bims-enlima Biomed News
on Engineered living materials
Issue of 2025–05–04
47 papers selected by
Rahul Kumar, Tallinna Tehnikaülikool
  1. Bioxolography Using Diphenyliodonium Chloride and N-Vinylpyrrolidone Enables Rapid High-Resolution Volumetric 3D Printing of Spatially Encoded Living Matter.
  2. Designing with Printed Responsive Biomaterials: A Review.
  3. Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins.
  4. Light-Controlled Synthetic Communication Networks via Paired Connexon Nanopores.
  5. A responsive living material prepared by diffusion reveals extracellular enzyme activity of cyanobacteria.
  6. Powerful protein editors offer new ways of probing living cells.
  7. Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid.
  8. Why cellular computations challenge our design principles.
  9. High-Resolution Patterned Delivery of Chemical Signals From 3D-Printed Picoliter Droplet Networks.
  10. 3D-Printed Mycelium Biocomposites: Method for 3D Printing and Growing Fungi-Based Composites.
  11. A Facile and Versatile Platform for Cytosolic Delivery of Proteins in Nanoshells of DNA or RNA: Packaging Options in Multiplexed Delivery.
  12. Hybrid Formative-Additive Manufacturing.
  13. 3D Printable Biocomposites with Tunable Environmental Degradability.
  14. Monitoring in real time and far-red imaging of H2O2 dynamics with subcellular resolution.
  15. Implementing complex nucleic acid circuits in living cells.
  16. Matrix Stiffness and Biochemistry Govern Colorectal Cancer Cell Growth and Signaling in User-Programmable Synthetic Hydrogels.
  17. Spatial entropy drives the maintenance and dissemination of transferable plasmids.
  18. Inducing mechanical self-healing in polymer glasses.
  19. Modeling and design of 3D printed hyperelastic lattice metamaterials with bionic S-shaped stress-strain behaviors.
  20. Shape and topology morphing of closed surfaces integrating origami and kirigami.
  21. Active and passive crosslinking of cytoskeleton scaffolds tune the effects of cell inclusions on composite structure.
  22. Scalable Cell-Free Production of Active T7 RNA Polymerase.
  23. Integrase enables synthetic intercellular logic via bacterial conjugation.
  24. Ab initio structure solutions from nanocrystalline powder diffraction data via diffusion models.
  25. Modulating fatty acid metabolism and composition of CHO cells by feeding high levels of fatty acids complexed using methyl-β-cyclodextrin.
  26. Red Light-Activated Reversible Inhibition of Protein Functions by Assembled Trap.
  27. Effects of ligand vs. linker on phase behavior and mechanical properties of nanoparticle gels.
  28. Robust and Highly Stretchable UV-Curable Rubber/Polyurethane-Based Resins Reinforced with Photocurable Cellulose Acetate.
  29. Chemically-fueled phase transition of a redox-responsive polymer.
  30. Process Intensification for Recombinant Protein Production in E. coli via Identification of Active Nodes in Cellular Metabolism and Dynamic Flux Balance Analysis.
  31. Fabrication of Microgel-Reinforced Hydrogels via Vat Photopolymerization.
  32. Editing proteins inside a cell.
  33. Designing yield stress fluids for advanced materials processing using derivatives of pH-responsive branched co-polymer surfactants.
  34. Enzyme- and DNAzyme-Driven Transient Assembly of DNA-Based Phase-Separated Coacervate Microdroplets.
  35. Tunable mechanical properties and phase transitions in nanoconfined polyzwitterionic UCST hydrogels.
  36. Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii.
  37. Feedback-responsive cell factories for dynamic modulation of the unfolded protein response.
  38. Selective inhibition of stromal mechanosensing suppresses cardiac fibrosis.
  39. Viscoelastic extracellular matrix enhances epigenetic remodeling and cellular plasticity.
  40. Artificial Intelligence tool for prediction of ECM mimics hydrogel formulations via click chemistry.
  41. Structurally Colored Sustainable Sea Silk from Atrina pectinata.
  42. Metabolic engineering of Escherichia coli for 4-nitrophenylalanine production via the 4-aminophenylalanine synthetic pathway.
  43. Supramolecular Conductive Hydrogels With Homogeneous Ionic and Electronic Transport.
  44. ATOMICA: Learning Universal Representations of Intermolecular Interactions.
  45. Maltodextrin transport in the extremely thermophilic, lignocellulose degrading bacterium Anaerocellum bescii (f. Caldicellulosiruptor bescii).
  46. High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples.
  47. Development of a bioreactor and volumetric bioprinting protocol to enable perfused culture of biofabricated human epithelial mammary ducts and endothelial constructs.
  1. Adv Mater. 2025 Apr 26. e2501052
    Bioxolography Using Diphenyliodonium Chloride and N-Vinylpyrrolidone Enables Rapid High-Resolution Volumetric 3D Printing of Spatially Encoded Living Matter.
    Alexis Wolfel, Castro Johnbosco, Annalise Anspach, Marieke Meteling, Jos Olijve, Niklas Felix König, Jeroen Leijten.
      Light-based volumetric bioprinting enables fabrication of cubic centimeter-sized living materials with micrometer resolution in minutes. Xolography is a light sheet-based volumetric printing technology that offers unprecedented volumetric generation rates and print resolutions for hard plastics. However, the limited solubility and reactivity of current dual-color photoinitiators (DCPIs) in aqueous media have hindered their application for high-resolution bioprinting of living matter. Here, we present a novel three-component formulation that drastically improves photoreactivity and thereby enables high-resolution, rapid, and cytocompatible Xolographic biofabrication of intricately architected yet mechanically robust living materials. To achieve this, various relevant additives are systematically explored, which revealed that diphenyliodonium chloride and N-vinylpyrrolidone strongly enhance D-mediated photoreactivity, as confirmed by dual-color photo-rheology. This enables Xolographic bioprinting of gelatin methacryloyl-based bioresins, producing >1 cm3 constructs at ≈20 µm positive and 125 µm negative resolution within minutes. Multimaterial printing, molecular patterning, and grayscale-mediated mechanical patterning are explored to programmably create intricate, biomimetic, and concentration-controlled architectures. We demonstrate the Bioxolographic printing of various cell types, showing excellent cell viability, compatibility with long-term culture, and ability for nascent protein deposition. These results position Bioxolography as a transformative platform for rapid, scalable, high-resolution fabrication of functional living materials with encoded chemical and mechanical properties.
    Keywords:  bioxolography; high‐resolution; spatial patterning; volumetric bioprinting
    DOI:  https://doi.org/10.1002/adma.202501052
  2. 3D Print Addit Manuf. 2025 Apr;12(2): 155-168
    Designing with Printed Responsive Biomaterials: A Review.
    Laia Mogas-Soldevila, Katia Zolotovsky.
      This review explores additive manufacturing (AM) strategies across disciplines for designing with responsive biomaterials and presents a vision of how printed responsive biomaterials (PRBs) can be integrated into everyday objects and buildings to enhance environmental and human health. Advancements in biomaterials science, biological materials manufacturing, synthetic biology, biomedical engineering, bio design, and living architecture are ushering in a new era characterized by multisensory interactions within everyday products and built environments. The material systems developed in recent research demonstrate the ability to interact with their environments through biological, chemical, or physical processes, yielding functionalities desirable in daily-use products. These include self-healing, health diagnostics, pathogen neutralization, adjustable stiffness, strain detection, threat visualization, shapeshifting, toxin trapping, stress correction, waste processing, and energy generation. Here we review examples of AM of biobased environmentally interactive materials using biopolymer composites, electrochemical and resistive devices, active molecules, bio sensors, living cells, spores, or cell-free sites, resulting in genetically active, and physical and chemical interactive systems. We highlight their robustness and evaluate their potential for scaling up into designs and architectures on Earth and beyond.
    Keywords:  active matter; additive manufacturing; biomaterials; environmental interaction; living materials; responsive materials; sustainable systems
    DOI:  https://doi.org/10.1089/3dp.2024.0004
  3. Science. 2025 May;388(6746): eadr5499
    Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins.
    Jenna N Beyer, Yevgeniy V Serebrenik, Kaitlyn Toy, Mohd Altaf Najar, Emily Feierman, Nicole R Raniszewski, Erica Korb, Ophir Shalem, George M Burslem.
      The ability to study proteins in their native cellular context is crucial to our understanding of biology. In this work, we report a technology for intracellular protein editing, drawing from split intein-mediated protein splicing, genetic code expansion, and endogenous protein tagging. This approach enables us to rapidly and site-specifically install residues and chemical handles into a protein. We demonstrate the power of this platform to edit cellular proteins, inserting epitopes, protein-specific sequences, and noncanonical amino acids. Notably, we use an endogenous tagging approach to apply our protein editing technology to endogenous proteins with minimal perturbation. We anticipate that the protein editing technology presented in this work will be applied to a diverse set of problems and phenomena in live mammalian cells.
    DOI:  https://doi.org/10.1126/science.adr5499
  4. bioRxiv. 2025 Apr 11. pii: 2025.04.11.648033. [Epub ahead of print]
    Light-Controlled Synthetic Communication Networks via Paired Connexon Nanopores.
    Ahmed Z Sihorwala, Alexander J Lin, Isabela Ramirez-Velez, Siqi Yang, Shwetadwip Chowdhury, Jeanne C Stachowiak, Brian Belardi.
      Living cells employ dynamic networks for intercellular communication and cooperation, leading to tissue-wide activity. One emerging challenge in the field of bottom-up synthetic biology is emulating such sophisticated behaviors in liposome-based synthetic cells (SCs). Fabricating communication networks in lipid bilayer-based SCs remains a challenge as signaling molecules must transit through two consecutive membranes to transfer information between different SCs. Here, we address this obstacle by engineering connexin channels that directly connect the lumens of adhering SC membranes. We focus on orthogonal channel-forming connexins, namely connexin 43 and connexin 32, and re-design their channel activity to be UV- and near IR-responsive, respectively. By combining engineered connexins into a single SC assembly, we demonstrate orthogonal transfer of reactive signaling molecules between SCs, giving rise to unique reaction products and network states in a wavelength-dependent manner - an important step toward synthetic communication networks.
