Embedding Living Cells with a Mechanically Reinforced and Functionally Programmable Hydrogel Fiber Platform

Integrase enables synthetic intercellular logic via bacterial conjugation

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.

Engineered Living Memory Microspheroid-Based Archival File System for Random Accessible In Vivo DNA Storage

Given its exceptional durability and high information density, deoxyribonucleic acid (DNA) has the potential to meet the escalating global demand for data storage if it can be stored efficiently and accessed randomly in exabyte-to-yottabyte-scale databases. Here, this work introduces the Engineered Living Memory Microspheroid (ELMM) as a novel material for DNA data storage, retrieval, and management. This work engineers a plasmid library and devises a random access strategy pairing plasmid function with DNA data in a key-value format. Each DNA segment is integrated with its corresponding plasmid, introduced into bacteria, and encapsulated within matrix material via droplet microfluidics within 5 min. ELMMs can be stored at room temperature following lyophilization and, upon rehydration, each type of ELMM exhibits specific functions expressed by the plasmids, allowing for physical differentiation based on these characteristics. This work demonstrates fluorescent expression as the plasmid function and employs fluorescence-based sorting access image files in a prototype database. By utilizing N optical channels, to retrieve 2N file types, each with a minimum of 10 copies. ELMM offers a digital-to-biological information solution, ensuring the preservation, access, replication, and management of files within large-scale DNA databases.

Cellular mechanical memory: a potential tool for mesenchymal stem cell-based therapy

Recent studies have shown that mechanical properties such as extracellular matrix stiffness, fluid flow, weight loading, compression, and stretching can affect cellular functions. Some examples of cell responses to mechanical properties could be the migration of cancer cells from rigid to soft surfaces or the differentiation of fibroblasts into myofibroblasts. Cellular responses to mechanical changes can modify the insertion of proteins in the extracellular matrix (ECM), causing an increase in tissue stiffness with functional consequences. In general, mechanical and physical factors can affect any kind of cell phenotype in culture conditions and in vivo tissues. Cells sense mechanical stimuli by applying force and restructuring their shape and functions in response to the resistance of the stimuli. Furthermore, mechanical triggers can develop a "memory" for altering cellular plasticity and adaptation. This phenomenon is called cellular mechanical memory (CMM), a singular feature of mesenchymal stem cells (MSCs). Controlled targeting of CMM may resolve the scarcity of viable cells needed for cell based therapy (CBT) and implement studies concerning cancer research, fibrosis, and senescence. This review focusses on cells from the mesodermal lineage, such as MSCs, fibroblasts and chondrocytes, and the role of CMM as a potential target for CBT.

Living plastics from plasticizer-assisted thermal molding of silk protein

The pursuit of materials, particularly plastics, with a minimal ecological footprint throughout their circular lifecycle, is crucial for advancing sustainable materials development. Living materials composed of embedded yet active organisms can leverage endogenous biotic resources to achieve functional materials that align with sustainability goals. However, current living material systems face challenges such as weak mechanical properties, limited environmental adaptability, and restricted cellular functionality. In this study, we propose an approach to sustainable living materials by incorporating active organisms into silk-based plastics through a plasticizer-assisted thermal molding process. We investigate the mechanism of structure formation in these materials, correlating manufacturing performance to the resulting secondary structure. These silk-based plastics provide a protective matrix for probiotics, ensuring their survival through the harsh gastrointestinal tract and enhancing intestinal delivery. Similarly, soil rhizobacteria encapsulated within the plastics exhibit long-term protease activity, accelerating plastic degradation upon soil exposure. This work demonstrates the potential of sustainable plastics as a form of living materials, where active organisms are processed, entrapped, retain metabolic functions, and are protected in harsh environments.

Blue-Purple evaluation: Chromoproteins facilitate the identification of BioBrick compatibility

Synthetic BioBricks introduce novel capabilities to manipulate genetic information, direct transcription-translation processes, and program cellular behaviors in living organisms. To maintain the stability and functionality of synthetic BioBricks, assembled DNA fragments should be mutually compatible without inducing negative effects such as metabolic burden or cellular toxicity in host cells. However, a simple, rapid, and reliable method to evaluate BioBrick compatibility remains to be developed. In this study, we report BP (Blue/Purple, Ban/Pick) evaluation, a method utilizing chromoproteins to facilitate the identification of BioBrick compatibility in one-pot reactions. By visualizing and quantifying the ratio of blue to purple Escherichia coli (E. coli) colonies on LB-agar plates, we can easily validate the compatibility of desired BioBrick constructions. To demonstrate our design, we characterized BioBrick assemblies with antitoxin-toxin pair ccdA-ccdB, lysis protein E, or heterologous protein sfGFP. Among these, we successfully identified several compatible assemblies. We anticipate that BP evaluation will enhance biotechnological assessments of BioBrick compatibility in vivo and expand the application of chromoproteins in synthetic biology.

