Fakultät Naturwissenschaften

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Biologie, Ernährungs-wissenschaften und Lebensmittelwissenschaften sind die Schwerpunkte der Fakultät. Die Forschung befasst sich mit Schlüsselthemen der Life Sciences.

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10 W-Average-Power Single-Frequency Ti:sapphire Laser with Tuning Agility – A Breakthrough in High-Resolution 3D Water-Vapor Measurement
(2018) Metzendorf, Simon; Wulfmeyer, Volker
The differential absorption lidar (DIAL) technique is well suited for measuring the humidity field of the atmosphere with high spatial and temporal resolution as well as accuracy. The water-vapor DIAL of the University of Hohenheim is a mobile, ground-based, scanning system. The DIAL methodology and the application in the Hohenheim-DIAL impose stringent requirements on the laser transmitter. In this thesis, a new laser transmitter was realized and employed. It is a pulsed, actively frequency-stabilized titanium-sapphire laser system, pumped with a Nd:YAG master-oscillator power-amplifier (MOPA) and alternately seeded by two diode lasers. As pump source, two commercially custom-made, diode-pumped, Q-switched, and frequency-doubled Nd:YAG lasers in MOPA architecture were employed. The relevant properties for pumping the Ti:sapphire laser were studied. The second Nd:YAG MOPA provides a considerably higher average output power (up to P = 63 W at 532 nm, or a pulse energy of up to E = 210 mJ at a repetition rate of f = 300 Hz) and an almost ideal top-hat beam profile. Thus, efficient end-pumping of the Ti:sapphire crystal was enabled without any optical damage. The components for injection seeding of the titanium-sapphire laser, making narrowband operation at two alternating frequencies (online and offline) possible, were substantially improved. Now, advanced commercial external-cavity diode lasers (ECDL) are applied. With an analog regulation signal of a wavelength meter, the frequency of an ECDL can be stabilized precisely to a defined value (standard deviation < 1 MHz). Optionally, the frequency can be tuned according to various mathematical functions. The online-offline-switching is accomplished with a fiber switch. The crosstalk is extraordinarily low (< -61 dB), the switching time sufficiently short (~ 1.5 ms), and the spatial overlap of the signals, due to the waveguide, almost perfect. The power of the seeders in front of the resonator is more than sufficient, 17-20 mW. The Ti:sapphire laser consists of a ring resonator with four mirrors in a bow-tie layout. With adequate components, the operation wavelength at 818 nm is pre-selected and unidirectional propagation is ensured. The laser crystal is installed in an in-house-manufactured cooling mount, of which two designs were utilized and compared. The gain-switched Ti:sapphire laser was developed to operate in a dynamically stable state of the thermal lens, which arises in the crystal at high powers. To this end, the resonator was theoretically analyzed beforehand and the focal length of the thermal lens measured. The implementation of a cylindrical lens compensates the stronger contraction of the eigenmode in the tangential plane. By these means, a stable operation with an average output power of P = 10 W (corresponding to E = 33.3 mJ at f = 300 Hz; pulse duration ~ 30 ns) was realized. With a modified configuration of the cylindrical lens a maximum output power of P_max = 11.8 W (E_max = 39.3 mJ) was achieved. These values are the highest which were obtained so far for a laser of this kind, i.e., a laser transmitter whose power originates from a single radiation source (without further amplification or conversion). The laser cavity is actively stabilized to the frequency of the seeder, following a Pound-Drever-Hall technique. This yields permanent single-frequency operation with very high frequency stability (standard deviation < 2 MHz) and a narrow linewidth (< 63 MHz). These results correspond to the resolution limit of the characterizing wavelength meter. Laser emission occurs in the fundamental transverse mode, TEM_00 (M² <= 1.06). The laser system of the Hohenheim-DIAL has been successfully operated on several field campaigns. Its robustness has been demonstrated, for instance, during an uninterrupted operation for over 30 hours and an overseas transport to the USA which the system endured without damage. This work presents a vertical pointing and two scanning water-vapor DIAL measurements, confirming a high resolution and accuracy. The vertical measurement was executed for the first time at 10 W laser operation. Furthermore, two special DIAL measurements are discussed: The measurements on a strongly backscattering target demonstrate a high spectral purity >= 99.97% of the laser transmitter. Finally, an atmospheric measurement with a tuning online wavelength shows the frequency-agility of the laser and allows to determine the water-vapor absorption line experimentally. The comparison with the spectrum of a database shows a very good agreement (~ 5-10 % deviation in the absorption cross sections absolute value).
3-D observations of absolute humidity from the land surface to the lower troposphere with scanning differential absorption lidar
(2016) Späth, Florian Heiko; Wulfmeyer, Volker
The water vapor (WV) distribution in the atmospheric boundary layer (ABL) is spatially and temporally highly variable. To investigate this behavior, the Institute of Physics and Meteorology at the University of Hohenheim (UHOH) developed a unique scanning differential absorption lidar (DIAL). This instrument allows for water vapor measurements with high temporal and spatial resolutions of the orders of seconds and tens of meters in the range of several kilometers from the surface up to the lower troposphere. Additionally, the UHOH DIAL system can perform scanning measurements which allows for observations down to the surface as well as for observations of the horizontal moisture variability. Within this thesis, three aspects regarding high-resolution observations of moisture in the ABL with scanning DIAL are demonstrated: 1) the development of a new seeder system for the laser transmitter, 2) the presentation of three scan modes, and 3) applications of 2-D to 3-D WV DIAL data. The newly developed seeder system is based on distributed feedback (DFB) laser diodes as seed lasers and an electro-optical deflector as optical switch. The setup and its specifications are presented. Scanning measurements were performed to capture the spatial WV structures. For this purpose, three scan modes with measurement examples are presented: 1) Range-height indicator (RHI) scans provide vertical cross-section images of the atmospheric humidity distribution. The presented series of four measurements show several humidity layers with different WV content and their evolution. Clouds appear in the last scan. 2) A volume scan captures the whole three-dimensional WV structure made out of several conical scans of different elevation angles. The horizontal variation of the layer heights can be related to the terrain profile with a small hill near the DIAL site. 3) Low elevation scans observe the WV distribution directly above the surface. Thus, relationships of the ground characteristics and vegetation with the humidity content above can be investigated. It is shown that there was more moisture above a maize field and above a forest than above grassland. For the analysis of scanning measurements, new analysis and visualization routines as well as new methods for the error estimation were developed. More scientific applications of high-resolution WV data from DIAL measurements are presented in three publications. A evaluation study compared humidity profiles from model simulations with different land-surface schemes with horizontal mean profiles of scanning DIAL measurements. High-resolution humidity fluctuations from vertical measurements were used to determine higher-order moments up to the fourth-order as well as skewness and kurtosis. Furthermore, such WV profiles were combined with profiles of temperature and vertical wind velocities and used for the development of new turbulence parameterizations and for model validation.