    DOI:  https://doi.org/10.1101/2025.04.11.648033
  5. Proc Natl Acad Sci U S A. 2025 May 06. 122(18): e2424405122
    A responsive living material prepared by diffusion reveals extracellular enzyme activity of cyanobacteria.
    Lisa Tang, Nathan T Soulier, Rebecca Wheeler, Jonathan K Pokorski, James W Golden, Susan S Golden, Jinhye Bae.
      Stimuli-responsive engineered living materials (ELMs) can respond to environmental or biochemical cues and have broad utility in biological sensors and machines, but have traditionally been limited to biocompatible scaffolds. This is because they are typically made by mixing cells into a precursor solution before crosslinking. Here, we demonstrate a diffusion mechanism for incorporating cells of the cyanobacterium Synechococcus elongatus sp. PCC 7942 (S. elongatus) into nanoclay-poly-N-isopropylacrylamide (NC-PNIPAm), a hydrogel with a cytotoxic precursor, by exploiting its temperature-dependent shape-morphing behavior. Subsequent growth of S. elongatus caused a decrease in the bending curvature and stiffness (local Young's modulus) of NC-PNIPAm due to partial degradation by an unannotated enzyme. Creation and observation of this cyanobacteria-hydrogel ELM showcases a method for diffusing cells into a hydrogel as well as characterizing an extracellular enzyme.
    Keywords:  amidase; biomaterials; cyanobacteria; engineered living materials
    DOI:  https://doi.org/10.1073/pnas.2424405122
  6. Nature. 2025 May 01.
    Powerful protein editors offer new ways of probing living cells.
    Asher Mullard.
      
    Keywords:  Biochemistry; CRISPR-Cas9 genome editing; Cell biology
    DOI:  https://doi.org/10.1038/d41586-025-01358-8
  7. Nat Microbiol. 2025 May 01.
    Engineered orthogonal and obligate bacterial commensalism mediated by a non-standard amino acid.
    Amanda M Forti, Michaela A Jones, Defne N Elbeyli, Neil D Butler, Aditya M Kunjapur.
      Microorganisms can be genetically engineered for intrinsic biological containment based on synthetic chemical provision. However, reliance on an exogenous chemical limits the contexts where a contained microorganism could survive. Here we design an orthogonal obligate commensalism in Escherichia coli that autonomously creates environments permissive for survival of a partner microbe. We engineer one E. coli strain (the producer) to biosynthesize a non-standard amino acid (nsAA) from simple carbon sources through heterologous expression. We engineer a second E. coli strain (the utilizer) to rely on the same nsAA for growth as a synthetic auxotroph, with a 14-day escape rate of 2.8 × 10-9 escapees per colony-forming unit. Co-culture experiments show utilizer dependence on the producer, with no escape detected during co-inoculation of ~107 colony-forming units of utilizer and a non-producer E. coli strain. Dependence is maintained within a simplified synthetic maize root-associated community. This work provides ecological insights and presents a potential biocontainment strategy independent of an exogenous chemical.
    DOI:  https://doi.org/10.1038/s41564-025-01999-5
  8. Semin Cell Dev Biol. 2025 Apr 30. pii: S1084-9521(25)00026-6. [Epub ahead of print]171 103616
    Why cellular computations challenge our design principles.
    Lewis Grozinger, Bruno Cuevas-Zuviría, Ángel Goñi-Moreno.
      Biological systems inherently perform computations, inspiring synthetic biologists to engineer biological systems capable of executing predefined computational functions for diverse applications. Typically, this involves applying principles from the design of conventional silicon-based computers to create novel biological systems, such as genetic Boolean gates and circuits. However, the natural evolution of biological computation has not adhered to these principles, and this distinction warrants careful consideration. Here, we explore several concepts connecting computational theory, living cells, and computers, which may offer insights into the development of increasingly sophisticated biological computations. While conventional computers approach theoretical limits, solving nearly all problems that are computationally solvable, biological computers have the opportunity to outperform them in specific niches and problem domains. Crucially, biocomputation does not necessarily need to scale to rival or replicate the capabilities of electronic computation. Rather, efforts to re-engineer biology must recognise that life has evolved and optimised itself to solve specific problems using its own principles. Consequently, intelligently designed cellular computations will diverge from traditional computing in both implementation and application.
    Keywords:  Biocomputation; Cellular computing; Complexity; Synthetic biology
    DOI:  https://doi.org/10.1016/j.semcdb.2025.103616
  9. Adv Mater. 2025 Apr 30. e2412292
    High-Resolution Patterned Delivery of Chemical Signals From 3D-Printed Picoliter Droplet Networks.
    Jorin Riexinger, Thomas Caganek, Xingzao Wang, Yutong Yin, Khoa Chung, Linna Zhou, Hagan Bayley, Ravinash Krishna Kumar.
      Synthetic cells, such as giant unilamellar vesicles, can be engineered to detect and release chemical signals to control target cell behavior. However, control over target-cell populations is limited due to poor spatial or temporal resolution and the inability of synthetic cells to deliver patterned signals. Here, 3D-printed picoliter droplet networks are described that direct gene expression in underlying bacterial populations by patterned release of a chemical signal with temporal control. Shrinkage of the droplet networks prior to use achieves spatial control over gene expression with ≈50 µm resolution. Ways to store chemical signals in the droplet networks and to activate release at controlled points in time are also demonstrated. Finally, it is shown that the spatially-controlled delivery system can regulate competition between bacteria by inducing the patterned expression of toxic bacteriocins. This system provides the groundwork for the use of picoliter droplet networks in fundamental biology and in medicine in applications that require the controlled formation of chemical gradients (i.e., for the purpose of local control of gene expression) within a target group of cells.
    Keywords:  3D printing; antimicrobial agent; droplet interface bilayers (DIBs); droplet network; gene expression; nanopore; patterning; synthetic tissue
    DOI:  https://doi.org/10.1002/adma.202412292
  10. 3D Print Addit Manuf. 2025 Apr;12(2): 98-111
    3D-Printed Mycelium Biocomposites: Method for 3D Printing and Growing Fungi-Based Composites.
    Danli Luo, Junchao Yang, Nadya Peek.
      Despite recent advances in 3D printing and additive manufacturing, the main materials in rapid prototyping are derived from finite resources such as petroleum-based plastics. Researchers are developing alternatives to exhaustible and potentially environmentally harmful materials through biomaterials. Mycelium biocomposites are one promising area of inquiry; when mycelium decomposes biomass, it produces a composite biomaterial, which is fully compostable and has beneficial structural and hydrophobic properties. However, mold-based fabrication methods for biocomposites require tooling and limit the possible shapes. We introduce a novel method for directly 3D printing mycelium biocomposites without the need for molds or tooling. Our method comprises three main contributions: Mycofluid, a mycelium-inoculated paste that uses spent coffee grounds, a recycled biomass; Fungibot, a custom hardware system for 3D printing biopastes like Mycofluid; and a method for incubating mycelial growth within fresh 3D prints resulting in mycelium biocomposite parts. We illustrate our contributions through a series of objects showcasing our method and the material qualities of the parts. Notably, we demonstrate how living mycelium can fuse separate prints, enabling complex geometries that are otherwise challenging to 3D print as one part.
    Keywords:  3D printing; compostable materials; digital fabrication; mycelium; open-source hardware
    DOI:  https://doi.org/10.1089/3dp.2023.0342
  11. Biomacromolecules. 2025 May 01.
    A Facile and Versatile Platform for Cytosolic Delivery of Proteins in Nanoshells of DNA or RNA: Packaging Options in Multiplexed Delivery.
    Pilar O'Neal, Kareem Washington, Bram Estes, Preethi L Chandran.
      Polyethylenimine (PEI) polymers are used to compact DNA into nanoparticles for delivery into cells. We have shown that PEI-mannose polymers compact DNA into nanoshell-like particles, which can load proteins as well. Here we show that these DNA containers are uniquely versatile for scavenging proteins, irrespective of size, charge, and hydrophobicity from dilute solutions. The number of DNA containers for loading proteins can be controlled independently of the protein loading per container by changing the amounts of DNA and protein in solution. This provides control of the fraction of cells receiving the payload and the relative amounts of DNA and protein per cell. The proteins released inside cells retain enzymatic activity. The proposed technology provides a new way to approach protein delivery by hitchhiking proteins within a facile and well-established DNA-delivery mechanism and by utilizing sugar biophysics to load a wide range of proteins in a single-step process.
    DOI:  https://doi.org/10.1021/acs.biomac.5c00149
  12. Adv Mater. 2025 Apr 28. e2417609
    Hybrid Formative-Additive Manufacturing.
    Nathan C Brown, Jochen Mueller.
      Material extrusion additive manufacturing (AM) provides extensive design flexibility and exceptional material versatility, enabling the fabrication of complex, multifunctional objects ranging from embedded electronics to soft robotics and vascularized tissues. The bottom-up creation of these objects typically requires discretization into layers and voxels. However, the voxel size, determined by the nozzle diameter, limits extrusion rate, creating a conflict between resolution and speed. To address these inherent scalability challenges, the study proposes a hybrid formative-additive manufacturing technology that combines the respective strengths of each method-speed and quality with complexity and flexibility. The approach involves 3D-printing complex geometries, multimaterial features, and bounding walls of bulky, lower-resolution volumes, which are rapidly filled via casting or molding. By precisely controlling the materials' rheological properties-while maintaining similar solidified properties and high interfacial strength-several typical AM flaws, such as bulging and internal voids, are eliminated, achieving exponentially faster production speeds for objects with varying feature sizes.
