Bacterial Growth, Communication, and Guided Chemotaxis in 3D-Bioprinted Hydrogel Environments

A Cautionary Perspective on Hydrogel-Induced Concentration Gradient Generation for Studying Chemotaxis

The achievement of consistent and static chemical gradients is critically important in the study of diffusion and chemotaxis at the micro- and nanoscales. In this context, a number of groups have reported on hydrogel-based systems for generating concentration gradients. Here, we analyze the behavior of agarose and gelatin-based hydrogels in hybridization chambers of different heights. Our focus is on the issues that are caused by the presence of robust bulk fluid flows in such systems due to the solutes present in the hydrogel and/or the surrounding fluid. We describe the key insights derived from these experiments, offering practical guidelines for establishing gradients using hydrogel-based systems and make the community aware of different variables that can make the experiments nonreproducible and prone to misinterpretations.

Limiting the Broadcast Range of a Secreting Cell during Intercellular Signaling Using Protease-Mediated Degradation

Synthetic biology is revolutionizing our approaches to biocomputing, diagnostics, and environmental monitoring through the use of designed genetic circuits that perform a function within a single cell. More complex functions can be performed by multiple cells that coordinate as they perform different subtasks. Cell-cell communication using molecular signals is particularly suited for aiding in this communication, but the number of molecules that can be used in different communication channels is limited. Here we investigate how proteases can limit the broadcast range of communicating cells. We find that adding barrierpepsin to Saccharomyces cerevisiae cells in two-dimensional multicellular networks that use α-factor signaling prevents cells beyond a specific radius from responding to α-factor signals. Such limiting of the broadcast range of cells could allow multiple cells to use the same signaling molecules to direct different communication processes and functions, provided that they are far enough from one another. These results suggest a means by which complex synthetic cellular networks using only a few signals for communication could be created by structuring a community of cells to create distinct broadcast environments.

Decoding the "Fingerprint" of Implant Materials: Insights into the Foreign Body Reaction

Foreign body reaction (FBR) is a prevalent yet often overlooked pathological phenomenon, particularly within the field of biomedical implantation. The presence of FBR poses a heavy burden on both the medical and socioeconomic systems. This review seeks to elucidate the protein "fingerprint" of implant materials, which is generated by the physiochemical properties of the implant materials themselves. In this review, the activity of macrophages, the formation of foreign body giant cells (FBGCs), and the development of fibrosis capsules in the context of FBR are introduced. Additionally, the relationship between various implant materials and FBR is elucidated in detail, as is an overview of the existing approaches and technologies employed to alleviate FBR. Finally, the significance of implant components (metallic materials and non-metallic materials), surface CHEMISTRY (charge and wettability), and physical characteristics (topography, roughness, and stiffness) in establishing the protein "fingerprint" of implant materials is also well documented. In conclusion, this review aims to emphasize the importance of FBR on implant materials and provides the current perspectives and approaches in developing implant materials with anti-FBR properties.

Cell-Free Protein Expression in Polymer Materials

While synthetic biology has advanced complex capabilities such as sensing and molecular synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics make the incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over the cellular viability or release of genetically modified organisms. Here, we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobials in situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable biofunctionality in a ubiquitous class of synthetic materials.

Bacterial Patterning: A Promising Biofabrication Technique

Bacterial patterning has emerged as a pivotal biofabrication technique in the biomedical field. In the past 2 decades, a diverse array of bacterial patterning approaches have been developed to enable the precise manipulation of the spatial distribution of bacterial patterns for various applications. Despite the significance of these advancements, there is a deficiency of review articles providing an overview of bacterial patterning technologies. In this mini-review, we systematically summarize the progress of bacterial patterning over the past 2 decades. This review commences with an elucidation of the definition and fundamental principles of bacterial patterning. Subsequently, we introduce the established bacterial patterning strategies, accompanied by discussions about the advantages and limitations of each approach. Furthermore, we showcase the biomedical applications of these strategies, highlighting their efficacy in spatial control of biofilms, biosensing, and biointervention. Finally, this mini-review is concluded with a summary and an outlook on future challenges and opportunities. It is anticipated that this mini-review can serve as a concise guide for those who are interested in this exciting and rapidly evolving research area.

