basicsynbio and the BASIC SEVA collection: software and vectors for an established DNA assembly method

Synthetically Engineered Bacterial Extracellular Vesicles and IL-4-Encapsulated Hydrogels Sequentially Promote Osteoporotic Fracture Repair

Osteoporosis (OP) is a systemic disease characterized by decreased bone density and quality, leading to fragile bones and osteoporotic fractures (OPF). Conventional treatments for OPF often exhibit limited therapeutic efficacy and significant side effects. Synthetic biology-based bacterial extracellular vesicles (BEVs) offer a safe and effective alternative for OPF treatment. Here, we constructed bioengineered BEVs loaded with pBMP-2-VEGF (BEVs-BP) and encapsulated them together with IL-4 in GelMA hydrogels to form IL-4/BEVs-BP@GelMA. Initially, IL-4 alleviated chronic inflammation by modulating immune cells, while BEVs-BP subsequently enhanced osteogenesis and vascularization by upregulating BMP-2 and VEGF expression. In vitro, IL-4/BEVs-BP@GelMA polarized M1 macrophages toward the M2 phenotype, enhanced osteogenesis, and increased angiogenesis. Moreover, BEVs-BP effectively promoted the maturation and mineralization of bone organoids in vivo. Finally, IL-4/BEVs-BP@GelMA successfully accelerated osteoporotic fracture repair in mice. In summary, we developed an easy-to-build and powerful bone repair biomaterial, IL-4/BEVs-BP@GelMA, which offers a therapeutic strategy for osteoporotic fracture management.

Fine-Tuning Genetic Circuits via Host Context and RBS Modulation

The choice of organism to host a genetic circuit, the chassis, is often defaulted to model organisms due to their amenability. The chassis-design space has therefore remained underexplored as an engineering variable. In this work, we explored the design space of a genetic toggle switch through variations in nine ribosome binding site compositions and three host contexts, creating 27 circuit variants. Characterization of performance metrics in terms of toggle switch output and host growth dynamics unveils a spectrum of performance profiles from our circuit library. We find that changes in host context cause large shifts in overall performance, while modulating ribosome binding sites leads to more incremental changes. We find that a combined ribosome binding site and host context modulation approach can be used to fine-tune the properties of a toggle switch according to user-defined specifications, such as toward greater signaling strength, inducer sensitivity, or both. Other auxiliary properties, such as inducer tolerance, are also exclusively accessed through changes in the host context. We demonstrate here that exploration of the chassis-design space can offer significant value, reconceptualizing the chassis organism as an important part in the synthetic biologist's toolbox with important implications for the field of synthetic biology.

Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology

Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to "model status," synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the "chassis effect." It remains a major challenge to uncover which genome-encoded and biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of genetic circuit performance. This was accomplished using a comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis effect and characterize the performance dynamics of a genetic inverter circuit operating within 6 Gammaproteobacteria. Our results solidify the notion that genetic devices are strongly impacted by the host context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar performance of the genetic inverter, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.