bims-enlima Biomed News
on Engineered living materials
Issue of 2025–01–12
sixteen papers selected by
Rahul Kumar, Tallinna Tehnikaülikool



  1. Nat Chem Biol. 2025 Jan 08.
      Engineering cells to sense and respond to environmental cues often focuses on maximizing gene regulation at the single-cell level. Inspired by population-level control mechanisms like the immune response, we demonstrate dynamic control and amplification of gene regulation in bacterial populations using programmable plasmid-mediated gene transfer. By regulating plasmid loss rate, transfer rate and fitness effects via Cas9 endonuclease, F conjugation machinery and antibiotic selection, we modulate the fraction of plasmid-carrying cells, serving as an amplification factor for single-cell-level regulation. This approach expands the dynamic range of gene expression and allows orthogonal control across populations. Our platform offers a versatile strategy for dynamically regulating gene expression in engineered microbial communities.
    DOI:  https://doi.org/10.1038/s41589-024-01817-9
  2. Langmuir. 2025 Jan 04.
      3D printing techniques are increasingly being explored to produce hydrogels, versatile materials with a wide range of applications. While photopolymerization-based 3D printing can produce customized hydrogel shapes and intricate structures, its reliance on rigid printing conditions limits material properties compared to those of extrusion printing. To address this limitation, this study employed an alternative approach by printing an organogel precursor using vat polymerization with organic solvents instead of water, followed by solvent exchange after printing to create the final hydrogel material. Using mask stereolithography (mSLA), we evaluated the effects of solvent choice on a novel and recently developed 3D-printed supramolecular hydrogel, cross-linked with quaternized chitosan/acrylate salt. In this study, we compared the conventional solvent dimethyl sulfoxide (DMSO) with the bioderived solvent Cyrene. Our findings reveal that hydrogels produced with Cyrene-based 3D printing exhibit weaker strength but high swelling capacity and elasticity, resilience to cyclic loading, and the ability to produce detailed and accurate 3D-printed objects. These results provide insights into the solvent-dependent mechanical and physical characteristics of 3D-printed hydrogels and underscore the potential of Cyrene as a sustainable alternative for polymeric synthesis.
    DOI:  https://doi.org/10.1021/acs.langmuir.4c03887
  3. Adv Mater. 2025 Jan 05. e2413096
      The article explores materials sustainability through a bio-inspired lens and discusses paradigms that can reshape the understanding of material synthesis, processing, and usage. It addresses various technological fields, from structural engineering to healthcare, and emphasizes natural material cycles as a blueprint for efficient recycling and reuse. The study shows that material functionality depends on both chemical composition and structural modifications, which emphasizes the role of material processing. The article identifies strategies such as mono-materiality and multifunctionality, and explores how responsivity, adaptivity, modularity, and cellularity can simplify material assembly and disassembly. Bioinspired strategies for reusing materials, defect tolerance, maintenance, remodeling, and healing may extend product lifespans. The principles of circularity, longevity, and parsimony are reconsidered in the context of "active materiality", a dynamic bio-inspired paradigm. This concept expands the traditional focus of material science from structure-function relationships to include the development of materials capable of responding or adapting to external stimuli. Concrete examples demonstrate how bio-inspired strategies are being applied in engineering and technology to enhance the sustainability of materials. The article concludes by emphasizing interdisciplinary collaboration as a key factor for developing a sustainable and resilient materials economy in harmony with nature's material cycles.
    Keywords:  active materials; adaptive; bioinspiration; biological materials; responsive