    Keywords:  3D printing; direct ink writing; material extrusion; non‐Newtonian materials; rheology
    DOI:  https://doi.org/10.1002/adma.202417609
  13. 3D Print Addit Manuf. 2025 Apr;12(2): 122-130
    3D Printable Biocomposites with Tunable Environmental Degradability.
    Hannah B Gazdus, Sabrina C Shen, Nicolas A Lee, Markus J Buehler.
      The growing environmental impacts of solid waste accumulation have resulted in an increased demand for biodegradable alternatives to conventional plastics. While several products have begun to gain popularity as biodegradable or compostable plastics, these often still negatively impact terrestrial and aquatic environments, as they frequently require precise conditions in order to fully decompose. Furthermore, standards for measuring biodegradation rates are often complex and poorly representative of real disposal sites, limiting their widespread use and applicability. In this study, we present four simple tests to assess the environmental degradability of materials without specialized equipment and demonstrate them with a series of 3D printable biotic composites composed of pectin, chitosan, and cellulose, abundant and organic biopolymers known to be degradable by common microorganisms. Five different compositions were degraded in live soil, worm burial, high humidity, and aqueous environments, and demonstrated rapid degradation with up to 100% mass loss after 21 days for a pectin-based material buried in worm-laden oil. Degradability was further found to be tunable, with decreasing degradation rate as chitosan content increased. Our results confirm that biotic composites degrade more rapidly than conventional plastics and provide accessible methods that can enable more widespread material testing for the development of sustainable material alternatives, especially to gather basic environmental degradation information representative of typical solid waste discard conditions. We anticipate that these degradation methods and the materials degraded therein will provide further impetus for reducing waste from 3D printing and for considering end of life when designing products.
    Keywords:  biocomposite; biodegradable; compostable; sustainability
    DOI:  https://doi.org/10.1089/3dp.2024.0014
  14. Nat Chem Biol. 2025 Apr 28.
    Monitoring in real time and far-red imaging of H2O2 dynamics with subcellular resolution.
    Justin Daho Lee, Amanda Nguyen, Chelsea E Gibbs, Zheyu Ruby Jin, Yuxuan Wang, Aida Moghadasi, Sarah J Wait, Hojun Choi, Kira M Evitts, Anthony Asencio, Samantha B Bremner, Shani Zuniga, Vedant Chavan, Inez K A Pranoto, C Andrew Williams, Annette Smith, Farid Moussavi-Harami, Michael Regnier, David Baker, Jessica E Young, David L Mack, Elizabeth Nance, Patrick M Boyle, Andre Berndt.
      Monitoring H2O2 dynamics in conjunction with key biological interactants is critical for elucidating the physiological outcome of cellular redox regulation. Optogenetic hydrogen peroxide sensor with HaloTag with JF635 (oROS-HT635) allows fast and sensitive chemigenetic far-red H2O2 imaging while overcoming drawbacks of existing red fluorescent H2O2 indicators, including oxygen dependency, high pH sensitivity, photoartifacts and intracellular aggregation. The compatibility of oROS-HT635 with blue-green-shifted optical tools allows versatile optogenetic dissection of redox biology. In addition, targeted expression of oROS-HT635 and multiplexed H2O2 imaging enables spatially resolved imaging of H2O2 targeting the plasma membrane and neighboring cells. Here we present multiplexed use cases of oROS-HT635 with other green fluorescence reporters by capturing acute and real-time changes in H2O2 with intracellular redox potential and Ca2+ levels in response to auranofin, an inhibitor of antioxidative enzymes, via dual-color imaging. oROS-HT635 enables detailed insights into intricate intracellular and intercellular H2O2 dynamics, along with their interactants, through spatially resolved, far-red H2O2 imaging in real time.
    DOI:  https://doi.org/10.1038/s41589-025-01891-7
  15. Sci Adv. 2025 May 02. 11(18): eadv6512
    Implementing complex nucleic acid circuits in living cells.
    Jiajia Sun, Xiewei Xiong, Wei Lai, Zhongdong Wu, Heming Wang, Lei Yang, Niannian Xue, Qunyan Yao, Guangqi Song, Yicheng Zhao, Li Li, Fei Wang, Chunhai Fan, Hao Pei.
      Synthetic nucleic acid-based computing has demonstrated complex computational capabilities in vitro. However, translating these circuits into living cells remains challenging because of instability and cellular interference. We introduce an allosteric strand exchange (ASE) strategy for complex intracellular computing. Leveraging conformational cooperativity to regulate strand exchange, ASE offers a modular platform for designing intracellular circuits with flexible programmability. We engineer a scalable circuit architecture based on ASE that can execute AND and OR logic and scale to an eight-input expression. We demonstrate ASE-based circuits can detect messenger RNAs with high specificity in mammalian cells via AND logic computation. The capacity of ASE-based circuits to accept messenger RNAs as inputs enables integration of endogenous cellular information for efficient multi-input information processing, demonstrated by a multi-input molecular classifier monitoring key cell reprogramming events. Reprogramming ASE-based circuit to interface with CRISPR-Cas9 enables programmable control of Cas9-targeting activity for gene editing, highlighting their potential for advancing intracellular biocomputation.
    DOI:  https://doi.org/10.1126/sciadv.adv6512
  16. ACS Biomater Sci Eng. 2025 Apr 30.
    Matrix Stiffness and Biochemistry Govern Colorectal Cancer Cell Growth and Signaling in User-Programmable Synthetic Hydrogels.
    Irina Kopyeva, Ross C Bretherton, Jessica L Ayers, Ming Yu, William M Grady, Cole A DeForest.
      Colorectal cancer (CRC) studies in vitro have been conducted almost exclusively on 2D cell monolayers or suspension spheroid cultures. Though these platforms have shed light on many important aspects of CRC biology, they fail to recapitulate essential cell-matrix interactions that often define in vivo function. Toward filling this knowledge gap, synthetic hydrogel biomaterials with user-programmable matrix mechanics and biochemistry have gained popularity for culturing cells in a more physiologically relevant 3D context. Here, using a poly(ethylene glycol)-based hydrogel model, we systematically assess the role of matrix stiffness and fibronectin-derived RGDS adhesive peptide presentation on CRC colony morphology and proliferation. Highlighting platform generalizability, we demonstrate that these hydrogels can support the viability and promote spontaneous spheroid or multicellular aggregate formation of six CRC cell lines that are commonly utilized in biomedical research. These gels are engineered to be fully degradable via a "biologically invisible" sortase-mediated reaction, enabling the triggered recovery of single cells and spheroids for downstream analysis. Using these platforms, we establish that substrate mechanics play a significant role in colony growth: soft conditions (∼300 Pa) encourage robust colony formation, whereas stiffer (∼2 kPa) gels severely restrict growth. Tuning the RGDS concentration did not affect the colony morphology. Additionally, we observe that epidermal growth factor receptor (EGFR) signaling in Caco-2 cells is influenced by adhesion ligand identity─whether the adhesion peptide was derived from collagen type I (DGEA) or fibronectin (RGDS)─with DGEA yielding a marked decrease in the level of downstream protein kinase phosphorylation. Taken together, this study introduces a versatile method to culture and probe CRC cell-matrix interactions within engineered 3D biomaterials.
    Keywords:  3D hydrogel model; colorectal cancer; sortase
    DOI:  https://doi.org/10.1021/acsbiomaterials.4c01632
  17. Mol Syst Biol. 2025 Apr 29.
    Spatial entropy drives the maintenance and dissemination of transferable plasmids.
    Wenzhi Xue, Juken Hong, Runmeng Zhao, Huaxiong Yao, Yi Zhang, Zhuojun Dai, Teng Wang.
      The dissemination of transferable plasmids, a major type of mobile genetic elements (MGEs), is one main driver of antibiotic resistance outbreaks. While the plasmid persistence condition in well-mixed environments has been extensively studied, most microbiota in nature are spatially heterogeneous. However, our knowledge regarding how spatial landscape shapes plasmid maintenance and dissemination remains limited. Here we establish a theoretical framework describing plasmid spread over a metacommunity of multiple patches. By analyzing the gene flow dynamics on randomly generated landscapes, we show that plasmid survival and dispersal are dictated by a simple feature of the landscape, spatial entropy. Reducing entropy speeds up plasmid range expansion and allows the global maintenance of many plasmids that are predicted to be lost by classic theories. The entropy's effects are experimentally validated in E. coli metacommunities transferring a conjugative plasmid. We further examine a vast collection of prokaryotic genomes and show that prokaryotes from low-entropy environments indeed carry more abundant MGEs and antibiotic resistance genes. Our work provides critical insights into the management and control of antimicrobial resistance.
    Keywords:  Antibiotic Resistance; Biofilm; Horizontal Gene Transfer; Plasmid; Spatial Entropy
    DOI:  https://doi.org/10.1038/s44320-025-00110-8
  18. Nat Commun. 2025 May 01. 16(1): 4085
    Inducing mechanical self-healing in polymer glasses.
    José Ruiz-Franco, Andrea Giuntoli.
      Polymer glasses such as the plastics used in pipes, structural materials, and medical devices are ubiquitous in daily life. The nature of their low molecular mobility is still poorly understood and it leads to brittle mechanical behavior, damage, and fracture over time. It also prevents the design of self-healing mechanisms that expand the material's lifespan, as more commonly done in recent years for higher mobility amorphous polymers such as gels and rubbers. We demonstrate through numerical simulations that controlled oscillatory deformations enhance the local molecular mobility of glassy polymers without compromising their structural or mechanical stability. We apply this principle to increase the molecular mobility around the surface of a cylindrical crack, counterintuitively inducing fracture repair and recovering the mechanical properties of the pristine material. Our findings are a first step to establish a general physical mechanism of self-healing in glasses that may inspire the design and processing of new glassy materials.
