Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.

Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for Mycobacterium tuberculosis and Salmonella Typhi, we compare the genotyping results obtained with the k-mer-based tools BioHansel and SKA, with those of the organism-specific tools TBProfiler and genotyphi, which use gold-standard reference-mapping approaches. We show that the genotyping results are fully concordant across these different methods, and that the k-mer-based tools are significantly faster. We also test the ability of the BioHansel quality assurance module to detect intra-lineage contamination and demonstrate that it is effective, even in populations with low genetic diversity. We demonstrate the scalability of the tool using a dataset of ~8100 S. Typhi public genomes and provide the aggregated results of geographical distributions as part of the tool's output. BioHansel is an open source Python 3 application available on PyPI and Conda repositories and as a Galaxy tool from the public Galaxy Toolshed. In a public health context, BioHansel enables rapid and high-resolution classification of bacterial pathogens with low genetic diversity.

Synthesis of reactive 1,3-diphenyl-6-aryl-substituted fulvene chromophores.

This data article describes a detailed synthetic strategy and experimental data for the synthesis of brominated fulvene chromophores as reactive precursors/monomers for conjugated organic materials. Metal-mediated coupling reactions of brominated fulvenes would result in conjugated small molecules or polymers that would find application as organic light emitting diodes (OLEDs) and photovoltaic (PV) applications.

A durable template for carbosilane dendrimer synthesis.

Many types of organosilicon dendrimers are known, but the carbosilane dendrimers are by far the most widely studied. This Viewpoint article describes the impact of a communication published in 1992 by Alexander van der Made, one of the pioneers in the field.

Multifunctional thiols from the highly selective reaction of mercaptoalcohols with chlorosilanes.

Multifunctional thiols were synthesized by the selective reaction of chlorosilanes with mercaptoalcohols. Reaction of the mercaptoalcohols through the thiol group was not observed. Utilizing this method, thiols of varying structural diversity were prepared.

Irradiation- and thermoinduced synthesis of Ag nanoparticles within amphiphilic carbosilane-thioether dendrimers.

We report on the preparation of new amphiphilic carbosilane-thioether dendrimers by thiol-ene chemistry and their application in the in situ formation of silver nanoparticles (AgNPs) with unusual versatility in approach. In the presence of the dendrimers, AgNPs can be prepared in either water or organic solvents, and by simply using UV irradiation or heat in the reduction step without the need for a chemical reducing agent. Monodisperse size-tunable AgNPs possessing a simple cubic crystal structure were characterized by TEM, SAED, XRD, and other techniques. Susceptibility examination of E. coli indicated strong antibacterial activity of the AgNPs in aqueous solution.

Silyl-substituted thioether ligands and their Ag(I) complexes.

Silyl-substituted thioether ligands were prepared that differed in the identity and number of ligating groups attached to silicon and the nature of the alkyl groups on silicon. The ligand syntheses involved deprotonation of a thioether with n-butyllithium followed by reaction with the appropriate chlorosilane. Yields were 45-75% after purification. The majority of the ligands reacted with silver(I) triflate to give stable crystalline products in high yields that could be characterized by single-crystal X-ray crystallography. Depending on the ligand, the structures of the products ranged from discrete complexes to infinite polymeric structures. Apparent argentophilic interactions were commonly observed in the solid-state structures of the complexes (Ag-Ag = 2.909-3.196 A).

Spacer flexibility in bis(pyridyl) ligands: chelating organosilicon pyridylethynyl ligands.

Two new bis(pyridylethynyl) ligands with organosilicon spacers have been synthesized. The ligands react readily with silver(I) to form crystalline complexes, both of which are revealed to be triflate-bridged dimers by X-ray crystallographic analysis. The complex with the flexible siloxane-based ligand possesses considerably less bond angle distortion.

Transmetalation as a route to novel styryllithium reagents.

[structure: see text] Transmetalation of beta-tributyl(styryl)stannanes with n-BuLi gives the functional equivalents of the corresponding styryllithium intermediates. Reaction of the intermediates with chlorotrimethylsilane, iodomethane, or dimethyl sulfate gives the substituted styryl products in moderate to good yields. In all cases, the configuration about the double bond was retained in the products.