PHASTEST: faster than PHASTER, better than PHAST.

PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in bacterial genomes. Given that bacterial genome sequencing has become so routine, the need for fast tools to comprehensively annotate bacterial genomes has become progressively more important. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors, it also provides more complete whole genome annotations and much improved genome visualization capabilities. In standardized tests, we found that PHASTEST is 31% faster and 2-3% more accurate in prophage identification than PHASTER. Specifically, PHASTEST can process a typical bacterial genome in 3.2 min (raw sequence) or in 1.3 min when given a pre-annotated GenBank file. Improvements in PHASTEST's ability to annotate bacterial genomes now make it a particularly powerful tool for whole genome annotation. In addition, PHASTEST now offers a much more modern and responsive visualization interface that allows users to generate, edit, annotate and interactively visualize (via zooming, rotating, dragging, panning, resetting), colourful, publication quality genome maps. PHASTEST continues to offer popular options such as an API for programmatic queries, a Docker image for local installations, support for multiple (metagenomic) queries and the ability to perform automated look-ups against thousands of previously PHAST-annotated bacterial genomes. PHASTEST is available online at https://phastest.ca.

MiMeDB: the Human Microbial Metabolome Database.

The Human Microbial Metabolome Database (MiMeDB) (https://mimedb.org) is a comprehensive, multi-omic, microbiome resource that connects: (i) microbes to microbial genomes; (ii) microbial genomes to microbial metabolites; (iii) microbial metabolites to the human exposome and (iv) all of these 'omes' to human health. MiMeDB was established to consolidate the growing body of data connecting the human microbiome and the chemicals it produces to both health and disease. MiMeDB contains detailed taxonomic, microbiological and body-site location data on most known human microbes (bacteria and fungi). This microbial data is linked to extensive genomic and proteomic sequence data that is closely coupled to colourful interactive chromosomal maps. The database also houses detailed information about all the known metabolites generated by these microbes, their structural, chemical and spectral properties, the reactions and enzymes responsible for these metabolites and the primary exposome sources (food, drug, cosmetic, pollutant, etc.) that ultimately lead to the observed microbial metabolites in humans. Additional, extensively referenced data about the known or presumptive health effects, measured biosample concentrations and human protein targets for these compounds is provided. All of this information is housed in richly annotated, highly interactive, visually pleasing database that has been designed to be easy to search, easy to browse and easy to navigate. Currently MiMeDB contains data on 626 health effects or bioactivities, 1904 microbes, 3112 references, 22 054 reactions, 24 254 metabolites or exposure chemicals, 648 861 MS and NMR spectra, 6.4 million genes and 7.6 billion DNA bases. We believe that MiMeDB represents the kind of integrated, multi-omic or systems biology database that is needed to enable comprehensive multi-omic integration.

Probe molecule chemisorption-low energy ion scattering study of surface active sites present in the orthorhombic Mo-V-(Te-Nb)-O catalysts for propane (amm)oxidation.