    DOI:  https://doi.org/10.1038/s41467-025-59426-6
  19. Mater Horiz. 2025 Apr 28.
    Modeling and design of 3D printed hyperelastic lattice metamaterials with bionic S-shaped stress-strain behaviors.
    Le Dong, Mengjie Zhang, Dong Wang.
      Lattice metamaterials made of stiff polymers, ceramics, and metals have been extensively designed to reproduce the mechanical behaviors of biological tissues, holding promising applications in biomedical devices and tissue engineering. However, lattice metamaterials composed of soft materials have been far less explored due to challenges posed by material nonlinearity and large deformations. Here, hyperelastic lattice metamaterials with curved microstructures are fabricated by 3D printing elastomers and are developed to mimic bionic S-shaped stress-strain behaviors. We propose a design framework for 3D printed hyperelastic lattice metamaterials that integrates digital geometry generation, hierarchical mechanics modeling, and validation by finite element (FE) simulations and experiments. The microstructures are modeled through deriving a Timoshenko-type beam theory governed by hyperelastic strain energy potentials. The model is then combined with the deformation and equilibrium analysis considering non-rigid connections between microstructures to predict the mechanical responses of hyperelastic lattice metamaterials. Using the developed design framework, programmable S-shaped stress-strain behaviors and high fracture strains (over 800%) are achieved. We demonstrate S-shaped stress-strain curves that match skeletal and cardiac muscles and highly stretchable lattice sensors for remote controls. This study provides design methods and theoretical guidelines for hyperelastic lattice metamaterials, holding promise for robotic sensors with bionic performance and functionality.
    DOI:  https://doi.org/10.1039/d4mh01582g
  20. Sci Adv. 2025 May 02. 11(18): eads5659
    Shape and topology morphing of closed surfaces integrating origami and kirigami.
    Xiangxin Dang, Shujia Chen, Ali Elias Acha, Lei Wu, Damiano Pasini.
      A closed surface is generally more resistant to deformation and shape changes than an open surface. An empty closed box, for example, is stiffer and more stable than when it is open. The presence of an opening makes it less constrained, more deformable, and easier to morph, as demonstrated by several studies on open-surface morphing across patterns, materials, and scales. Here, we present a platform to morph closed surfaces with bistability that harnesses a balanced integration of origami and kirigami principles. By harmonizing panel rotation around creases nearly tangent to the closed surface and panel rotation around hinges nearly perpendicular to the closed surface, we show that origami-kirigami assemblages can shape-morph between a cube and a sphere, scale between spheres of dissimilar size, and change topology between a sphere and a torus, with programmed bistability. The framework offers a promising strategy for designing bistable reconfigurable structures and metamaterials with enclosed configurations.
    DOI:  https://doi.org/10.1126/sciadv.ads5659
  21. Soft Matter. 2025 Apr 28.
    Active and passive crosslinking of cytoskeleton scaffolds tune the effects of cell inclusions on composite structure.
    Katarina Matic, Nimisha Krishnan, Eric Frank, Michael Arellano, Aditya Sriram, Moumita Das, Megan T Valentine, Michael J Rust, Rae M Robertson-Anderson, Jennifer L Ross.
      Incorporating cells within active biomaterial scaffolds is a promising strategy to develop forefront materials that can autonomously sense, respond, and alter the scaffold in response to environmental cues or internal cell circuitry. Using dynamic biocompatible scaffolds that can self-alter their properties via crosslinking and motor-driven force-generation opens even greater avenues for actuation and control. However, the design principles associated with engineering active scaffolds embedded with cells are not well established. To address this challenge, we design a dynamic scaffold material of bacteria cells embedded within a composite cytoskeletal network of actin and microtubules that can be passively or actively crosslinked by either biotin-streptavidin or multimeric kinesin motors. Using quantitative microscopy, we demonstrate the ability to embed cells of volume fractions 0.4-2% throughout the network without compromising the structural integrity of the network or inhibiting crosslinking or motor-driven dynamics. Our findings suggest that both passive and active crosslinking promote entrainment of cells within the network, while depletion interactions play a more important role in uncrosslinked networks. Moreover, we show that large-scale structures emerge with the addition of cell fractions as low as 0.4%, but these structures do not influence the microscale structural length scale of the materials. Our work highlights the potential of our composite biomaterial in designing autonomous materials controlled by cells, and provides a roadmap for effectively coupling cells to complex composite materials with an eye towards using cells as in situ factories to program material modifications.
    DOI:  https://doi.org/10.1039/d4sm01527d
  22. Biotechnol Bioeng. 2025 Apr 29.
    Scalable Cell-Free Production of Active T7 RNA Polymerase.
    Ryan N Rezvani, Rochelle Aw, Wei Chan, Krishnathreya Satish, Han Chen, Adi Lavy, Swechha Rimal, Divyesh A Patel, Govind Rao, James R Swartz, Matthew P DeLisa, Erik Kvam, Ashty S Karim, Antje Krüger, Weston Kightlinger, Michael C Jewett.
      The SARS-CoV-2 pandemic highlighted the urgent need for biomanufacturing paradigms that are robust and fast. Here, we demonstrate the rapid process development and scalable cell-free production of T7 RNA polymerase, a critical component in mRNA vaccine synthesis. We carry out a 1-L cell-free gene expression (CFE) reaction that achieves over 90% purity, low endotoxin levels, and enhanced activity relative to commercial T7 RNA polymerase. To achieve this demonstration, we implement rolling circle amplification to circumvent difficulties in DNA template generation, and tune cell-free reaction conditions, such as temperature, additives, purification tags, and agitation, to boost yields. We achieve production of a similar quality and titer of T7 RNA polymerase over more than four orders of magnitude in reaction volume. This proof of principle positions CFE as a viable solution for decentralized biotherapeutic manufacturing, enhancing preparedness for future public health crises or emergent threats.
    Keywords:  T7 RNA polymerase; biomanufacturing; cell‐free gene expression; in vitro transcription and translation; protein synthesis; scale‐up
    DOI:  https://doi.org/10.1002/bit.28993
  23. Cell Syst. 2025 Apr 22. pii: S2405-4712(25)00101-2. [Epub ahead of print] 101268
    Integrase enables synthetic intercellular logic via bacterial conjugation.
    Fang Ba, Yufei Zhang, Luyao Wang, Xiangyang Ji, Wan-Qiu Liu, Shengjie Ling, Jian Li.
      Integrases have been widely used in synthetic biology for genome engineering and genetic circuit design. They mediate DNA recombination to alter the genotypes of single cell lines in vivo, with these changes being permanently recorded and inherited via vertical gene transfer. However, integrase-based intercellular DNA messaging and its regulation via horizontal gene transfer remain underexplored. Here, we introduce a versatile strategy to design, build, and test integrase-based intercellular DNA messaging through bacterial conjugation. First, we screened conjugative plasmids and recipient cells for efficient conjugation. Then, we established a layered framework to describe the interactions among hierarchical E. coli strains and implemented dual-layer Boolean logic gates to demonstrate intercellular DNA messaging and management. Finally, we expanded the design to include four-layer single-processing pathways and dual-layer multi-processing systems. This strategy advances intercellular DNA messaging, hierarchical signal processing, and the application of integrase in systems and synthetic biology.
    Keywords:  DNA messaging; bacterial conjugation; genetic circuit design; integrase; recombinase; synthetic biology
    DOI:  https://doi.org/10.1016/j.cels.2025.101268
  24. Nat Mater. 2025 Apr 28.
    Ab initio structure solutions from nanocrystalline powder diffraction data via diffusion models.
    Gabe Guo, Tristan Luca Saidi, Maxwell W Terban, Michele Valsecchi, Simon J L Billinge, Hod Lipson.
      A major challenge in materials science is the determination of the structure of nanometre-sized objects. Here we present an approach that uses a generative machine learning model based on diffusion processes that are trained on 45,229 known structures. The model factors measured the diffraction pattern as well as the relevant statistical priors on the unit cell of atomic cluster structures. Conditioned only on the chemical formula and the information-scarce finite-sized broadened powder diffraction pattern, we find that our model, PXRDnet, can successfully solve the simulated nanocrystals as small as 10 Å across 200 materials of varying symmetries and complexities, including structures from all seven crystal systems. We show that our model can successfully and verifiably determine structural candidates four out of five times, with an average error among these candidates being only 7% (as measured by the post-Rietveld refinement R-factor). Furthermore, PXRDnet is capable of solving structures from noisy diffraction patterns gathered in real-world experiments. We suggest that data-driven approaches, bootstrapped from theoretical simulation, will ultimately provide a path towards determining the structure of previously unsolved nanomaterials.
    DOI:  https://doi.org/10.1038/s41563-025-02220-y
  25. Metab Eng. 2025 Apr 25. pii: S1096-7176(25)00069-2. [Epub ahead of print]91 158-169
    Modulating fatty acid metabolism and composition of CHO cells by feeding high levels of fatty acids complexed using methyl-β-cyclodextrin.
    Bradley Priem, Xiangchen Cai, Yu-Jun Hong, Karl Gilmore, Zijun Deng, Sabrina Chen, Harnish Mukesh Naik, Michael J Betenbaugh, Maciek R Antoniewicz.
