Massenspektrometrie-Messungen Durchgeführt Unter Bedingungen der Ultraschnellen Stress-Confinement

The subject of this dissertation was to demonstrate the advantages of performing mass spectrometry measurements under the conditions of stress-confinement. To be in a position to discuss such measurements, there was the need to develop a high-performance time-of-flight mass spectrometer in-house, since commercially available instruments do not allow the scientist the freedom to adequately study the underlying physical mechanisms. Furthermore, due to the high complexity of the datasets generated by these studies, there was a definite need for novel data analysis routines to improve the quality of the available information. Laser desorption mass spectrometry is an established, but not yet adequately quantitative analytical technique. One of the primary reasons for this unfortunate limitation is because the desorption and ionisation processes are highly coupled. Consequently, this does not allow the ionisation efficiency to be varied without varying the amount of material desorbed and vice versa. The only way to get past this inherent deadlock is to separate these two processes. Interestingly, molecular dynamics simulations have suggested that when performing mass spectrometry measurements under stress-confinement conditions the desorption and ionisation processes would become separable. It is for this reason why there was a basic need to understand the desorption and ionisation mechanisms under these conditions since an appropriate understanding could potentially facilitate laser desorption mass spectrometry to become more quantitative. Within this thesis, it has been established that there are numerous advantages to performing mass spectrometry studies under conditions of stress-confinement. The practicality of this concept was demonstrated both at atmospheric conditions by using a picosecond infrared laser for studying bulk water samples and under high-vacuum by utilising a femtosecond ultraviolet laser with standard matrices. The atmospheric studies indicated that the infrared laser produces mass spectra which qualitatively compares well to that of electrospray ionisation, but enjoyed the benefits of laser control. Importantly, it was shown that no source of secondary ionisation is required. To my knowledge, the vacuum experiments demonstrated for the first time that desorption and ionisation processes are separable with the application of ultrashort pulses. This observation was made by studying survival yields (intensity of the fragment ions relative to a parent ion) of thermometer ions for a range of laser pulse energies. Moreover, a Bayesian deconvolution algorithm was developed to improve the quantification of these fragmentation channels. By decoupling the desorption and ionisation processes, I believe that laser desorption mass spectrometry measurements can genuinely be made quantitative.Das Thema vorliegender Dissertation war die Durchfuhrung von Massenspektrometrie-Messungen im Hinblick auf die Analyse der vorteilhaften Bedingungen des sogenanten stress-confinement''. Hierfur war es notig eine leistungsstarkes Massenspektrometer zu konstruieren und in Betrieb zu nehmen, da kommerziell verfugbare Instrumente den Blick auf die zugrunde liegenden Mechanismen erschweren. Auf Grund der hohen Komplexitat der generierten Datensatze gab es Bedarf an neuartigen Auswertungsansatzen, um die Qualitat der extrahierbaren Informationen zu verbessern. Die Laserdesorption-Massenspektrometrie ist zwar eine etablierte, jedoch noch nicht vollstandig quantitative Analysetechnik. Einer der Hauptgrunde fur diese Begrenzung liegt darin, dass die Desorptions- und Ionisationsprozesse stark gekoppelt sind. Dies fuhrt dazu, dass die Ionisationseffizienz nicht unabhangig von der Menge des desertierten Materials variiert werden kann und umgekehrt. Um diese Begrenzung zu uberwinden mussen die beiden Prozesse getrennt werden. Molekulare Dynamiksimulationen haben gezeigt, dass bei der Durchfuhrung von Massenspektrometrie unter stress-confinement'' Bedingungen die Prozesse trennbar werden. Aus diesem Grund ist ein Verstandnis um die Desorptions- und Ionisationsprozesse unter diesen speziellen Bedingungen von grosser Bedeutung, da unter Umstanden der Schritt zu einem qualitativen Verfahren moglich wird. Im Rahmen dieser Arbeit wurde festgestellt, dass es zahlreiche Vorteile massenspektrometrische Untersuchungen unter stress-confinement'' Bedingungen durchzufuhren. Die Praxistauglichkeit dieses Konzepts wurde sowohl bei atmospharischen Bedingungen, unter Einsatz eines Pikosekunden-Infrarotlasers zur Untersuchung wassriger Proben, als auch unter Hochvakuum bei gleichzeitigem Einsatz eines ultravioletten Femtosekunden-Lasers appliziert auf Standardmatrizen, validiert. Die atmospharischen Studien zeigten ferner, dass sich die Massenspektren mittels Infrarotlaser qualitativ gut mit jenen der Elektrospray-Ionisation vergleichen lassen, jedoch ist die verbesserte experimentelle Kontrolle der Ionisation mittels Laser von Vorteil. Bei diesem Verfahren ist also keine sekundare Ionisation mehr erforderlich. Meiner Kenntnis nach konnten die Vakuumexperimente erstmals zeigen, dass Desorptions- und Ionisationsprozesse unter Anwendung von ultrakurzen Laserpulsen voneinander trennbar sind. Diese Beobachtung konnte durch die Analyse der Ausbeuten (Intensitat der Fragment-Ionen relativ zu einem Hauption) von Thermometer-Ionen fur eine Reihe von Laserpulsenergien gemacht werden. Schliesslich ist ein Bayesscher Entfaltungsalgorithmus entwickelt worden, um die Quantifizierung der vorhandenen Fragmentierungskanale zu verbessern. Uber die Entkopplung der Desorptions- und Ionisationsprozesse wird die Laserdesorption-Massenspektrometrie letztlich, so scheint es, quantitativ durchfuhrbar

