@phdthesis{Harbart2024,
  author    = {Harbart, Vanessa},
  title     = {The effect of protected cultivation on the nutritional quality of lettuce (Lactuca sativa var capitata L.) with a focus on antifogging additives in polyolefin covers},
  doi       = {10.25932/publishup-62937},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-629375},
  school      = {Universit{\"a}t Potsdam},
  pages     = {IV, 115},
  year      = {2024},
  abstract  = {Protected cultivation in greenhouses or polytunnels offers the potential for sustainable production of high-yield, high-quality vegetables. This is related to the ability to produce more on less land and to use resources responsibly and efficiently. Crop yield has long been considered the most important factor. However, as plant-based diets have been proposed for a sustainable food system, the targeted enrichment of health-promoting plant secondary metabolites should be addressed. These metabolites include carotenoids and flavonoids, which are associated with several health benefits, such as cardiovascular health and cancer protection. Cover materials generally have an influence on the climatic conditions, which in turn can affect the levels of secondary metabolites in vegetables grown underneath. Plastic materials are cost-effective and their properties can be modified by incorporating additives, making them the first choice. However, these additives can migrate and leach from the material, resulting in reduced service life, increased waste and possible environmental release. Antifogging additives are used in agricultural films to prevent the formation of droplets on the film surface, thereby increasing light transmission and preventing microbiological contamination. This thesis focuses on LDPE/EVA covers and incorporated antifogging additives for sustainable protected cultivation, following two different approaches. The first addressed the direct effects of leached antifogging additives using simulation studies on lettuce leaves (Lactuca sativa var capitata L). The second determined the effect of antifog polytunnel covers on lettuce quality. Lettuce is usually grown under protective cover and can provide high nutritional value due to its carotenoid and flavonoid content, depending on the cultivar. To study the influence of simulated leached antifogging additives on lettuce leaves, a GC-MS method was first developed to analyze these additives based on their fatty acid moieties. Three structurally different antifogging additives (reference material) were characterized outside of a polymer matrix for the first time. All of them contained more than the main fatty acid specified by the manufacturer. Furthermore, they were found to adhere to the leaf surface and could not be removed by water or partially by hexane. The incorporation of these additives into polytunnel covers affects carotenoid levels in lettuce, but not flavonoids, caffeic acid derivatives and chlorophylls. Specifically, carotenoids were higher in lettuce grown under polytunnels without antifog than with antifog. This has been linked to their effect on the light regime and was suggested to be related to carotenoid function in photosynthesis. In terms of protected cultivation, the use of LDPE/EVA polytunnels affected light and temperature, and both are closely related. The carotenoid and flavonoid contents of lettuce grown under polytunnels was reversed, with higher carotenoid and lower flavonoid levels. At the individual level, the flavonoids detected in lettuce did not differ however, lettuce carotenoids adapted specifically depending on the time of cultivation. Flavonoid reduction was shown to be transcriptionally regulated (CHS) in response to UV light (UVR8). In contrast, carotenoids are thought to be regulated post-transcriptionally, as indicated by the lack of correlation between carotenoid levels and transcripts of the first enzyme in carotenoid biosynthesis (PSY) and a carotenoid degrading enzyme (CCD4), as well as the increased carotenoid metabolic flux. Understanding the regulatory mechanisms and metabolite adaptation strategies could further advance the strategic development and selection of cover materials.},
  language  = {en}
}
@phdthesis{MichalikOnichimowska2022,
  author    = {Michalik-Onichimowska, Aleksandra},
  title     = {Real-time monitoring of (photo)chemical reactions in micro flow reactors and levitated droplets by IR-MALDI ion mobility and mass spectrometry},