      Chinese Hamster Ovary (CHO) cells are widely used in the pharmaceutical industry to produce therapeutic proteins. Increasing the productivity of CHO cells through media development and genetic engineering is a significant industry objective. Past research demonstrated the benefits of modulating fatty acid composition of CHO cells through genetic engineering. In this study, we describe an alternative approach to modulate fatty acid composition by directly feeding high levels of fatty acids in CHO cell culture. To accomplish this, we developed and optimized a pharmaceutically relevant feeding strategy using methyl-β-cyclodextrin (MBCD) to solubilize fatty acids. To quantify fatty acid composition of CHO cells, a new GC-MS protocol was developed and validated. In fed batch cultures, we found that the degree of saturation of fatty acids in CHO cell mass, i.e. the relative abundances of saturated, monounsaturated and polyunsaturated fatty acids, can be controlled by the choice of fatty acid supplement and feeding strategy. Feeding unsaturated fatty acids such as palmitoleic acid, oleic acid, and linoleic acid had the greatest impact the fatty acid composition of CHO cells, increasing their respective abundances in cell mass by upwards of 25x, 1.5x, and 50x, respectively. 13C-Tracing further revealed that the supplemented fatty acids were involved in a range of elongation, desaturation, and β-oxidation reactions to yield both common and uncommon fatty acids such as vaccenic acid and hypogeic acid. Finally, we show that CHO-K1 and CHO-GS cells take up fatty acids solubilized with MBCD at rates comparable to delivery using bovine serum albumin. Taken together, this work paves the way for new feed media formulations containing fatty acids to optimize CHO cell physiology in industrial cell cultures.
    Keywords:  (13)C tracing; Biomass composition; Fatty acid metabolism; Mammalian cell culture; Mass spectrometry
    DOI:  https://doi.org/10.1016/j.ymben.2025.04.005
  26. ACS Synth Biol. 2025 Apr 30.
    Red Light-Activated Reversible Inhibition of Protein Functions by Assembled Trap.
    Peng Zhou, Yongkang Jia, Tianyu Zhang, Abasi Abudukeremu, Xuan He, Xiaozhong Zhang, Chao Liu, Wei Li, Zengpeng Li, Ling Sun, Shouhong Guang, Zhongcheng Zhou, Zhiheng Yuan, Xiaohua Lu, Yang Yu.
      Red light, characterized by superior tissue penetration and minimal phototoxicity, represents an ideal wavelength for optogenetic applications. However, the existing tools for reversible protein inhibition by red light remain limited. Here, we introduce R-LARIAT (red light-activated reversible inhibition by assembled trap), a novel optogenetic system enabling precise spatiotemporal control of protein function via 660 nm red-light-induced protein clustering. Our system harnesses the rapid and reversible binding of engineered light-dependent binders (LDBs) to the bacterial phytochrome DrBphP, which utilizes the endogenous mammalian biliverdin chromophore for red light absorption. By fusing LDBs with single-domain antibodies targeting epitope-tagged proteins (e.g., GFP), R-LARIAT enables the rapid sequestration of diverse proteins into light-responsive clusters. This approach demonstrates high light sensitivity, clustering efficiency, and sustained stability. As a proof of concept, R-LARIAT-mediated sequestration of tubulin inhibits cell cycle progression in HeLa cells. This system expands the optogenetic toolbox for studying dynamic biological processes with high spatial and temporal resolution and holds the potential for applications in living tissues.
    Keywords:  DrBphP; LARIAT; LDB; nanobody; optogenetics; red light
    DOI:  https://doi.org/10.1021/acssynbio.4c00585
  27. Soft Matter. 2025 Apr 30.
    Effects of ligand vs. linker on phase behavior and mechanical properties of nanoparticle gels.
    Qizan Chen, Dinesh Sundaravadivelu Devarajan, Arash Nikoubashman, Michael P Howard, Jeetain Mittal.
      Nanoparticle gels have attracted considerable attention due to their highly tunable properties. One strategy for producing nanoparticle gels involves using strong local attractions between polymeric molecules, such as DNA hybridization or dynamic covalent chemistry, to form percolated nanoparticle networks. These molecules can be used in two distinct roles: as "ligands" with one end grafted to a nanoparticle or as "linkers" with both ends free. Here, we explore how these roles shape the phase behavior and mechanical properties of gel-like nanoparticle assemblies using coarse-grained simulations. We systematically vary the interaction strength and bending stiffness of both ligands and linkers. We find that phase separation can be limited to low nanoparticle volume fractions by making the ligands rigid, consistent with previous studies on linked nanoparticle gels. At fixed interaction strength and volume fraction, both ligand- and linker-mediated nanoparticle assemblies show similar mechanical responses as bending stiffness is varied. However, a comparison between the two association schemes reveals that the linked nanoparticles form rigid percolated networks that are less stretchable than the ligand-grafted gels, despite exhibiting similar tensile strength. We attribute these differences between ligands and linkers to the distinct structural arrangement of nanoparticles within the gel. Our findings highlight the potential to use different association schemes to tune specific mechanical properties.
    DOI:  https://doi.org/10.1039/d4sm01301h
  28. Macromol Rapid Commun. 2025 Apr 28. e2500214
    Robust and Highly Stretchable UV-Curable Rubber/Polyurethane-Based Resins Reinforced with Photocurable Cellulose Acetate.
    Bin Yang, Kun Wang, Xiaoming Shi, Yongxian Zhao, Junyi Chen.
      Tough and stretchable elastomeric resins are useful materials, particularly for coatings and additive manufacturing, which constructs 3D objects through the successive deposition of curable materials. Though elastomeric resins are valued for their flexibility and mechanical resilience, remain limited in availability. In this work, a photocurable resin capable of producing highly elastic material is designed and synthesized. The resin is derived from polybutadiene-based thermoset polyurethane, which is degraded and functionalized through olefin cross-metathesis reaction. The elastomeric resin can be efficiently cured by UV light, affording robust elastomers with an excellent elongation rate (>1300%). The study reveals that the molecular architecture of the resin plays an important role in UV curing and the resulting elastomer properties. Model studies suggest the fragment architecture within the resin prevents shrinkage during UV-curing, which is a common and undesired phenomenon for photocurable elastomers. Moreover, the elastomeric resin's physical properties are tuned by incorporating a cellulose-based reinforcing component (CA-MA) and systematically adjusting the formulation. Tensile testing indicated that the addition of CA-MA significantly enhanced the modulus and toughness (46 MJ m-3) of the UV cured elastomer. Finally, the resin is used as a component in SLA-based 3D printing transforming the elastomeric resin into complex 3D structures.
    Keywords:  UV‐curing; cellulose reinforcement; elastomer; rubber‐based polyurethane; structure‐property relationship
    DOI:  https://doi.org/10.1002/marc.202500214
  29. Sci Technol Adv Mater. 2025 ;26(1): 2494496
    Chemically-fueled phase transition of a redox-responsive polymer.
    Takafumi Enomoto, Aya M Akimoto, Ryo Yoshida.
      In living systems, dynamic biomacromolecular assemblies are driven and regulated by energy dissipative chemical reaction networks, enabling various autonomous functions. Inspired by this biological principle, we report a chemically-fueled phase transition of a poly(N-isopropylacrylamide) (PNIPAAm)-based polymer bearing viologen units (P(NIPAAm-V)), wherein redox changes drive coil-to-globule phase transitions. Upon the addition of a reducing agent, viologen moieties in P(NIPAAm-V) are converted into their reduced state, resulting in enhanced hydrophobicity and polymer aggregation. Coexistence of a platinum catalyst couples these redox-driven structural changes to hydrogen evolution, which oxidizes the viologen radicals, thus restoring the polymer chains to their hydrated random coil state. As a result, transient polymer assemblies form and subsequently disassemble upon depletion of the reducing agent, leading to a temporally controlled out-of-equilibrium phase transition. Moreover, by tuning the platinum concentration and reaction temperature, we achieve precise control of both the size and lifetime of these assemblies. Notably, viologen moieties constitute only about 1% of the polymer repeating units, underscoring that chemically-fueled phase transition is efficient strategy for dynamically regulating molecular assemblies. These findings demonstrate that chemically-fueled phase transitions in redox-responsive polymers offer a promising blueprint for designing dynamic, biomimetic materials capable of spatiotemporally regulated structural transformations.
    Keywords:  Chemically-fueled self-assembly; coil-to-globule phase transition; hydrogen evolution; poly(N-isopropylacrylamide); viologen
    DOI:  https://doi.org/10.1080/14686996.2025.2494496
  30. Biotechnol Bioeng. 2025 Apr 30.
    Process Intensification for Recombinant Protein Production in E. coli via Identification of Active Nodes in Cellular Metabolism and Dynamic Flux Balance Analysis.
    Hardik Dodia, Charandatta Muddana, Vivek Mishra, Avinash Vellore Sunder, Pramod P Wangikar.
      Complex media supplemented with a carbon source are commonly used in bioprocesses for recombinant protein production in Escherichia coli. Optimizing these processes is challenging and requires precise understanding of cellular metabolism and nutrient requirements. Compared to a design of experiments approach that necessitates extensive experimentation, metabolic modeling using a genome scale metabolic model (GEM) offers a more predictive and systematic approach to guide process optimization by identifying specific metabolic bottlenecks. In addition, spent media analysis (SMA) can unravel the preferential utilization of different media components during the bioprocess. Here, we integrated the updated E. coli GEM with time course SMA data from a fed-batch process and performed dynamic flux balance analysis (dFBA) to identify metabolites that function as active nodes and are vital for cellular function. These are potential target supplements to boost cellular activity and in turn the recombinant protein productivity. Using an iterative approach of performing fermentation, SMA, and metabolic modeling, we intensified the bioprocess in just five experimental trials, resulting in a six-fold increase in protein productivity. Our new feeding strategy involved yeast extract with amino acid supplementation (Ser, Thr, Asp, and Glu) and increased oxygen transfer rates. This approach demonstrates significant promise for application in bioprocess intensification.
    Keywords:  active nodes; bioprocess intensification; complex media; recombinant protein production; spent media analysis
    DOI:  https://doi.org/10.1002/bit.29012
  31. ACS Macro Lett. 2025 Apr 29. 603-609
    Fabrication of Microgel-Reinforced Hydrogels via Vat Photopolymerization.
