RESUMEN
One important direction of synthetic biology is to establish desired spatial structures from microbial populations. Underlying this structural development process are different driving factors, among which bacterial motility and chemotaxis serve as a major force. Here, we present an individual-based, biophysical computational framework for mechanistic and multiscale simulation of the spatiotemporal dynamics of motile and chemotactic microbial populations. The framework integrates cellular movement with spatial population growth, mechanical and chemical cellular interactions, and intracellular molecular kinetics. It is validated by a statistical comparison of single-cell chemotaxis simulations with reported experiments. The framework successfully captures colony range expansion of growing isogenic populations and also reveals chemotaxis-modulated, spatial patterns of a two-species amensal community. Partial differential equation-based models subsequently validate these simulation findings. This study provides a versatile computational tool to uncover the fundamentals of microbial spatial ecology as well as to facilitate the design of synthetic consortia for desired spatial patterns.
Asunto(s)
Quimiotaxis , Biología Sintética , Simulación por Computador , Bacterias , Movimiento Celular , Modelos BiológicosRESUMEN
Microbial communities are complex living systems that populate the planet with diverse functions and are increasingly harnessed for practical human needs. To deepen the fundamental understanding of their organization and functioning as well as to facilitate their engineering for applications, mathematical modeling has played an increasingly important role. Agent-based models represent a class of powerful quantitative frameworks for investigating microbial communities because of their individualistic nature in describing cells, mechanistic characterization of molecular and cellular processes, and intrinsic ability to produce emergent system properties. This review presents a comprehensive overview of recent advances in agent-based modeling of microbial communities. It surveys the state-of-the-art algorithms employed to simulate intracellular biomolecular events, single-cell behaviors, intercellular interactions, and interactions between cells and their environments that collectively serve as the driving forces of community behaviors. It also highlights three lines of applications of agent-based modeling, namely, the elucidation of microbial range expansion and colony ecology, the design of synthetic gene circuits and microbial populations for desired behaviors, and the characterization of biofilm formation and dispersal. The review concludes with a discussion of existing challenges, including the computational cost of the modeling, and potential mitigation strategies.
Asunto(s)
Microbiota , Humanos , Modelos Teóricos , Análisis de Sistemas , Algoritmos , Interacciones Microbianas , Consorcios MicrobianosRESUMEN
The reductive functionalization of the CîO unit of carbonates, carboxylic acids, esters, and CO2, respectively has received great attention since its introduction. This method is often used industrially for the synthesis of high value-added energy products in chemistry. This opens up a new way forward to reduce greenhouse gases and the consumption of traditional energy sources. Herein, we report an earth-abundant, cheap, and readily available aluminum dihydride, which can catalyze the reduction of a range of carbonates, esters, carboxylic acids, and CO2, respectively in the presence of pinacolborane as a reducing agent. Moreover, we demonstrate that the reaction can proceed to obtain good yield products under mild conditions, with low catalyst loading and solvent-free reactions. The mechanism of the catalytic reduction of carbonates has been investigated.
RESUMEN
Commercially available compound ZnEt2 acts as an efficient precatalyst for the solvent-free hydrophosphinations of heterocumulenes using Ph2PH as reagent. As far as we knew, this has been not reported in group 12 metal catalyzing reactions. A suggested mechanism of this reaction is explored, and the intermediate [{Ph2PC(NiPr)2}ZnEt]2 is obtained and characterized by a single-crystal X-ray structural analysis.
RESUMEN
Synthetic biology is advancing into a new phase where real-world applications are emphasized. There is hence an urgent need for mathematical modeling that can quantitatively describe the behaviors of genetic devices in natural, fluctuating environments. We utilize an integrative circuit-host modeling framework to examine the dynamics of a genetic switch and its host cell in varying environments. For both steady-state and transient cases, we find increasing nutrient reduces the bistability region of the phase space and eventually drives the switch from bistability to monostability. In response, cellular growth and proteome partitioning experience the same transition. Antibiotic perturbations cause the similar circuit and host responses as nutrient variations. However, one difference is the trend of growth rate, which augments with nutrient but declines with antibiotic levels. The framework provides a mechanistic scheme to account for both the dynamic and static characteristics of the circuit-host system upon environmental perturbations, underscoring the intimacy of gene circuits and their hosts and elucidating the complexity of circuit behaviors arising from environmental variations.
Asunto(s)
Biología Sintética/métodos , Redes Reguladoras de Genes/fisiología , Genes de Cambio/genética , Modelos GenéticosRESUMEN
We engineered Escherichia coli cells to bind to cyanobacteria by heterologously producing and displaying lectins of the target cyanobacteria on their surface. To prove the efficacy of our approach, we tested this design on Microcystis aeruginosa with microvirin (Mvn), the lectin endogenously produced by this cyanobacterium. The coding sequence of Mvn was C-terminally fused to the ice nucleation protein NC (INPNC) gene and expressed in E. coli. Results showed that E. coli cells expressing the INPNC::Mvn fusion protein were able to bind to M. aeruginosa and the average number of E. coli cells bound to each cyanobacterial cell was enhanced 8-fold. Finally, a computational model was developed to simulate the binding reaction and help reconstruct the binding parameters. To our best knowledge, this is the first report on the binding of two organisms in liquid culture mediated by the surface display of lectins and it may serve as a novel approach to mediate microbial adhesion.