Rapid deconvolution of low-resolution time-of-flight data using Bayesian inference

The deconvolution of low-resolution time-of-flight data has numerous advantages, including the ability to extract additional information from the experimental data. We augment the well-known Lucy-Richardson deconvolution algorithm using various Bayesian prior distributions and show that a prior of second-differences of the signal outperforms the standard Lucy-Richardson algorithm, accelerating the rate of convergence by more than a factor of four, while preserving the peak amplitude ratios of a similar fraction of the total peaks. A novel stopping criterion and boosting mechanism are implemented to ensure that these methods converge to a similar final entropy and local minima are avoided. Improvement by a factor of two in mass resolution allows more accurate quantification of the spectra. The general method is demonstrated in this paper through the deconvolution of fragmentation peaks of the 2,5-dihydroxybenzoic acid matrix and the benzyltriphenylphosphonium thermometer ion, following femtosecond ultraviolet laser desorption

A consistent molecular hydrogen isotope chemistry scheme based on an independent bond approximation

The isotopic composition of molecular hydrogen (H<sub>2</sub>) produced by photochemical oxidation of methane (CH<sub>4</sub>) and Volatile Organic Compounds (VOCs) is a key quantity in the global isotope budget of (H<sub>2</sub>). The many individual reaction steps involved complicate its investigation. Here we present a simplified structure-activity approach to assign isotope effects to the individual elementary reaction steps in the oxidation sequence of CH<sub>4</sub> and some other VOCs. The approach builds on and extends the work by Gerst and Quay (2001) and Feilberg et al. (2007b). The description is generalized and allows the application, in principle, also to other compounds. The idea is that the C-H and C-D bonds – seen as reactive sites – have similar relative reaction probabilities in isotopically substituted, but otherwise identical molecules. The limitations of this approach are discussed for the reaction CH<sub>4</sub>+Cl. The same approach is applied to VOCs, which are important precursors of H<sub>2</sub> that need to be included into models. Unfortunately, quantitative information on VOC isotope effects and source isotope signatures is very limited and the isotope scheme at this time is limited to a strongly parameterized statistical approach, which neglects kinetic isotope effects. Using these concepts we implement a full hydrogen isotope scheme in a chemical box model and carry out a sensitivity study to identify those reaction steps and conditions that are most critical for the isotope composition of the final H<sub>2</sub> product. The reaction scheme is directly applicable in global chemistry models, which can thus include the isotope pathway of H<sub>2</sub> produced from CH<sub>4</sub> and VOCs in a consistent way

