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We present classical and hybrid modeling approaches for genetic regulatory networks focusing on promoter analysis for negatively and positively autoregulated networks. The main aim of this thesis is to introduce an alternative mathematical approach to model gene regulatory networks based on piecewise deterministic Markov processes (PDMP). During somitogenesis, a process describing the early segmentation in vertebrates, molecular oscillators play a crucial role as part of a segmentation clock. In mice, these oscillators are called Hes1 and Hes7 and are commonly modeled by a system of two delay differential equations including a Hill function, which describes gene repression by their own gene products. The Hill coefficient, which is a measure of nonlinearity of the binding processes in the promoter, is assumed to be equal to two, based on the fact that Hes1 and Hes7 form dimers.However, by standard arguments applied to binding analysis, we show that a higher Hill coefficient is reasonable. This leads to results different from those in literature which requires a more sophisticated model. For the Hes7 oscillator we present a system of ordinary differential equations including a Michaelis-Menten term describing a nonlinear degradation of the proteins by the ubiquitinpathway. As demonstrated by the Hes1 and Hes7 oscillator, promoter behavior can have strong influence on the dynamical behavior of genetic networks. Since purely deterministic systems cannot reveal phenomenons caused by the inherent random fluctuations, we propose a novel approach based on PDMPs. Such models allow to model binding processes of transcription factors to binding sites in a promoter as random processes, where all other processes like synthesis, degradation or dimerization of the gene products are modeled in deterministic manner. We present and discuss a simulation algorithm for PDMPs and apply it to three types of genetic networks: an unregulated gene, a toggle switch, and a positively autoregulated network. The different regulation characteristics are analyzed and compared by numerical means. Furthermore, we determine analytical solutions of the stationary distributions of one negatively, and three positively autoregulated networks. Based on these results, we analyze attenuation of noise in a negative feedback loop, and the question of graded or binary response in autocatalytic networks.
The introduction of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) enabled the separation and visualization of a substantial fraction of an organism’s entire proteome, and when mass spectrometry entered protein science, these proteins became even amenable to identification on a grand scale. Nevertheless, important classes of proteins elude a separation on classical 2 D gels, as the ones showing extremes in isoelectric point or molecular weight, and foremost very hydrophobic proteins naturally embedded in lipid membranes. This thesis aimed at the establishment and adaptation of alternatives to 2-D PAGE. New techniques allowing for an identification and quantification of critical protein classes were designed and adopted to physiological questions in the Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus. In a comprehensive study on cytoplasmic proteins of S. aureus COL the number of proteins identified by a 2-D gel based approach could be extended by 650 proteins employing gel free technologies. Application of these complementary methods resulted in the establishment of a comprehensive reference map of the cytosolic proteome in growing and non-growing S. aureus cells which can serve as basis for further physiological investigations. Gel free separation of complex protein digests was likewise used in a quantitative study on heat stress in B. subtilis. By implementation of the iTRAQ® technology four different physiological states could be relatively quantified in one experiment. A parallel generation of 2-D gel based data enabled the depiction of strengths and weaknesses of protein quantitation by both, spot intensities on 2-D gels and iTRAQ® signal intensities in MS/MS spectra. Furthermore, new insights into heat sensitivity of pivotal enzymes involved in amino acid biosynthesis could be delivered. The institution of gel free approaches and advancements in 2-D PAGE provide the tools to penetrate into yet unamenable scopes of proteomes. A review on proteome coverage in B. subtilis gives an overview on the strategies which have been explored for most comprehensive protein identification in various sub-proteomes. Although more than one third of B. subtilis’ open reading frames could be demonstrated on protein level, one has to be aware of the fact that it still is a long way to achieve complete coverage of its proteome. Integral membrane proteins make up about one quarter of the entirety of proteins in a cell. Despite their large portion they are clearly understudied due to the intricacy of identification. Their low abundance and non-accessibility of membrane-spanning domains represent major experimental difficulties. The establishment of a protocol efficiently depleting cytosolic proteins by membrane shaving and targeting trans-membrane peptides by novel digestion strategies essentially facilitated identification of highly hydrophobic integral membrane proteins. This protocol was not only successfully applied to the membrane proteome of growing S. aureus cells, but was shown to be applicable in B. subtilis as well. Both studies displayed the novel membrane shaving approach to be highly complementary to a previously established separation of membrane proteins via 1 D PAGE. A combination of the two techniques resulted in identification of about half of the theoretical membrane proteome in both bacteria, and hence layed the foundation for advanced and quantitative analyses. In this regard, 14N/15N metabolically labeled membrane samples of growing and non-growing cells of S. aureus COL were relatively quantified revealing a significant difference in amount for more than one third of the proteins. A corresponding experimental setup was used to compare the membrane proteomes of S. aureus SA113 and its mutant deficient in the lysylphosphatidylglycerol synthetase MprF. Interesting quantitative differences were obtained for proteins most likely involved in the regulation of cellular surface net charge as well as for virulence-associated proteins.