A backscatter lidar forward operator for aerosol-representing atmospheric chemistry models
(2020) Geisinger, Armin; Wulfmeyer, Volker
State-of-the-art atmospheric chemistry models are capable of simulating the transport and evolution of aerosols and trace gases but there is a lack of reliable methods for model validation and data assimilation. Networks of automated ceilometer lidars (ACLs) could be used to fill this gap. These networks are already used for the detection of clouds and aerosols, providing a 3D dataset of atmospheric backscatter profiles. But as the aerosol number concentration cannot be obtained from the ACL data alone; one needs a backscatter-lidar forward model to simulate lidar profiles from the model variables. Such an operator allows then for a qualitative and quantitative model validation based on ACL data. In this work, a newly developed backscatter-lidar forward operator and the related sensitivity studies are presented and results of the forward operator applied on model output data are compared to measured ACL profiles in the frame of a case study. As case study, the eruption of the Icelandic volcano Eyjafjallajökull in 2010 was chosen and extensively analyzed. The Consortium for Small-scale Modeling - Aerosols and Reactive Trace gases (COSMO-ART) model of DWD (Deutscher Wetterdienst) was operated during this event for ash-transport simulations over Europe. For the forward model, the attenuated backscatter coefficient is used as lidar-independent variable, which only relies on the laser wavelength. To calculate the attenuated backscatter coefficient, the size-dependent aerosol number concentration and the scattering properties of each aerosol type and size have to be simulated. While the aerosol number concentration is a model output variable, the scattering properties were determined by extensive scattering calculations. As these scattering calculations require assumptions about the aerosol refractive indices and shapes, sensitivity studies were performed to estimate the uncertainties related to the particle properties as represented by the model system. An analysis of the particle shape effect for the extinction and backscatter coefficients resulted in huge differences of the scattering properties between spherical, ellipsoidal and cylindrical particle shapes. Due to a particle shape mixture in typical volcanic ash plumes, the application of non-spherical scattering calculation methods for estimating the effective optical properties requires more information related to the particle shape distribution (specifically: a particle size and shape distribution). As such information was not available for the present case study, it was necessary to assume spherical shaped volcanic ash particles but estimate the uncertainty related to this assumption within the frame of additional sensitivity studies. Finally, the forward modeled lidar profiles were compared to ACL measurements from stations of the German ACL network. The comparison required an extraction of common time and height intervals of the ACL and forward modeled COMSO-ART data as well as reshaping the datasets to the same vertical and temporal resolution. Significant differences between ACL profiles and the output of the forward operator applied to the COSMO-ART data were found. Some ash layer structures were at similar coordinates which is remarkable due to the uncertainties related to the model dynamics and the limited amount of measurement data that could be used for model validation. In detail, however, the major fraction of the compared time and height interval differed both in the relative signal intensity and the layer structures of the volcanic ash plume. Based on such quantitative comparison, a future data assimilation system could correct the model prediction of the forward modeled attenuated backscatter coefficient, the time of arrival, as well as the vertical structure of the volcanic ash plume. In summary, the continuous and distributed data stream provided by ACL stations was found to deliver valuable verification information for dispersion simulations of aerosol events. But major issues have been determined which limit current realizations of backscatter-lidar forward operators for aerosol transport simulations: First, it is suggested that the ACL systems improve their dynamic range and perform automatic calibration to increase the precision of ACL data and for calculating the measured attenuated backscatter coefficient with a minimum leftover of uncertainties. This will allow for the calculation of the attenuated backscatter coefficient in the presence of clouds as well as of faint aerosol signals. Second, the aerosols scattering properties have to be analyzed even more extensively which includes both the variety of aerosol sizes or types as well as the size distribution information. From the findings within this study, the particle size distribution was indentified to be a critical component when using monodisperse size classes.
A high-power laser transmitter for ground-based and airborne water-vapor measurements in the troposphere
(2009) Schiller, Max; Wulfmeyer, Volker
A gain-switched high-power single-frequency Ti:sapphire laser was developed. It is pumped with a frequency-doubled diode-pumped Nd:YAG laser. The laser fulfills the requirements for a transmitter of a water-vapor differential absorption lidar (DIAL), intended for accurate high temporally- and spatially-resolved measurements from the ground to the upper troposphere. The laser was developed using thermal, resonator-design, spectral, and pulse-evolution models. There were layouts assembled for operation at 935 nm and 820 nm optimized for airborne and groundbased measurements, respectively. A birefringent filter and an external-cavity diode laser as an injection seeder are controlling the spectral properties of the transmitter. With a frequency stability of < 60 MHz rms, an emission bandwidth of < 160 MHz, and a spectral purity of > 99.7 %, the total error from the laser properties is smaller than 5 % for water-vapor measurements in the troposphere. The laser beam profile is near-Gaussian with M2 < 2. The achieved laser power was 4.5 W at 935 nm and 7 W at 820 nm at repetition rate of 250 Hz. These values are the highest reported for a single-frequency Ti:sapphire laser. As a part of a ground-based water-vapor DIAL system, the transmitter was deployed during the measurement campaign COPS (Convective and Orographically-induces Precipitation Study). Comparisons with radiosondes confirmed a high precision of the acquired water-vapor day- and nighttime measurements.
A mobile, scanning eye-safe lidar for the study of atmospheric aerosol particles and transport processes in the lower troposphere
(2009) Pal, Sandip; Wulfmeyer, Volker
A high-power eye-safe scanning aerosol lidar system in the ultraviolet wavelength region is introduced for the study of the optical properties of aerosol particles and transport processes in the atmosphere, especially in the atmospheric boundary layer (ABL). This system operates with an average power of 9 W in combination with a 40-cm scanner with a speed of up to 10° s-1. A modified version of the lidar inversion algorithm is developed for the retrieval of optical properties of aerosols from scanning lidar measurements. The lidar data can be analyzed with previously unachieved temporal and spatial resolution of 0.03 s and 3 m, respectively.
A scanning eye-safe rotational Raman lidar in the ultraviolet for measurements of tropospheric temperature fields
(2009) Radlach, Marcus; Wulfmeyer, Volker
Within the frame of the virtual Institute COSI-TRACKS the first scanning rotational Raman lidar has been developed and deployed successfully in two large field campaigns. This has allowed new investigations of the convective boundary layer and contributed to studies on the initiation of convection during the PRINCE campaign (PRediction, Identification and trackiNg of Convective cElls) in July 2006 and the COPS experiment (Convective and Orographically-induced Precipitation Study) from June to August 2007. The University of Hohenheim rotational Raman lidar was deployed in both these campaigns on Hornisgrinde (48.61 °N, 8.20 °E, 1161 m above sea level), the highest peak in the Northern Black Forest in southwest Germany. The lidar provides measurements of atmospheric temperature fields in the troposphere with high spatial and temporal resolution at day and night. Daytime scanning temperature measurements within a range of 3 km using a temporal resolution of 169 s and a moving average of 300 m in range show statistical temperature uncertainties of less than 1 K while pointing at 21 directions. Temperature uncertainties of less than 1 K are achieved during nighttime up to a range of 8 km using a temporal resolution of 3 minutes and a range resolution of 300 m. The lidar resolves also turbulence in the convective boundary layer, e.g., at 470 m height with a temporal resolution of 10 s and statistical uncertainties of only 0.41 K. In addition to temperature, also the particle backscatter coefficient and the particle extinction coefficient are measured independently. The instrument operates with a primary wavelength of 355 nm. This has instrumental advantages compared to 532 nm but also yields eye-safety beyond a range of 500 m which facilitates the deployment. Highly efficient spectral separation of the atmospheric backscatter signals is performed by a polychromator with narrow-band interference filters in a sequential setup. The spectral characteristics of these filters were optimized with respect to high measurement performance in the daytime planetary boundary layer and the lower free troposphere. Pioneering measurements of the 2-dimensional temperature distribution in the lower troposphere in the vicinity of a mountain ridge are presented.