Superfast Gelation of Spider Silk-Based Artificial Silk Protein

Spider silk proteins (spidroins) have garnered attention in biomaterials research due to their ability to self-assemble into hydrogels. However, reported spidroin hydrogels require high protein concentration and prolonged gelation time. Our study engineered an artificial spidroin that exhibits unprecedented rapid self-assembly into hydrogels at physiologically relevant conditions, achieving gelation at a low concentration of 6 mg/mL at 37 °C without external additives. Remarkably, at a 30 mg/mL concentration, our engineered protein forms hydrogels within 30 s, a feature we termed "superfast gelation". This rapid formation is modulated by ions, pH, and temperature, offering versatility in biomedical applications. The hydrogel's capacity to encapsulate proteins and support E. coli growth while inducing RFP expression provides a novel platform for drug delivery and bioengineering applications. Our findings introduce a superfast, highly adaptable, and cytocompatible hydrogel that self-assembles under mild conditions, underscoring the practical implication of rapid gelation in biomedical research and clinical applications.

Genetic mixing and demixing on expanding spherical frontiers

Genetic fluctuation during range expansion is a key process driving evolution. When a bacterial population is expanding on a 2D surface, random fluctuations in the growth of the pioneers at the front line cause a strong demixing of genotypes. Even when there is no selective advantage, sectors of low genetic diversity are formed. Experimental studies of range expansions in surface-attached colonies of fluorescently labelled micro-organisms have contributed significantly to our understanding of fundamental evolutionary dynamics. However, experimental studies on genetic fluctuations in 3D range expansions have been sparse, despite their importance for tumour or biofilm development. We encapsulated populations of two fluorescent Escherichia coli strains in inoculation droplets (volumes [Formula: see text] nl). The confined ensemble of cells grew when embedded in a hydrogel-with nutrients-and developed 3D colonies with well-defined, sector-like regions. Using confocal laser scanning microscopy, we imaged the development of 3D colonies and the emergence of sectors. We characterized how cell concentration in the inoculation droplet controls sectors, growth rate, and the transition from branched colonies to quasi-spherical colonies. We further analysed how sectors on the surface change over time. We complement these experimental results with a modified 3D Eden growth model. The model in 3D spherical growth predicts a phase, where sectors are merging, followed by a steady increase (constant rate), and the experimentally analysed sectors were consistent with this prediction. Therefore, our results demonstrate qualitative differences between radial (2D) and spherical (3D) range expansions and their importance in gene fixation processes.

Gene expression dynamics in input-responsive engineered living materials programmed for bioproduction

Engineered living materials (ELMs) fabricated by encapsulating microbes in hydrogels have great potential as bioreactors for sustained bioproduction. While long-term metabolic activity has been demonstrated in these systems, the capacity and dynamics of gene expression over time is not well understood. Thus, we investigate the long-term gene expression dynamics in microbial ELMs constructed using different microbes and hydrogel matrices. Through direct gene expression measurements of engineered E. coli in F127-bisurethane methacrylate (F127-BUM) hydrogels, we show that inducible, input-responsive genetic programs in ELMs can be activated multiple times and maintained for multiple weeks. Interestingly, the encapsulated bacteria sustain inducible gene expression almost 10 times longer than free-floating, planktonic cells. These ELMs exhibit dynamic responsiveness to repeated induction cycles, with up to 97% of the initial gene expression capacity retained following a subsequent induction event. We demonstrate multi-week bioproduction cycling by implementing inducible CRISPR transcriptional activation (CRISPRa) programs that regulate the expression of enzymes in a pteridine biosynthesis pathway. ELMs fabricated from engineered S. cerevisiae in bovine serum albumin (BSA) - polyethylene glycol diacrylate (PEGDA) hydrogels were programmed to express two different proteins, each under the control of a different chemical inducer. We observed scheduled bioproduction switching between betaxanthin pigment molecules and proteinase A in S. cerevisiae ELMs over the course of 27 days under continuous cultivation. Overall, these results suggest that the capacity for long-term genetic expression may be a general property of microbial ELMs. This work establishes approaches for implementing dynamic, input-responsive genetic programs to tailor ELM functions for a wide range of advanced applications.