    DOI:  https://doi.org/10.1002/adma.202413096
  4. Acc Chem Res. 2025 Jan 06.
      ConspectusLight-driven polymerizations and their application in 3D printing have revolutionized manufacturing across diverse sectors, from healthcare to fine arts. Despite the popularized notion that with 3D printing "imagination is the only limit", we and others in the scientific community have identified fundamental hurdles that restrict our capabilities in this space. Herein, we describe the ZAP group's efforts in developing photochemical systems that respond to nontraditional colors of light to elicit the rapid, spatiotemporally controlled formation of plastics. Our research addresses key limitations in current photopolymerization methods, such as the reliance on high-energy UV light, oxygen sensitivity, and narrow materials scope. We present a comprehensive overview of our advancements in both light-fueled radical and nonradical chemistry and its implementation in vat photopolymerization 3D printing using panchromatic resins. In radical chemistry, we have developed a class of boron dipyrromethene (BODIPY) dye molecules that act as photoradical generators (PRGs). Upon exposure to visible or near-infrared (NIR) light, these molecules induced efficient polymerization of acrylics. Structural modifications, including the installment of halogens, twisted aromatic groups, nitrogen bridgeheads, and thiophenes, have imbued activity across this wide spectral range. Systematic photophysical characterization of these dyes revealed the presence of long-lived excited (high in energy) states, from which we accredited the enhancements in polymerization efficiency. In turn, curing (converting a liquid to solid) with low intensity visible-to-NIR light was possible in mere seconds; a requirement for many light-based 3D printing technologies. Our efforts in nonradical chemistry have been motivated by the need for new materials with properties and functionality currently inaccessible using radical-based 3D printing approaches (e.g., tough and recyclable), while also providing an avenue toward multimaterial fabrication. We have developed photobase generators (PBGs) - dyes that release basic cargo upon light exposure-to catalyze polymerizations beyond acrylic-only resins. These include coumarinylmethyl- and BODIPY-tetramethylguanidine (TMG) derivatives, as well as onium photocages, which enabled photocuring of thiol-ene and thiol-isocyanate resins. Lastly, we have pioneered rapid, high-resolution visible-to-NIR light-based 3D printing. Our work includes the development of reactive photoredox catalyst systems for speed, additives for oxygen-tolerance, NIR-light reactivity for nanoparticle composites, models for streamlined optimization, and triplet fusion for high resolution. These advancements led to build speeds up to 45 mm/h with features <100 μm, rivaling contemporary UV-based technologies. The impact of our research extends beyond academic interest, offering practical solutions for additive manufacturing of (multi)functional materials. By enabling the use of lower-energy light sources, our work paves the way for environmentally friendly, cost-effective, and versatile 3D printing. It opens new possibilities for printing with previously incompatible materials, including UV-sensitive compounds and high-refractive-index nanocomposites. Nascent developments in multimaterial 3D printing via color- and dose-controlled light exposure are enabling the production of objects with precise placement of materials having disparate composition and properties. As we continue to develop photopolymerizations and light-based 3D printing, we anticipate transformative applications in fields ranging from tissue engineering to advanced electronics manufacturing. This will bring the community one step closer to fulfill the dream of creators only being "limited by imagination".
    DOI:  https://doi.org/10.1021/acs.accounts.4c00680
  5. PLoS One. 2025 ;20(1): e0317350
      The extrusion bioprinting of collagen material has many applications relevant to tissue engineering and regenerative medicine. Freeform Reversible Embedding of Suspended Hydrogels (FRESH) technology is capable of 3D printing collagen material with the specifications and details needed for precise tissue guidance, a crucial requirement for effective tissue repair. While FRESH has shown repeated success and reliability for extrusion printing, the mechanical properties of completed collagen prints can be improved further by post-print crosslinking methodologies. Photoinitiator-based crosslinking methods are simple and have proven effective in strengthening protein-based materials. The ruthenium and sodium persulfate photoinitiator system (Ru(bpy)3/SPS) has been suggested as an effective crosslinking method for collagen materials. Herein, we describe the procedure our group has developed to combine extrusion-based 3D printing of type-1 collagen using FRESH technology with Ru(bpy)3/SPS photoinitiated crosslinking methods to improve the strength and stability of 3D printed collagen structures. Mechanical testing and cell biocompatibility assessments were performed to investigate the impact of Ru(bpy)3/SPS photoinitiated crosslinking and highlight the potential limitations of this method. These results demonstrate a significant improvement in the compressive strength of type-1 collagen samples as the Ru(bpy)3/SPS concentration increases. Additionally, type-1 collagen samples crosslinked with up to 1/10 mM Ru(bpy)3/SPS support PC12 cell viability over a period of 7 days. The primary limitations that were observed and described in detail in this protocol are: the FRESH slurry preparation, printing environment, extrusion printer hardware, and quality of the ruthenium reagent.
    DOI:  https://doi.org/10.1371/journal.pone.0317350
  6. Sci Adv. 2025 Jan 10. 11(2): eadq6652
      In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a foundation to explore the interactions of chromatin and transcription at the single-cell level in human health.