Approximate Turing Kernelization for Problems Parameterized by Treewidth

We extend the notion of lossy kernelization, introduced by Lokshtanov et al. [STOC 2017], to approximate Turing kernelization. An $\alpha$-approximate Turing kernel for a parameterized optimization problem is a polynomial-time algorithm that, when given access to an oracle that outputs $c$-approximate solutions in $O(1)$ time, obtains an $(\alpha \cdot c)$-approximate solution to the considered problem, using calls to the oracle of size at most $f(k)$ for some function $f$ that only depends on the parameter. Using this definition, we show that Independent Set parameterized by treewidth $\ell$ has a $(1+\varepsilon)$-approximate Turing kernel with $O(\frac{\ell^2}{\varepsilon})$ vertices, answering an open question posed by Lokshtanov et al. [STOC 2017]. Furthermore, we give $(1+\varepsilon)$-approximate Turing kernels for the following graph problems parameterized by treewidth: Vertex Cover, Edge Clique Cover, Edge-Disjoint Triangle Packing and Connected Vertex Cover. We generalize the result for Independent Set and Vertex Cover, by showing that all graph problems that we will call "friendly" admit $(1+\varepsilon)$-approximate Turing kernels of polynomial size when parameterized by treewidth. We use this to obtain approximate Turing kernels for Vertex-Disjoint $H$-packing for connected graphs $H$, Clique Cover, Feedback Vertex Set and Edge Dominating Set

Carbonic anhydrases CA1 and CA4 function in atmospheric CO2-modulated disease resistance

Main conclusion Carbonic anhydrases CA1 and CA4 attenuate plant immunity and can contribute to altered disease resistance levels in response to changing atmospheric CO2 conditions. Abstract β-Carbonic anhydrases (CAs) play an important role in CO2 metabolism and plant development, but have also been implicated in plant immunity. Here we show that the bacterial pathogen Pseudomonas syringae and application of the microbe-associated molecular pattern (MAMP) flg22 repress CA1 and CA4 gene expression in Arabidopsis thaliana. Using the CA double-mutant ca1ca4, we provide evidence that CA1 and CA4 play an attenuating role in pathogen- and flg22-triggered immune responses. In line with this, ca1ca4 plants exhibited enhanced resistance against P. syringae, which was accompanied by an increased expression of the defense-related genes FRK1 and ICS1. Under low atmospheric CO2 conditions (150 ppm), when CA activity is typically low, the levels of CA1 transcription and resistance to P. syringae in wild-type Col-0 were similar to those observed in ca1ca4. However, under ambient (400 ppm) and elevated (800 ppm) atmospheric CO2 conditions, CA1 transcription was enhanced and resistance to P. syringae reduced. Together, these results suggest that CA1 and CA4 attenuate plant immunity and that differential CA gene expression in response to changing atmospheric CO2 conditions contribute to altered disease resistance levels

Emission ratio and isotopic signatures of molecular hydrogen emissions from tropical biomass burning

In this study, we identify a biomass-burning signal in molecular hydrogen (H₂) over the Amazonian tropical rainforest. To quantify this signal, we measure the mixing ratios of H₂ and several other species as well as the H₂ isotopic composition in air samples that were collected in the BARCA (Balanço Atmosférico Regional de Carbono na Amazônia) aircraft campaign during the dry season. We derive a relative H₂ emission ratio with respect to carbon monoxide (CO) of 0.31 ± 0.04 ppb ppb⁻¹ and an isotopic source signature of −280 ± 41‰ in the air masses influenced by tropical biomass burning. In order to retrieve a clear source signal that is not influenced by the soil uptake of H₂, we exclude samples from the atmospheric boundary layer. This procedure is supported by data from a global chemistry transport model. The ΔH₂ / ΔCO emission ratio is significantly lower than some earlier estimates for the tropical rainforest. In addition, our results confirm the lower values of the previously conflicting estimates of the H₂ isotopic source signature from biomass burning. These values for the emission ratio and isotopic source signatures of H₂ from tropical biomass burning can be used in future bottom-up and top-down approaches aiming to constrain the strength of the biomass-burning source for H₂. Hitherto, these two quantities relied only on combustion experiments or on statistical relations, since no direct signal had been obtained from in-situ observations

