li, Jeremy M Baskin.

Cells contain thousands of different lipids. Their rapid and redundant metabolism, dynamic movement, and many interactions with other biomolecules have justly earned lipids a reputation as a vexing class of molecules to understand. Further, as the cell's hydrophobic metabolites, lipids assemble into supramolecular structures─most commonly bilayers, or membranes─from which they carry out myriad biological functions. Motivated by this daunting complexity, researchers across disciplines are bringing order to the seeming chaos of biological lipids and membranes. Here, we formalize these efforts as "synthetic lipid biology". Inspired by the idea, central to synthetic biology, that our abilities to understand and build biological systems are intimately connected, we organize studies and approaches across numerous fields to create, manipulate, and analyze lipids and biomembranes. These include construction of lipids and membranes from scratch using chemical and chemoenzymatic synthesis, editing of pre-existing membranes using optogenetics and protein engineering, detection of lipid metabolism and transport using bioorthogonal chemistry, and probing of lipid-protein interactions and membrane biophysical properties. What emerges is a portrait of an incipient field where chemists, biologists, physicists, and engineers work together in proximity─like lipids themselves─to build a clearer description of the properties, behaviors, and functions of lipids and membranes.

DOI: https://doi.org/10.1021/acs.chemrev.4c00761
Nat Chem Biol. 2025 Jan 13.

A cell-free biosensor signal amplification circuit with polymerase strand recycling.

Yueyi Li, Tyler Lucci, Matias Villarruel Dujovne, Jaeyoung Kirsten Jung, Daiana A Capdevila, Julius B Lucks.

Cell-free systems are powerful synthetic biology technologies that can recapitulate gene expression and sensing without the complications of living cells. Cell-free systems can perform more advanced functions when genetic circuits are incorporated. Here we expand cell-free biosensing by engineering a highly specific isothermal amplification circuit called polymerase strand recycling (PSR), which leverages T7 RNA polymerase off-target transcription to recycle nucleic acid inputs within DNA strand displacement circuits. We first construct simple PSR circuits to detect different RNA targets with high specificity. We then interface PSR circuits to amplify signals from allosteric transcription factor-based biosensors for small molecule detection. A double equilibrium model of transcription factor-DNA/ligand binding predicts that PSR can improve biosensor sensitivity, which we confirm experimentally by improving the limits of detection by 10-fold to submicromolar levels for two biosensors. We believe this work expands the capabilities of cell-free circuits and demonstrates PSR's potential for diverse applications in biotechnology.

DOI: https://doi.org/10.1038/s41589-024-01816-w
Biomaterials. 2025 Jan 06. pii: S0142-9612(24)00607-0. [Epub ahead of print]317 123071

Injectable ionic hydrogel conductors: Advancing material design to transform cardiac pacing.

Gabriel J Rodriguez-Rivera, Allison Post, Mathews John, Derek Bashe, Fei Xu, Trace Larue, Abbey Nkansah, Megan Wancura, Malgorzata Chwatko, Christina Waldron, Nikhith Kalkunte, Janet Zoldan, Mathieu Arseneault, Abdou Elgalad, Manuel K Rausch, Mehdi Razavi, Elizabeth Cosgriff-Hernandez.

  Direct pacing of the mid myocardium where re-entry originates can be used to prevent ventricular arrhythmias and circumvent the need for painful defibrillation or cardiac ablation. However, there are no pacing electrodes small enough to navigate the coronary veins that cross these culprit scar regions. To address this need, we have developed an injectable ionically conductive hydrogel electrode that can fill the epicardial coronary veins and transform them into flexible electrodes. A new hydrogel chemistry based on a polyether urethane diacrylamide macromer was developed that matches myocardial stiffness and is resistant to hydrolysis. Conductivity was imparted using ionic precursor solutions with values in the range of 2-3X of native myocardium that was retained after implantation. Ionic hydrogel electrodes provided stable electrical stimuli over many cycles and across a substantial length of the cardiac vein. Rapid in situ cure was achieved with redox initiation after injection from a double-barrel syringe with a mixing head. An ex vivo porcine model was used to identify the requisite viscosity and cure rate for hydrogel retention and homogeneity. Finally, successful in vivo deployment and pacing in a porcine model demonstrated that the ionic hydrogel electrode filled the anterior interventricular vein to depths far more distal and refined than current technologies. Collectively, these studies demonstrate the potential of this injectable ionic hydrogel electrode to pace previously inaccessible mid-myocardial tissue and pave the pathway for painless defibrillation.

Keywords:  Arrhythmias; Biomaterials; Conductive; Hydrogels; Injectable; Pacing

DOI:  https://doi.org/10.1016/j.biomaterials.2024.123071
iScience. 2025 Jan 17. 28(1): 111541

Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes.

Shaunak Kar, Elizabeth C Gardner, Kamyab Javanmardi, Daniel R Boutz, Raghav Shroff, Andrew P Horton, Thomas H Segall-Shapiro, Andrew D Ellington, Jimmy Gollihar.

  T7 RNA polymerase (RNAP) has enabled orthogonal control of gene expression and recombinant protein production across diverse prokaryotic host chassis organisms for decades. However, the absence of 5' methyl guanosine caps on T7 RNAP-derived transcripts has severely limited its utility and widespread adoption in eukaryotic systems. To address this shortcoming, we evolved a fusion enzyme combining T7 RNAP with the single subunit capping enzyme from African swine fever virus using Saccharomyces cerevisiae. We isolated highly active variants of this fusion enzyme, which exhibited roughly two orders of magnitude higher protein expression compared to the wild-type enzyme. We demonstrate the programmable control of gene expression using T7 RNAP-based genetic circuits in yeast and validate enhanced performance of these engineered variants in mammalian cells. This study presents a robust, orthogonal gene regulatory system applicable across diverse eukaryotic hosts, enhancing the versatility and efficiency of synthetic biology applications.

Keywords:  biomolecular engineering; genetics; molecular biology

DOI:  https://doi.org/10.1016/j.isci.2024.111541
Nature. 2025 Jan 17.

AI-designed proteins tackle century-old problem - making snake antivenoms.

Ewen Callaway.



Keywords:  Synthetic biology

DOI:  https://doi.org/10.1038/d41586-025-00133-z
bioRxiv. 2025 Jan 05. pii: 2025.01.05.631398. [Epub ahead of print]

Design of an exclusive obligate symbiosis for organism-based biological containment.