    DOI:  https://doi.org/10.1126/sciadv.adq6652
  7. ACS Appl Mater Interfaces. 2025 Jan 07.
      Field-effect transistor (FET) biosensors have significantly attracted interest across various disciplines because of their high sensitivity, time-saving, and label-free characteristics. However, it remains a grand challenge to interface the FET biosensor with complex liquid media. Unlike standard liquid electrolytes containing purified protein content, directly exposing FET biosensors to complex biological fluids introduces significant sensing noise, which is caused by the abundance of nonspecific proteins, viruses, and bacteria that adsorb to the biosensor surfaces. In this work, we leverage the hydrogel encapsulation on an MXene-graphene-based FET, which selectively allows the permeation of viruses (e.g., SARS-CoV-2) and bacteria (e.g., E. coli), leading to the high-specificity detection of those biomarkers. The results demonstrated that hydrogel encapsulation could successfully detect the SARS-CoV-2 biomarker at 1 fg/mL while preventing the diffusion of E. coli biomarkers, and the obtained signal output amplitude is twice that of sensors without hydrogel encapsulation, demonstrating significant advantages over conventional bare sensors.
    Keywords:  /iE. coli bacteria; SARS-CoV-2 virus; field-effect-transistor (FET); hydrogel gating; selective transport/screening
    DOI:  https://doi.org/10.1021/acsami.4c12130
  8. bioRxiv. 2024 Dec 18. pii: 2024.12.17.628963. [Epub ahead of print]
      Applications of genetic code expansion in live cells are widespread and continually emerging, yet they have been limited by their reliance on the supplementation of non-standard amino acids (nsAAs) to cell culturing media. While advances in cell-free biocatalysis are improving nsAA synthesis cost and sustainability, such processes remain reliant on multi-step processes of product isolation followed by supplementation to engineered cells. Here, we report the design of a modular and genetically encoded system that combines the steps of biosynthesis of diverse phenylalanine derivatives, which are the most frequently used family of nsAAs for genetic code expansion, and their site-specific incorporation within target proteins using a single engineered bacterial host. Unlike previous demonstrations in which individual nsAAs were targeted for biosynthesis and site-specific incorporation, our system serves as a platform that exhibits broad substrate specificity towards commercially ubiquitous, achiral building blocks of aryl aldehydes or carboxylic acids. We demonstrate that this modular system enables high fidelity biosynthesis and incorporation of nsAAs for multiple industrially relevant nsAAs, such as the incorporation of 4,4-L-biphenylalanine within proteins after supplementation with biphenylaldehyde and the incorporation of 4-azido-L-phenylalanine within proteins after supplementation with 4-azido-benzoic acid. Finally, we show that the combination of nsAA biosynthesis and incorporation steps can extend the chemical reach of the intrinsic biological containment strategy of synthetic auxotrophy from nsAAs to low-cost and achiral building blocks. We anticipate that our system will aid industrial-scale manufacturing of proteins that contain nsAAs and democratize access to expensive or commercially unavailable chemistries for labs that lack separations or synthesis expertise.
    DOI:  https://doi.org/10.1101/2024.12.17.628963
  9. Metab Eng. 2025 Jan 06. pii: S1096-7176(25)00001-1. [Epub ahead of print]
      Advanced genome engineering enables precise and customizable modifications of bacterial species, and toolsets that exhibit broad-host compatibility are particularly valued owing to their portability. Tn5 transposon vectors have been widely used to establish random integrations of desired DNA sequences into bacterial genomes. However, the iteration of the procedure remains challenging because of the limited availability and reusability of selection markers. We addressed this challenge with CIFR, a mini-Tn5 integration system tailored for iterative genome engineering. The pCIFR vectors incorporate attP and attB sites flanking an antibiotic resistance marker used to select for the insertion. Subsequent removal of antibiotic determinants is facilitated by the Bxb1 integrase paired to a user-friendly counter-selection marker, both encoded in auxiliary plasmids. CIFR delivers engineered strains harboring stable DNA insertions and free of any antibiotic resistance cassette, allowing for the reusability of the tool. The system was validated in Pseudomonas putida, Escherichia coli, and Cupriavidus necator, underscoring its portability across diverse industrially relevant hosts. The CIFR toolbox was calibrated through combinatorial integrations of chromoprotein genes in P. putida, generating strains displaying a diverse color palette. We also introduced a carotenoid biosynthesis pathway in P. putida in a two-step engineering process, showcasing the potential of the tool for pathway balancing. The broad utility of the CIFR toolbox expands the toolkit for metabolic engineering, allowing for the construction of complex phenotypes while opening new possibilities in bacterial genetic manipulations.