Adaptation of model organisms and environmental bacilli to glyphosate gives insight to species-specific peculiarities of the shikimate pathway
(2024) Schwedt, Inge; Commichau, Fabian M.
Glyphosate (GS), the active ingredient of the popular herbicide Roundup, inhibits the 5-enolpyruvyl shikimate-3-phosphate (EPSP) synthase of the shikimate pathway, which is present in archaea, bacteria, Apicomplexa, algae, fungi, and plants. In these organisms, the shikimate pathway is essential for de novo synthesis of aromatic amino acids, folates, quinones and other metabolites. Therefore, the GS-dependent inhibition of the EPSP synthase results in cell death. Previously, it has been observed that isolates of the soil bacteria Burkholderia anthina and Burkholderia cenocepacia are resistant to high amounts of GS. In the framework of this PhD thesis, it could be demonstrated that B. anthina isolates are not intrinsically resistant to GS. However, B. anthina rapidly adapts to the herbicide at the genome level and the characterization of GS-resistant suppressor mutants led to the discovery of a novel GS resistance mechanism. In B. anthina, the acquisition of loss-of-function mutations in the ppsR gene increases GS resistance. The ppsR gene encodes a regulator of the phosphoenolpyruvate (PEP) synthetase PpsA. In the absence of a functional PpsR protein, the bacteria synthesize more PEP, which competes with GS for binding in the active site of the EPSP synthase, increasing GS resistance. The EPSP synthase in B. anthina probably does not allow changes in the amino acid sequence as it is the case in other organisms. Indeed, the Gram-negative model organism Escherichia coli evolves GS resistance by the acquisition of mutations that either reduce the sensitivity of the EPSP synthase or increase the cellular concentration of the enzyme. Unlike E. coli, the EPSP synthase is also critical for the viability of Gram-positive model bacterium Bacillus subtilis. This observation is surprising because the enzyme belongs to the class of GS-insensitive EPSP synthases. In fact, the EPSP synthase is essential for growth of B. subtilis. The determination of the nutritional requirements allowing the growth of B. subtilis and E. coli mutants lacking EPSP synthase activity revealed that the demand for shikimate pathway intermediates is higher in the former organism. This finding explains why laboratory as well as environmental Bacilli exclusively adapt to GS by the mutational inactivation of glutamate transporter genes. Here, it was also shown that a B. subtilis mutant lacking EPSP synthase activity grows in minimal medium only when additional mutations accumulate in genes involved in the regulation of aerobic/anaerobic metabolism and central carbon metabolism. The characterization of these additional mutants will help to elucidate the peculiarities of the shikimate pathway in B. subtilis. Moreover, the mutants could be useful to identify the aromatic amino acid transporters that still await their discovery.
Adaptations of maize to low phosphate availability
establishing regulatory networks from large-scale quantitative proteomic profiling
(2022) He, Mingjie; Schulze, Waltraud
Maize (Zea mays) is an important crop in global for human food, animal feed and industrial usage. Suboptimal phosphorus (P) availability is one of the primary constraints for maize growth and productivity (Jianbo Shen et al., 2011; L.pez-Arredondo et al., 2014). Over 70% arable land suffers from P-deficiency, and plants can take up small amounts of P from the soil due to P-fixation. However, over-application of P fertilizer has frequently happened in last decades and resulted in environmental pollution (L.pez- Arredondo et al., 2014). Modern agriculture calls for maintaining productivity while reducing synthetic-P fertilizer inputs and losses, thus, requiring breeding of novel cultivars to increase phosphate use efficiency (PUE) (Balemi and Negisho, 2012; X., Li, Mang, et al., 2021; Mardamootoo et al., 2021). Understanding the regulation of maize to low phosphate(LP)-availability at the molecular level will offer unlimited potential for the development of selection markers and engineering targets in breeding programs. Nowadays, “OMIC” approaches and computational science are developing rapidly. They are advanced tools for investigation of molecular adaptations on a large-scale and in a systemic view. Thereby, the major research task within this thesis is to reveal P-deficiency induced responsive components and regulations at protein level based on proteomic profiles, aiming to provide promising candidate genes/proteins for research on the molecular mechanisms of adaptation to LP-stress, and potentially to provide promising candidate gene/proteins for development of selection markers and engineering targets to obtain desired traits, in the long term goal of improving PUE in novel cultivars. In Chapter 1, we focused on six genotypes (EP1, F2, F142, F160, SF1, SM1) with close genetic background but several contrasting traits to LP-stress, such as PUE (X., Li, Mang, et al., 2021). They were cultured in pot with either sufficient or inefficient P-fertilizer in a climate chamber for one month. The young seedlings were sampled by root and shoot for analysis of multiple traits, transcriptome and proteome. Firstly, we constructed the co-expression network of proteins and transcripts separately using WGCNA method (Langfelder and Horvath, 2008), which predicted potential protein-protein interactions or their co-regulations. Secondly, we categorized proteins/transcripts to modules according to their different coexpression patterns, thus, identified potential determining relationships of modules-traits. Thirdly, we compared the responses between transcripts and proteins, presenting their responses being concordant or dis-concordant. Fourthly, we identified common and genotype-specific P-starvation response modules and biological processes. Finally, we focused on protein kinases, which play roles as regulators, to demonstrated protein kinases-centered network and validated protein interactions between mitogenactivated protein kinase-kinase 1 (MEK1, Zm00001d043609) either with sucrose synthase1 (SH1,Zm00001d045042) or translation elongation factor 1-gamma 3 (eEF1B-γ, Zm00001d046352). MEK1 is a potential genotype-specific regulator via sucrose metabolism and translation elongation process. In Chapter 2, we aimed to adapted an experimental workflow for phosphoproteome analysis in maize, addressing the interference to phosphoproteome quantification by fibers, secondary metabolites and low abundant of phosphorylated proteins. In this manuscript, we described a rapid and universal protocol for both proteome and phosphoproteome analysis that is suitable for cereal crops. The results of phosphoproteome in maize root testing samples showed that proteins within kinase-centered network in Chapter 1 can be largely quantified based on this workflow. It provides a possible way to analyze phosphorylation dynamics to P-starvation responses, it allows further investigation for kinase-centered 1 network in Chapter 1 to identify phosphorylation pairs of “protein kinase – protein substrate”, which will largely expand a view on P-starvation regulations through posttranslational modifications.