    Cody O Crosby, Abhishek P Dhand, Jonathan T Taasan, Jason A Burdick.
      We report a facile method for the vat photopolymerization (i.e., digital light processing, DLP) of microgel-reinforced hydrogels that leverages both light and dark polymerization for curing. As an example, norbornene modified hyaluronic acid (NorHA) microgels at varying volume fractions swollen in acrylamide monomer are implemented as resins. When processed with DLP, acrylamide polymerization and cross-linking results in the formation of a secondary, continuous network that percolates through the microgels. At even low volume fractions (e.g., 30% v/v), the addition of microgels results in up to 4-fold increases in the stress at failure and work of fracture and a reduction in hydrogel swelling. The microgel-reinforced hydrogels are 3D printed into intricate shapes (e.g., metamaterial lattices) while maintaining uniform microgel distributions, and microgels with varied cross-link densities, cross-linkers, and fabrication methods are also investigated. This work expands the potential of microgel-reinforced hydrogels across applications where geometric freedom is essential.
    DOI:  https://doi.org/10.1021/acsmacrolett.5c00086
  32. Science. 2025 May;388(6746): 472
    Editing proteins inside a cell.
    J Trae Hampton, Wenshe Ray Liu.
      Pairs of split protein segments can modify a variety of target proteins in a living cell.
    DOI:  https://doi.org/10.1126/science.adx5085
  33. Soft Matter. 2025 May 01.
    Designing yield stress fluids for advanced materials processing using derivatives of pH-responsive branched co-polymer surfactants.
    Emma L Jones, Zhidong Luo, Rishav Agrawal, Sean Flynn, Megan Carr, Will Sharratt, Esther García-Tuñón.
      Through careful formulation design from a structure-properties perspective, this work demonstrates the potential of pH-responsive branched co-polymer surfactants (BCSs) in emulsion engineering and advanced materials processing. A library of BCS derivatives, with controlled spatial distribution of hydrogen bonding motifs and different branching levels, is synthesised via a modified Strathclyde method with varying conditions in solids content and PEGMA chain length. High dilution during the co-polymerisation leads to linear co-polymers, while an increase of monomers concentration favours branching reactions. This diverse set of BCSs can be exploited to stabilise pH-responsive suspension and emulsions containing activated charcoal (AC) or strontium titanate (STO) to create an array of yield stress soft materials. Large amplitude oscillatory shear (LAOS) experiments reveal their diverse rheological properties and yielding behaviours, that correlate primarily with powders properties and concentration, the degree of branching of BCS macromolecules, and to some extent, with the PEGMA length or BCS molecular weight. Based on the rheological characterisation, two formulations are selected and optimised for direct coagulation casting of AC suspensions and direct ink writing (DIW) of STO to create macroscopic structures. The optimised STO emulsion gels for DIW show a dramatic shift in printing behaviour before and after triggering the pH-controlled assembly. LAOS analyses using Fourier-transform (FT) rheology and the sequence of physical processes (SPP) confirm that the pH triggered assembly of STO emulsion gels results in the transition from a stable microstructure that shows a smooth flow transition, to an aggregated and unstable microstructure that becomes easily disrupted under shear. The higher harmonics and SPP analysis enable the correlation of yielding and printing behaviours. Overall, the findings highlight the critical role that BCSs play in providing electro-steric stabilisation of suspensions and emulsion gels in the processing of advanced materials. Combining polymer chemistry, formulation design and rheology, we optimise responsive formulations to create complex macroscopic structures with hierarchical features.
    DOI:  https://doi.org/10.1039/d4sm01473a
  34. J Am Chem Soc. 2025 Apr 30.
    Enzyme- and DNAzyme-Driven Transient Assembly of DNA-Based Phase-Separated Coacervate Microdroplets.
    Yunlong Qin, Yang Sung Sohn, Rachel Nechushtai, Fan Xia, Fujian Huang, Itamar Willner.
      An assembly of dissipative, transient, DNA-based microdroplet (MD) coacervates in the presence of auxiliary enzymes (endonucleases and nickases) or MD-embedded DNAzyme is introduced. Two pairs of different Y-shaped DNA core frameworks modified with toehold tethers are cross-linked by complementary toehold-functionalized duplexes, engineered to be cleaved by EcoRI or HindIII endonucleases, or cross-linked by palindromic strands that include pre-engineered Nt.BbvCI or Nb.BtsI nicking sites, demonstrating transient evolution/depletion of phase-separated MD coacervates. By mixing the pairs of endonuclease- or nickase-responsive MDs, programmed or gated transient formation/depletion of MD frameworks is presented. In addition, by cross-linking a pre-engineered Y-shaped core framework with a sequence-designed fuel strand, phase separation of MD coacervates with embedded Mg2+-DNAzyme units is introduced. The DNAzyme-catalyzed cleavage of a ribonucleobase-modified hairpin substrate, generating the waste product of the metabolite fragments, leads to the metabolite-driven separation of the cross-linked coacervates, resulting in the temporal evolution and depletion of the DNAzyme-functionalized MDs. By employing a light-responsive caged hairpin structure, the light-modulated fueled evolution and depletion of the DNAzyme-active MDs are presented. The enzyme- or DNAzyme-catalyzed transient evolution/depletion of the MD coacervates provides protocell frameworks mimicking dynamic transient processes of native cells. The possible application of MDs as functional carriers for the temporal, dose-controlled release of loads is addressed.
    DOI:  https://doi.org/10.1021/jacs.5c00637
  35. Soft Matter. 2025 Apr 29.
    Tunable mechanical properties and phase transitions in nanoconfined polyzwitterionic UCST hydrogels.
    Sebastian Loescher, Chen Liang, Remi Plamont, Josef Breu, Olli Ikkala, Hang Zhang.
      Stimuli-responsive hydrogels with thermal phase transitions serve as pivotal components in advancing biomedical and soft robotics applications. In contrast to widely studied LCST-type thermo-responsive hydrogels, UCST-type hydrogels provide reverse thermo-responses. However, conventional UCST-type hydrogels suffer from weak mechanical properties and fixed phase transition kinetics. Here, we present polyzwitterionic UCST-type hydrogels under coplanar nanoconfinement by large aspect ratio hectorite nanosheets. The nanoconfinement significantly enhances the strength and stiffness of the hydrogels. In addition, the nanosheets serve as kinetic barriers for water diffusion. This regulates the swelling and shrinking kinetics of the polyzwitterionic hydrogels and thus allows for tunable phase transitions dependent on the thermal history of the hydrogels. Furthermore, we demonstrate that the incorporation of gold nanoparticles allows precise control of the optical properties of the hydrogel through photothermal means. These findings pave the way for engineering both the mechanical and thermoresponsive properties in polyzwitterionic hydrogels, thus broadening their applications in smart soft materials.
    DOI:  https://doi.org/10.1039/d5sm00317b
  36. Metab Eng. 2025 Apr 30. pii: S1096-7176(25)00071-0. [Epub ahead of print]
    Ribo-seq guided design of enhanced protein secretion in Komagataella phaffii.
    Aida Tafrishi, Troy Alva, Justin Chartron, Ian Wheeldon.
      The production of recombinant proteins requires the precise coordination of various biological processes, including protein synthesis, folding, trafficking, and secretion. The overproduction of a heterologous protein can impose various bottlenecks on these networks. Identifying and alleviating these bottlenecks can guide strain engineering efforts to enhance protein production. The methylotrophic yeast Komagataella phaffii is used for its high capacity to produce recombinant proteins. Here, we use ribosome profiling to identify bottlenecks in protein secretion during heterologous expression of human serum albumin (HSA). Validation of this analysis showed that the knockout of non-essential genes whose gene products target the ER, through co- and post-translational mechanisms, and have high ribosome utilization can increase production of a heterologous protein, HSA. A triple knockout in co-translationally translocated carbohydrate and acetate transporter Gal2p, cell wall maintenance protein Ydr134cp, and the post-translationally translocated cell wall protein Aoa65896.1 increased HSA production by 35%. This data-driven strain engineering approach uses cell-level information to identify gene targets for phenotype improvement. This specific case identifies hits and creates strains with improved HSA production, with Ribo-seq and bioinformatic analysis to identify non-essential ER targeted proteins that are high ribosome utilizers.
    Keywords:  CRISPR-Cas9 genome editing; Rational strain design; Recombinant protein secretion; Ribosome profiling; strain engineering
    DOI:  https://doi.org/10.1016/j.ymben.2025.04.007
  37. Nat Commun. 2025 May 02. 16(1): 4106
    Feedback-responsive cell factories for dynamic modulation of the unfolded protein response.
    Daniela Barrios, Bhagyashree Bachhav, Wendolyn Carlos-Alcalde, Carlos D Llanos, Wenchang Zhou, Laura Segatori.
      Engineering cell factories that support the production of large quantities of protein therapeutics remains a significant biomanufacturing challenge. The overexpression of secretory proteins causes proteotoxic stress, affecting cell viability and protein productivity. Proteotoxic stress leads to the activation of the Unfolded Protein Response (UPR), a series of signal transduction pathways regulating protein quality control mechanisms aimed at restoring homeostasis. Sustained UPR activation culminates with the induction of apoptosis. Current strategies for enhancing the production of therapeutic proteins have focused on the deregulated modulation of key components of the UPR. These strategies have resulted in limited and often protein-specific improvements as they may lead to adaptation and cell toxicity and do not account for natural population heterogeneities. We report here feedback-responsive cell factories that sense proteotoxic stress and, in response, modulate the UPR to enhance stress attenuation and delay cell death, addressing the limitations of current strategies. We demonstrate that our cell engineering approach enables dynamic UPR modulation upon proteotoxic stress. The sense-and-respond systems that mediate dynamic UPR modulation enhance the production of the therapeutic enzyme tissue plasminogen activator and the bispecific antibody blinatumomab. Our feedback-responsive cell factories provide an innovative strategy for dynamically adjusting the innate cellular stress response and enhancing therapeutic protein manufacturing.
