MI-Pack: Increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways

Metabolite identification is of central importance to metabolomics as it provides the route to new knowledge. Automated identification of the thousands of peaks detected by high resolution mass spectrometry is currently not possible, largely due to the finite mass accuracy of the spectrometer and the complexity that one peak can be assigned to one or more empirical formula(e) and each formula maps to one or more metabolites. Biological samples are not, however, composed of random metabolite mixtures, but instead comprise of thousands of compounds related through specific chemical transformations. Here we evaluate if prior biological knowledge of these transformations can improve metabolite identification accuracy.Our identification algorithm - which uses metabolite interconnectivity from the KEGG database to putatively identify metabolites by name - is based on mapping an experimentally-derived empirical formula difference for a pair of peaks to a known empirical formula difference between substrate-product pairs derived from KEGG, termed transformation mapping (TM). To maximize identification accuracy, we also developed a novel semi-automated method to calculate a mass error surface associated with experimental peak-pair differences. The TM algorithm with mass error surface has been extensively validated using simulated and experimental datasets by calculating false positive and false negative rates of metabolite identification. Compared to the traditional identification method of database searching accurate masses on a single-peak-by-peak basis, the TM algorithm reduces the false positive rate of identification by > 4-fold, while maintaining a minimal false negative rate. The mass error surface, putative identification of metabolite names, and calculation of false positive and false negative rates collectively advance and improve upon related previous research on this topic [1, 2]. We conclude that inclusion of prior biological knowledge in the form of metabolic pathways provides one route to more accurate metabolite identification.     

TcdB of Clostridioides difficile Mediates RAS-Dependent Necrosis in Epithelial Cells

A Clostridioides difficile infection (CDI) is the most common nosocomial infection worldwide. The main virulence factors of pathogenic C. difficile are TcdA and TcdB, which inhibit small Rho-GTPases. The inhibition of small Rho-GTPases leads to the so-called cytopathic effect, a reorganization of the actin cytoskeleton, an impairment of the colon epithelium barrier function and inflammation. Additionally, TcdB induces a necrotic cell death termed pyknosis in vitro independently from its glucosyltransferases, which are characterized by chromatin condensation and ROS production. To understand the underlying mechanism of this pyknotic effect, we conducted a large-scale phosphoproteomic study. We included the analysis of alterations in the phosphoproteome after treatment with TcdA, which was investigated for the first time. TcdA exhibited no glucosyltransferase-independent necrotic effect and was, thus, a good control to elucidate the underlying mechanism of the glucosyltransferase-independent effect of TcdB. We found RAS to be a central upstream regulator of the glucosyltransferase-independent effect of TcdB. The inhibition of RAS led to a 68% reduction in necrosis. Further analysis revealed apolipoprotein C-III (APOC3) as a possible crucial factor of CDI-induced inflammation in vivo.     

Säurekatalysierte Umsetzungen von Aromaten mit Alkanen und Cycloalkanen. IX. Alkylierungen mit 2,2,4-Trimethylpentan (Isooctan)

Acid-catalyzed Reactions of Aromatic Hydrocarbons with Alkanes and Cycloalkanes. IX. Alkylations with 2,2,4-Trimethylpentane (Isooctane) The non-conventional alkylation of benzene, toluene, ethyl- and isopropylbenzene, fluoro- and chlorobenzene with 2,2,4-trimethylpentane in the presence of acid catalysts is described. The composition of the rather complex reaction mixtures is determined by gas-liquid chromatography and mass spectrometry, tert. butylarenes being the main products beside alkylsubstituted indanes and tetralines. Their formation is interpreted as a competition between fragmentation and isomerization of the alkylating agent. By use of trifluoromethanesulfonic acid or combinations of catalysts from HF or HSO₃F with variant metallic fluorides at lower temperatures the selectivity of the reaction may be partially raised.     

Correlation of III/V semiconductor etch results with physical parameters of high-density reactive plasmas excited by electron cyclotron resonance

Reactive ion etching is the interaction of reactive plasmas with surfaces. To obtain a detailed understanding of this process, significant properties of reactive composite low-pressure plasmas driven by electron cyclotron resonance (ECR) were investigated and compared with the radial uniformity of the etch rate. The determination of the electronic properties of chlorine-and hydrogen-containing plasmas enabled the understanding of the pressure-dependent behavior of the plasma density and provided better insights into the electronic parameters of reactive etch gases. From the electrical evaluation of I(V ) characteristics obtained using a Langmuir probe, plasmas of different compositions were investigated. The standard method of Druyvesteyn to derive the electron energy distribution functions by the second derivative of the I(V ) characteristics was replaced by a mathematical model which has been evolved to be more robust against noise, mainly, because the first derivative of the I(V ) characteristics is used. Special attention was given to the power of the energy dependence in the exponent. In particular, for plasmas that are generated by ECR with EM modes, the existence of Maxwellian distribution functions is not to be taken as a self-evident fact, but the bi-Maxwellian distribution was proven for Ar-and Kr-stabilized plasmas. In addition to the electron temperature, the global uniform discharge model has been shown to be useful for calculating the neutral gas temperature. To what extent the invasive method of using a Langmuir probe could be replaced with the non-invasive optical method of emission spectroscopy, particularly actinometry, was investigated, and the resulting data exhibited the same relative behavior as the Langmuir data. The correlation with etchrate data reveals the large chemical part of the removal process—most striking when the data is compared with etching in pure argon. Although the relative amount of the radial variation of plasma density and etch rate is approximately ±5%, the etch rate shows a slightly concave shape in contrast to the plasma density.     