Engineering Hygroscopic MOF-Based Silk Via Bioinspired Interfacial Assembly for Fast Moisture Manipulation

Metal-organic frameworks (MOFs) have emerged as exceptional moisture sorbents in low humidity conditions. However, their typical powdered form often results in agglomeration, impeding water diffusion kinetics and practical handling. To enhance the accessibility and diversify the integration of MOFs, a universal and scalable bionic interfacial assembly method is introduced for fabricating MOF-based silk. The resulting silk, enriched with a high content of MOF-303, demonstrates a significant water adsorption capacity of 315.1 mg g-1 at 25% relative humidity, exhibiting a three fold faster water absorption compared with that of stacked MOFs powder on a gram-scale. Furthermore, it achieves efficient water release, with a rate of 8.1 mg g-1 min-1 under sunlight after surface photothermal modification. Through one-step drawing assembly, electrothermal wires can be incorporated into MOF-based silk and demonstrate fast and reversible moisture adsorption/desorption for indoor humidity control. It is envisioned that this assembling method and integrated functional silk will yield valuable insights into the rational engineering of MOFs toward practical applications in moisture management, molecule absorption, etc.

Engineered Bacteria as Living Biosensors in Dermal Tattoos

Dermal tattoo biosensors are promising platforms for real-time monitoring of biomarkers, with skin used as a diagnostic interface. Traditional tattoo sensors have utilized small molecules as biosensing elements. However, the rise of synthetic biology has enabled the potential employment of engineered bacteria as living analytical tools. Exploiting engineered bacterial sensors will allow for potentially more sensitive detection across a broad biomarker range, with advanced processing and sense/response functionalities using genetic circuits. Here, the interfacing of bacterial biosensors as living analytics in tattoos is shown. Engineered bacteria are encapsulated into micron-scale hydrogel beads prepared through scalable microfluidics. These biosensors can sense both biochemical cues (model biomarkers) and biophysical cues (temperature changes, using RNA thermometers), with fluorescent readouts. By tattooing beads into skin models and confirming sensor activity post-tattooing, our study establishes a foundation for integrating bacteria as living biosensing entities in tattoos.

Rainbow screening: Chromoproteins enable visualized molecular cloning

Molecular cloning facilitates the assembly of heterologous DNA fragments with vectors, resulting in the generation of plasmids that can steadily replicate in host cells. To efficiently and accurately screen out the expected plasmid candidates, various methods, such as blue-white screening, have been developed for visualization. However, these methods typically require additional genetic manipulations and costs. To simplify the process of visualized molecular cloning, here we report Rainbow Screening, a method that combines Gibson Assembly with chromoproteins to distinguish Escherichia coli (E. coli) colonies by naked eyes, eliminating the need for additional genetic manipulations or costs. To illustrate the design, we select both E. coli 16s rRNA and sfGFP expression module as two inserted fragments. Using Rainbow Screening, false positive colonies can be easily distinguished on LB-agar plates. Moreover, both the assembly efficiency and the construct accuracy can exceed 80%. We anticipate that Rainbow Screening will enrich the molecular cloning methodology and expand the application of chromoproteins in biotechnology and synthetic biology.

Exploring the Application and Prospects of Synthetic Biology in Engineered Living Materials

At the intersection of synthetic biology and materials science, engineered living materials (ELMs) exhibit unprecedented potential. Possessing unique "living" attributes, ELMs represent a significant paradigm shift in material design, showcasing self-organization, self-repair, adaptability, and evolvability, surpassing conventional synthetic materials. This review focuses on reviewing the applications of ELMs derived from bacteria, fungi, and plants in environmental remediation, eco-friendly architecture, and sustainable energy. The review provides a comprehensive overview of the latest research progress and emerging design strategies for ELMs in various application fields from the perspectives of synthetic biology and materials science. In addition, the review provides valuable references for the design of novel ELMs, extending the potential applications of future ELMs. The investigation into the synergistic application possibilities amongst different species of ELMs offers beneficial reference information for researchers and practitioners in this field. Finally, future trends and development challenges of synthetic biology for ELMs in the coming years are discussed in detail.