The Bacillus subtilis Minimal Genome Compendium

To better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology

Design and evaluation of a new intersection model to minimize congestions using VISSIM software

Traffic modelling and simulation is one of the frequent tools used in road infrastructure design. Software tools designed for traffic simulations are an important supportive tool in decision-making and in choosing the optimal solution. The aim of this paper is to introduce the application of the VISSIM program, in the design and testing a model of the traffic-light-controlled intersection. The traffic on the selected congested intersection is modelled and simulated first for the current state, then for two models with modifications that are to increase the throughput of the intersection. The monitored criterion of the intersection throughput is the length of queues. Both adjustments have led to a significant reduction of the number of vehicles waiting in direction of the greatest congestions. In the first model, the average line length was reduced by 75%, and in the second model, the modifications lead to a fluent passage of right-turn vehicles and a significant reduction in vehicle lines for other directions

On Silylated Oxonium and Sulfonium Ions and Their Interaction with Weakly Coordinating Borate Anions

Attempts have been made to prepare salts with the labile tris(trimethylsilyl)chalconium ions, [(Me3Si)3E]+ (E=O, S), by reacting [Me3Si-H-SiMe3][B(C6F5)4] and Me3Si[CB] (CB−=carborate=[CHB11H5Cl6]−, [CHB11Cl11]−) with Me3Si-E-SiMe3. In the reaction of Me3Si-O-SiMe3 with [Me3Si-H-SiMe3][B(C6F5)4], a ligand exchange was observed in the [Me3Si-H-SiMe3]+ cation leading to the surprising formation of the persilylated [(Me3Si)2(Me2(H)Si)O]+ oxonium ion in a formal [Me2(H)Si]+ instead of the desired [Me3Si]+ transfer reaction. In contrast, the expected homoleptic persilylated [(Me3Si)3S]+ ion was formed and isolated as [B(C6F5)4]− and [CB]− salt, when Me3Si-S-SiMe3 was treated with either [Me3Si-H-SiMe3][B(C6F5)4] or Me3Si[CB]. However, the addition of Me3Si[CB] to Me3Si-O-SiMe3 unexpectedly led to the release of Me4Si with simultaneous formation of a cyclic dioxonium dication of the type [Me3Si-μO-SiMe2]2[CB]2 in an anion-mediated reaction. DFT studies on structure, bonding and thermodynamics of the [(Me3Si)3E]+ and [(Me3Si)2(Me2(H)Si)E]+ ion formation are presented as well as mechanistic investigations on the template-driven transformation of the [(Me3Si)3E]+ ion into a cyclic dichalconium dication [Me3Si-μE-SiMe2]22+. © 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA

Quantitative IR Readout of Fulgimide Monolayer Switching on Si(111) Surfaces

International audienc

Adenosine Triphosphate Neutralizes Pneumolysin-induced Neutrophil Activation.

Background: In tissue infections, adenosine triphosphate (ATP) is released into extracellular space and contributes to purinergic chemotaxis. Neutrophils are important players in bacterial clearance and recruited to the site of tissue infections. Pneumococcal infections can lead to uncontrolled hyper-inflammation of the tissue along with substantial tissue damage through excessive neutrophil activation and uncontrolled granule release. We aimed to investigate the role of ATP in neutrophil response to pneumococcal infections. Methods: Primary human neutrophils were exposed to the pneumococcal strain TIGR4 and its pneumolysin deficient mutant or directly to different concentrations of recombinant pneumolysin. Neutrophil activation was assessed by measurement of secreted azurophilic granule protein resistin and profiling of the secretome, using mass spectrometry. Results: Pneumococci are potent inducers of neutrophil degranulation. Pneumolysin was identified as a major trigger of neutrophil activation. This process is partially lysis independent and inhibited by ATP. Pneumolysin and ATP interact with each other in the extracellular space leading to reduced neutrophil activation. Proteome analyses of the neutrophil secretome confirmed that ATP inhibits pneumolysin-dependent neutrophil activation. Conclusions: Our findings suggest that despite its cytolytic activity, pneumolysin serves as a potent neutrophil activating factor. Extracellular ATP mitigates pneumolysin induced neutrophil activation

Formation of Carboxy- and Amide-Terminated Alkyl Monolayers on Silicon(111) Investigated by ATR-FTIR, XPS, and X‑ray Scattering: Construction of Photoswitchable Surfaces

We have prepared high-quality, densely packed, self-assembled monolayers (SAMs) of carboxy-terminated alkyl chains on Si(111). The samples were made by thermal grafting of methyl undec-10-enoate under an inert atmosphere and subsequent cleavage of the ester functionality to disclose the carboxylic acid end-group. X-ray photoelectron spectroscopy (XPS) and grazing incidence X-ray diffraction (GIXD) indicate a surface coverage of about 50% of the initially H-terminated sites. In agreement, GIXD implies a rectangular unit mesh of 6.65 and 7.68 Å side lengths, containing two molecules in a regular zigzag-like substitution pattern for the ester- and carboxy-terminated monolayer. Hydrolysis of the remaining H–Si(111) bonds at the surface furnished HO–Si(111) groups according to XPS and attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR) studies. The amide-terminated alkyl SAM on Si(111) assembled in a 2-(6-chloro-1<i>H</i>-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate (HCTU)-mediated one-pot coupling reaction under an inert atmosphere, whereby the active ester forms in situ prior to the reaction with an amino-functionalized photoswitchable fulgimide. ATR-FTIR and XPS studies of the fulgimide samples revealed closely covered amide-terminated SAMs. Reversible photoswitching of the headgroup was read out by applying XPS, ATR-FTIR, and difference absorption spectra in the mid-IR. In XPS, we observed a reversible breathing of the amide/imide C1s and N1s signals of the fulgimide. The results demonstrate the general suitability of HCTU as a reagent for amide couplings to carboxy-terminated alkyl SAMs and the on-chip functionalization toward photoswitchable Si(111) surfaces