No abstract

Lanthipeptides have extensive therapeutic and industrial applications. However, because many are bactericidal, traditional in vivo platforms are limited in their capacity to discover and mass produce novel lanthipeptides as bacterial organisms are often critical components in these systems. Herein, the development of a cell‐free protein synthesis (CFPS) platform that enables rapid genome mining, screening, and guided overproduction of lanthipeptides in vivo is described. For proof‐of‐concept studies, a type I lanthipeptide, nisin, is selected. Four novel lanthipeptides with antibacterial activity are identified among all nisin analogs in the National Center for Biotechnology Information (NCBI) database in a single day. Further, the CFPS platform is coupled with a screening assay for anti‐gram‐negative bacteria growth, resulting in the identification of a potent nisin mutant, M5. The titers of nisin and the nisin analog are found to be improved with CFPS platform guidance. Owing to the similarities in biosynthesis, the CFPS platform is broadly applicable to other lanthipeptides, thereby providing a universal method for lanthipeptide discovery and overproduction.

The phase-field method coupled with the Navier-Stokes equations is a rather new approach for scale-resolving numerical simulation of interfacial two-phase flows. The intention is to implement it as finite-volume method in the open source library for computational continuum mechanics OpenFOAM and make it freely available. An overview on the governing equations is given and the numerical method is shortly discussed. The focus is on application and validation of the code for some fundamental wetting phenomena, namely the capillary rise in a narrow channel and the spreading of a droplet on a flat surface, which is chemically homogeneous or regularly patterned. The numerical results on static meshes agree well with analytical solutions and experimental/numerical results from literature. Also, first 3D finite-volume simulations with adaptive mesh refinement near the interface are presented as a key element to achieve CPU-time efficient simulations.

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The effective mechanical and acoustic properties of two-dimensional pentamode metamaterials (PMs) with different structural parameters are investigated in this paper. It is found that with varying structural parameters, the effective bulk modulus and density remain constant as the same as those of water, while the figure of merit, i.e., the ratio of the bulk modulus to the shear modulus (B/G) gradually increases due to the decrease of the shear modulus. However, full wave simulations reveal that with the increase of B/G, the acoustic scattering becomes more and more intense, which indicates that the acoustic properties of pentamode metamaterials gradually deviate from those of water. These anomalous acoustic behaviors are proposed to arise from the existence of the bending modes in pentamode microstructures. Our results show that for pentamode metamaterials, the mechanical properties cannot be simply translated to their acoustic properties, and the structural parameters affect the mechanical and acoustic properties in much different ways.

Microfluidic devices often contain several phases. Their design can be supported by interface-resolving numerical simulations, requiring accurate methods and validated computer codes. Especially challenging are submillimetre air bubbles in water due to their large density contrast and dominance of surface tension. Here, we evaluate two numerical methods implemented in OpenFOAM ® , namely the standard solver interFoam with an algebraic volume-of-fluid method relying on a sharp interface representation and phaseFieldFoam relying on the phase-field method with diffuse interface representation. For a circular bubble in static equilibrium, we explore the impacts of uniform grid resolution and bubble size on bubble shape, mass conservation, pressure jump and spurious currents. While the standard interFoam solver exhibits excellent mass conservation with errors below 0.1% on fine grids, it lacks the accuracy to predict reasonable physics for a bubble in microfluidic systems. At higher resolution, large spurious currents significantly displace and deform the bubble, which is oscillating with resolution dependent mode and frequency. Furthermore, the pressure jump is consistently underestimated by more than 10%. The solver phaseFieldFoam suffers from much larger mass losses of up to 2%, which decrease as the ratio between interface thickness and bubble diameter decreases provided the diffuse interface region is adequately resolved. Spurious currents are very low and the bubble remains circular preserving its initial position with an error in pressure jump below 1%.

No abstract

Ubiquitin-specific protease (UBP) family is the largest group of deubiquitinases, which plays important roles in eukaryotic organisms. Comprehensive analysis of UBP genes has not been conducted in the plant pathogenic fungi. In this study, 11 putative UBP genes were identified and characterized in the rice blast fungus Magnaporthe oryzae. Expression profile analysis showed that UBP3, UBP6, UBP12 and UBP14 were highly expressed in different tissues of M. oryzae. In all ubp mutants, especially Δubp3, Δubp12 and previously reported Δubp14, the ubiquitination levels were evidently elevated, which is consistent with their molecular roles in de-ubiquitination. The Δubp1, Δubp3, Δubp4, Δubp8 and Δubp14 mutants were reduced in colony growth. Most of the ubp mutants were severely reduced in conidia production capacity, indicating important roles of the UBPs in conidia formation. Except for Δubp2 and Δubp16, all of the other mutants were decreased in virulence to host plants and defective in invasive growth. These ubp mutants also induced massive ROS accumulation in host cells. We also found that the UBPs may function as both positive and negative regulators in stress response and nutrient utilization of M. oryzae. Collectively, UBPs are important for development, stress response, nutrient utilization and infection of M. oryzae.