Infrared laser absorption spectroscopy (IRLAS) employing both tuneable diode and quantum cascade lasers (TDLs, QCLs) has been applied with both high sensitivity and high time resolution to plasma diagnostics and trace gas measurements.
TDLAS combined with a conventional White type multiple pass cell was used to detect up to 13 constituent molecular species in low pressure Ar/H2/N2/O2 and Ar/CH4/N2/O2 microwave discharges, among them the main products such as H2O, NH3, NO and CO, HCN respectively. The hydroxyl radical has been measured in the mid infrared (MIR) spectral range in-situ in both plasmas yielding number densities of between 1011 ... 1012 cm-3. Strong indications of surface dominated formation of either NH3 or N2O and NO were found in the H2-N2-O2 system. In methane containing plasmas a transition between deposition and etching conditions and generally an incomplete oxidation of the precursor were observed.
The application of QCLs for IRLAS under low pressure conditions employing the most common tuning approaches has been investigated in detail. A new method of analysing absorption features quantitatively when the rapid passage effect is present is proposed. If power saturation is negligible, integrating the undisturbed half of the line profile yields accurate number densities without calibrating the system. By means of a time resolved analysis of individual chirped QCL pulses the main reasons for increased effective laser line widths could be identified. Apart from the well-known frequency down chirp non-linear absorption phenomena and bandwidth limitations of the detection system may significantly degrade the performance and accuracy of inter pulse spectrometers. The minimum analogue bandwidth of the entire system should normally not fall below 250 MHz.
QCLAS using pulsed lasers has been used for highly time resolved measurements in reactive plasmas for the first time enabling a time resolution down to about 100 ns to be achieved. A temperature increase of typically less than 50 K has been established for pulsed DC discharges containing Ar/N2 and traces of NO. The main NO production and depletion reactions have been identified from a comparison of model calculations and time resolved measurements in plasma pulses of up to 100 ms. Considerable NO struction is observed after 5 ... 10 ms due to the impact of N atoms.
Finally, thermoelectrically cooled pulsed and continuous wave (cw) QCLs have been employed for high finesse cavity absorption spectroscopy in the MIR. Cavity ring down spectroscopy (CRDS) has been performed with pulsed QCLs and was found to be limited by the intrinsic frequency chirp of the laser suppressing an efficient intensity build-up inside the cavity. Consequently the accuracy and advantage of an absolute internal absorption calibration is not achievable. A room temperature cw QCL was used in a complementary cavity enhanced absorption spectroscopy (CEAS) configuration which was equipped with different cavities of up to ~ 1.3 m length. This spectrometer yielded path lengths of up to 4 km and a noise equivalent absorption down to 4 x 10-8 cm-1Hz-1/2. The corresponding molecular concentration detection limit (e.g. for CH4, N2O and C2H2 at 1303 cm-1/7.66 μm) was generally below 1 x 1010 cm-3 for 1 s integration times and one order of magnitude less for 30 s integration times. The main limiting factor for achieving even higher sensitivity is the residual mode noise of the cavity. Employing a ~ 0.5 m long cavity the achieved sensitivity was good enough for the selective measurement of trace atmospheric constituents at 2.2 mbar.
(A paperback version is published by Logos under ISBN 978-3-8325-2345-9.)