Aircraft air data system based on the measurement of Raman and elastic backscatter via active optical remote-sensing
(2012) Fraczek, Michael Darius; Wulfmeyer, Volker
Flight safety in all weather conditions demands exact and reliable determination of flight-critical air parameters. Conventional aircraft air data systems can be impacted by probe failure caused by mechanical damage or impairment due to different environmental influences. In this thesis, a novel measurement concept for optically measuring the air temperature, density, pressure, moisture and particle backscatter for aircrafts is presented. The detection of volcanic ash is possible as well. This concept is independent from assumptions about the atmospheric state and eliminates the drawbacks of conventional aircraft probes. The measurement principle is based on a laser emitting pulses into the atmosphere from inside the aircraft and a receiver detecting the light signals backscattered from a defined region just outside the disturbed area of the fuselage air flow. With four receiver channels, different spectral portions of the Raman backscatter of dry air and water vapor, as well as the elastic backscatter are extracted. Measurements at daytime and in any atmospheric condition, including very dense clouds, are possible. In the framework of this thesis, a first laboratory prototype of such a measurement system using 532 nm laser radiation was developed, comprising all relevant theoretical and experimental studies. These were notably the comparative feasibility assessment of the measurement methodology, the computational modeling of the measurement concept, the laboratory setup and the experimental validation. Detailed and realistic performance and optimization calculations were made based on the parameters of the first prototype. The impact and the correction of systematic errors due to solar background and elastic signal cross-talk appearing in optically dense clouds were analyzed in computational simulations. The simulations supplement the experimental results for measurement scenarios that are not generable in the laboratory. The laboratory experiments validate the predictions from the simulations with regard to systematic errors and statistical measurement uncertainties. Where possible, the experimental setup and the signal and data analysis were optimized. Residual differences between the experimental and the model results were analyzed in detail. Concrete further hardware optimizations were suggested. The resulting experimental systematic measurement errors at air temperatures varying from 238 K to 308 K under constant air pressure are < 0.05 K, < 0.07 % and < 0.06 % for temperature, density and pressure, respectively. The systematic errors for measurements at air pressures varying from 200 hPa to 950 hPa under constant air temperature are < 0.22 K, < 0.36 % and < 0.31 %, respectively. The experimentally achieved 1-σ statistical measurement uncertainties for the analysis of each single detected signal pulse range from 0.75 K to 2.63 K for temperature, from 0.43 % to 1.21 % for density, and from 0.51 % to 1.50 % for pressure, respectively, for measurement altitudes from 0 m to 13400 m. In order to meet measurement error requirements specified in aviation standards, minimum laser pulse energies were experimentally determined to be used with the designed measurement system. With regard to 100-pulse-averaged temperature measurements, the pulse energy at 532 nm has to be larger than 11 mJ (35 mJ), when regarding 1-σ (3-σ) uncertainties at all measurement altitudes. For 100-pulse-averaged pressure measurements, the laser pulse energy has to be respectively larger than 95 mJ (355 mJ). Based on these experimental results, the laser pulse energy requirements were extrapolated to the ultraviolet wavelength region as well, resulting in much lower laser pulse energy demand. The successful results of this thesis do not only prove the viability of the concept implementation, but also demonstrate its high potential for aircraft air data system application.
Aktivierung eines neuartigen Apoptose-Signalweges durch den Proteinkinaseinhibitor Staurosporin
(2009) Daubrawa, Merle; Graeve, Lutz
The protein kinase inhibitor staurosporine induces apoptosis via the activation of the intrinsic pathway. First staurosporine was described as a specific PKC inhibitor. Today it is known as a broad range kinase inhibitor and is used as a potent apoptosis inductor. However, the mechanism of the apoptotic effect remains elusive. Furthermore, staurosporine obviously exhibit the potential to eliminate chemotherapy resistant tumors by the induction of a novel intrinsic apoptotic signaling pathway. Different derivatives of staurosporine, e.g. UCN-01, PKC-412 or Enzastaurin are already tested in clinical trials phase I-II for cancer therapy. In the present work it could be shown that overexpression of Bcl-2 does not impede the caspase-dependent induction of apoptosis in J16- and JE6.1-Jurkat T-lymphocytes or in DT40 B-lymphocytes following staurosporine treatment . After generation of apaf-1 -/- DT40 cells it was demonstrated that staurosporine induces apoptosis despite the absence of Apaf-1 and therefore independently of the apoptosome. Together with the generated caspase-9 -/- DT40 cells, caspase-9 was identified as the central effector protein of both staurosporine-induced apoptotic pathways. The involvement of published and putative caspase-9 kinases could not be confirmed by the usage of specific inhibitors. Using phospho-mimicking and phospho-deficient caspase-9 variants, S183 could be identified as an essential phosphorylation site during staurosporine-induced apoptosis. In addition, after treatment with anticancer drugs apoptosome formation was blocked by an N-terminal tag of caspase-9. However, this tag could not prevent staurosporine-induced apoptosis. In further studies the potential role of cathepsines for this novel apoptosis signaling pathway could be analysed by their specific inhibition. In order to investigate the involvement of multiple kinases in this novel apoptotic signaling pathway, combination experiments with specific inhibitors of the respective kinases should be accomplished. Further investigations should clarify whether the influence of S183 on staurosporine-induced apoptosis is based on conformational alteration or on phosphorylation of caspase-9. The generation of additional caspase-9 variants including deltaCARD-caspase-9 or non-cleavable caspase-9 could lead to a deeper understanding of the role of caspase-9 for staurosporine-induced apoptosis. For this purpose caspase-9 -/- DT40 cells and cells reconstituted with different caspase-9 variants could be employed. The phosphorylation pattern of caspase-9 could be determined by mass spectrometric analysis. Xenograft or chorio allantois membrane models were used to investigate if the staurosporine derivative UCN-01 is also able to induce this novel apoptosis signaling pathway in vivo. The identification of both the mechanisms and the effector proteins of this staurosporine-induced apoptotic signaling pathway should provide the opportunity to develop novel agents for the elimination of chemotherapy-resistant tumors.