Methanol and allyl alcohol chemisorption and surface reaction in combination with low energy ion scattering (LEIS) were employed to determine the outermost surface compositions and chemical nature of active surface sites present on the orthorhombic (M1) Mo-V-O and Mo-V-Te-Nb-O phases. These orthorhombic phases exhibited vastly different behavior in propane (amm)oxidation reactions and, therefore, represented highly promising model systems for the study of the surface active sites. The LEIS data for the Mo-V-Te-Nb-O catalyst indicated surface depletion for V (-23%) and Mo (-27%), and enrichments for Nb (+55%) and Te (+165%) with respect to its bulk composition. Only minor changes in the topmost surface composition were observed for this catalyst under the conditions of the LEIS experiments at 400 degrees C, which is a typical temperature employed in these propane transformation reactions. These findings strongly suggested that the bulk orthorhombic Mo-V-Te-Nb-O structure may function as a support for the unique active and selective surface monolayer in propane (amm)oxidation. Moreover, direct evidence was obtained that the topmost surface VO(x) sites in the orthorhombic Mo-V-Te-Nb-O catalyst were preferentially covered by chemisorbed allyloxy species, whereas methanol was a significantly less discriminating probe molecule. The surface TeO(x) and NbO(x) sites on the Mo-V-Te-Nb-O catalyst were unable to chemisorb these probe molecules to the same extent as the VO(x) and MoO(x) sites. Our findings suggested that different surface locations for V(5+) ions in the orthorhombic Mo-V-O and Mo-V-Te-Nb-O catalysts may be primarily responsible for vastly different catalytic behavior exhibited by the Mo-V-O and Mo-V-Te-Nb-O phases. Although the proposed isolated V(5+) pentagonal bipyramidal sites in the orthorhombic Mo-V-O phase may be capable of converting propane to propylene with modest selectivity, the selective 8-electron transformation of propane to acrylic acid and acrylonitrile may require the presence of several surface VO(x) redox sites lining the entrances to the hexagonal and heptagonal channels of the orthorhombic Mo-V-Te-Nb-O phase. The study of allyl alcohol oxidation over the Mo-V-O and Mo-V-Te-Nb-O catalysts further suggested that water plays a critical role during the oxidation of acrolein intermediate to acrylic acid over the orthorhombic (M1 phase) Mo-V-Te-Nb-O catalysts. Finally, the present study strongly indicated that chemical probe chemisorption combined with low energy ion scattering (LEIS) is a novel and highly promising surface characterization technique for the investigation of the active surface sites present in the bulk mixed metal oxides.

Roles of surface Te, Nb, and Sb oxides in propane oxidation to acrylic acid over bulk orthorhombic Mo-V-O phase.

The outermost surfaces and subsurface layers of the orthorhombic (M1) Mo-V-O catalysts promoted with Te, Nb, and Sb oxide species at submonolayer surface coverage were examined by low-energy ion scattering (LEIS). This study indicated that the Nb oxide species was preferentially located at the topmost surface, while the subsurface Te and Sb concentrations declined gradually into the bulk. Although the original Mo-V-O catalyst was essentially unselective in propane oxidation to acrylic acid, significant improvement in the selectivity to acrylic acid was observed when Te, Nb, and Sb oxides were present as the surface species at submonolayer coverage. These findings further suggested that the formation of the surface V-O-M bonds (M = Nb, Te, or Sb) was highly beneficial for both the activity and selectivity of the orthorhombic Mo-V-O catalysts in propane oxidation to acrylic acid. The highest selectivity was observed when both Nb and Te (or Sb) oxide species were present at the surface. The selectivity trends established for the surface-promoted Mo-V-O catalyst parallel those found previously for the corresponding bulk Mo-V-M-O catalysts. These results further indicated that the introduction of surface metal oxide species is a highly promising method to prepare well-defined model catalysts for studies of the structure-activity/selectivity relationships as well as optimize the catalytic performance of the bulk mixed Mo-V-M-O catalysts for selective (amm)oxidation of propane.

A study of the surface region of the Mo-V-Te-O catalysts for propane oxidation to acrylic acid.

The bulk mixed Mo-V-Te oxides possess high activity and selectivity in propane oxidation to acrylic acid and represent well-defined model catalysts for studies of the surface molecular structure-activity/selectivity relationships in this selective oxidation reaction. The elemental compositions, metal oxidation states, and catalytic functions of V, Mo, and Te in the surface region of the model Mo-V-Te-O system were examined employing low energy ion scattering (LEIS) and X-ray photoelectron spectroscopy (XPS). This study indicated that the surfaces of these catalysts are terminated with a monolayer, which possesses a different elemental composition from that of the bulk. The rates of propane consumption and formation of propylene and acrylic acid depended on the topmost surface V concentration, whereas no dependence of these reaction rates on either the surface Mo or Te concentrations was observed. These findings suggested that the bulk Mo-V-Te-O structure may function as a support for the unique active and selective surface monolayer in propane oxidation to acrylic acid. The results of this study have important practical consequences for the development of improved selective oxidation catalysts by introducing surface metal oxide components to form new surface active V-O-M sites for propane oxidation to acrylic acid.