Amanda M Forti, Michaela A Jones, Defne N Elbeyli, Neil D Butler, Aditya M Kunjapur.

Biological containment is a critical safeguard for genetically engineered microbes prior to their environmental release to prevent proliferation in unintended regions. However, few biocontainment strategies can support the longer-term microbial survival that may be desired in a target environment without repeated human intervention. Here, we introduce the concept of an orthogonal obligate commensalism for the autonomous creation of environments that are permissive for survival of a biocontained microbe. We engineer one microbe to produce a non-standard amino acid (nsAA), and we engineer synthetic auxotrophy in a second microbe via reliance on this nsAA for growth. We show that this obligate commensalism is highly effective, with the survival of our commensal organism during co-culture dependent on the presence of our producer strain. We also show that this commensalism is orthogonal to a small microbial consortium isolated from maize roots, with survival of the synthetic auxotroph conditional upon the presence of the nsAA-producing strain in the consortium. Overall, our study demonstrates a transition from a chemical to a biological dependence for biocontained organisms that could lay the groundwork for biocontained synthetic ecologies.

DOI: https://doi.org/10.1101/2025.01.05.631398
Chemistry. 2025 Jan 14. e202404360

Programing Green Light-Responsive Hydrogels: from Photo-Weakening to Photo-unresponsiveness and Photo-Strengthening.

Saskia Frank, Seraphine Wegner.

  Light-responsive hydrogels are highly valued for their dynamic mechanical properties and biocompatibility. In this study, we present a hydrogel system that can either soften or strengthen on green light exposure, or remain unresponsive to light, depending on the addition of adenosyl cobalamin (AdoCbl) and Co2+. These protein-based hydrogels were formed using genetically encoded SpyTag-SpyCatcher chemistry and included green light-sensitive CarHc protein domains. As previously reported, these hydrogels formed in the dark with the addition of AdoCbl, due to the tetramerization of the CarHc domains. Under green light exposure, the CarHc tetramers disassembled, leading to a rapid transition from gel to sol. Interestingly, we discovered that an excess of AdoCbl leads to photo-strengthening rather than photo-weakening. This occurred because light exposure induces interchain crosslinks between AdoCbl and poly-histidine tags (His6-tags) of the proteins. Furthermore, incorporating Co2+ ions enhanced hydrogel stiffness by coordinating to His6-tags. This not only suppressed photo-weakening but also promoted photo-strengthening behaviour. These findings highlight the role of His6-tags in photochemical crosslinking with excess AdoCbl and in coordination to Co2+ ions, providing a novel strategy for designing tuneable, light responsiveness in materials.

Keywords:  AdoCbl; CarH; coordination hydrogels; photoresponsive; protein hydrogels

DOI:  https://doi.org/10.1002/chem.202404360
Nat Mater. 2025 Jan 13.

Morphology remodelling and membrane channel formation in synthetic cells via reconfigurable DNA nanorafts.

Sisi Fan, Shuo Wang, Longjiang Ding, Thomas Speck, Hao Yan, Stephan Nussberger, Na Liu.

The shape of biological matter is central to cell function at different length scales and determines how cellular components recognize, interact and respond to one another. However, their shapes are often transient and hard to reprogramme. Here we construct a synthetic cell model composed of signal-responsive DNA nanorafts, biogenic pores and giant unilamellar vesicles (GUVs). We demonstrate that reshaping of DNA rafts at the nanoscale can be coupled to reshaping of GUVs at the microscale. The nanorafts collectively undergo reversible transitions between isotropic and short-range local order on the lipid membrane, programmably remodelling the GUV shape. Assisted by the biogenic pores, during GUV shape recovery the locally ordered DNA rafts perforate the membrane, forming sealable synthetic channels for large cargo transport. Our work outlines a versatile platform for interfacing reconfigurable DNA nanostructures with synthetic cells, expanding the potential of DNA nanotechnology in synthetic biology.

DOI: https://doi.org/10.1038/s41563-024-02075-9
Science. 2025 Jan 17. 387(6731): 269-277

3D polycatenated architected materials.

Wenjie Zhou, Sujeeka Nadarajah, Liuchi Li, Anna Guell Izard, Hujie Yan, Aashutosh K Prachet, Payal Patel, Xiaoxing Xia, Chiara Daraio.

Architected materials derive their properties from the geometric arrangement of their internal structural elements. Their designs rely on continuous networks of members to control the global mechanical behavior of the bulk. In this study, we introduce a class of materials that consist of discrete concatenated rings or cage particles interlocked in three-dimensional networks, forming polycatenated architected materials (PAMs). We propose a general design framework that translates arbitrary crystalline networks into particle concatenations and geometries. In response to small external loads, PAMs behave like non-Newtonian fluids, showing both shear-thinning and shear-thickening responses, which can be controlled by their catenation topologies. At larger strains, PAMs behave like lattices and foams, with a nonlinear stress-strain relation. At microscale, we demonstrate that PAMs can change their shapes in response to applied electrostatic charges. The distinctive properties of PAMs pave the path for developing stimuli-responsive materials, energy-absorbing systems, and morphing architectures.

DOI: https://doi.org/10.1126/science.adr9713
Angew Chem Int Ed Engl. 2025 Jan 13. e202407359

Digital and Tunable Genetically Encoded Tension Sensors Based on Engineered Coiled-Coils.

Shuhong Liu, Jinchan Liu, Alexander Foote, Hiroaki Ogasawara, Sarah Al Abdullatif, Victor S Batista, Khalid Salaita.

  Genetically encoded tension sensors (GETSs) allow for quantifying forces experienced by intracellular proteins involved in mechanotransduction. The vast majority of GETSs are comprised of a FRET pair flanking an elastic "spring-like" domain that gradually extends in response to force. Because of ensemble averaging, the FRET signal generated by such analog sensors conceals forces that deviate from the average, and hence it is unknown if a subset of proteins experience greater magnitudes of force. We address this problem by developing digital GETSs comprised of coiled-coils (CCs) with tunable mechanical thresholds. We validate the mechanical response of CC digital probes using thermodynamic stability prediction, AlphaFold2 modeling, steered molecular dynamics simulations, and single molecule force microscopy. Live cell measurements using optimized CC tension sensors that are inserted into vinculin demonstrate that 13% of this mechanosensor experiences forces > 9.9 pN within focal adhesions. This reveals greater magnitudes of vinculin force than had previously been reported and demonstrates that coiled-coil tension sensors enable more facile and precise tension measurements in living systems.