Review of applications of SIMDEUM, a stochastic drinking water demand model with small temporal and spatial scale

Many researchers have developed drinking water demand models with various temporal and spatial scales. A limited number of models are available at a temporal scale of one second and a spatial scale of a single home. Reasons for building these models were described in the papers in which the models were introduced, along with a discussion on potential applications. However, the predicted applications are seldom re-examined. As SIMDEUM, a stochastic end-use model for drinking water demand, has often been applied in research and practice since it was developed, we are reexamining its applications in this paper. SIMDEUM’s original purpose was to calculate maximum demands in order to be able to design self-cleaning networks. Yet, the model has been useful in many more applications. This paper gives an overview of the many fields of application of SIMDEUM and shows where this type of demand model is indispensable and where it has limited practical value. This overview also leads to an understanding of requirements on demand models in various applications

Review of applications for SIMDEUM, a stochastic drinking water demand model with a small temporal and spatial scale

Many researchers have developed drinking water demand models with various temporal and spatial scales. A limited number of models is available at a temporal scale of 1 s and a spatial scale of a single home. The reasons for building these models were described in the papers in which the models were introduced, along with a discussion on their potential applications. However, the predicted applications are seldom re-examined. SIMDEUM, a stochastic end-use model for drinking water demand, has often been applied in research and practice since it was developed. We are therefore re-examining its applications in this paper. SIMDEUM's original purpose was to calculate maximum demands in order to design self-cleaning networks. Yet, the model has been useful in many more applications. This paper gives an overview of the many fields of application for SIMDEUM and shows where this type of demand model is indispensable and where it has limited practical value. This overview also leads to an understanding of the requirements for demand models in various applications

Rewiring of the Jasmonate Signaling Pathway in Arabidopsis during Insect Herbivory

Plant defenses against insect herbivores and necrotrophic pathogens are differentially regulated by different branches of the jasmonic acid (JA) signaling pathway. In Arabidopsis, the basic helix-loop-helix leucine zipper transcription factor (TF) MYC2 and the APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain TF ORA59 antagonistically control these distinct branches of the JA pathway. Feeding by larvae of the specialist insect herbivore Pieris rapae activated MYC2 transcription and stimulated expression of the MYC2-branch marker gene VSP2, while it suppressed transcription of ORA59 and the ERF-branch marker gene PDF1.2. Mutant jin1 and jar1-1 plants, which are impaired in the MYC2-branch of the JA pathway, displayed a strongly enhanced expression of both ORA59 and PDF1.2 upon herbivory, indicating that in wild-type plants the MYC2-branch is prioritized over the ERF-branch during insect feeding. Weight gain of P. rapae larvae in a no-choice setup was not significantly affected, but in a two-choice setup the larvae consistently preferred jin1 and jar1-1 plants, in which the ERF-branch was activated, over wild-type Col-0 plants, in which the MYC2-branch was induced. In MYC2- and ORA59-impaired jin1-1/RNAi-ORA59 plants this preference was lost, while in ORA59-overexpressing 35S:ORA59 plants it was gained, suggesting that the herbivores were stimulated to feed from plants that expressed the ERF-branch rather than that they were deterred by plants that expressed the MYC2-branch. The feeding preference of the P. rapae larvae could not be linked to changes in glucosinolate levels. Interestingly, application of larval oral secretion into wounded leaf tissue stimulated the ERF-branch of the JA pathway, suggesting that compounds in the oral secretion have the potential to manipulate the plant response toward the caterpillar-preferred ERF-regulated branch of the JA response. Our results suggest that by activating the MYC2-branch of the JA pathway, plants prevent stimulation of the ERF-branch by the herbivore, thereby becoming less attractive to the attacker