Analyse altersabhängiger Änderungen der DNA-Methylierung
(2024) Holländer, Olivia; Fricke, Florian
This study investigated age-dependent DNA methylation patterns to estimate chronological age. DNA methylation is a covalent bond of a methyl group at the 5'-carbon atom of a cytosine, which in mammals occurs almost exclusively in sequences of cytosine-phosphate-guanine, so-called CpG sites. For criminal proceedings, it is highly relevant whether a person has reached a legally relevant age limit of 14, 18 or 21 years. Estimating the age is also relevant for unaccompanied refugee minors who are entitled to special protection by law. There is often a lack of valid documents that can confirm that they are minors. Furthermore, estimating the age of unknown perpetrators of biological crime scene evidence can support police investigations in order to narrow down the circle of possible trace donors. In 2016, the German Ethics Commission expressed that they do not consider the medical methods currently used to estimate age to be suitable, as they violate the fundamental rights to physical integrity, human dignity and the general right to privacy. As buccal mucosal swabs or saliva samples represent a practicable, cost-effective and, above all, non-invasive alternative, an estimation model based on buccal mucosa was sought. The first research hypothesis covered age estimation of adolescents and young individuals. First, 88 age-dependent CpG sites of the eight markers PDE4C, ELOVL2, ITGA2B, ASPA, EDARADD, SST, KLF14 and SLC12A5 were analysed by bisulphite conversion and subsequent pyrosequencing. For this purpose, 141 buccal mucosal swabs from individuals between 21 and 69 years of age were analysed. In 54 of the 88 CpG sites analysed (in six markers PDE4C, ELOVL2, EDARADD, SST, KLF14 and SLC12A5), age-dependent methylation patterns were identified. This study showed that a reliable estimation of age is possible using as little as three CpG sites (PDE4C, EDARADD and KLF14) and that this model can also be successfully transferred to another sequencing method, namely minisequencing. In the second step, research focused on estimating the age of adolescent individuals. For this purpose, buccal swabs from 230 individuals between 1 and 88 years of age were used. Eight CpG sites of already established markers (PDE4C, EDARADD, SST, KLF14, ELOVL2, FHL2, C1orf132 and TRIM59) were analysed using mini sequencing. After analysing the correlation of the methylation status of the individual CpG sites with the chronological age of the test subjects, a logarithmic rather than linear relationship from birth to adulthood was observed, particularly for the markers ELOVL2 and TRIM59. To deal with this phenomenon, 20 years was defined as the ‘cut-off’ value, at which the chronological age is transformed in order to adjust the chronological age to the epigenetic age. A MAD of 4.680 years was thus achieved in the training set and a MAD of 4.695 years in the independent validation set. The estimates were most accurate in the lower age segment from 0 to 19 years (MAD of only 2.64 years), thus achieving the goal of a model that is suitable for age estimation for adolescents and young adults. To answer the second research hypothesis, the contribution of hydroxymethylation to the improvement of age estimation models was analysed. The term DNA methylation usually refers to 5-methylcytosine (5mC), but bisulphite conversion cannot distinguish between 5- hydroxymethylcytosine (5hmC) and 5mC. By subjecting a portion of the sample to an oxidation step prior to bisulphite conversion, in which 5hmC is oxidised and later treated like an unmethylated cytosine, 5mC and 5hmC can be analysed separately. Methylation values of 40 CpG sites in eight markers (EDARADD, PDE4C, SST, KLF14, SLC12A5, TOX2, LRRN2 and STK12A) were analysed by pyrosequencing in 108 individuals. Estimation models including 5hmC markers or take ydroxymethylation into account reveal similar accuracy as those that only take 5mC markers (so-called ‘true 5mC methylation’) into account and models based on the gold standard (undifferentiated 5mC+5hmC values). In any case, this makes 5hmC another promising marker for forensic age estimation. However, no significant improvement in estimation accuracy was achieved, which is why the second research hypothesis could not be confirmed. The 5hmC methylation values of individual CpG sites showed weak to moderate correlations with chronological age. The literature indicates that 5hmC shows better genome- wide correlation with age than 5mC and that it also regulates different genes. This suggests that the best 5hmC markers for age estimation may not yet have been found. Methods that can analyse longer sections of the genome are better suited for a future search for the best markers.
Analyse des Flow-abhängigen Symmetriebruchs im Frosch Xenopus
die Funktion des Nodal-Inhibitors Coco
(2015) Getwan, Maike; Blum, Martin
The bilaterally symmetrical vertebrate body plan is characterized by the three body axes, anterior-posterior (AP), dorsal-ventral (DV) and the left-right (LR). The LR-axis is the last one to be specified during embryonic development. Its impact on the morphology of the developing organism is visible after a few days in Xenopus laevis, because of the orientation of the visceral organs, such as the heart, gut and the gall bladder. The first molecular differences between the left and right side can already be detected after one day during early neurulation. It is found at the gastrocoel-roof-plate (GRP), a ciliated epithelium which is essential for symmetry breakage. Cilia rotate to produce a leftward fluid movement, which represses the Cerberus/DAN gene Coco in the lateral cells of the epithelium. As Coco acts as an inhibitor of the coexpressed TGFß-type growth factor Nodal (Xnr1), Xnr1 is flow-dependently released from repression on the left side. Xnr1 is capable to induce a unilateral gene-cascade in the left lateral plate mesoderm (LPM) consisting of Nodal itself, its antagonist Lefty/ antivin and the homeobox gene Pitx2c. A central question in this setting concerns the mechanism by which flow results in the repression of Coco. The analysis of Coco transcription gave a first hint, indicating that Coco mRNA is post-transcriptionally degraded and/ or that its translation is blocked. Gene regulation at the level of mRNA usually occurs through the untranslated regions (UTR), in most cases via the 3UTR. To examine the role of the Coco 3UTR for its regulation, protector-RNAs were used which should protect endogenous Coco mRNA from potential inhibitors. Injections led to the interruption of the flow-dependent Coco repression, verifying regulation of Coco via the 3UTR. As 3UTRs are target sites for microRNAs, loss of function experiments of the processing enzyme Dicer were performed. These experiments verified the involvement of miRNAs in the regulation of Coco. Further analyses identified miR-15a as a central player. The interruption of its synthesis or the specific protection of its binding site within the Coco 3UTR prevented flow-dependent down-regulation of Coco. Epistatic experiments demonstrated that the LR-axis of embryos with inhibited flow could be rescued by addition of the miR-15a precursor on the left side. In summary this thesis work revealed miRNAs as a primary target of leftward flow, upstream of the Nodal inhibitor Coco.
Analyse relevanter Signalwege der strahleninduzierten COX-2 Expression in Tumorzellen
(2007) Krebiehl, Guido Klaus; Rodemann, H.-Peter
Summary: Cancer is a health problem worldwide and the number of new cases is rising. Surgery, radiotherapy and chemotherapy are the major treatment modalities. New developments in radiotherapy make radiation alone and in combination with chemotherapy to an important therapy becoming more and more mattering. The success of a therapy often depends on the genetic profile of a tumor. This makes analysis of molecular processes in cells after radiation an important aspect in radiotherapy developing an effective strategy for tumor treatment. COX-2 is overexpressed in a lot of tumors and correlates with a poor prognosis. Moreover COX-2 can be induced by ionizing radiation. This makes COX-2 an interesting molecular target in radiation therapy and in cancer therapy in general. Studies with specific COX-2 inhibitors came to different results in different cell lines. The aim of the presented study was to investigate the survival and the proliferation of prostate cancer cells after treatment with ionizing radiation alone and in combination with specific COX-2 inhibitor Celecoxib and the analysis of signaling pathways leading to radiation induced COX-2 expression. The following major results were obtained: 1. Treatment with Celecoxib had no influence on the radiosensitivity of the prostate cancer cell lines investigated. 2. The proliferation of different cell lines was inhibited by the treatment with Celecoxib. 3. The inhibition of the proliferation seems to be independent of the level of COX-2 of the cell lines. 4. Apoptosis can not be induced by Celecoxib in clinical relevant doses in the cell lines investigated. 5. Induction of COX-2 expression by ionizing radiation depends on the cell line investigated. 6. The MAPK-signaling pathways play a major role at COX-2 expression. In conclusion the results of the presented study indicate that COX-2 can be an important molecular target in radiation therapy. Although this depends on the cell line investigated. As well, the signaling pathways leading to a radiation induced expression of COX-2 are individual for each cell line. Thus the application of Celecoxib during radiation therapy can be positive on the treatment of different tumors.