Keywords:  biophysics * protein engineering * biosensors * FRET

DOI:  https://doi.org/10.1002/anie.202407359
Sci Adv. 2025 Jan 17. 11(3): eadq5011

Programmed shape transformations in cell-laden granular composites.

Nikolas Di Caprio, Alex J Hughes, Jason A Burdick.

Tissues form during development through mechanical compaction of their extracellular matrix (ECM) and shape morphing, processes that result in complex-shaped structures that contribute to tissue function. While observed in vivo, control over these processes in vitro to understand both tissue development and guide tissue formation has remained challenging. Here, we use combinations of mesenchymal stromal cell spheroids and hydrogel microparticles (microgels) with varied hydrolytic stability to fabricate programmable and dynamic granular composites that control compaction and tissue formation over time. Mixed microgel populations of varying stability provide a further handle to alter compaction, and the level of compaction guides the uniformity and level of ECM deposition within tissues. Last, spatially patterned granular composites of varying compaction enable shape transformations (i.e., bending/curvature) that are stable with culture and are predicted by finite element models.

DOI: https://doi.org/10.1126/sciadv.adq5011
Nat Commun. 2025 Jan 16. 16(1): 719

A compliant metastructure design with reconfigurability up to six degrees of freedom.

Humphrey Yang, Dinesh K Patel, Tate Johnson, Ke Zhong, Gina Olson, Carmel Majidi, Mohammad F Islam, Teng Zhang, Lining Yao.

Compliant mechanisms with reconfigurable degrees of freedom are gaining attention in the development of kinesthetic haptic devices, robotic systems, and mechanical metamaterials. However, available devices exhibit limited programmability and form-customizability, restricting their versatility. To address this gap, we propose a metastructure concept featuring reconfigurable motional freedom and tunable stiffness, adaptable to various form factors and applications. These devices incorporate passive flexures and actively stiffness-changing rods to modify kinematic freedom. A rational design pipeline informs the flexures' topological arrangements, geometric parameters, and control signals based on targeted mobilities, enabling the creation of unitary joints with up to six degrees of freedom. Our demonstrative application examples include a wrist device that has an effective stiffness of 0.370 Nm/deg (unlocked state, 5% displacement) to 2.278 Nm/deg (locked state, 1% displacement) to enable dynamic joint mobility control, a haptic thimble device (2.27-52.815 Nmm-1 at 1% displacement) that mimics the sensation of touching physical materials ranging from soft gel to metal surfaces, and a wearable device composed of multiple joints tailored for the arm and hand to augment haptic experiences or facilitate muscle training. We believe the presented method can help democratize compliant metastructures development and expand their versatility for broader contexts.

DOI: https://doi.org/10.1038/s41467-024-55591-2
Acta Biomater. 2025 Jan 09. pii: S1742-7061(25)00017-0. [Epub ahead of print]

Interpenetrating networks of fibrillar and amorphous collagen promote cell spreading and hydrogel stability.

Lucia G Brunel, Chris M Long, Fotis Christakopoulos, Betty Cai, Patrik K Johansson, Diya Singhal, Annika Enejder, David Myung, Sarah C Heilshorn.

  Hydrogels composed of collagen, the most abundant protein in the human body, are widely used as scaffolds for tissue engineering due to their ability to support cellular activity. However, collagen hydrogels with encapsulated cells often experience bulk contraction due to cell-generated forces, and conventional strategies to mitigate this undesired deformation often compromise either the fibrillar microstructure or cytocompatibility of the collagen. To support the spreading of encapsulated cells while preserving the structural integrity of the gels, we present an interpenetrating network (IPN) of two distinct collagen networks with different crosslinking mechanisms and microstructures. First, a physically self-assembled collagen network preserves the fibrillar microstructure and enables the spreading of encapsulated human corneal mesenchymal stromal cells. Second, an amorphous collagen network covalently crosslinked with bioorthogonal chemistry fills the voids between fibrils and stabilizes the gel against cell-induced contraction. This collagen IPN balances the biofunctionality of natural collagen with the stability of covalently crosslinked, engineered polymers. Taken together, these data represent a new avenue for maintaining both the fiber-induced spreading of cells and the structural integrity of collagen hydrogels by leveraging an IPN of fibrillar and amorphous collagen networks. STATEMENT OF SIGNIFICANCE: Collagen hydrogels are widely used as scaffolds for tissue engineering due to their support of cellular activity. However, collagen hydrogels often undergo undesired changes in size and shape due to cell-generated forces, and conventional strategies to mitigate this deformation typically compromise either the fibrillar microstructure or cytocompatibility of the collagen. In this study, we introduce an innovative interpenetrating network (IPN) that combines physically self-assembled, fibrillar collagen-ideal for promoting cell adhesion and spreading-with covalently crosslinked, amorphous collagen-ideal for enhancing bulk hydrogel stability. Our IPN design maintains the native fibrillar structure of collagen while significantly improving resistance against cell-induced contraction, providing a promising solution to enhance the performance and reliability of collagen hydrogels for tissue engineering applications.

Keywords:  Cell morphology; Collagen; Crosslinking; Hydrogel contraction; Interpenetrating network

DOI:  https://doi.org/10.1016/j.actbio.2025.01.009
Angew Chem Int Ed Engl. 2025 Jan 13. e202421448

Two-Level Spatially Localized Proximity Labeling for Cross-Biological-Hierarchy Measurement and Manipulation.

Liusheng Chen, Yiran Li, Yuna Guo, Guyu Wang, Nan Feng, Jiahui Sun, Yihong Zhong, Yunyan Yao, Lin Ding, Huangxian Ju.

  Proximity labeling (PL) has emerged as a powerful technique for the in situ elucidation of biomolecular interaction networks. However, PL methods generally rely on single-biological-hierarchy control of spatial localization at the labeling site, which limits their application in multi-tiered biological systems. Here, we introduced another enzymatic reaction upstream of an enzyme-based PL reaction and targeted the two enzymes to markers indicating different biological hierarchies, establishing a two-level spatially localized proximity labeling (P2L) platform for in situ molecular measurement and manipulation. Using the cellular- and glycan-level as the hierarchical models, we demonstrated the ability of P2L to efficiently execute a two-step logic operation and to discriminate target cells with different levels of glycosylation within mixed cell populations. By mounting clickable handles via P2L, we reprogrammed the robust covalent assembly of cells at designated sites. The combination of P2L with proteomics led to the profiling of the protein microenvironment of specific glycans on target cells, revealing changes in tumor-cell-surface interactions under immune pressure from a glycan perspective. P2L provides not only a solution for revealing the heterogeneity of biological systems, but also new insights in the fields of intelligent logic computation, enzyme engineering, tissue engineering, etc.

