Application of Complexity Measures to Stratospheric Dynamics

This thesis examines the utility of mathematical complexity measures for the analysis of stratospheric dynamics. Through theoretical considerations and tests with artificial data sets, e.g., the iteration of the logistic map, suitable parameters are determined for the application of the statistical entropy measures sample entropy (SE) and Rényi entropy (RE) to methane (a long-lived stratospheric tracer) data from simulations of the SOCOL chemistry-climate model. The SE is shown to be useful for quantifying the variability of recurring patterns in a time series and is able to identify tropical patterns similar to those reported by previous studies of the ``tropical pipe'' region. However, the SE is found to be unsuitable for use in polar regions, due to the non-stationarity of the methane data at extra-tropical latitudes. It is concluded that the SE cannot be used to analyse climate complexity on a global scale. The focus is turned to the RE, which is a complexity measure of probability distribution functions (PDFs). Using the second order RE and a normalisation factor, zonal PDFs of ten consecutive days of methane data are created with a Bayesian optimal binning technique. From these, the RE is calculated for every day (moving 10-day window). The results indicate that the RE is a promising tool for identifying stratospheric mixing barriers. In Southern Hemisphere winter and early spring, RE produces patterns similar to those found in other studies of stratospheric mixing. High values of RE are found to be indicative of the strong fluctuations in tracer distributions associated with relatively unmixed air in general, and with gradients in the vicinity of mixing barriers, in particular. Lower values suggest more thoroughly mixed air masses. The analysis is extended to eleven years of model data. Realistic inter-annual variability of some of the RE structures is observed, particularly in the Southern Hemisphere. By calculating a climatological mean of the RE for this period, additional mixing patterns are identified in the Northern Hemisphere. The validity of the RE analysis and its interpretation is underlined by showing that qualitatively similar patterns can be seen when using observational satellite data of a different tracer. Compared to previous techniques, the RE has the advantage that it requires significantly less computational effort, as it can be used to derive dynamical information from model or measurement tracer data without relying on any additional input such as wind fields. The results presented in this thesis strongly suggest that the RE is a useful new metric for analysing stratospheric mixing and its variability from climate model data. Furthermore, it is shown that the RE measure is very robust with respect to data gaps, which makes it ideal for application to observations. Hence, using the RE for comparing observations of tracer distributions with those from model simulations potentially presents a novel approach for analysing mixing in the stratosphere

Stable isotope dilution assay for the accurate determination of mycotoxins in maize by UHPLC-MS/MS

A fast, easy-to-handle and cost-effective analytical method for 11 mycotoxins currently regulated in maize and other cereal-based food products in Europe was developed and validated for maize. The method is based on two extraction steps using different acidified acetonitrile–water mixtures. Separation is achieved using ultrahigh-performance liquid chromatography (UHPLC) by a linear water–methanol gradient. After electrospray ionisation, tandem mass spectrometric detection is performed in dynamic multiple reaction monitoring mode. Since accurate mass spectrometric quantification is hampered by matrix effects, uniformly [13C]-labelled mycotoxins for each of the 11 compounds were added to the sample extracts prior to UHPLC-MS/MS analysis. Method performance parameters were obtained by spiking blank maize samples with mycotoxins before as well as after extraction on six levels in triplicates. The twofold extraction led to total recoveries of the extraction steps between 97% and 111% for all target analytes, including fumonisins. The [13C]-labelled internal standards efficiently compensated all matrix effects in electrospray ionisation, leading to apparent recoveries between 88% and 105% with reasonable additional costs. The relative standard deviations of the whole method were between 4% and 11% for all analytes. The trueness of the method was verified by the measurement of several maize test materials with well-characterized concentrations. In conclusion, the developed method is capable of determining all regulated mycotoxins in maize and presuming similar matrix effects and extraction recovery also in other cereal-based foods

Specialized Peptidoglycan Hydrolases Sculpt the Intra-bacterial Niche of Predatory Bdellovibrio and Increase Population Fitness

Bdellovibrio are predatory bacteria that have evolved to invade virtually all Gram-negative bacteria, including many prominent pathogens. Upon invasion, prey bacteria become rounded up into an osmotically stable niche for the Bdellovibrio, preventing further superinfection and allowing Bdellovibrio to replicate inside without competition, killing the prey bacterium and degrading its contents. Historically, prey rounding was hypothesized to be associated with peptidoglycan (PG) metabolism; we found two Bdellovibrio genes, bd0816 and bd3459, expressed at prey entry and encoding proteins with limited homologies to conventional dacB/PBP4 DD-endo/carboxypeptidases (responsible for peptidoglycan maintenance during growth and division). We tested possible links between Bd0816/3459 activity and predation. Bd3459, but not an active site serine mutant protein, bound β-lactam, exhibited DD-endo/carboxypeptidase activity against purified peptidoglycan and, importantly, rounded up E. coli cells upon periplasmic expression. A ΔBd0816 ΔBd3459 double mutant invaded prey more slowly than the wild type (with negligible prey cell rounding) and double invasions of single prey by more than one Bdellovibrio became more frequent. We solved the crystal structure of Bd3459 to 1.45 Å and this revealed predation-associated domain differences to conventional PBP4 housekeeping enzymes (loss of the regulatory domain III, alteration of domain II and a more exposed active site). The Bd3459 active site (and by similarity the Bd0816 active site) can thus accommodate and remodel the various bacterial PGs that Bdellovibrio may encounter across its diverse prey range, compared to the more closed active site that “regular” PBP4s have for self cell wall maintenance. Therefore, during evolution, Bdellovibrio peptidoglycan endopeptidases have adapted into secreted predation-specific proteins, preventing wasteful double invasion, and allowing activity upon the diverse prey peptidoglycan structures to sculpt the prey cell into a stable intracellular niche for replication

c-di-AMP Is a New Second Messenger in Staphylococcus aureus with a Role in Controlling Cell Size and Envelope Stress.

Published versio

Metabolomic Analysis of Marine Microalgae Using High Resolution Mass Spectrometry for Taxonomic Comparisons and Screening of Marine Biotoxins

Out of the circa 5000 microalgae known, around 100 marine species of unicellular algae have been shown to produce several hundred biotoxins worldwide. Such biotoxins may be harmful to man through consumption of fish and shellfish exposed to such algae or through direct contact. Many official methods aimed at the detection of such toxins had traditionally been based on biological assays, due to the lack of reference compounds. Recently, legislation for shellfish safety in Europe introduced targeted MS screening for lipophilic toxins. Due to globalization of trade and climate change, there is a need to develop methods for untargeted screening to fully protect consumer safety, e.g. LC-HRMS. For this purpose we studied the metabolomes of marine microalgae using HRMS technique