  doi       = {10.25932/publishup-55729},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-557298},
  school      = {Universit{\"a}t Potsdam},
  pages     = {v, 68},
  year      = {2022},
  abstract  = {Eine nachhaltigere chemische Industrie erfordert eine Minimierung der L{\"o}sungsmittel und Chemikalien. Daher werden Optimierung und Entwicklung chemischer Prozesse vor einer Produktion in großem Maßstab in kleinen Chargen durchgef{\"u}hrt. Der entscheidende Schritt bei diesem Ansatz ist die Skalierbarkeit von kleinen Reaktionssystemen auf große, kosteneffiziente Reaktoren. Die Vergr{\"o}ßerung des Volumens des Reaktionsmediums geht immer mit der Vergr{\"o}ßerung der Oberfl{\"a}che einher, die mit dem begrenzenden Gef{\"a}ß in Kontakt steht. Da das Volumen kubisch, w{\"a}hrend die Oberfl{\"a}che quadratisch mit zunehmendem Radius skaliert, nimmt ihr Verh{\"a}ltnis nicht linear zu. Viele an der Grenzfl{\"a}che zwischen Oberfl{\"a}che und Fl{\"u}ssigkeit auftretende Ph{\"a}nomene k{\"o}nnen die Reaktionsgeschwindigkeiten und Ausbeuten beeinflussen, was zu falschen Prognosen aufgrund der kleinskaligen Optimierung f{\"u}hrt. Die Anwendung von schwebenden Tropfen als beh{\"a}lterlose Reaktionsgef{\"a}ße bietet eine vielversprechende M{\"o}glichkeit, die oben genannten Probleme zu vermeiden. In der vorgestellten Arbeit wurde eine effiziente Kopplung von akustisch schwebenden Tropfen und IM Spektrometer f{\"u}r die Echtzeit{\"u}berwachung chemischer Reaktionen entwickelt, bei denen akustisch schwebende Tropfen als Reaktionsgef{\"a}ße fungieren. Das Design des Systems umfasst die ber{\"u}hrungslose Probenahme und Ionisierung, die durch Laserdesorption und -ionisation bei 2,94 µm realisiert wird. Der Umfang der Arbeit umfasst grundlegende Studien zum Verst{\"a}ndnis der Laserbestrahlung von Tropfen im akustischen Feld. Das Verst{\"a}ndnis dieses Ph{\"a}nomens ist entscheidend, um den Effekt der zeitlichen und r{\"a}umlichen Aufl{\"o}sung der erzeugten Ionenwolke zu verstehen, die die Aufl{\"o}sung des Systems beeinflusst. Der Aufbau umfasst eine akustische Falle, Laserbestrahlung und elektrostatische Linsen, die bei hoher Spannung unter Umgebungsdruck arbeiten. Ein effektiver Ionentransfer im Grenzfl{\"a}chenbereich zwischen dem schwebenden Tropfen und dem IMS muss daher elektrostatische und akustische Felder vollst{\"a}ndig ber{\"u}cksichtigen. F{\"u}r die Probenahme und Ionisation wurden zwei unterschiedliche Laserpulsl{\"a}ngen untersucht, n{\"a}mlich im ns- und µs-Bereich. Die Bestrahlung {\"u}ber µs-Laserpulse bietet gegen{\"u}ber ns-Pulse mehrere Vorteile: i) das Tropfenvolumen wird nicht stark beeinflusst, was es erm{\"o}glichet, nur ein kleines Volumen des Tropfens abzutasten; ii) die geringere Fluenz f{\"u}hrt zu weniger ausgepr{\"a}gten Schwingungen des im akustischen Feld eingeschlossenen Tropfens und der Tropfen wird nicht aus dem akustischen Feld r{\"u}ckgeschlagen, was zum Verlust der Probe f{\"u}hren w{\"u}rde; iii) die milde Laserbestrahlung f{\"u}hrt zu einer besseren r{\"a}umlichen und zeitlichen Begrenzung der Ionenwolken, was zu einer besseren Aufl{\"o}sung der detektierten Ionenpakete f{\"u}hrt. Schließlich erm{\"o}glicht dieses Wissen die Anwendung der Ionenoptik, die erforderlich ist, um den Ionenfluss zwischen dem im akustischen Feld suspendierten Tropfen und dem IM Spektrometer zu induzieren. Die Ionenoptik aus 2 elektrostatischen Linsen in der N{\"a}he des Tropfens erm{\"o}glicht es, die Ionenwolke effektiv zu fokussieren und direkt zum IM Spektrometer-Eingang zu f{\"u}hren. Diese neuartige Kopplung hat sich beim Nachweis einiger basischer Molek{\"u}le als erfolgreich erwiesen. Um die Anwendbarkeit des Systems zu belegen, wurde die Reaktion zwischen N-Boc Cysteine Methylester und Allylalkohol in einem Chargenreaktor durchgef{\"u}hrt und online {\"u}berwacht. F{\"u}r eine Kalibrierung wurde der Reaktionsfortschritt parallel mittels 1H-NMR verfolgt. Der beobachtete Reaktionsumsatz von mehr als 50\% innerhalb der ersten 20 Minuten demonstrierte die Eignung der Reaktion, um die Einsatzpotentiale des entwickelten Systems zu bewerten.},
  language  = {en}
}
@phdthesis{Riebe2016,
  author    = {Riebe, Daniel},
  title     = {Experimental and theoretical investigations of molecular ions by spectroscopy as well as ion mobility and mass spectrometry},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-94632},
  school      = {Universit{\"a}t Potsdam},