Keywords:  Cellular assembly; Enzymatic cascade; Logic computation; Two-level spatial localization; proximity labeling

DOI:  https://doi.org/10.1002/anie.202421448
Nat Chem Biol. 2025 Jan 13.

Transforming an ATP-dependent enzyme into a dissipative, self-assembling system.

Yiying Li, Jie Zhu, Zhiyin Zhang, Jiapeng Wei, Fengbin Wang, Georg Meisl, Tuomas P J Knowles, Edward H Egelman, F Akif Tezcan.

Nucleoside triphosphate (NTP)-dependent protein assemblies such as microtubules and actin filaments have inspired the development of diverse chemically fueled molecular machines and active materials but their functional sophistication has yet to be matched by design. Given this challenge, we asked whether it is possible to transform a natural adenosine 5'-triphosphate (ATP)-dependent enzyme into a dissipative self-assembling system, thereby altering the structural and functional mode in which chemical energy is used. Here we report that FtsH (filamentous temperature-sensitive protease H), a hexameric ATPase involved in membrane protein degradation, can be readily engineered to form one-dimensional helical nanotubes. FtsH nanotubes require constant energy input to maintain their integrity and degrade over time with the concomitant hydrolysis of ATP, analogous to natural NTP-dependent cytoskeletal assemblies. Yet, in contrast to natural dissipative systems, ATP hydrolysis is catalyzed by free FtsH protomers and FtsH nanotubes serve to conserve ATP, leading to transient assemblies whose lifetimes can be tuned from days to minutes through the inclusion of external ATPases in solution.

DOI: https://doi.org/10.1038/s41589-024-01811-1
Biomacromolecules. 2025 Jan 13. 26(1): 490-502

Nanofibrous Peptide Hydrogels Leveraging Histidine to Modulate pH-Responsive Supramolecular Assembly and Antibody Release.

Gabriel Saenz, Brett H Pogostin, Carson C Cole, Anushka Agrawal, Danielle Chew-Martinez, Marija Dubackic, Antara Pal, Ulf Olsson, Kevin J McHugh, Jeffrey D Hartgerink.

In this work, we investigate the pH-responsive behavior of multidomain peptide (MDP) hydrogels containing histidine. Small-angle X-ray scattering confirmed that MDP nanofibers sequester nonpolar residues into a hydrophobic core surrounded by a shell of hydrophilic residues. MDPs with histidine on the hydrophilic face formed nanofibers at all pH values tested, but the morphology of the fibers was influenced by the protonation state and the location of histidine in the MDP sequence. MDPs with histidine residues within the hydrophobic face disassemble below physiological pH and form nanofibers at higher pH. Taking advantage of their stimulus-triggered behavior, an anti-PD-1 antibody was loaded into histidine MDP hydrogels to examine pH-dependent differences in payload delivery in vitro. Hydrogels composed of MDPs with histidine on the hydrophilic face demonstrated pH-dependent payload retention. Additionally, they showed significantly slower antibody release and reduced antibody diffusion rates in vitro compared to MDP hydrogels lacking histidine.

DOI: https://doi.org/10.1021/acs.biomac.4c01296
ACS Nano. 2025 Jan 12.

Temperature-Directed Morphology Transformation Method for Precision-Engineered Polymer Nanostructures.

Valentin A Bobrin, Surya E Sharma-Brymer, Michael J Monteiro.

  With polymer nanoparticles now playing an influential role in biological applications, the synthesis of nanoparticles with precise control over size, shape, and chemical functionality, along with a responsive ability to environmental changes, remains a significant challenge. To address this challenge, innovative polymerization methods must be developed that can incorporate diverse functional groups and stimuli-responsive moieties into polymer nanostructures, which can then be tailored for specific biological applications. By combining the advantages of emulsion polymerization in an environmentally friendly reaction medium, high polymerization rates due to the compartmentalization effect, chemical functionality, and scalability, with the precise control over polymer chain growth achieved through reversible-deactivation radical polymerization, our group developed the temperature-directed morphology transformation (TDMT) method to produce polymer nanoparticles. This method utilized temperature or pH responsive nanoreactors for controlled particle growth and with the added advantages of controlled surface chemical functionality and the ability to produce well-defined asymmetric structures (e.g., tadpoles and kettlebells). This review summarizes the fundamental thermodynamic and kinetic principles that govern particle formation and control using the TDMT method, allowing precision-engineered polymer nanoparticles, offering a versatile and an efficient means to produce 3D nanostructures directly in water with diverse morphologies, high purity, high solids content, and controlled surface and internal functionality. With such control over the nanoparticle features, the TDMT-generated nanostructures could be designed for a wide variety of biological applications, including antiviral coatings effective against SARS-CoV-2 and other pathogens, reversible scaffolds for stem cell expansion and release, and vaccine and drug delivery systems.

Keywords:  RAFT polymerization; antiviral coating; asymmetric nanoparticles; drug delivery; emulsion polymerization; multifunctional nanoparticles; nanoreactors; smart polymers; stem cells; vaccine

DOI:  https://doi.org/10.1021/acsnano.4c14506
Appl Environ Microbiol. 2025 Jan 14. e0246524

Single-cell phenotyping of extracellular electron transfer via microdroplet encapsulation.

Gina Partipilo, Emily K Bowman, Emma J Palmer, Yang Gao, Rodney S Ridley, Hal S Alper, Benjamin K Keitz.

  Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes via extracellular electron transfer (EET). Unfortunately, developing genotype-phenotype relationships for electroactive organisms is challenging because EET is necessarily removed from the cell of origin. Microdroplet emulsions, which encapsulate individual cells in aqueous droplets, have been used to study a variety of extracellular phenotypes but have not been applied to investigate EET. Here, we describe the development of a microdroplet emulsion system to sort and enrich EET-capable organisms from complex populations. We validated our system using the model electrogen Shewanella oneidensis and described the tooling of a benchtop microfluidic system for oxygen-limited conditions. We demonstrated the enrichment of strains exhibiting electroactive phenotypes from mixed wild-type and EET-deficient populations. As a proof-of-concept application, we collected samples from iron sedimentation in Town Lake (Austin, TX) and subjected them to microdroplet enrichment. We measured an increase in electroactive organisms in the sorted population that was distinct compared to a population growing in bulk culture with Fe(III) as the sole electron acceptor. Finally, two bacterial species not previously shown to be EET-capable, Cronobacter sakazakii and Vagococcus fessus, were further cultured and characterized for electroactivity. Our results demonstrate the utility of microdroplet emulsions for isolating and identifying EET-capable bacteria.IMPORTANCEThis work outlines a new high-throughput method for identifying electroactive bacteria from mixed populations. Electroactive bacteria play key roles in iron trafficking, soil remediation, and pollutant degradation. Many existing methods for identifying electroactive bacteria are coupled to microbial growth and fitness-as a result, the contributions from weak or poor-growing electrogens are often muted. However, extracellular electron transfer (EET) has historically been difficult to study in high-throughput in a mixed population since extracellular reduction is challenging to trace back to the parent cell and there are no suitable fluorescent readouts for EET. Our method circumvents these challenges by utilizing an aqueous microdroplet emulsion wherein a single cell is statistically isolated in a pico- to nano-liter-sized droplet. Then, via fluorescence obtained from copper reduction, the mixed population can be fluorescently sorted and gated by performance. Utilizing our technique, we characterize two previously unrecognized weak electrogens Vagococcus fessus and Cronobacter sakazakii.

Keywords:  electroactive; iron-reducing; microbiology; microfluidics

DOI:  https://doi.org/10.1128/aem.02465-24
Food Chem. 2025 Jan 09. pii: S0308-8146(25)00078-0. [Epub ahead of print]471 142828

3D bioprinting: Advancing the future of food production layer by layer.

Nisansala Chandimali, Seon-Gyeong Bak, Eun Hyun Park, Sun Hee Cheong, Sang-Ik Park, Seung-Jae Lee.

  3D bioprinting is an advanced manufacturing technique that involves the precise layer-by-layer deposition of biomaterials, such as cells, growth factors, and biomimetic scaffolds, to create three-dimensional living structures. It essentially combines the complexity of biology with the principles of 3D printing, making it possible to fabricate complex biological structures with extreme control and accuracy. This review discusses how 3D bioprinting is developing as an essential step in the creation of alternative food such as cultured meat and seafood. In light of the growing global issues associated with food sustainability and the ethical challenges raised by conventional animal agriculture, 3D bioprinting is emerging as a key technology that will transform food production in the years to come. This paper also addresses in detail each of the components that make up bioprinting systems, such as the bioinks and scaffolds used, the various types of bioprinter models, and the software systems that control the production process. It offers a thorough examination of the processes involved in printing diverse food items using bioprinting. Beyond the scope of this conversation, 3D bioprinting, which provides superior precision and scalability in tissue engineering, is a crucial node in the broader system of cultured meat and seafood production. But like any emerging technology, 3D bioprinting has its limitations. In light of this, this study emphasizes the necessity of ongoing research and development to advance bioprinting towards widespread use and, ultimately, promote a more resilient, ethical, and sustainable food supply system.

Keywords:  Bio ink; Bioprinter; Cultured meat; Scaffolds; Tissue engineering

DOI:  https://doi.org/10.1016/j.foodchem.2025.142828
FEMS Microbes. 2025 ;6 xtae035

Silica hydrogels as a carbon-free solid media for the culture of diverse organisms.

Druhi Vaid, Alisa Zubir, Alistair Hanak, Tanda Qi, Daniela Delneri, Lu Shin Wong.

  Bacteriological agar plates are commonly used to carry out experiments for the selective growth of microorganisms and the isolation of single-strain colonies. However, the presence of agar itself may be a confounding factor since it may serve as a source of carbon and energy. Moreover, there have been ongoing constraints on the production and sourcing of agar. These concerns have led to an interest in the development of agar substitutes. Silica hydrogels are entirely inorganic carbon-free polymeric materials that lack any source of micronutrients. Herein, a revised method for the preparation of silica hydrogels as a solid culture medium is reported. These gels can be formulated with a range of nutrient-rich or minimal media supplemented with various carbon sources, and can be manipulated in the same manner as agar gels. Their use for the culture and isolation of diverse microorganisms, including both Gram-positive and Gram-negative bacteria, yeast, and filamentous fungi is demonstrated. These silica hydrogels supplemented with either antibiotics or other molecules of interest can also be used for microbial selection experiments.

Keywords:  biocompatible; hydrogel; inorganic gel; selective culture media; solid culture media; tetraethoxysilane

DOI:  https://doi.org/10.1093/femsmc/xtae035
Curr Opin Biotechnol. 2025 Jan 09. pii: S0958-1669(24)00187-3. [Epub ahead of print]91 103251

Optimizing the value of bioinks and robotics to advance in vivo bioprinting.

Friederike Dehli, Oscar O'Dwyer Lancaster-Jones, Daniela Duarte Campos.

In vivo bioprinting strategies aim at facilitating immediate integration of engineered tissues with the host's biological system. As integral parts of current bioprinting technologies, bioinks and robotics should be holistically considered for new biomedical applications. This implies that chosen bioinks should exhibit rheological properties that are compatible with the fabrication method and vice versa, bioprinting tools might need to be redesigned and reconstructed to fit the characteristics of the needed bioinks that after solidification act as supporting matrices for living cells. In this piece, we identify current challenges in merging the best of these two principles, we highlight relevant studies that have addressed this need, and we propose ideas how to approach this challenge in the next years.

DOI: https://doi.org/10.1016/j.copbio.2024.103251
Chemistry. 2025 Jan 13. e202403808

Visible-light-switchable Molecular Glues for Reversible Control of Protein Function.

Jun Zhang, Laura K Herzog, Shuang Li, Xi Chen, Yaowen Wu.

