Sample amount alternatives for data adjustment in comparative cyanobacterial metabolomics

Here we describe an integrative protocol for metabolite extraction and the measurement of three cellular constituents, chlorophyll a, total protein, and glycogen from the same small volume of cyanobacterial cultures that can be used as alternative sample amount parameters for data adjustment in comparative metabolome studies. We conducted recovery experiments to assess the robustness and reproducibility of the measurements obtained for the cellular constituents. Also, we have chosen three profile-intrinsic parameters derived from gas chromatography-mass spectrometry (GC/MS) data in order to test their utility for spectral data adjustment. To demonstrate the relevance of these six parameters, we analyzed three cyanobacteria with greatly different morphologies, comprising a unicellular, a filamentous, and a filamentous biofilm-forming strain. Comparative analysis of GC/MS data from cultures grown under standardized conditions indicated that adjustment of the corresponding metabolite profiles by any of the measured cellular constituents or chosen intrinsic parameters led to similar results with respect to sample cohesion and strain separation. Twenty-one metabolites significantly enriched for the carbohydrate and amine superclasses are mainly responsible for strain separation, with a majority of the remaining metabolites contributing to sample group cohesion. Therefore, we conclude that any of the parameters tested in this study can be used for spectral data adjustment of cyanobacterial strains grown under controlled conditions. However, their use for the differentiation between different stresses or physiological states within a strain remains to be shown. Interestingly, both the adjustment approaches and statistical tests applied effected the detection of metabolic differences and their patterns among the analyzed strains.     

Drugs of abuse screening in urine as part of a metabolite-based LC-MS<Superscript>n</Superscript> screening concept

Today, immunoassays and several chromatographic methods are in use for drug screening in clinical and forensic toxicology and in doping control. For further proof of the authors’ new metabolite-based liquid chromatography-mass spectrometry (LC-MSⁿ) screening concept, the detectability of drugs of abuse and their metabolites using this screening approach was studied. As previously reported, the corresponding reference library was built up with MS² and MS³ wideband spectra using a LXQ linear ion trap with electrospray ionization in the positive mode and full scan information-dependent acquisition. In addition to the parent drug spectra recorded in methanolic solution, metabolite spectra were identified after protein precipitation of urine from rats after administration of the corresponding drugs and added to the library. This consists now of data of over 900 parent compounds, including 87 drugs of abuse, and of over 2,300 metabolites and artifacts, among them 436 of drugs of abuse. Recovery, process efficiency, matrix effects, and limits of detection for selected drugs of abuse were determined using spiked human urine, and the resulting data have been acceptable. Using two automatic data evaluation tools (ToxID and SmileMS), the intake of 54 of the studied drugs of abuse could be confirmed in urine samples of drug users after protein precipitation and LC separation. The following drugs classes were covered: stimulants, designer drugs, hallucinogens, (synthetic) cannabinoids, opioids, and selected benzodiazepines. The presented LC-MSⁿ method complements the well-established gas chromatography-mass spectroscopy procedure in the authors’ laboratory.     

Metabolism studies of the <Emphasis Type="Italic">Kratom</Emphasis> alkaloid speciociliatine,a diastereomer of the main alkaloid mitragynine,in rat and human urine using liquid chromatography-linear ion trap mass spectrometry

Mitragyna speciosa (Kratom) is currently used as a drug of abuse. When monitoring its abuse in urine, several alkaloids and their metabolites must be considered. In former studies, mitragynine (MG), its diastereomer speciogynine (SG), and paynantheine and their metabolites could be identified in rat and human urine using LC-MSⁿ. In Kratom users' urines, besides MG and SG, further isomeric compounds were detected. To elucidate whether the MG and SG diastereomer speciociliatine (SC) and its metabolites represent further compounds, the phase I and II metabolites of SC were identified first in rat urine after the administration of the pure alkaloid. Then, the identified rat metabolites were screened for in the urine of Kratom users using the above-mentioned LC-MSⁿ procedure. Considering the mass spectra and retention times, it could be confirmed that SC and its metabolites are so far the unidentified isomers in human urine. In conclusion, SC and its metabolites can be used as further markers for Kratom use, especially by consumption of raw material or products that contain a high amount of fruits of the Malaysian plant M. speciosa.     

Approximation in quantale-enriched categories

Our work is a foundational study of the notion of approximation in Q-categories and in (U,Q)-categories, for a quantale Q and the ultrafilter monad U. We introduce auxiliary, approximating and Scott-continuous distributors, the way-below distributor, and continuity of Q- and (U,Q)-categories. We fully characterize continuous Q-categories (resp. (U,Q)-categories) among all cocomplete Q-categories (resp. (U,Q)-categories) in the same ways as continuous domains are characterized among all dcpos. By varying the choice of the quantale Q and the notion of ideals, and by further allowing the ultrafilter monad to act on the quantale, we obtain a flexible theory of continuity that applies to partial orders and to metric and topological spaces. We demonstrate on examples that our theory unifies some major approaches to quantitative domain theory.     

On the completion monad via the Yoneda embedding in quasi-uniform spaces

Making use of the presentation of quasi-uniform spaces as generalised enriched categories, and employing in particular the calculus of modules, we define the Yoneda embedding, prove a (weak) Yoneda Lemma, and apply them to describe the Cauchy completion monad for quasi-uniform spaces.     