    Keywords:  C. necator; E. coli; Genome engineering; Metabolic engineering; Pseudomonas; Synthetic biology; transposon
    DOI:  https://doi.org/10.1016/j.ymben.2025.01.001
  10. Nat Commun. 2025 Jan 09. 16(1): 517
      Complementary transistors are critical for circuits with compatible input/output signal dynamic range and polarity. Organic electronics offer biocompatibility and conformability; however, generation of complementary organic transistors requires introduction of separate materials with inadequate stability and potential for tissue toxicity, limiting their use in biomedical applications. Here, we discovered that introduction of source/drain contact asymmetry enables spatial control of de/doping and creation of single-material complementary organic transistors from a variety of conducting polymers of both carrier types. When integrated with the vertical channel design and internal ion reservoirs of internal ion-gated organic electrochemical transistors, we produced matched complementary IGTs (cIGTs) that formed high-performance conformable amplifiers with 200 V/V uniform gain and 2 MHz bandwidth. These amplifiers showed long-term in vivo stability, and their miniaturized biocompatible design allowed implantation in developing rodents to monitor network maturation. cIGTs expand the use of organic electronics in standard circuit designs and enhance their biomedical potential.
    DOI:  https://doi.org/10.1038/s41467-024-55284-w
  11. Mater Today Bio. 2025 Feb;30 101384
      This study explores the utilization of digital light processing (DLP) printing to fabricate complex structures using native gelatin as the sole structural component for applications in biological implants. Unlike approaches relying on synthetic materials or chemically modified biopolymers, this research harnesses the inherent properties of gelatin to create biocompatible structures. The printing process is based on a crosslinking mechanism using a di-tyrosine formation initiated by visible light irradiation. Formulations containing gelatin were found to be printable at the maximum documented concentration of 30 wt%, thus allowing the fabrication of overhanging objects and open embedded. Cell adhesion and growth onto and within the gelatin-based 3D constructs were evaluated by examining two implant fabrication techniques: (1) cell seeding onto the printed scaffold and (2) printing compositions that contain cells (cell-laden). The preliminary biological experiments indicate that both the cell-seeding and cell-laden strategies enable making 3D cultures of chondrocytes within the gelatin constructs. The mechanical properties of the gelatin scaffolds have a compressive modulus akin to soft tissues, thus enabling the growth and proliferation of cells, and later degrade as the cells differentiate and form a grown cartilage. This study underscores the potential of utilizing non-modified protein-only bioinks in DLP printing to produce intricate 3D objects with high fidelity, paving the way for advancements in regenerative tissue engineering.
    Keywords:  3D printing; Cell-laden; Digital light processing (DLP); Non-modified; di-tyrosine
    DOI:  https://doi.org/10.1016/j.mtbio.2024.101384
  12. Nat Commun. 2025 Jan 04. 16(1): 400
      Natural materials with highly oriented heterogeneous structures are often lightweight but strong, stiff but tough and durable. Such an integration of diverse incompatible mechanical properties is highly desired for man-made materials, especially weak hydrogels which are lack of high-precision structural design. Herein, we demonstrate the fabrication of hierarchically aligned heterogeneous hydrogels consisting of a compactly crosslinked sheath and an aligned porous core with alignments of nanofibrils at multi-scales by a sequential self-assembly assisted salting out method. The produced hydrogel offers ultrahigh mechanical properties among the reported hydrogels, elastomers and natural materials, including a toughness of 1031 MJ · m-3, strength of 55.3 MPa, strain of 3300%, stiffness of 6.8 MPa, fracture energy of 552.7 kJ · m-2 and fatigue threshold of 40.9 kJ · m-2. Furthermore, such a tough and strong hydrogel facilely achieves stable regeneration and rapid adhesion owing to the highly crystallized and aligned network structure. The regenerated specimen presents the reinforced strength, toughness and fatigue resistance over 10 regeneration cycles. This work provides a simple method to produce hydrogels with bioinspired heterostructures and combinational properties for real applications.
    DOI:  https://doi.org/10.1038/s41467-024-55677-x
  13. J Mater Chem B. 2025 Jan 10.
      Most synthetic hydrogels are formed through radical polymerization to yield a homogenous covalent meshwork. In contrast, natural hydrogels form through mechanisms involving both covalent assembly and supramolecular interactions. In this communication, we expand the capabilities of covalent poly(ethylene glycol) (PEG) networks through co-assembly of supramolecular peptide nanofibers. Using a peptide hydrogelator derived from the tryptophan zipper (Trpzip) motif, we demonstrate how in situ formation of nanofiber networks can tune the stiffness of PEG-based hydrogels, while also imparting shear thinning, stress relaxation, and self-healing properties. The hybrid networks show enhanced toughness and durability under tension, providing scope for use in load bearing applications. A small quantity of Trpzip peptide renders the non-adhesive PEG network adhesive, supporting adipose derived stromal cell adhesion, elongation, and growth. The integration of supramolecular networks into covalent meshworks expands the versatility of these materials, opening up new avenues for applications in biotechnology and medicine.