Tunable diode laser absorption spectroscopy of argon metastable atoms in Ar/C2H2 dusty plasmas
(2009)
The tunable diode laser absorption spectroscopy method was used to measure Ar metastable density in order to study the dust growth process in hydrocarbon-containing plasmas. A simple model was proposed that successfully interprets the experimental results of pristine plasmas. The model is also suitable for explaining the influence of dust particle size on metastable density and for examining the dust growth process. The metastable density responded strictly to the formation of dust particles and their growth in processing plasmas. Using metastable density as an indicator is, therefore, a non-intrusive and effective method for the study of the dust growth process in hydrocarbon-containing plasmas.
The Caribbean is a geologically complex region with several different plate boundary interactions. Geodynamic reconstructions of the northwestern Caribbean region have been particularly controversial in terms of the number of arcs, subduction polarity, and timing of collision. This thesis develops a refined tectonic reconstruction for the northwestern Caribbean based on a review of geological data of Cuba and a regional analysis within the northwestern Caribbean context. With regard to plausibility, significant emphasis was put on the degree and qualitiy of visualization. Three crustal sections across key areas in western, central, and eastern Cuba have been constructed in order to conduct an evolutionary interpretation in three dimensions. Western and central Cuba constitute an orogenic belt resulting from the collision of a mid- to Late Cretaceous volcanic arc - the "Great Caribbean Arc" - with the southern paleomargin of North America. The collision process apparently started in the Campanian, but major north- to northeast-directed thrusting processes at the southern Bahamas margin culminated during the Paleocene. A continous southwest-dipping polarity of the "Great Caribbean Arc", at least from the Aptian-Albian, can be infered from (1) its Late Cretaceous approach towards the North American margin, (2) the magnitude of top to the north directed tectonic transport in the Cuba orogenic belt, and (3) the internal structures of the metamorphic fore-arc assemblages and their evolution on the north side of the arc. An Early Cretaceous southwest-dipping origin of the "Great Caribbean Arc" along the northern fringe of the Chortís Block appears to be in all probability. This concept provides a link between (1) middle Late Cretaceous collision processes along the Matagua suture zone, (2) the Turonian termination of "Great Caribbean Arc"-activity on Jamaica, and (3) the late Campanian onset of collision in the Cuba orogenic belt. The collision of the "Great Caribbean Arc" with the Bahamas margin hampered relative northward motion of the Caribbean Plate from the late Campanian onward. Continued northward push finally resulted in the commencement of north-dipping subduction. Late Cretaceous commencement of north-dipping subduction was accompanied by superposition of oceanic crust and large-scale north-directed gravity sliding on the upper plate, as documented by ophiolitic slide-masses and Maastrichtian olistostromes in eastern Cuba (Nipe - Cristal and Moa Baracoa ophiolite massifs) as well as on Jamaica (ophiolites of the Bath-Dunrobin Complex) and the southern peninsula of Hispaniola. Progress of north-dipping subduction was responsible for the emergence of a Paleocene to Middle Eocene volcanic arc which spanned the northwestern Caribbean along the southern boundary of the Yucatán Basin while the Chortís Block and the Nicaragua Rise were still in a paleoposition to the south of the Maya Block. North-dipping subduction and the associated volcanic arc isolated the Yucatán Basin from its original affiliation to the Caribbean Plate. Relative northward motion of the Caribbean Plate and activity of the Paleogene volcanic arc stopped after the Eocene arrival of thickened oceanic crust of the Caribbean Large Igneous Province at the north-dipping subduction zone. After the late Early Eocene commencement of spreading at the Mid-Cayman Rise, North America - Caribbean relative motion was taken up along the sinistral Oriente Fault with estimated amounts of 800 to 1000 km offset since the Middle Eocene. This transform margin dissmembered the northwestern Caribbean extend of the Paleocene to Middle Eocene volcanic arc. Its eastern bend was uncoupled in the course of this process and may be represented by the Aves Ridge. South-central Hispaniola can be restored to a Middle Eocene position to the south of eastern Cuba, which accounts for an approximate Cenozoic displacement of 200 to 300 km. Therefore, most of the western prolongation of the Oriente Fault must be accommodated at the northern bounding-faults of the southern peninsula of Hispaniola. The proposed synthesis is in clear accordance with the paradigm of plate tectonics, corroborating its capability to incorporate even a complex region like the Caribbean.