  pages     = {143},
  year      = {2016},
  abstract  = {The aim of this thesis was the elucidation of different ionization methods (resonance-enhanced multiphoton ionization - REMPI, electrospray ionization - ESI, atmospheric pressure chemical ionization - APCI) in ion mobility (IM) spectrometry. In order to gain a better understanding of the ionization processes, several spectroscopic, mass spectrometric and theoretical methods were also used. Another focus was the development of experimental techniques, including a high resolution spectrograph and various combinations of IM and mass spectrometry. The novel high resolution 2D spectrograph facilitates spectroscopic resolutions in the range of commercial echelle spectrographs. The lowest full width at half maximum of a peak achieved was 25 pm. The 2D spectrograph is based on the wavelength separation of light by the combination of a prism and a grating in one dimension, and an etalon in the second dimension. This instrument was successfully employed for the acquisition of Raman and laser-induced breakdown spectra. Different spectroscopic methods (light scattering and fluorescence spectroscopy) permitting a spatial as well as spectral resolution, were used to investigate the release of ions in the electrospray. The investigation is based on the 50 nm shift of the fluorescence band of rhodamine 6G ions of during the transfer from the electrospray droplets to the gas phase. A newly developed ionization chamber operating at reduced pressure (0.5 mbar) was coupled to a time-of-flight mass spectrometer. After REMPI of H2S, an ionization chemistry analogous to H2O was observed with this instrument. Besides H2S+ and its fragments, H3S+ and protonated analyte ions could be observed as a result of proton-transfer reactions. For the elucidation of the peaks in IM spectra, a combination of IM spectrometer and linear quadrupole ion trap mass spectrometer was developed. The instrument can be equipped with various ionization sources (ESI, REMPI, APCI) and was used for the characterization of the peptide bradykinin and the neuroleptic promazine. The ionization of explosive compounds in an APCI source based on soft x-radiation was investigated in a newly developed ionization chamber attached to the ion trap mass spectrometer. The major primary and secondary reactions could be characterized and explosive compound ions could be identified and assigned to the peaks in IM spectra. The assignment is based on the comparison of experimentally determined and calculated IM. The methods of calculation currently available exhibit large deviations, especially in the case of anions. Therefore, on the basis of an assessment of available methods, a novel hybrid method was developed and characterized.},
  language  = {en}
}
@phdthesis{Kopka2008,
  author    = {Kopka, Joachim},
  title     = {Applied metabolome analysis : exploration, development and application of gas chromatography-mass spectrometry based metabolite profiling technologies},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-40597},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {The uptake of nutrients and their subsequent chemical conversion by reactions which provide energy and building blocks for growth and propagation is a fundamental property of life. This property is termed metabolism. In the course of evolution life has been dependent on chemical reactions which generate molecules that are common and indispensable to all life forms. These molecules are the so-called primary metabolites. In addition, life has evolved highly diverse biochemical reactions. These reactions allow organisms to produce unique molecules, the so-called secondary metabolites, which provide a competitive advantage for survival. The sum of all metabolites produced by the complex network of reactions within an organism has since 1998 been called the metabolome. The size of the metabolome can only be estimated and may range from less than 1,000 metabolites in unicellular organisms to approximately 200,000 in the whole plant kingdom. In current biology, three additional types of molecules are thought to be important to the understanding of the phenomena of life: (1) the proteins, in other words the proteome, including enzymes which perform the metabolic reactions, (2) the ribonucleic acids (RNAs) which constitute the so-called transcriptome, and (3) all genes of the genome which are encoded