    DOI:  https://doi.org/10.1039/d4tb02002b
  14. bioRxiv. 2024 Dec 23. pii: 2024.12.22.629992. [Epub ahead of print]
      Tyrosine phosphorylation is an important post-translational modification that regulates many biochemical signaling networks in multicellular organisms. To date, 46,000 tyrosines have been observed in human proteins, but relatively little is known about the function and regulation of most of these sites. A major challenge has been producing recombinant phospho-proteins in order to test the effects of phosphorylation. Mutagenesis to acidic amino acids often fails to replicate the size and charge of a phosphorylated tyrosine residue and synthetic amino acid incorporation has high cost with relatively low yield. Here, we demonstrate an approach, inspired by how native tyrosine kinases find targets in cells - through a secondary targeting interaction, augmenting innate catalytic specificity of a tyrosine kinase, without overriding it. We engineered complementary vector systems for multiple approaches to producing high yields of phosphoprotein products in E. coli. Here, we test phosphorylation as a function of the targeting interaction (an SH3-polyproline sequence) affinity, different reaction methods across kinases of different specificity. This system presents an inexpensive and tractable system to producing phosphoproteins and phosphopeptides and we demonstrate how it can be used for testing antibody specificity on targets of EGFR and PD-1. This methodology is a generalizable approach for enhancing the enzymatic action on a recombinant protein via the flexibility of in vitro reactions and co-expression approaches. We refer to this as SISA-KiT, for Signaling Inspired Synthetically Augmented Kinase Toolkit.
    DOI:  https://doi.org/10.1101/2024.12.22.629992
  15. Langmuir. 2025 Jan 05.
      Biofouling on polymeric membranes poses a significant challenge in protein production and separation processes. We report here on the use of zwitterionic peptides composed of alternating lysine (K) and glutamic acid (E) residues to reduce biomolecular fouling on gold substrates and polymeric membranes within a protein production-mimicking environment. Our findings demonstrate that both gold chips and polymeric membranes functionalized with longer sequence zwitterionic peptides, along with a hydrophilic linker, exhibit superior antifouling performance across various protein-rich environments. Furthermore, increasing the grafting density of these peptides on substrates enhances their antifouling properties. We believe that this work sheds light on the antifouling capabilities of zwitterionic peptides in cell culture environments, advancing our understanding and paving the way for the development of zwitterionic peptide-based antifouling materials for polymeric membranes.
    DOI:  https://doi.org/10.1021/acs.langmuir.4c04384
  16. ACS Nano. 2025 Jan 06.
      Transmembrane signaling receptors, such as integrins, organize as nanoclusters that provide several advantages, including increasing avidity, sensitivity (increasing the signal-to-noise ratio), and robustness (signaling threshold) of the signal in contrast to signaling by single receptors. Furthermore, compared to large micron-sized clusters, nanoclusters offer the advantage of rapid turnover for the disassembly of the signal. However, whether nanoclusters function as signaling hubs remains poorly understood. Here, we employ fluorescence nanoscopy combined with photoactivation and photobleaching at subdiffraction limited resolution of ∼100 nm length scale within a focal adhesion to examine the dynamics of diverse focal adhesion proteins. We show that (i) subregions of focal adhesions are enriched in an immobile population of integrin β3 organized as nanoclusters, which (ii) in turn serve to organize nanoclusters of associated key adhesome proteins-vinculin, focal adhesion kinase (FAK) and paxillin, demonstrating that signaling proceeds by formation of nanoclusters rather than through individual proteins. (iii) Distinct focal adhesion protein nanoclusters exhibit distinct protein dynamics, which is closely correlated to their function in signaling. (iv) Long-lived nanoclusters function as signaling hubs─wherein immobile integrin nanoclusters organize phosphorylated FAK to form stable nanoclusters in close proximity to them, which are disassembled in response to inactivation signal by removal of force and in turn activation of phosphatase PTPN12. (v) Signaling takes place in response to external signals such as force or geometric arrangement of the nanoclusters and when the signal is removed, these nanoclusters disassemble. We term these functional nanoclusters as integrin signaling transit and relay nodes (STARnodes). Taken together, these results demonstrate that integrin STARnodes seed signaling downstream of the integrin receptors by organizing hubs of signaling proteins (FAK, paxillin, vinculin) to relay the incoming signal intracellularly and bring about robust function.
    Keywords:  FAK; focal adhesion; integrin; nanoclusters; protein dynamics; signaling
    DOI:  https://doi.org/10.1021/acsnano.4c03214