  Chemically induced dimerization/proximity (CID/CIP) systems controlled by chemical dimerizers (also known as molecular glues) provide valuable means for understanding and manipulating complex, dynamic biological systems. In this study, we present the development of versatile chemo-optogenetic systems utilizing azobenzene-based photoswitchable molecular glues (sMGs) for reversible protein dimerization controlled by visible light. These systems allow multiple cycles of light-induced dimerization, overcoming the limitations of irreversible photolysis in previous systems. Through optimizing photoswitch properties and linker strategies, we achieved efficient and reversible control using blue, green, and red light. We demonstrate that these systems enable rapid and reversible control of protein function in vitro and in cells. The findings represent a significant advancement in chemo-optogenetics, offering opportunities to expand applications requiring precise spatiotemporal regulation of dynamic biological processes.

Keywords:  Chemo-optogenetic system, Chemically induced dimerization, Molecular glue, Photoswitches, Visible light

DOI:  https://doi.org/10.1002/chem.202403808
Nature. 2025 Jan 09.

Revealed: the fatty cells that are the 'bubble wrap' of the body.

Max Kozlov.



Keywords:  Cell biology

DOI:  https://doi.org/10.1038/d41586-025-00012-7
ACS Appl Mater Interfaces. 2025 Jan 15.

Vat Photopolymerization Additive Manufacturing of WC-Co Hardmetals Enabled by In Situ Polymerization-Induced Microencapsulation.

Zhanhe Liu, Zirui Liu, Kechao Zhou, Zihang Chen, Kaihua Shi, Xinyu Wang, Chaoqun Peng, Richu Wang, Shlomo Magdassi, Jin He, Xiaofeng Wang.

  The additive manufacturing of hardmetals has attracted great attention recently but faces significant challenges in low printing resolution and low mechanical strength. Herein, the fabrication of hardmetal parts with complex structures and high surface quality by vat photopolymerization assisted with a sintering process has been achieved. This was enabled by in situ polymerization-induced microencapsulation of WC powder, which simultaneously enhances the photocuring ability and sedimentation stability of the WC-Co slurry. The WC powder is microencapsulated by a polystyrene (PS, WC@PS) coating with a thickness of ∼20 nm. The curing depth of the WC-Co slurry with WC@PS was dramatically increased from 32 to 336 μm compared to the slurry with original WC, exhibiting an average increment of 650%. The 3D-printed hardmetal parts exhibited a relative density of 99.5%, a Rockwell hardness of 86.9 HRA, and a surface roughness Ra of 2.26 μm, approaching the theoretical limits in classical powder metallurgy-derived WC-Co hardmetal parts. With high density and hardness, it is shown that a printed drilling bit can easily drill through metal sheets. This work paves a path for the vat photopolymerization 3D printing of miniature complex hardmetal components combined with high surface quality and high performance.

Keywords:  additive manufacturing (AM); complex shape; hardmetals; surface modification; vat photopolymerization

DOI:  https://doi.org/10.1021/acsami.4c20608
Angew Chem Int Ed Engl. 2025 Jan 17. e202423172

Optimized directed evolution of E. coli leucyl-tRNA synthetase adds many noncanonical amino acids into the eukaryotic genetic code including ornithine and Nε-acetyl-methyllysine.

Elise D Ficaretta, Tarah J Yared, Subrata Bhattacharjee, Lena A Voss, Rachel L Huang, Abhishek Chatterjee.

  Site-specific incorporation of noncanonical amino acids (ncAAs) into proteins in eukaryotes has predominantly relied on the pyrrolysyl-tRNA synthetase/tRNA pair. However, access to additional easily engineered pairs is crucial for expanding the structural diversity of the ncAA toolbox in eukaryotes. The Escherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair presents a particularly promising alternative. This pair has been engineered to charge a small yet structurally diverse group of ncAAs in eukaryotic cells. However, expanding the substrate scope of EcLeuRS has been difficult due to the suboptimal yeast-based directed evolution platform used for its engineering. In this study, we address this limitation by optimizing the yeast-based directed evolution platform for efficient selection of ncAA-selective EcLeuRS mutants. Using the optimized selection system, we demonstrate rapid isolation of many novel EcLeuRS mutants capable of incorporating various ncAAs in mammalian cells, including ornithine and Nε-acetyl-methyllysine, a recently discovered post-translational modification in mammalian cells.

Keywords:  Genetic code expansion, Post-translational modifications, aminoacyl-tRNA synthetases, protein engineering, directed evolution

DOI:  https://doi.org/10.1002/anie.202423172
Nature. 2025 Jan 15.

Targeting protein-ligand neosurfaces with a generalizable deep learning tool.

Anthony Marchand, Stephen Buckley, Arne Schneuing, Martin Pacesa, Maddalena Elia, Pablo Gainza, Evgenia Elizarova, Rebecca M Neeser, Pao-Wan Lee, Luc Reymond, Yangyang Miao, Leo Scheller, Sandrine Georgeon, Joseph Schmidt, Philippe Schwaller, Sebastian J Maerkl, Michael Bronstein, Bruno E Correia.

Molecular recognition events between proteins drive biological processes in living systems1. However, higher levels of mechanistic regulation have emerged, in which protein-protein interactions are conditioned to small molecules2-5. Despite recent advances, computational tools for the design of new chemically induced protein interactions have remained a challenging task for the field6,7. Here we present a computational strategy for the design of proteins that target neosurfaces, that is, surfaces arising from protein-ligand complexes. To develop this strategy, we leveraged a geometric deep learning approach based on learned molecular surface representations8,9 and experimentally validated binders against three drug-bound protein complexes: Bcl2-venetoclax, DB3-progesterone and PDF1-actinonin. All binders demonstrated high affinities and accurate specificities, as assessed by mutational and structural characterization. Remarkably, surface fingerprints previously trained only on proteins could be applied to neosurfaces induced by interactions with small molecules, providing a powerful demonstration of generalizability that is uncommon in other deep learning approaches. We anticipate that such designed chemically induced protein interactions will have the potential to expand the sensing repertoire and the assembly of new synthetic pathways in engineered cells for innovative drug-controlled cell-based therapies10.

DOI: https://doi.org/10.1038/s41586-024-08435-4
ACS Nano. 2025 Jan 14.

Symmetric Diblock Copolymers Form Versatile and Switchable Ultrasmall Nanoparticles.

Artem Petrov, Guillermo A Hernández-Mendoza, Alfredo Alexander-Katz.

