Metabolite Damage and Damage Control in a Minimal Genome

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal. IMPORTANCE Metabolite damage and repair mechanisms are being increasingly recognized. We present here compelling genetic and biochemical evidence for the universal importance of these mechanisms by demonstrating that stripping a genome down to its barest essentials leaves metabolite damage control systems in place. Furthermore, our metabolomic and cheminformatic results point to the existence of a network of metabolite damage and damage control reactions that extends far beyond the corners of it that have been characterized so far. In sum, there can be little room left to doubt that metabolite damage and the systems that counter it are mainstream metabolic processes that cannot be separated from life itself

Sample preparation procedure for the determination of polycyclic aromatic hydrocarbons in petroleum vacuum residue and bitumen

This paper describes a novel method of sample preparation for the determination of trace concentrations of polycyclic aromatic hydrocarbons (PAHs) in high-boiling petroleum products. Limits of quantitation of the investigated PAHs in materials of this type range from tens of nanograms per kilogram to <20 μg/kg. The studies revealed that in order to separate most of interferences from the analytes without a significant loss of PAHs, it is necessary to use size exclusion chromatography as the first step of sample preparation, followed by adsorption using normal-phase liquid chromatography. The use of orthogonal separation procedure described in the paper allows the isolation of only a group of unsubstituted and substituted aromatic hydrocarbons with a specific range of molar mass. The lower the required limit of quantitation of PAHs, the larger is the scale of preparative liquid chromatography in both steps of sample preparation needed. The use of internal standard allows quantitative results to be corrected for the degree of recovery of PAHs during the sample preparation step. Final determination can be carried out using HPLC-FLD, GC-MS, or HPLC-UV–VIS/DAD. The last technique provides a degree of identification through the acquired UV–VIS spectra

Kinetic Analysis and Development of a Complete Catalytic Oxidation of Methane Experiment for Unit Operations II

Catalysts are widely used in the chemical process industry to increase yields of industrial reactions. Using the packed bed reactors at WPI, which contain palladium and platinum catalysts, the kinetics of complete methane oxidation over were examined. The activation energy and reaction orders were calculated for this reaction over both catalysts and was found to be within the range provided by literature. The system was redesigned to deliver quicker and simpler results via the replacement of the gas chromatograph with CO2 meters. It was determined that the CO2 meters were a sufficient replacement for the purposes of unit operations experimentation. A new experimental procedure was designed to provide a more complete study and understanding of catalysis for chemical engineering students

Sociale veiligheid in de Nederlandse wetenschap - Van papier naar praktijk

Om ongewenst gedrag aan wetenschappelijke instellingen te bestrijden is het nodig veel meer aan preventie te doen. De huidige aanpak richt zich vooral op klachtafhandeling, maar de sociale veiligheid aan universiteiten en onderzoeksinstituten verbetert pas echt door gedrag op de werkvloer structureel onderwerp van gesprek te maken

Sociale veiligheid in de Nederlandse wetenschap - Van papier naar praktijk

Om ongewenst gedrag aan wetenschappelijke instellingen te bestrijden is het nodig veel meer aan preventie te doen. De huidige aanpak richt zich vooral op klachtafhandeling, maar de sociale veiligheid aan universiteiten en onderzoeksinstituten verbetert pas echt door gedrag op de werkvloer structureel onderwerp van gesprek te maken. Dat vraagt om een andere cultuur die is verankerd in een nieuwe manier van leiding geven. De KNAW heeft op verzoek van de minister van OCW de gids Sociale veiligheid in de Nederlandse wetenschap - Van papier naar praktijk gemaakt met handreikingen en tips om de problemen met ongewenst gedrag te voorkomen of vroegtijdig bij te sturen. Hiermee wil de KNAW een proces in gang zetten waarmee de sociale veiligheid in de Nederlandse wetenschap wordt vergroot