Seasonal and diurnal variation of PM2.5 apparent particle density in urban air in Augsburg, Germany

The apparent particle density of particulate matter with aerodynamic diameter < 2.5 microm (rho2.5) was determined at an urban site in Augsburg, Germany and its correlation with chemical composition and meteorological conditions was investigated. rho2.5 showed strong day-to-day variation from 1.05 to 2.36 g cm(-3) (5 to 95% percentile), and nearly 64% of the daily variability could be explained by a multiple variable regression model. A minimum in the morning and afternoon (about 1.5 g cm(-3)), and a maximum (near 1.8 g cm(-3)) during midday was observed. The minima represent fresh primary aerosol emissions, which were related to traffic soot particles with low density due to their agglomerate structure, especially observed in the early morning hours of weekdays. The maximum is likely due to increased secondary particle production and the presence of more aged particles with the built-up of the convectively mixed boundary layer. rho2.5 has the potential to serve as a crude tracer for chemical composition and atmospheric processing and might play an important role when considering the associations between health effects and ambient particles.     

Laser flash photolysis studies on homo-and copolymers of phenylisopropenyl ketone and of pivalophenone in solution

Benzene solutions of poly(phenylisopropenyl ketone) (PPIK), of copolymers of PIK and styrene and of phenyl-t-butyl ketone (pivalophenone) were irradiated with light flashes (duration 25 nsec) at wavelength 347 nm. The spectra observed at the end of the flash were attributed to the triplet state (T-T-spectra). A fraction of the triplets in the polymers was deactivated by T-T annihilation, as evidenced by lifetimes decreasing with increasing absorbed dose rate. Upon extrapolation to zero intensity the following triplet decay rate constants K_T were obtained:

$\text{(1.0 ± 0.1) 10}{}^7\text{sec}{}^{\mathrm{?}}\text{(}\text{PPIK}\text{),}$

$\text{(8 ± 1) 10}{}^6\text{sec}{}^{\mathrm{?1}}\text{(}\text{CPStPlK12}\text{), (6 ± 1) 10}{}^6\text{sec}{}^{\mathrm{?1}}\text{(}\text{CPStPlK3.7}\text{)}$

$\text{(3 ± 1) 10}{}^6\text{sec}{}^{\mathrm{?1}}\text{(}\text{CPStPlK1}\text{)}$

$\text{(2.5 ± 0.2) 10}{}^6\text{sec}{}^{\mathrm{?1}}\text{(}\text{pivalophenone}\text{)}$

.In PPIK and pivalophenone the dominant chemical route of triplet deactivation is α-cleavage. The relatively high k_T value found with PPIK is presumably due to next neighbour interaction. In copolymers with a high content of isolated PIK units type I processes (α-cleavage) become less probable due to weak next neighbour influence. Thus type II processes dominate in copolymers although being slower than type I processes in homo PPIK. The rate constant of the reaction of PIK triplets in homo PPIK with 2-propanol in benzene solution is (2.0 ± 0.2)10⁶ l/mol sec, whereas pivalophenone triplets react almost 10 times slower with 2-propanol. The difference is assumed to be due to a rather strong interaction of 2-propanol with ground state as well as with excited pivalophenone.     

Monoclinic Zirconia Bodies by Thermoplastic Ceramic Extrusion

Two ultrafine, undoped ZrO₂ powders with median primary particle sizes of 9 and 25 nm were used to prepare ceramic suspensions for thermoplastic extrusion. The organic vehicle consisted of an industrial-grade poly(ethylene- co -vinyl acetate) (EVA) or polyethylene (PE-HD) and decanoic acid as a dispersing agent. The powder volume loadings achieved were 44% and 52% by volume for the two powders, respectively. The amount of dispersant needed was calculated from a new model based on available chemisorption sites on the powder surface. Mixing and extrusion were conducted using a conventional modular plastic processing unit. Green bodies were dewaxed up to 450°C in an inert atmosphere and sintered to full density in air at 1060° and 1100°C, respectively. Analysis of the ceramic phase content and the microstructure of the bodies is presented.