  Block copolymers (BCPs) can form nanoparticles having different morphologies that can be used as photonic nanocrystals and are a platform for drug delivery, sensors, and catalysis. In particular, BCP nanoparticles having disk-like shape have been recently discovered. Such nanodisks can be used as the next-generation antitumor drug delivery carriers; however, the applicability of the existing nanodisks is limited due to their poor or unknown ability to respond to external stimuli. In this work, we showed that the simplest symmetric diblock copolymers in equilibrium can form nanodisks that can be reversibly switched into a multitude of various nanoparticles potentially applicable in nanophotonics, biomedicine, and hierarchical self-assembly. These structures include patchy and onion-like nanoparticles, striped ellipsoids, mixed morphology nanocolloids, and spherical micelles. The transitions between nanodisks and the aforementioned nanoparticles are sharp, direct, and can be achieved by tuning the block-block and polymer-solvent incompatibility. We demonstrated that this versatility of nanoparticle morphologies can be achieved upon reducing the nanoparticle size to approximately two lamellar periods of the BCP. Upon aggregation of such small nanocolloids, a larger assembly can be formed. In turn, these bigger particles could form many other structures including a chain-like supramolecular aggregate of nanodisks and a multilayered disk-like nanoparticle. We obtained our results by performing self-consistent field theory calculations according to an algorithm designed to produce equilibrium nanoparticle morphology. This work demonstrates that nanodisks prepared from the simplest type of BCPs are extremely tunable; therefore, symmetric diblock copolymers can become a platform for producing the next-generation stimuli-responsive nanoparticles.

Keywords:  block copolymers; nanodisks; nanoparticles; self-assembly; self-consistent field theory; stimuli-responsiveness

DOI:  https://doi.org/10.1021/acsnano.4c14236
ACS Biomater Sci Eng. 2025 Jan 13.

Evaluation of Silica and Bioglass Nanomaterials in Pulp-like Living Materials.

Daline Mbitta Akoa, Anthony Avril, Christophe Hélary, Anne Poliard, Thibaud Coradin.

  Although silicon is a widespread constituent in dental materials, its possible influence on the formation and repair of teeth remains largely unexplored. Here, we studied the effect of two silicic acid-releasing nanomaterials, silica and bioglass, on a living model of pulp consisting of dental pulp stem cells seeded in dense type I collagen hydrogels. Silica nanoparticles and released silicic acid had little effect on cell viability and mineralization efficiency but impacted metabolic activity, delayed matrix remodeling, and led to heterogeneous cell distribution. Bioglass improved cell metabolic activity and led to a homogeneous dispersion of cells and mineral deposits within the hydrogel. These results suggest that the presence of calcium ions in bioglass is not only favorable to cell proliferation but can also counterbalance the negative effects of silicon. Both chemical and biological processes should therefore be considered when investigating the effects of silicon-containing materials on dental tissues.

Keywords:  bioglass; dental materials; dental pulp stem cells; reparative dentin; silicic acid

DOI:  https://doi.org/10.1021/acsbiomaterials.4c01898
Nature. 2025 Jan;637(8046): 594-600

Transducing chemical energy through catalysis by an artificial molecular motor.

Peng-Lai Wang, Stefan Borsley, Martin J Power, Alessandro Cavasso, Nicolas Giuseppone, David A Leigh.

Cells display a range of mechanical activities generated by motor proteins powered through catalysis1. This raises the fundamental question of how the acceleration of a chemical reaction can enable the energy released from that reaction to be transduced (and, consequently, work to be done) by a molecular catalyst2-7. Here we demonstrate the molecular-level transduction of chemical energy to mechanical force8 in the form of the powered contraction and powered re-expansion of a cross-linked polymer gel driven by the directional rotation of artificial catalysis-driven9 molecular motors. Continuous 360° rotation of the rotor about the stator of the catalysis-driven motor-molecules incorporated in the polymeric framework of the gel twists the polymer chains of the cross-linked network around one another. This progressively increases writhe and tightens entanglements, causing a macroscopic contraction of the gel to approximately 70% of its original volume. The subsequent addition of the opposite enantiomer fuelling system powers the rotation of the motor-molecules in the reverse direction, unwinding the entanglements and causing the gel to re-expand. Continued powered twisting of the strands in the new direction causes the gel to re-contract. In addition to actuation, motor-molecule rotation in the gel produces other chemical and physical outcomes, including changes in the Young modulus and storage modulus-the latter is proportional to the increase in strand crossings resulting from motor rotation. The experimental demonstration of work against a load by a synthetic organocatalyst, and its mechanism of energy transduction6, informs both the debate3,5,7 surrounding the mechanism of force generation by biological motors and the design principles6,10-14 for artificial molecular nanotechnology.

DOI: https://doi.org/10.1038/s41586-024-08288-x
Nano Lett. 2025 Jan 13.

Nanospiked Cellulose Gauze That Attracts Bacteria with Biomolecules for Reducing Bacterial Load in Burn Wounds.

Yuuki Hata, Hiromi Miyazaki, Sayaka Okamoto, Takeshi Serizawa, Shingo Nakamura.

  Nanostructuring surfaces is an emergent strategy to endow materials with abilities to combat pathogenic bacteria. Nevertheless, it remains challenging to create nanospike structures on the curved surfaces of polymer materials, including gauze and other microfibrous medical materials. Additionally, the effects of nanostructured surfaces on bacteria in the presence of proteins and in vivo remain largely unexplored. Herein, we demonstrated the decoration of gauze microfiber surfaces with nanospike structures via the self-assembly of cello-oligosaccharides and investigated the effects of the nanospiked gauze on bacteria in the presence of proteins. The nanospiked gauze had low bacterial adhesion properties in the absence of proteins, whereas in the presence of proteins, it promoted bacterial adhesion. Analyses suggested that the adsorbed protein layers on the nanospikes were involved in the promoted bacterial adhesion. Furthermore, the bacterial adhesion-promoting effects were exploited to remove pathogenic bacteria from burn wounds with exudate containing proteins using the nanospiked gauze.

Keywords:  Cello-oligosaccharide; bacterial adhesion; nanostructured surface; self-assembly; wound dressing

DOI:  https://doi.org/10.1021/acs.nanolett.4c05773
ACS Synth Biol. 2025 Jan 12.

Construction and Characterization of MoClo-Compatible Vectors for Modular Protein Expression in E. coli.

Jochem R Nielsen, Michael J Lewis, Wei E Huang.