Application of quantum cascade laser absorption spectroscopy to studies of fluorocarbon molecules
(2009)
The recent advent of quantum cascade lasers (QCLs) enables room-temperature mid-infrared spectrometer operation which is particularly favourable for industrial process monitoring and control, i.e. the detection of transient and stable molecular species. Conversely, fluorocarbon containing radio-frequency discharges are of special interest for plasma etching and deposition as well as for fundamental studies on gas phase and plasma surface reactions. The application of QCL absorption spectroscopy to such low pressure plasmas is typically hampered by non-linear effects connected with the pulsed mode of the lasers. Nevertheless, adequate calibration can eliminate such effects, especially in the case of complex spectra where single line parameters are not available. In order to facilitate measurements in fluorocarbon plasmas, studies on complex spectra of CF4 and C3F8 at 7.86 μm (1269 – 1275 cm-1) under low pressure conditions have been performed. The intra-pulse mode, i.e. pulses of up to 300 ns, was applied yielding highly resolved spectral scans of ∼ 1 cm-1 coverage. Effective absorption cross sections were determined and their temperature dependence was studied in the relevant range up to 400 K and found to be non-negligible.
Fluorocarbon containing capacitively coupled radio frequency (cc-rf) plasmas are widely used in technical applications and as model systems for fundamental investigations of complex plasmas. Absorption spectroscopy based on pulsed quantum cascade lasers (QCL) was applied in the mid-IR spectral range of 1269-1275 cm-1. Absolute densities of the precursor molecule CF4 and of the stable product C3F8 were measured with a time resolution of up to 1 ms in pulsed CF4/H2 asymmetrical cc-rf (13.56 MHz) discharges. For this purpose both the non-negligible temperature dependence of the absorption coefficients and the interference of the absorption features of CF4 and C3F8 had to be taken into account in the target spectral range. Therefore, at two different spectral positions composite absorption spectra were acquired under the same plasma conditions in order to discriminate between CF4 and C3F8 contributions. A total consumption of∼ 12 % was observed for CF4 during a 1 s plasma pulse, whereas C3F8 appeared to be produced mainly from amorphous fluorocarbon layers deposited at the reactor walls. A gas temperature increase by ∼ 100 K in the plasma pulse was estimated from the measurements. Additionally, not yet identified unresolved absorption (potentially from the excited CF4 molecule) was found during the àon-phase'.
Discovery of novel Baeyer-Villiger monooxygenases and their application in organic synthesis.
(2009)
The application of BVMOs in kinetic resolution is a versatile alternative for the synthesis of optically pure esters. Within this thesis BVMOs proved to be highly active against a broad range of linear and aryl aliphatic ketones yielding a variety of enantiopure products. Among the beta-hydroxy ketones several CHMOs and BVMOPsfl showed the best results (E > 100), whereas the application of the latter enzyme also allowed access to the abnormal esters (regioisomeric excess > 40%). Interestingly, some enzymes showed a reduced activity and selectivity with a growing chain length of the ketone, suggesting that middle-chain ketones (C8-C10) might be preferred. Moreover, the production of optically pure 1,2-diols was observed (yields 8-50%), resulting from an in vivo hydrolysis of the 2-hydroxy alkyl acetates. Regarding the N-protected beta-amino ketones, results were different. While the majority of CHMOs catalyzed linear substrates showing high enantioselectivities (for CHMOBrevi1 and CHMOBrachy E > 100, c = 40-50%), BVMOPsfl did not convert nitrogen bearing linear ketones, although this might also be justified with the methylcarbamate protecting group. Interestingly, the number of BVMOs catalyzing oxidation of spatially more demanding linear branched beta-amino ketones was greatly reduced, indicating steric hindrance that was also combined with a decrease in selectivity. Similar to the observation for beta-hydroxy ketones, also the 2 amino alkyl acetates hydrolyzed furnishing 2-amino alcohols (yields 9-52%). Moreover, hydrolysis of the “abnormal“ esters allowed an alternative access to valuable native and non-native β-amino acids. In a two step process, using CDMO from R. ruber and CAL-B, it was possible to generate N-protected (+)-beta-leucine. During kinetic resolutions of aryl aliphatic ketones it was observed that the highest enantio¬selectivities could be achieved utilizing HAPMOJD1, HAPMOACB and PAMO, enzymes