within the double strands of desoxyribonucleic acid (DNA). Investigations of each of these molecular levels of life require analytical technologies which should best enable the comprehensive analysis of all proteins, RNAs, et cetera. At the beginning of this thesis such analytical technologies were available for DNA, RNA and proteins, but not for metabolites. Therefore, this thesis was dedicated to the implementation of the gas chromatography - mass spectrometry technology, in short GC-MS, for the in-parallel analysis of as many metabolites as possible. Today GC-MS is one of the most widely applied technologies and indispensable for the efficient profiling of primary metabolites. The main achievements and research topics of this work can be divided into technological advances and novel insights into the metabolic mechanisms which allow plants to cope with environmental stresses. Firstly, the GC-MS profiling technology has been highly automated and standardized. The major technological achievements were (1) substantial contributions to the development of automated and, within the limits of GC-MS, comprehensive chemical analysis, (2) contributions to the implementation of time of flight mass spectrometry for GC-MS based metabolite profiling, (3) the creation of a software platform for reproducible GC-MS data processing, named TagFinder, and (4) the establishment of an internationally coordinated library of mass spectra which allows the identification of metabolites in diverse and complex biological samples. In addition, the Golm Metabolome Database (GMD) has been initiated to harbor this library and to cope with the increasing amount of generated profiling data. This database makes publicly available all chemical information essential for GC-MS profiling and has been extended to a global resource of GC-MS based metabolite profiles. Querying the concentration changes of hundreds of known and yet non-identified metabolites has recently been enabled by uploading standardized, TagFinder-processed data. Long-term technological aims have been pursued with the central aims (1) to enhance the precision of absolute and relative quantification and (2) to enable the combined analysis of metabolite concentrations and metabolic flux. In contrast to concentrations which provide information on metabolite amounts, flux analysis provides information on the speed of biochemical reactions or reaction sequences, for example on the rate of CO2 conversion into metabolites. This conversion is an essential function of plants which is the basis of life on earth. Secondly, GC-MS based metabolite profiling technology has been continuously applied to advance plant stress physiology. These efforts have yielded a detailed description of and new functional insights into metabolic changes in response to high and low temperatures as well as common and divergent responses to salt stress among higher plants, such as Arabidopsis thaliana, Lotus japonicus and rice (Oryza sativa). Time course analysis after temperature stress and investigations into salt dosage responses indicated that metabolism changed in a gradual manner rather than by stepwise transitions between fixed states. In agreement with these observations, metabolite profiles of the model plant Lotus japonicus, when exposed to increased soil salinity, were demonstrated to have a highly predictive power for both NaCl accumulation and plant biomass. Thus, it may be possible to use GC-MS based metabolite profiling as a breeding tool to support the selection of individual plants that cope best with salt stress or other environmental challenges.},
  language  = {en}
}
@phdthesis{Baessler2008,
  author    = {B{\"a}ßler, Olivia},
  title     = {Identifizierung und Charakterisierung IgE- reaktiver Proteine in der Tomate (Lycopersicon esculentum)},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-26953},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Zur Detektion neuer IgE- reaktiver Proteine wurde in dieser Arbeit ein zweidimensionales Proteintrennverfahren verwendet. Resultierende Proteinfraktionen wurden mithilfe von 18 tomatensensibiliesierten Patientenseren im Immunoblot getestet. Detektierte Proteine in der SDS-PAGE wurden mittels LC-MS/MS identifiziert. Dadurch konnten 2 Tomatensamenproteine, die im Immunoblot ein IgE- reaktives Signal zeigten eindeutig mittels Massenspektrometrie identifiziert werden. Diese Proteine sind Legumin und Vicilin. Durch Sequenzabgleich und Proteinstrukturmodellierung im Vergleich zu bereits bekannten Allergenen (Erdnuss und Cashewnuss), konnte eine hohe Homologie gezeigt werden.},