Analyse viraler Promotoren von Phycodnaviren und deren Interaktion mit Transkriptionsfaktoren
(2025) Wahl, Benjamin; Pfitzner, Artur
Acanthocystis turfacea Chlorella Virus 1 (ATCV-1) ist ein dsDNA-Virus aus der Gattung Chloroviren, welches Chlorella heliozoae infiziert. Das Virus besitzt 860 offene Leserahmen (open reading frames, ORF), die für die Gene codieren, die für einen korrekten Virusreplikationszyklus benötigt werden. Diese Gene werden in sehr frühe/frühe/späte Gene eingeteilt. Diese Einteilung basiert auf den Zeitpunkten der Expression der Gene. Für die Expression dieser Gene nutzt ATCV-1 virale Promotoren, die eine Mischung aus eukaryotischen und prokaryotischen Bestandteilen darstellen. Die erfolgreiche Initialisierung des Replikationszyklus mit Hilfe von sehr frühen und frühen Genen ist essenziell für eine vollständige Virusreplikation. In früheren Arbeiten konnten Gene in Paramecium busaria Chlorella Virus 1 (PBCV-1) identifiziert werden, die als sehr frühe Gene klassifiziert wurden. Das Ziel dieser Arbeit beinhaltet die Untersuchung sehr früher/ früher Gene und deren Promotoren. Im zweiten Teil der Arbeit sollte die Interaktion von Proteinen, deren Promotor ein Hex-Motiv (XXXCGTGG) enthalten, mit verschiedenen Faktoren untersucht werden. Basierend auf Sequenzvergleich-Analysen zwischen den sehr frühen Genen aus PBCV-1 und den Genen aus ATCV-1 wurden 20 Gene identifiziert. Die Promotoren dieser Gene wurden auf ihre Motive analysiert. Mit Hilfe einer RT-qPCR konnte gezeigt werden, dass diese Gene in der sehr frühen Phase der Virusreplikation (5 min p.i.) alle aktiv waren. Die Analyse in Pflanzen konnte zeigen, dass das Hex-Motiv in Verbindung mit mindestens einer TATA-Box ideal für die Expression der frühen Promotoren ist. Weitere Analysen konnten zeigen, dass für eine generelle Expression in Pflanzen mindestens zwei TATA-Box-Motiv in Verbindung mit anderen Motiven existieren müssen. In HEK293-Zellen konnte für die Promotoren mit dem Hex-Motiv ebenfalls eine Aktivität demonstriert werden. In der Arbeit konnte gezeigt werden, dass das Arg7-ASL-System zur Untersuchung der Aktivität von viralen Promotoren genutzt werden konnte. Alle frühen Promotoren zeigten eine Aktivität in Chlamydomonas reinhardtii, inklusive Promotoren anderer Viren. Promotoren mit dem Hex-Motiv zeigten, im Vergleich zu Promotoren ohne dieses Motiv, eine Interaktion mit einer Vielzahl von unterschiedlichen Transkriptionsfaktoren, die zu den bZIP-Transkriptionsfaktoren gezählt werden. Mit Hilfe zweier Proteine, Z174L und Z765R, deren Promotoren das Hex-Motiv besitzen, konnten mehrere mögliche Interaktionspartner mit Hilfe von „proximity based labeling“, darunter Proteine wie z.B. Actin, Thioredoxin und ein Histon-Acetlytransferase-Protein, identifiziert werden. Diese Proteine können mit der Transkription in Verbindung gebracht werden, was die vermutete Funktion von Z765R als Transkriptionsfaktor stützt. Z174L ist vermutlich ein Transkriptionsfaktor bzw. eine Endonuklease. Auch hierfür konnten Proteine, die diese Hypothese unterstützen, mit Hilfe der Massenspektrometrie identifiziert werden. In dem dritten Teil der Arbeit konnte mit Hilfe von Yeast-1-Hybrid-Analysen und dem Promotor von Z063L ein neues Protein, Activating protein 63 (Ap63), in Chlamydomonas reinhardtii identifiziert werden. Dieses Protein besitzt Motive, die mit DNA-Bindung in Verbindung gebracht werden. Kombiniert mit Analysen der Sequenz, handelt es sich bei dem hier entdeckten Protein vermutlich um einen Transkriptionsfaktor. Das Gesamtbild dieser Studie zeigt auf, wie abhängig das Virus von seinem Wirt für eine erfolgreiche Replikation ist und wie breit das Spektrum der Virus-Wirt-Interaktion ist. Die sehr frühe Genexpression (5 min p.i.) spielt eine essenzielle Rolle für die Replikation. Hierfür macht sich das Virus Proteine (vor allem Transkriptionsfaktoren) des Wirts zunutze, um die gesamte Genexpression der Wirtszelle auf die Virusreplikation umzuprogrammieren.
Analyse von Pathogenresistenzmechanismen in Tomate (Solanum lycopersicum L.)
(2008) Gerhardts, Anja; Pfitzner, Artur J. P.
For many organisms plants serve as a source of nutrients and energy, but because of their static location they are exposed to various harmful environmental influences. Due to this factor they have developed complex defence mechanisms e. g. for protection against pathogens. An important aspect of these defence mechanisms is the expression of intrinsic resistance genes (R) that detect pathogenic avirulence gene products (Avr) thereby causing a hypersensitive response (HR) in the infected cells and consequently inhibiting the systemic infection of the plant. In this work the resistance genes Tm-2 and Tm-2² of tomato were isolated, cloned and sequenced. The allelic R genes are members of the CC-NBS-LRR group of resistance genes, which is widely spread in plants, and differ only in four amino acids. This is surprising because using resistance breaking ToMV strains Weber et al. (2004) showed that both resistance gene products interact differently with the movement protein (30 kDa MP = Avr) of the virus. To gain further insight into this phenomenon of different pathogen detection, chimeric exchange constructs (A1 and A2) were designed through restriction in the region between the NBS and the LRR domain. These four constructs were used for transformation of MM tomatoes as well as NN and nn tobacco plants. The expression of the resistance gene constructs in MM an nn lines did not confer the expected resistance to ToMV. Nevertheless in older infected nn transformants a formation of spontaneous necrosis was observed, which indicates a delayed development of HR. One possible explanation could be that the presence of only the resistance gene product is not sufficient to detect the viral movement protein and that other host cellular components are involved in this process (as in the guard hypothesis by Dangl and Jones, 2001). This assumption is supported by our yeast two hybrid interaction experiments which showed that a direct interaction of Tm-2 and 30 kDa MP can be excluded. For the NN transformants differences in functionality of the constructs was observed. While NN/Tm-2 and NN/A2 plants showed extreme resistance to ToMV wild type (ToMV0) and the Tm-2² resistance breaking strain ToMV2², the Tm-2² and A1 constructs conferred less resistance to ToMV0 and the Tm-2 resistance breaking strain ToMV1-2. This finding also supports the assumption that there is a difference in pathogen detection between the two alleles. Furthermore it shows that the detection takes place within the LRR region because the exchange construct that behaves in the same way as the endogenous resistance gene carries the C-terminal LRR domain of this allele. The hydroxycinnamoyl-CoA:tyramine N-(Hydroxycinnamoyl)transferase (THT) was found to be another candidate for transmission of pathogen resistance during HR (Gerhardts, 2003). Our in vivo results show that the products of the THT enzymatic reaction induced during HR does not only have an antimicrobiotic effect on the pathogen (von Roepenack-Lahaye et al., 2003; Newman et al., 2001) but also has an apoptotic effect on the plant cell itself.