typically preferring aromatic substrates. Biotransformation with 3-phenyl-2-butanone revealed an E-value > 100 for HAPMOJD1 (S-selective). Nevertheless, also BVMOPsfl converted this sub¬strate (E = 43), and also CHMOAcineto and CPMO oxidized it, although selectivity was rather low (E < 5). Interestingly, BVMOKT2440 was the only examined enzyme showing R selectivity (E = 13). Additionally, increasing the scale and performing biotransformation in a baffled flask could increase enantioselectivity of BVMOPsfl from E = 43 to 82. The discovery of novel enzymes with diverse properties is still a main goal of the biotechnological industry. Within these studies, two BVMOs (BVMOKT2440 and HAPMOJD1) could be successfully amplified from genomic DNA using different PCR-methods. Then, expression in E. coli was optimized, revealing that the reduction of expression temperature, implementation of E. coli JM109 or RosettaTM (DE3), possessing the pRARE plasmid to facilitate translation of rare codons in the latter case, and/or co-expression of chaperones (pGro7: GroEL/ES-familiy) could increase the amount of soluble and active protein. Both enzymes were subjected to biocatalysis and it was found that BVMOKT2440 preferentially oxidized linear ketones, while HAPMOJD1 dominantly converted aryl aliphatic ketones. The latter enzyme could be purified by anion exchange and affinity chromatography allowing examination of kinetic parameters. Thereby, HAPMOJD1 displayed lowest KM-values for acetophenone derivatives bearing their substituent in para-position (KM < 320 µM). Moreover, also aldehydes and heteroaromatic compounds were oxidized and also sulfoxidation was observed. Interestingly it was found, that both BVMO genes are located in the direct neighborhood of a dehydrogenase and a hydrolase. This led to the suggestion that these enzymes may be metabolically connected in the degradation of their natural substrate.
Medulloblastoma is one of the most common malignant childhood brain tumors. Although advances in multimodal treatment have significantly improved the survival rate, the outcome of children is still very poor. Therefore, there is an urgent need to develop novel approaches that can increase survival and reduce long term side effects of patients. Histone deacetylase inhibitors (HDIs) have emerged as a promising new class of antineoplastic agents in cancer therapy. Among them, suberoylanilide hydroxamic acid (SAHA, vorinostat, Zolinza®) is a highly potential HDI which has been approved for treatment of cutaneous T-cell lymphoma and is currently used for treatment of various tumor cell types both in vivo and in vitro. However, only little information has been reported on the effects of SAHA on primary central nervous system (CNS) tumors including medulloblastoma. The DAOY cell line represents the most widely used model cell line for investigation of medulloblastoma. In a recent study, it was reported that SAHA induces apoptosis and cell cycle arrest of DAOY cells (Sonnemann et al., 2006). However, the molecular mechanisms underlying this antitumor activity are still not clear. Therefore, in this study, effects of SAHA on DAOY cells were analysed at the protein level by using both gel-based and gel-free proteomic approaches. A 2D proteome reference map of DAOY cells in pH range of 4-7 was created from control and 10 µM SAHA treated cells via a combined analysis using 2D electrophoresis and MALDI-TOF/TOF-MS. This reference map covers 1196 identified protein spots of more than 770 distinct proteins. This is the first report of a 2D proteome map of SAHA treated DAOY cells. Moreover, the number of covered proteins was increased with the aid of a 1D-RP-LC-ESI-MS/MS analysis. Both methods together gave rise to a total of over 1200 distinct protein species, which is the largest catalogue of proteins identified in DAOY cells so far. In SAHA treated cells, a series of proteins were found to be subjected to protein degradation after treatment with the drug, including mainly cytoskeleton proteins (e.g. beta-tubulin, beta/gamma-actin, vimentin, filamin interacting protein 1), heat shock protein HS90B and a component of the FACT chromosomal remodelling complex (SSRP1). Most of those proteins are known substrates for caspases. Interestingly, several of these protein degradations are reported as typical apoptotic events in brain cells such as fragmentations of lamin A/C, alpha-spectrin, myosin-9 and SSRP1. The 2D reference map was then used as an annotated database for further investigation of changes in protein expression and protein modification profiles of DAOY cells following SAHA treatment. By using the 2D-DIGE technique, SAHA was found to induce significant