    DOI:  https://doi.org/10.1038/s41467-025-58994-x
  38. Nature. 2025 Apr 30.
    Selective inhibition of stromal mechanosensing suppresses cardiac fibrosis.
    Sangkyun Cho, Siyeon Rhee, Christopher M Madl, Arianne Caudal, Dilip Thomas, Hyeonyu Kim, Ana Kojic, Hye Sook Shin, Abhay Mahajan, James W Jahng, Xi Wang, Phung N Thai, David T Paik, Mingqiang Wang, McKay Mullen, Natalie M Baker, Jeremy Leitz, Souhrid Mukherjee, Virginia D Winn, Y Joseph Woo, Helen M Blau, Joseph C Wu.
      Matrix-derived biophysical cues are known to regulate the activation of fibroblasts and their subsequent transdifferentiation into myofibroblasts1-6, but whether modulation of these signals can suppress fibrosis in intact tissues remains unclear, particularly in the cardiovascular system7-10. Here we demonstrate across multiple scales that inhibition of matrix mechanosensing in persistently activated cardiac fibroblasts potentiates-in concert with soluble regulators of the TGFβ pathway-a robust transcriptomic, morphological and metabolic shift towards quiescence. By conducting a meta-analysis of public human and mouse single-cell sequencing datasets, we identify the focal-adhesion-associated tyrosine kinase SRC as a fibroblast-enriched mechanosensor that can be targeted selectively in stromal cells to mimic the effects of matrix softening in vivo. Pharmacological inhibition of SRC by saracatinib, coupled with TGFβ suppression, induces synergistic repression of key profibrotic gene programs in fibroblasts, characterized by a marked inhibition of the MRTF-SRF pathway, which is not seen after treatment with either drug alone. Importantly, the dual treatment alleviates contractile dysfunction in fibrotic engineered heart tissues and in a mouse model of heart failure. Our findings point to joint inhibition of SRC-mediated stromal mechanosensing and TGFβ signalling as a potential mechanotherapeutic strategy for treating cardiovascular fibrosis.
    DOI:  https://doi.org/10.1038/s41586-025-08945-9
  39. Nat Commun. 2025 Apr 30. 16(1): 4054
    Viscoelastic extracellular matrix enhances epigenetic remodeling and cellular plasticity.
    Yifan Wu, Yang Song, Jennifer Soto, Tyler Hoffman, Xiao Lin, Aaron Zhang, Siyu Chen, Ramzi N Massad, Xiao Han, Dongping Qi, Kun-Wei Yeh, Zhiwei Fang, Joon Eoh, Luo Gu, Amy C Rowat, Zhen Gu, Song Li.
      Extracellular matrices of living tissues exhibit viscoelastic properties, yet how these properties regulate chromatin and the epigenome remains unclear. Here, we show that viscoelastic substrates induce changes in nuclear architecture and epigenome, with more pronounced effects on softer surfaces. Fibroblasts on viscoelastic substrates display larger nuclei, lower chromatin compaction, and differential expression of distinct sets of genes related to the cytoskeleton and nuclear function, compared to those on elastic surfaces. Slow-relaxing viscoelastic substrates reduce lamin A/C expression and enhance nuclear remodeling. These structural changes are accompanied by a global increase in euchromatin marks and local increase in chromatin accessibility at cis-regulatory elements associated with neuronal and pluripotent genes. Consequently, viscoelastic substrates improve the reprogramming efficiency from fibroblasts into neurons and induced pluripotent stem cells. Collectively, our findings unravel the roles of matrix viscoelasticity in epigenetic regulation and cell reprogramming, with implications for designing smart materials for cell fate engineering.
    DOI:  https://doi.org/10.1038/s41467-025-59190-7
  40. Biomater Adv. 2025 Apr 28. pii: S2772-9508(25)00150-5. [Epub ahead of print]175 214323
    Artificial Intelligence tool for prediction of ECM mimics hydrogel formulations via click chemistry.
    Francesca Cadamuro, Marco Piazzoni, Elia Gamba, Beatrice Sonzogni, Fabio Previdi, Francesco Nicotra, Antonio Ferramosca, Laura Russo.
      A user-friendly machine learning (ML) predictive tool is reported for designing extracellular matrix (ECM)-mimetic hydrogels with tailored rheological properties. Developed for regenerative medicine and 3D bioprinting, the model leverages click chemistry crosslinking to fine-tune the mechanical behaviour of gelatin- and hyaluronic acid-based hydrogels. Using both experimental rheological data and synthetic datasets, our supervised ML approach accurately predicts hydrogel compositions, significantly reducing the cost and time associated with trial-and-error approach. Despite advancements in the field, existing models remain limited in their ability to mimic the ECM due to the use of non-natural polymers, reliance on a single type of biologically active macromolecule, and physical crosslinking reactions with limited tuneability. Additionally, their lack of generalizability confines them to specific formulations and demands extensive experimental data for training. This predictive platform represents a major advancement in biomaterial design, improving reproducibility, scalability, and efficiency. By integrating rational design, it accelerates tissue engineering research and expands access to customized ECM-mimetic hydrogels with tailored viscoelastic properties for biomedical applications, enabling both experts and non-experts in materials design.
    Keywords:  Artificial intelligence; Click chemistry; ECM mimics; Hydrogel; Machine learning
    DOI:  https://doi.org/10.1016/j.bioadv.2025.214323
  41. Adv Mater. 2025 Apr 29. e2502820
    Structurally Colored Sustainable Sea Silk from Atrina pectinata.
    Jimin Choi, Jun-Hyung Im, Young-Ki Kim, Tae Joo Shin, Patrick Flammang, Gi-Ra Yi, David J Pine, Dong Soo Hwang.
      The harvesting of sea silk, a luxurious golden textile traditionally obtained from the endangered mollusk Pinna nobilis, faces severe limitations due to conservation efforts, driving the search for sustainable alternatives. Atrina pectinata, a phylogenetically close relative within the Pinnidae family is identified, as a viable source of biomimetic sea silk. The byssal threads of A. pectinata can be processed using existing methods, providing a way to continue producing this historically significant textile. These threads exhibit a remarkable hierarchical structure with globular proteins organized across multiple scales and stabilized by supramolecular sugar-lectin interactions that influence their mechanical properties. Moreover, the threads display a brilliant golden hue arising from structural coloration, ensuring exceptional lightfastness, retaining their color for millennia. This discovery elucidates the biomolecular foundations of sea silk's unique properties and establishes A. pectinata as a sustainable candidate for producing exquisite golden textiles and bioinspired pigments, thereby addressing the growing demand for eco-friendly and long-lasting colored materials in the textile and pigment industries.
    Keywords:  golden silks; hierarchical structure; photonins; sea silks; structural color; sugar‐lectin interaction
    DOI:  https://doi.org/10.1002/adma.202502820
  42. Metab Eng. 2025 Apr 27. pii: S1096-7176(25)00070-9. [Epub ahead of print]
    Metabolic engineering of Escherichia coli for 4-nitrophenylalanine production via the 4-aminophenylalanine synthetic pathway.
    Ayana Mori, Yuuki Hirata, Mayumi Kishida, Daisuke Nonaka, Akihiko Kondo, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka.
      The non-natural amino acid 4-nitrophenylalanine is a crucial pharmaceutical ingredient and has extensive utility in protein engineering. Here, we demonstrated the production of 4-nitrophenylalanine by Escherichia coli with AurF, 4-aminobenzoate N-oxygenase from Streptomyces thioluteus. Firstly, eight distinct gene combinations, encompassing four variants of papA and two of papBC, were evaluated to optimize the production of 4-aminophenylalanine, a precursor of 4-nitrophenylalanine. The strain co-expressing both pabAB from E. coli and papBC from Streptomyces venezuelae attained the highest 4-aminophenylalanine production. In a fed-batch fermenter cultivation, 4-aminophenylalanine production of 22.5 g/L was achieved. To produce 4-nitrophenylalanine from glucose, we constructed strains co-expressing AurF alongside the genes responsible for 4-aminophenylalanine synthesis. The subsequent optimization of the plasmid copy numbers carrying each gene set resulted in an increase in the 4-nitrophenylalanine production titer. Transcription analysis revealed that the expression level of the 4-aminophenylalanine biosynthetic genes markedly contributed to 4-nitrophenylalanine production. After optimizing batch fermentation conditions, the titer of 4-nitrophenylalanine increased to 2.22 g/L. Overall, these results provide the basis for industrial microbial production of 4-nitrophenylalanine, contributing to the advancement of biotechnological methodologies for generating non-natural amino acids with specific functionalities.
    Keywords:  4-aminophenylalanine; 4-nitrophenylalanine; microbial production; nitro compounds
    DOI:  https://doi.org/10.1016/j.ymben.2025.04.006
  43. Adv Mater. 2025 Apr 28. e2415687
    Supramolecular Conductive Hydrogels With Homogeneous Ionic and Electronic Transport.
    Stephen J K O'Neill, Minoru Ashizawa, Alan M McLean, Ruben Ruiz-Mateos Serrano, Tokihiko Shimura, Masakazu Agetsuma, Motosuke Tsutsumi, Tomomi Nemoto, Christopher D J Parmenter, Jade A McCune, George G Malliaras, Naoji Matsuhisa, Oren A Scherman.