Analysis of aging-related changes and influencing factors on the metabolome of beef
(2023) Bischof, Greta; Gibis, Monika
Aging of beef is necessary to improve its flavor and tenderness. There are two most common aging types, dry-aging and wet-aging. Dry-aged beef is often associated with a higher eating quality than wet-aged beef. The term “dry-aged beef” is not legally defined, so authentication methods are needed to protect the consumers from food fraud. During beef aging, the metabolome of beef changes due to the postmortem metabolism. This dissertation focuses on the aging method as a postmortem process and the resulting changes in the metabolome. As a hypothesis of this study, it was postulated that the detection of these metabolic changes due to aging of beef is feasible by 1H NMR spectroscopy and based on these measurements the evaluation of an authentication model for the aging method of beef is possible. In order to test this hypothesis, a sample preparation and measurement method was developed and based on this, potential influencing factors such as sampling position in muscle, breed and sex were investigated on the metabolome of fresh and aged beef. In the first part of this thesis, the sample preparation and the 1H NMR measurement method were developed. In the sample preparation, the polar fraction of the metabolome was extracted from 200 mg of beef, allowing 24 samples to be prepared in parallel. The sample preparation and the measurement method were validated, and the first aged beef samples were analyzed to check if the aging-related changes in the metabolome could be detected by this method. In the second part of this thesis, the sampling position in the muscle were analyzed for changes or differences in the metabolome due to its location in the muscle. The results showed that the metabolome changes along the length of the M. longissimus thoracis et lumborum, but the influence of the aging type and aging time was more pronounced in the metabolome of beef. The comparison of the surface and the inner part of wet-aged and dry-aged beef showed that the metabolome of dry-aged beef differed greatly between the surface and the inner part, despite the exclusion of the moisture content by freeze-drying and the low microbial load. There were only slight differences between the surface and the inner part for wet-aged beef, which could be due to the influence of microbiota and their metabolites. Therefore, the sampling location in the M. longissimus thoracis et lumborum was determined as precisely as possible for the further studies. The muscles were cut into ten pieces from cranial to caudal and dry-aged or wet-aged for 0, 7, 14, 21, and 28 days, in duplicates. The third part of this thesis focuses on the potential influencing factors such as breed and sex of the animals. Fresh and aged beef samples from three cattle types (heifer, cow, and young bull) and two different breeds (‘Fleckvieh’ and ‘Schwarzbunt’) were analyzed by targeted and non-targeted 1H NMR spectroscopy. Both factors were shown to influence the metabolome of fresh and aged beef. Therefore, these factors had to be included in the authentication model based on both targeted and non-targeted model. The calculation of the authentication model was the main part of this thesis and showed a good prediction of cattle type, breed, aging time and aging type of beef. The authentication model was based on the combination of multiple models of PLS-R and PLS-DA. The model for predicting the cattle type showed an accuracy of 99 %, and the models for predicting the breed depending on the cattle type showed an accuracy of 100 %. Aging time could be predicted with an error of 2.28 days. The statistical models for aging type were separated by aging time based on the determination of aging time. The model for predicting the aging type of 28-day aged samples had an accuracy of 99 %. The other statistical models for predicting aging type were additionally separated by cattle type and breed, and their accuracy ranged from 90 % to 100 %. In conclusion, an authentication model to determine the cattle type, breed, aging time and aging type of beef was developed in this dissertation. Therefore, it is possible to authenticate beef samples using a single 1H NMR spectrum. In future studies, it would be useful to extend this authentication model to other samples of other breeds and influencing factors.
Analysis of the structure of tomato mosaic virus movement protein based on virus host interactions
(2011) Tanwir, Fariha; Pfitzner, Artur J. P.
Viruses are obligatory plant pathogens causing sever diseases, and ultimately great losses in crop yield. Plant viruses, once entered in the cell, make use of host machinery for its own replication and moves from one cell to the other. Natural resistance against virus attack is achieved by the presence of resistance genes (R genes). R genes recognize viral avirulence (Avr) factors in elicitor-receptor manner to initiate resistance cascade. In tomato, the resistance genes Tm-I, Tm-2 and Tm-22 are used to protect the plants against infection by tomato mosaic virus.Tm-2 and Tm-22 require recognition of the viral 30kDa movement protein (MP) for triggering resistance response. Sequence analysis of Tm-2 and Tm-22 resistance breaking viruses have shown an amino-acid exchange at position 133 (E>K) is found in all Tm-2 resistance breaking virus strains, whereas, amino-acid exchange at position 130 (K>E) is associated with Tm-22 resistance breaking phenotype (Calder and Palukaitis, 1992). This suggests a physical interaction between resistance genes and 30kDa MP. In the present study, a unique Split GFP approach is used to analyse the structure and localization of different domains of 30kDa MP in S. cerviceae and N. benthamiana. Different deletion mutants were fused between two non-overlapping halves of GFP and expressed. Results showed that both N and C terminus as well as the middle part of 30kDa MP (aa 80-150) is present in the cytoplasm with two integral membrane loops. These findings are in contrast with previous in-vitro results, which suggest that middle part of 30kDa MP is present in ER lumen, whereas N and C terminus in cytoplasm (Brill et al., 2000). Fluorescence microscopy revealed that GFP fused 30kDa MP deletion mutants were localized on the cytoplasmic side of plasmamembrane and near plasmodesmata. Membrane association of fusion protein confirmed the proper folding and functionality of deletion mutants. Therefore, the structural model of ToMV 30kDa MP has to be revised. Secondly, to identify the host factors involved in resistance mechanism, initiated by Tm-2 and Tm-22 resistance genes, tomato mosaic virus based vectors were constructed. Two different types of in-vivo transcription vectors were constructed, one containing both right and left border of the T-DNA (pBinSLN) and one without the right border (pBinSLN-RB). Self replication of these vectors were analysed in N. benthamiana, N. tabacum and S. lycopersicum. It was found that the deletion of RB does not affect virus replication, when agro-infiltrated in N. benthamiana. pBinSLN-RB was used further for the isolation of a stable and vigorous Tm-2 and Tm-22 resistance breaking ToMV strain through a novel selection scheme. ToMV2-22 contains two amino-acid exchanges at position 54(N>D) and 133(E>K). ToMV2-22 is the first mutant strain of ToMV, which can escape both Tm-2 and Tm-22 resistance simultaneously.