  language  = {de}
}
@phdthesis{Bahrke2008,
  author    = {Bahrke, Sven},
  title     = {Mass spectrometric analysis of chitooligosaccharides and their interaction with proteins},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-20179},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {Chitooligosaccharides are composed of glycosamin and N-acetylglycisamin residues. Gel permeations chromatography is employed for the separation of oligomers, cation exchange chromatography is used for the separation of homologes and isomers. Trideuterioacetylation of the chitooligosaccharides followed by MALDI-TOF mass spectrometry allowes for the quantitation of mixtures of homologes. vMALDI LTQ multiple-stage MS is employed for quantitative sequencing of complex mixtures of heterochitooligosaccharides. Pure homologes and isomers are applied to biological assays. Chitooligosaccahrides form high-affinity non-covalent complexes with HC gp-39 (human cartilage glycoprotein of 39 kDa). The affinity of the chitooligosaccharides depends on DP, FA and the sequence of glycosamin and N-acetylglycosamin moieties. (+)nanoESI Q TOF MS/MS is used for identification of a high-affinity binding chitooligosaccharide of a non-covalent chitinase B - chitooligosaccharide complex. DADAA is identified as the heterochitoisomer binding with highest affinity and biostability to HC gp-39. Fluorescence based enzyme assays confirm the results.},
  language  = {en}
}
@phdthesis{Birkemeyer2005,
  author    = {Birkemeyer, Claudia Sabine},
  title     = {Signal-metabolome interactions in plants},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7144},
  school      = {Universit{\"a}t Potsdam},
  year      = {2005},
  abstract  = {From its first use in the field of biochemistry, instrumental analysis offered a variety of invaluable tools for the comprehensive description of biological systems. Multi-selective methods that aim to cover as many endogenous compounds as possible in biological samples use different analytical platforms and include methods like gene expression profile and metabolite profile analysis. The enormous amount of data generated in application of profiling methods needs to be evaluated in a manner appropriate to the question under investigation. The new field of system biology rises to the challenge to develop strategies for collecting, processing, interpreting, and archiving this vast amount of data; to make those data available in form of databases, tools, models, and networks to the scientific community. On the background of this development a multi-selective method for the determination of phytohormones was developed and optimised, complementing the profile analyses which are already in use (Chapter I). The general feasibility of a simultaneous analysis of plant metabolites and phytohormones in one sample set-up was tested by studies on the analytical robustness of the metabolite profiling protocol. The recovery of plant metabolites proved to be satisfactory robust against variations in the extraction protocol by using common extraction procedures for phytohormones; a joint extraction of metabolites and hormones from plant tissue seems practicable (Chapter II). Quantification of compounds within the context of profiling methods requires particular scrutiny (Chapter II). In Chapter III, the potential of stable-isotope in vivo labelling as normalisation strategy for profiling data acquired with mass spectrometry is discussed. First promising results were obtained for a reproducible quantification by stable-isotope in vivo labelling, which was applied in metabolomic studies. In-parallel application of metabolite and phytohormone analysis to seedlings of the model plant Arabidopsis thaliana exposed to sulfate limitation was used to investigate the relationship between the endogenous concentration of signal elements and the 'metabolic phenotype' of a plant. An automated evaluation strategy was developed to process data of compounds with diverse physiological nature, such as signal elements, genes and metabolites - all which act in vivo in a conditional, time-resolved manner (Chapter IV). Final data analysis focussed on conditionality of signal-metabolome interactions.},
  subject      = {Pflanzenhormon},
  language  = {en}
}