  Cloning methods are fundamental to synthetic biology research. The capability to generate custom DNA constructs exhibiting predictable protein expression levels is crucial to the engineering of biology. Golden Gate cloning, a modular cloning (MoClo) technique, enables rapid and reliable one-pot assembly of genetic parts. In this study, we expand on the existing MoClo toolkits by constructing and characterizing compatible low- (p15A) and medium-copy (pBR322) destination vectors. Together with existing high-copy vectors, these backbones enable a protein expression range covering a 500-fold difference in normalized fluorescence output. We further characterize the expression- and burden profiles of each vector and demonstrate their use for the optimization of growth-coupled enzyme expression. The optimal expression of adhE (encoding alcohol dehydrogenase) for ethanol-dependent growth of Escherichia coli is determined using randomized Golden Gate Assembly, creating a diverse library of constructs with varying expression strengths and plasmid copy numbers. Through selective growth experiments, we show that relatively low expression levels of adhE facilitated optimal growth using ethanol as the sole carbon source, demonstrating the importance of adding low-copy vectors to the MoClo vector repertoire. This study emphasizes the importance of varying vector copy numbers in selection experiments to balance expression levels and burden, ensuring accurate identification of optimal conditions for growth. The vectors developed in this work are publicly available via Addgene (catalog #217582-217609).

Keywords:  GFP expression; MoClo; copy number; destination vectors; golden gate assembly; growth-coupled selection; origin of replication; plasmid; plasmid burden

DOI:  https://doi.org/10.1021/acssynbio.4c00564
bioRxiv. 2025 Jan 04. pii: 2025.01.04.631316. [Epub ahead of print]

A data-driven modeling framework for mapping genotypes to synthetic microbial community functions.

Yili Qian, Sarvesh D Menon, Nick Quinn-Bohmann, Sean M Gibbons, Ophelia S Venturelli.

Microbial communities play a central role in transforming environments across Earth, driving both physical and chemical changes. By harnessing these capabilities, synthetic microbial communities, assembled from the bottom up, offer valuable insights into the mechanisms that govern community functions. These communities can also be tailored to produce desired outcomes, such as the synthesis of health-related metabolites or nitrogen fixation to improve plant productivity. Widely used computational models predict synthetic community functions using species abundances as inputs, making it impossible to predict the effects of species not included in the training data. We bridge this gap using a data-driven community genotype function (dCGF) model. By lifting the representation of each species to a high-dimensional genetic feature space, dCGF learns a mapping from community genetic feature matrices to community functions. We demonstrate that dCGF can accurately predict communities in a fixed environmental context that are composed in part or entirely from new species with known genetic features. In addition, dCGF facilitates the identification of species roles for a community function and hypotheses about how specific genetic features influence community functions. In sum, dCGF provides a new data-driven avenue for modeling synthetic microbial communities using genetic information, which could empower model-driven design of microbial communities.

DOI: https://doi.org/10.1101/2025.01.04.631316
ACS Nano. 2025 Jan 17.

Complex Core-Shell Architectures through Spatially Organized Nano-Assemblies.

Xiangyu Jiang, Bo Jiang, Manrui Mu, Tongyi Wang, Shi Sun, Jiaxin Xu, Shutao Wang, Yan Zhou, Jun Zhang, Wenle Li.

  Core-shell structures demonstrate superior capability in customizing properties across multiple scales, offering valuable potential in catalysis, medicine, and performance materials. Integrating functional nanoparticles in a spatially controlled manner is particularly appealing for developing sophisticated architectures that support heterogeneous characteristics and tandem reactions. However, creating such complex structures with site-specific features remains challenging due to the dynamic microenvironment during the shell-forming process, which considerably impacts colloidal particle assembly. Here, we describe a method to spatially deploy nanoscale assemblies within microscale structures comprising a dense shell and a liquid core through colloidal surface decoration coupled with emulsion-based synthesis. Exploiting a spectrum of nanoparticles grafted with incrementally varying densities of organic ligands, we reveal that nanofeatures can be selectively sculpted onto the shell exterior, within the shell wall, and on the interior surface. The versatility of this mechanism is validated by systematically arranging nanoparticles with various compositions, shapes, and dimensions. Spatially integrated nanotitania endows the core-shell structures with localized photocatalytic abilities. Additionally, distinctive surface modifications enable the simultaneous yet independent implantation of diverse nanoparticles, yielding intricate architectures with programmable functions. This generalizable approach showcases a synthetic strategy to attain structural complexity and functional sophistication reminiscent of those of biological systems in nature.

Keywords:  complexity; core−shell structures; heterogeneous functionalities; nanoparticles; spatial distribution

DOI:  https://doi.org/10.1021/acsnano.4c17322
Sci Adv. 2025 Jan 17. 11(3): eadq7797

Morphogenesis of bacterial cables in polymeric environments.

Sebastian Gonzalez La Corte, Corey A Stevens, Gerardo Cárcamo-Oyarce, Katharina Ribbeck, Ned S Wingreen, Sujit S Datta.

Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, laboratory studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.

DOI: https://doi.org/10.1126/sciadv.adq7797
ACS Synth Biol. 2025 Jan 14.

Quantitative Measurement of Molecular Permeability to a Synthetic Bacterial Microcompartment Shell System.

Eric J Young, Henning Kirst, Matthew E Dwyer, Josh V Vermaas, Cheryl A Kerfeld.

  Naturally evolved and synthetically designed forms of compartmentalization benefit encapsulated function by increasing local concentrations of substrates and protecting cargo from destabilizing environments and inhibitors. Crucial to understanding the fundamental principles of compartmentalization are experimental systems enabling the measurement of the permeability rates of small molecules. Here, we report the experimental measurement of the small-molecule permeability of a 40 nm icosahedral bacterial microcompartment shell. This was accomplished by heterologous loading of light-producing luciferase enzymes and kinetic measurement of luminescence using stopped-flow spectrophotometry. Compared to free enzyme, the luminescence signal kinetics was slower when the luciferase was encapsulated in bacterial microcompartment shells. The results indicate that substrates and products can still exchange across the shell, and modeling of the experimental data suggest that a 50× permeability rate increase occurs when shell vertices were vacant. Overall, our results suggest design considerations for the construction of heterologous bacterial microcompartment shell systems and compartmentalized function at the nanoscale.

Keywords:  ATP; biophysics; compartmentalization; modeling; molecular permeability; synthetic biology

DOI:  https://doi.org/10.1021/acssynbio.4c00290