Multi-stage solvers optimized for damping and propagation

Explicit multi-stage solvers are routinely used to solve the semi-discretized equations that arise in Computational Fluid Dynamics (CFD) problems. Often they are used in combination with multi-grid methods. In that case, the role of the multi-stage solver is to efficiently reduce the high frequency modes on the current grid and is called a smoother. In the past, when optimizing the coefficients of the scheme, only the damping characteristics of the smoother were taken into account and the interaction with the remainder of the multi-grid cycle was neglected. Recently it had been found that coefficients that result in less damping, but allow for a higher Courant-Friedrichs-Lewy (CFL) number are often superior to schemes that try to optimize damping alone. While this is certainly true for multi-stage schemes used as a stand-alone solver, we investigate in this paper if using higher CFL numbers also yields better results in a multi-grid setting. We compare the results with a previous study we conducted and where a more accurate model of the multi-grid cycle was used to optimize the various parameters of the solver.We show that the use of the more accurate model results in better coefficients and that in a multi-grid setting propagation is of little importance.We also look into the gains to be made when we allow the parameters to be different for the pre- and post-smoother and show that even better coefficients can be found in this way.     

Generalizing the Keller�CSegel Model: Lyapunov Functionals, Steady State Analysis, and Blow-Up Results for Multi-species Chemotaxis Models in?the?Presence of Attraction and Repulsion Between Competitive Interacting Species

In this paper we extend the famous Keller–Segel model for the chemotactic movement of motile species to some multi-species chemotaxis equations. The presented multi-species chemotaxis models are more general than those introduced so far and also include some interaction effects that have not been studied before. For example, we consider multi-species chemotaxis models with attraction and repulsion between interacting motile species. For some of the presented new models we give sufficient conditions for the existence of Lyapunov functionals. These new results are related to those of Wolansky (Scent and sensitivity: equilibria and stability of chemotactic systems in the absence of conflicts, preprint, 1998; Eur. J. Appl. Math. 13:641–661, 2002). Furthermore, a linear stability analysis is performed for uniform steady states, and results for the corresponding steady state problems are established. These include existence and nonexistence results for non-constant steady state solutions in some special cases.     

2,2']paracyclophane-based π-conjugated molecular wires reveal molecular-junction behavior

The electronic coupling as well as the attenuation factor (β), which depends primarily on the nature of the molecular bridge and is used as a benchmark to test the molecular wire behavior, have been determined in a systematic study carried out on a series of ZnP/C(60) conjugates connected through a [2,2']paracyclophane-oligophenylenevinylene (pCp-oPPV). The convergent synthesis involves a series of Horner-Emmons olefination reactions or double palladium-catalized Heck-type reactions. ZnP-pCp-C(60) conjugates were finally obtained by the 1,3-dipolar cycloaddition reaction of the in situ-generated azomethyne ylide containing the ZnP-pCp moiety to the [60]fullerene using Prato conditions. Experimental (UV-vis, fluorescence, transient absorption spectroscopy, and solution electrochemistry) and theoretical studies revealed that the pCps act as molecular junctions. If hole transfer is assumed to be the dominant charge transfer (CT) mechanism, CT is facilitated in one direction (from C(60) to ZnP via pCp) but disfavored in the other direction (from ZnP to C(60) via pCp).     

Macroscopic investigation of the transient hydrodynamic memory behavior of preparative packed chromatography beds

The goal of the present work was to examine the hydrodynamic behavior of preparative scale packed chromatography beds during long-term cyclical operation at high loads using an experimental set-up with a high resolution measuring device of bed height. One agarose-based resin and one methacrylic-based resin were examined in a 140 mm column. Both resins exhibited hysteresis behavior during compression/relaxation cycles. The hystereses were less pronounced with decreasing hydrodynamic stress rate. The occurrence of hystereses was an indication for hydrodynamic memory behavior of the chromatography packing. During long-term cyclical operation at high loads of the column filled with methacrylic resin, oscillations of the steadily with time decreasing flow rate were observed for the first time. These oscillations were attributed to the viscoelasticity of the polymer particles network representing a system with materials with fading memory. Such nonlinear systems with feed-back are known to exhibit inherent self-oscillations. A decoupling of the two processes of bed compression and decrease of bed permeability was observed. The presented results explain why preparative packed-bed chromatography often yields unsatisfactory reproducible data and why unwanted phenomena like medium wall detachment or other symptoms of deteriorated chromatography beds are frequently observed.     

Toward making the mean spherical approximation of primitive model electrolytes analytic: an analytic approximation of the MSA screening parameter

The mean spherical approximation (MSA) for the primitive model of electrolytes provides reasonable estimates of thermodynamic quantities such as the excess chemical potential and screening length. It is especially widely used because of its explicit formulas so that numerically solving equations is minimized. As originally formulated, the MSA screening parameter Γ (akin to the reciprocal of the Debye screening length) does not have an explicit analytic formula; an equation for Γ must be solved numerically. Here, an analytic approximation for Γ is presented whose relative error is generally ?10(-5). If more accuracy is desired, one step of an iterative procedure (which also produces an explicit formula for Γ) is shown to give relative errors within machine precision in many cases. Even when ion diameter ratios are ～10 and ion valences are ～10, the relative error for the analytic approximation is still ?10(-3) and for the single iterative substitution it is ?10(-9).