Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks.

Outbreaks of virulent and/or drug-resistant bacteria have a significant impact on human health and major economic consequences. Genomic islands (GIs; defined as clusters of genes of probable horizontal origin) are of high interest because they disproportionately encode virulence factors, some antimicrobial-resistance (AMR) genes, and other adaptations of medical or environmental interest. While microbial genome sequencing has become rapid and inexpensive, current computational methods for GI analysis are not amenable for rapid, accurate, user-friendly and scalable comparative analysis of sets of related genomes. To help fill this gap, we have developed IslandCompare, an open-source computational pipeline for GI prediction and comparison across several to hundreds of bacterial genomes. A dynamic and interactive visualization strategy displays a bacterial core-genome phylogeny, with bacterial genomes linearly displayed at the phylogenetic tree leaves. Genomes are overlaid with GI predictions and AMR determinants from the Comprehensive Antibiotic Resistance Database (CARD), and regions of similarity between the genomes are also displayed. GI predictions are performed using Sigi-HMM and IslandPath-DIMOB, the two most precise GI prediction tools based on nucleotide composition biases, as well as a novel blast-based consistency step to improve cross-genome prediction consistency. GIs across genomes sharing sequence similarity are grouped into clusters, further aiding comparative analysis and visualization of acquisition and loss of mobile GIs in specific sub-clades. IslandCompare is an open-source software that is containerized for local use, plus available via a user-friendly, web-based interface to allow direct use by bioinformaticians, biologists and clinicians (at https://islandcompare.ca).

Ab initio metadynamics study on hydronium ion dynamics at acid-functionalized interfaces: effect of surface group density.

This article presents an ab initio metadynamics study of elementary hydronium ion transitions at dense arrays of surface groups with sulfonic acid head groups. Calculations simulate minimally hydrated conditions of the interfacial ionic system. The specific focus is on the influence of the surface group density on hydronium ion transport. Results reveal a high sensitivity of the activation free energy of hydronium translocations to the surface group density. A spontaneous concerted transition with low activation barrier is found at a surface group separation of 6.8 Å. When hydroniums translocate concertedly, the activation barrier of the transition drops by more than a factor of two to the value of 0.25 eV. An approach is presented to determine interaction constants of hydronium ions and anionic surface groups as well as the surface group flexibility from the analysis of frequency spectra. These properties are discussed in the context of a recently developed soliton theory of interfacial proton transport.

Collective proton dynamics at highly charged interfaces studied by ab initio metadynamics.

Surface proton conduction is of utmost importance in biology, materials science, and electrochemistry; yet experimental findings of ultrafast proton transport at densely packed arrays of anionic surface groups have remained controversial and unexplained. We present an ab initio molecular dynamics study of proton dynamics at sulfonic-acid terminated surface groups. Results furnish a highly efficient collective mechanism of hydronium ion translocations at a critical surface group separation of ~6.5 Å. Orientational fluctuations of SG trigger hydrogen bond breaking that sets off the hydronium ion motion. The activation free energy of this process is 0.3 eV (±0.1 eV). The soliton-like nature of this mechanism is owed to the trigonal symmetry of sulfonate anions and exceptionally strong interfacial hydrogen bonding. These insights should stimulate surface conductance studies at SG monolayers with sulfonic acid groups, and they bolster efforts in designing proton conducting polymers conducive to fuel cell operation above ~100 °C.

Ab initio study of oxygen reduction mechanism at Pt(4) cluster.

We used density functional theory to investigate the reaction pathway of oxygen reduction/water splitting at a tetrahedral Pt(4) cluster. Four extra water molecules were included to account for the effect of water in mediating elementary surface processes. We propose a 6-step reaction sequence that includes a proton transfer between neighbouring active sites. Thermochemical considerations and the nudged elastic band method were employed to calculate reaction and activation energies for the elementary reaction steps. We generated the free energy diagram along the reaction path for various applied potentials. This plot provides vital information on the stability of intermediates and the rate determining processes in oxygen reduction and water splitting. Results suggest that removal of the reaction product, viz. molecular oxygen or water, is an energetically strongly hindered step in either direction.