      Mechanically resilient hydrogels with ion-electron mixed transport properties effectively bridge biology with electronics. An ideal bioelectronic interface can be realized through introducing electronically conductive polymers into supramolecular hydrogels. However, inhomogeneous morphologies of conducting polymers, such as poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS), have limited mechanical properties and ion-electron interactions. Here, supramolecular conductive hydrogels that possess homogeneous ionic and electronic transport are achieved. The materials demonstrate high toughness (620 kJ m-3), stretchability (>1000%), softness (10.5 kPa), and conductivity (5.8 S cm-1), which surpasses commonly used inhomogeneous PEDOT:PSS-based hydrogels. The homogeneous network leads to higher charge injection capacitance and lower skin impedance compared to commercial electrodes or commonly used inhomogeneous PEDOT:PSS conducting networks. This significant advance arises from the homogeneous incorporation of the hydrophilic self-doped conducting polymer S-PEDOT, which has polymerized within a supramolecular polymer network template mediated by high-binding affinity host-guest crosslinks. Furthermore, the compatibility of S-PEDOT with hydrophilic secondary networks enables the realization of fully dryable and reswellable electronic devices, facilitating reusability and improving their ease of handling. It is anticipated that achieving such material architectures will offer a promising new direction in future synthesis and implementation of conductive hydrogels in the field of bioelectronics.
    Keywords:  bioelectronics; conducting polymers; host‐guest chemistry; reusable devices; supramolecular networks
    DOI:  https://doi.org/10.1002/adma.202415687
  44. bioRxiv. 2025 Apr 08. pii: 2025.04.02.646906. [Epub ahead of print]
    ATOMICA: Learning Universal Representations of Intermolecular Interactions.
    Ada Fang, Zaixi Zhang, Andrew Zhou, Marinka Zitnik.
      Molecular interactions underlie nearly all biological processes, but most machine learning models treat molecules in isolation or specialize in a single type of interaction, such as protein-ligand or protein-protein binding. This siloed approach prevents generalization across biomolecular classes and limits the ability to model interaction interfaces systematically. We introduce ATOMICA, a geometric deep learning model that learns atomic-scale representations of intermolecular interfaces across diverse biomolecular modalities, including small molecules, metal ions, amino acids, and nucleic acids. ATOMICA uses a self-supervised denoising and masking objective to train on 2,037,972 interaction complexes and generate hierarchical embeddings at the levels of atoms, chemical blocks, and molecular interfaces. The model generalizes across molecular classes and recovers shared physicochemical features without supervision. Its latent space captures compositional and chemical similarities across interaction types and follows scaling laws that improve representation quality with increasing biomolecular data modalities. We apply ATOMICA to construct five modality-specific interfaceome networks, termed ATOMICAN et s, which connect proteins based on interaction similarity with ions, small molecules, nucleic acids, lipids, and proteins. These networks identify disease pathways across 27 conditions and predict disease-associated proteins in autoimmune neuropathies and lymphoma. Finally, we use ATOMICA to annotate the dark proteome-proteins lacking known structure or function-by predicting 2,646 previously uncharacterized ligand-binding sites. These include putative zinc finger motifs and transmembrane cytochrome subunits, demonstrating that ATOMICA enables systematic annotation of molecular interactions across the proteome.
    DOI:  https://doi.org/10.1101/2025.04.02.646906
  45. J Bacteriol. 2025 Apr 30. e0040124
    Maltodextrin transport in the extremely thermophilic, lignocellulose degrading bacterium Anaerocellum bescii (f. Caldicellulosiruptor bescii).
    Hansen Tjo, Virginia Jiang, Jerelle A Joseph, Jonathan M Conway.
      Sugar transport into microbial cells is a critical, yet understudied step in the conversion of lignocellulosic biomass to metabolic products. Anaerocellum bescii (formerly Caldicellulosiruptor bescii) is an extremely thermophilic, anaerobic bacterium that readily degrades the cellulose and hemicellulose components of lignocellulosic biomass into a diversity of oligosaccharide substrates. Despite significant understanding of how this microorganism degrades lignocellulose, the mechanisms underlying its highly efficient transport of the released oligosaccharides into the cell are comparatively underexplored. Here, we identify and characterize the ATP-binding cassette (ABC) transporters in A. bescii governing maltodextrin transport. Utilizing past transcriptomic studies on Anaerocellum and Caldicellulosiruptor species, we identify two maltodextrin transporters in A. bescii and express and purify their substrate-binding proteins (Athe_2310 and Athe_2574) for characterization. Using differential scanning calorimetry and isothermal titration calorimetry, we show that Athe_2310 strongly interacts with shorter maltodextrins, such as maltose and trehalose, with dissociation constants in the micromolar range, while Athe_2574 binds longer maltodextrins, with dissociation constants in the sub-micromolar range. Using a sequence-structure-function comparison approach combined with molecular modeling, we provide context for the specificity of each of these substrate-binding proteins. We propose that A. bescii utilizes orthogonal ABC transporters to uptake malto-oligosaccharides of different lengths to maximize transport efficiency.
    IMPORTANCE: Here, we reveal the biophysical and structural basis for oligosaccharide transport by two maltodextrin ATP-binding cassette (ABC) transporters in Anaerocellum bescii. This is the first biophysical characterization of carbohydrate uptake in this organism and establishes a workflow for characterizing other oligosaccharide transporters in A. bescii and similar biomass-degrading thermophiles of interest for lignocellulosic bioprocessing. By deciphering the mechanisms underlying high-affinity sugar uptake in A. bescii, we shed light on an underexplored step between extracellular lignocellulose degradation and intracellular conversion of sugars to metabolic products. This understanding will expand opportunities for harnessing sugar transport in thermophiles to reshape lignocellulose bioprocessing as part of a renewable bioeconomy.
    Keywords:  ABC sugar transporter; Anaerocellum bescii; Caldicellulosiruptor; biophysics; lignocellulose; maltodextrin; maltose binding protein; substrate-binding protein; thermophile
    DOI:  https://doi.org/10.1128/jb.00401-24
  46. bioRxiv. 2025 Apr 08. pii: 2025.04.02.646189. [Epub ahead of print]
    High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples.
    Li Yao, Sagar R Shah, Abdullah Ozer, Junke Zhang, Xiuqi Pan, Tianyu Xia, Vrushali D Fangal, Alden King-Yung Leung, Meihan Wei, John T Lis, Haiyuan Yu.
      Biological systems exhibit remarkable heterogeneity, characterized by intricate interplay among diverse cell types. Resolving the regulatory processes of specific cell types is crucial for delineating developmental mechanisms and disease etiologies. While single-cell sequencing methods such as scRNA-seq and scATAC-seq have revolutionized our understanding of individual cellular functions, adapting bulk genome-wide assays to achieve single-cell resolution of other genomic features remains a significant technical challenge. Here, we introduce Deep-learning-based DEconvolution of Tissue profiles with Accurate Interpretation of Locus-specific Signals (DeepDETAILS), a novel quasi-supervised framework to reconstruct cell-type-specific genomic signals with base-pair precision. DeepDETAILS' core innovation lies in its ability to perform cross-modality deconvolution using scATAC-seq reference libraries for other bulk datasets, benefiting from the affordability and availability of scATAC-seq data. DeepDETAILS enables high-resolution mapping of genomic signals across diverse cell types, with great versatility for various omics datasets, including nascent transcript sequencing (such as PRO-cap and PRO-seq) and ChIP-seq for chromatin modifications. Our results demonstrate that DeepDETAILS significantly outperformed traditional statistical deconvolution methods. Using DeepDETAILS, we developed a comprehensive compendium of high-resolution nascent transcription and histone modification signals across 39 diverse human tissues and 86 distinct cell types. Furthermore, we applied our compendium to fine-map risk variants associated with Primary Sclerosing Cholangitis (PSC), a progressive cholestatic liver disorder, and revealed a potential etiology of the disease. Our tool and compendium provide invaluable insights into cellular complexity, opening new avenues for studying biological processes in various contexts.
    DOI:  https://doi.org/10.1101/2025.04.02.646189
  47. Biofabrication. 2025 Apr 29.
    Development of a bioreactor and volumetric bioprinting protocol to enable perfused culture of biofabricated human epithelial mammary ducts and endothelial constructs.
    Maj-Britt Buchholz, Paulina Nuñez Bernal, Nils Bessler, Camille Bonhomme, Riccardo Levato, Anne Rios.
      Tissue function depends on the 3D spatial organization of cells, extracellular matrix components, as well as dynamic nutrient gradients and mechanical forces. Advances in biofabrication technologies have enabled the creation of increasingly sophisticated tissue models, but achieving native-like tissue maturation post-fabrication remains a challenge. The development of bioreactors and microfluidic systems capable of introducing dynamic culture platforms and controlled mechanical and biochemical stimulation for biofabricated tissue analogues is therefore imperative to address this. In this technical note, we introduce a multi-step pipeline to fabricate, seed and perfuse geometrically complex hydrogel constructs with quality control protocols through the computational analysis of confocal multispectral 3D imaging data for each step of the process. Employing ultra-fast volumetric bioprinting, chips with tunable channel architectures were fabricated. Furthermore, an autoclavable and transparent perfusion bioreactor inspired by open-source designs was developed to enable controlled, long-term perfusion (up to 28 days) and real-time monitoring of cell behavior. As proof-of-concept, employing this pipeline, we fabricated a human mammary ductal model and an endothelialized vessel on-a-chip, demonstrating the compatibility of the platform with epithelial and endothelial cell lines, and investigated the effect of dynamic culture on tissue-specific cell organization. Dynamic perfusion underlined the influence of mechanical stimulation on cell organization and maturation. Various chip architectures, capable of recapitulating tissue-specific features (i.e. lobules) were printed, enabling the mono- and co-culture of human mammary epithelial and endothelial cells. Our pipeline, with the accompanying protocols and analysis scripts presented here, provide the potential to be applied for the dynamic culture of a wide range of tissues.
    Keywords:  Biofabrication; organ on-a-chip; perfusion bioreactor; volumetric bioprinting
    DOI:  https://doi.org/10.1088/1758-5090/add20f
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