changes in protein levels of DAOY cells, especially at the concentration of 10 µM while considerably fewer changes in the protein pattern were observed after treatment with the lower dose of 2 µM. Quantitative analysis of total protein extracts using the 2D-DIGE technique (employing pH range of 4-7) and spectral counting (employing a 1D-RP-LC separation) resulted in the identification of 213 differentially expressed proteins after treatment with 10 µM SAHA. Most of the targeted proteins belong to the groups of cytoskeleton proteins (e.g. lamin B1, calreticulin, dynexin), heat shock proteins (e.g. HSP71, HSP7C, CH60, GRP78) and brain signal transductors (e.g. 14-3-3E, 14-3-3T, CRK, MARCS). Other proteins that changed in levels after SAHA treatment include proteins involved in chromatin remodelling (e.g. RUBV1, RUBV2), transcription regulation (e.g. YBOX, CBX5), redox regulation (e.g. TXND4, TXND5, BIEA), metabolism (e.g. G6PI, K6PP, LDHB) and RNA processing (HNRP K). In addition, cathepsin D, one of autophagic executors, was increased by SAHA treatment while different subunits of the 26S proteasome complex were decreased in levels after addition of SAHA. Interestingly, we found alterations of mitochondrial proteins indicating the perturbation of mitochondrial function. VDACs are pore forming proteins located on the outer mitochondrial membrane which is known to play an important role in the release of apoptogenic proteins such as cytochrome-c from mitochondria to cytoplasm and induction of apoptosis. In this study, VDAC1 and VDAC3 were found to be overexpressed after incubation with SAHA, which might lead to an extensive release of apoptogenic proteins. This result is consistent with the study of Sonnemann and co-workers showing that SAHA induced the mitochondrial apoptotic pathway of DAOY cells (Sonnemann et al., 2006). Furthermore, these results are also in agreement with the previously known antitumor activities of SAHA reported for other cancer cell lines, e.g. the up-regulation of heat shock proteins, prostaglandin synthase 3, ubiquinol cytochrome c reductase or the down-regulation of MARCS proteins. …………………
Age-related brain injuries including stroke, are a major cause of physical and mental disabilities. Therefore studying the basic mechanism underlying functional recovery after brain stroke in middle aged subjected it is of considerable clinical interest. Data from our lab and elsewhere indicate that, behaviorally, middle aged rats were more severely impaired by stroke than were young rats, and they also showed diminished functional recovery. Infarct volume did not differ significantly in young and middle aged animals, but critical differences were apparent in the cytological response to stroke, most notably an age-related acceleration of the establishment of the glial scar. The early infarct in older rats is associated with a premature accumulation of BrdU-positive microglia and astrocytes, persistence of activated oligodendrocytes, a high incidence of neuronal degeneration, and accelerated apoptosis. In middle aged rats, neuroepithelial-positive cells were rapidly incorporated into the glial scar, but these neuroepithelial-like cells did not make a significant contribution to neurogenesis in the infarcted cortex in young or middle aged animals. Stroke is accompanied by a strong inflammatory reaction in the brain. We hypothesized that a mild systemic inflammatory reaction as caused by periodontal disease prior to stroke onset, may exert a neuroprotective effect in a rat model of focal ischemia. To test this hypothesis, marginal periodontitis was induced in BB/LL Wistar rats for 3 weeks. Two weeks after periodontitis initiation, focal cerebral ischemia was produced by reversible occlusion of the right middle cerebral artery. After a survival time of 7 days after ischemia, rat brains were analyzed. In addition, markers of systemic inflammation were determined in a different group of laboratory animals at 14 days after the onset of periodontitis. We found that rats with a mild systemic inflammation had a significantly reduced infarct volume and a significant reduction in the number of brain macrophages in the infarcted area. Conclusions: The available evidence indicates that the middle aged brain has the capability to mount a cytoproliferative response to injury, but the timing of the cellular and genetic response to cerebral insult is deregulated in middle aged animals, thereby further compromising functional recovery. In addition we found that that mild systemic inflammation elicited prior to stroke onset may have a neuroprotective effect in rats by reducing the infarct volume and tissue destruction by brain macrophages.