Rapid Screening and Synthesis of Abiotic Synthetic Receptors for Selective Bacterial Recognition

The major challenges that impede the preparation of abiotic synthetic receptors designed to feature selective bacterial recognition properties are the complexity, nonrobustness, and environmental adaptability of live microbes. Here, we describe a new rapid screening strategy to determine the optimal polymer formulation on 96-well plates and then produce abiotic synthetic receptors by imprinting the surface marker lipopolysaccharide (LPS) of Gram-negative bacteria. The resulting LPS-imprinted nanoparticles reveal remarkable affinity toward LPS with an equilibrium dissociation constant (K_D) value of 10^-12 M and can distinguish and selectively recognize specific bacteria in whole blood at concentrations down to 10 cells/mL. The incorporation of gold nanorods into imprinted nanoparticles allows selective microbial inactivation based on photothermal treatment. We have also demonstrated that the imprinted nanoparticles with high affinity for bacteria could induce bacteria clustering, drive the expression of quorum-sensing-controlled signal molecules, and eventually enhance the productivity of the cell factory.

The Next Frontier of 3D Bioprinting: Bioactive Materials Functionalized by Bacteria

3D bioprinting has become a flexible technical means used in many fields. Currently, research on 3D bioprinting is mainly focused on the use of mammalian cells to print organ and tissue models, which has greatly promoted progress in the fields of tissue engineering, regenerative medicine, and pharmaceuticals. In recent years, bacterial bioprinting has gradually become a rapidly developing research fields, with a wide range of potential applications in basic research, biomedicine, bioremediation, and other field. Here, this works reviews new research on bacterial bioprinting, and discuss its future research direction.

Multiscale Biofabrication: Integrating Additive Manufacturing with DNA-Programmable Self-Assembly

Structure and hierarchical organization are crucial elements of biological systems and are likely required when engineering synthetic biomaterials with life-like behavior. In this context, additive manufacturing techniques like bioprinting have become increasingly popular. However, 3D bioprinting, as well as other additive manufacturing techniques, show limited resolution, making it difficult to yield structures on the sub-cellular level. To be able to form macroscopic synthetic biological objects with structuring on this level, manufacturing techniques have to be used in conjunction with biomolecular nanotechnology. Here, a short overview of both topics and a survey of recent advances to combine additive manufacturing with microfabrication techniques and bottom-up self-assembly involving DNA, are given.

Oxygen-Generating Scaffolds: One Step Closer to the Clinical Translation of Tissue Engineered Products

The lack of oxygen supply in engineered constructs has been an ongoing challenge for tissue engineering and regenerative medicine. Upon implantation of an engineered tissue, spontaneous blood vessel formation does not happen rapidly, therefore, there is typically a limited availability of oxygen in engineered biomaterials. Providing oxygen in large tissue-engineered constructs is a major challenge that hinders the development of clinically relevant engineered tissues. Similarly, maintaining adequate oxygen levels in cell-laden tissue engineered products during transportation and storage is another hurdle. There is an unmet demand for functional scaffolds that could actively produce and deliver oxygen, attainable by incorporating oxygen-generating materials. Recent approaches include encapsulation of oxygen-generating agents such as solid peroxides, liquid peroxides, and fluorinated substances in the scaffolds. Recent approaches to mitigate the adverse effects, as well as achieving a sustained and controlled release of oxygen, are discussed. Importance of oxygen-generating materials in various tissue engineering approaches such as ex vivo tissue engineering, in situ tissue engineering, and bioprinting are highlighted in detail. In addition, the existing challenges, possible solutions, and future strategies that aim to design clinically relevant multifunctional oxygen-generating biomaterials are provided in this review paper.

Three-dimensional bioprinting: A cutting-edge tool for designing and fabricating engineered living materials

The design of engineered living materials (ELMs) is an emerging field developed from synthetic biology and materials science principles. ELMs are multi-scale bulk materials that combine the properties of self-healing and organism adaptability with the designed physicochemical or mechanical properties for functional applications in various fields, including therapy, electronics, and architecture. Among the many ELM design and manufacturing methods, three-dimensional (3D) bioprinting stands out for its precise control over the structure of the fabricated constructs and the spatial distribution of cells. In this review, we summarize the progress in the field, cell type and material selection, and the latest applications of 3D bioprinting to manufacture ELMs, as well as their advantages and limitations, hoping to deepen our understanding and provide new insights into ELM design. We believe that 3D bioprinting will become an important development direction and provide more contributions to this field.