Antimikrobielle Aktivität der Histone bei chronisch entzündlichen Darmerkrankungen
(2017) Kunkel, Yasmin; Stange, Eduard F.
The human intestine harbours a multitude of microorganisms. In addition to its func-tion as a protective layer against pathogens, it has to prevent an excessive immune answer against commensales simultaneously. Antimicrobial Peptides (AMPs) with their cationic character are playing an essential role in protection, because they are able to form voltage dependent channels on the surface of microorganism, which kill pathogens. In addition to the classical AMPs more antimicrobial active polypeptides, such as members of the histone family, were isolated. Histones are alkaline proteins, which are components of the chromatine. They are foremost responsible for packaging the DNA and for posttranslational modifications. Five different families can be differentiated: the core histones H2A, H2B, H3 and H4, as well as the linker histone H1. While extracellular histones show strong antimicrobial activity against a broad spectrum of microorganisms, the mechanism of their toxicity has not yet been sufficiently determined. If the antimicrobial protection layer of the intestine is weakened, due to a diminished expression of AMPs for instance, microorganisms can penetrate the mucosa and trigger inflammations. These findings have been confirmed in different tissues of patients with inflammatory bowel diseases (IBD), such as Crohn’s disease (CD) and ulcerative colitis (UC). The aim of this work is to determine whether histones play a role in IBD. In the first part a systematic analysis of the transcriptome (Q-PCR) and the transla-tome (Western Blotting) of the core histones of colonic tissue was performed. In tis-sues of patients with CD gene expression data showed generally an increase of his-tones. In the cases of H2A and H2B the increase was significant. The quantification on the protein level offered an extreme variance of the expression of all core histones, irrespective of the analysed group. Significant differences were not detected. However, in trend H2B was lower in inflammation. After the systematic analysis, histones were then isolated of human colonic tissue. Before the extracted histones were fractionated via RP-HPLC and screened via MALDI-TOF-MS, different methods for the isolation of histones had been compared. The antimicrobial activity of the isolated histones of different intestinal tissues and mucus showed no differences between healthy controls and patients with IBD in flow cytometric tests. A significant increase of the histone activity in inflamed tissues of UC was only detected against S. aureus. The impact of the extracted histones seems to be strain-specific and higher against gram-positive species. As expected, extracel-lular histones could be detected in the mucus by immunehistological staining. Through ELISAs, protein concentrations of H2A and H2B were determined in the mucus and thus a slight increase of the histone proteins in UC was observed. In the last part of this work, the interactions of recombinant histones among them-selves and with other AMPs were analysed by flow cytometric viability assays. A strain-specific increase of the antimicrobial activity of histones among themselves and with AMPs was found. Thereby synergistic effects occurred frequently. The in-teractions of histones against several bacteria were visualised by electron microscope images and furthermore an agglutination of the microorganisms as well as a massive loss of cell integrity were detected. Variantions of the histones’ transcriptome and the translatome, as well as variations of the antimicrobial activity of histones in CED would have been evaluated as patho-logic defects. However, in this work such effects could not been confirmed. Because of their enormous antimicrobial activity histones still play an important role in the protection against microorganisms in the colon. Further studies have to show, if his-tones possess a therapeutic potential, and if they can be used as new antibiotics. This work was able to verify the strong potential of histones against different pathogens, which is absolutely comparable with the potential of classic AMPs, and could pro-mote inspiration for subsequent studies.
Application of Global Positioning System slant path delay data for mesoscale modelverification and four-dimensional variational assimilation
(2010) Zus, Florian; Wulfmeyer, Volker
Observation modeling is required in order to make use of slant path delay data, processed from ground-based Global Positioning System (GPS) measurements, for verification purposes and numerical weather prediction. A rigorous ray-tracing algorithm based on the Euler-Lagrange equation derived from Fermat's principle is developed to simulate the propagation of GPS radio signals in a mesoscale model. The ray-tracing algorithm is based on a finite difference scheme and allows the direct numerical simulation of GPS slant path delays.
Application of nature-inspired optimization algorithms to improve the production efficiency of small and medium-sized bakeries
(2023) Babor, Md Majharul Islam; Hitzmann, Bernd
Increasing production efficiency through schedule optimization is one of the most influential topics in operations research that contributes to decision-making process. It is the concept of allocating tasks among available resources within the constraints of any manufacturing facility in order to minimize costs. It is carried out by a model that resembles real-world task distribution with variables and relevant constraints in order to complete a planned production. In addition to a model, an optimizer is required to assist in evaluating and improving the task allocation procedure in order to maximize overall production efficiency. The entire procedure is usually carried out on a computer, where these two distinct segments combine to form a solution framework for production planning and support decision-making in various manufacturing industries. Small and medium-sized bakeries lack access to cutting-edge tools, and most of their production schedules are based on personal experience. This makes a significant difference in production costs when compared to the large bakeries, as evidenced by their market dominance. In this study, a hybrid no-wait flow shop model is proposed to produce a production schedule based on actual data, featuring the constraints of the production environment in small and medium-sized bakeries. Several single-objective and multi-objective nature-inspired optimization algorithms were implemented to find efficient production schedules. While makespan is the most widely used quality criterion of production efficiency because it dominates production costs, high oven idle time in bakeries also wastes energy. Combining these quality criteria allows for additional cost reduction due to energy savings as well as shorter production time. Therefore, to obtain the efficient production plan, makespan and oven idle time were included in the objectives of optimization. To find the optimal production planning for an existing production line, particle swarm optimization, simulated annealing, and the Nawaz-Enscore-Ham algorithms were used. The weighting factor method was used to combine two objectives into a single objective. The classical optimization algorithms were found to be good enough at finding optimal schedules in a reasonable amount of time, reducing makespan by 29 % and oven idle time by 8 % of one of the analyzed production datasets. Nonetheless, the algorithms convergence was found to be poor, with a lower probability of obtaining the best or nearly the best result. In contrast, a modified particle swarm optimization (MPSO) proposed in this study demonstrated significant improvement in convergence with a higher probability of obtaining better results. To obtain trade-offs between two objectives, state-of-the-art multi-objective optimization algorithms, non-dominated sorting genetic algorithm (NSGA-II), strength Pareto evolutionary algorithm, generalized differential evolution, improved multi-objective particle swarm optimization (OMOPSO) and speed-constrained multi-objective particle swarm optimization (SMPSO) were implemented. Optimization algorithms provided efficient production planning with up to a 12 % reduction in makespan and a 26 % reduction in oven idle time based on data from different production days. The performance comparison revealed a significant difference between these multi-objective optimization algorithms, with NSGA-II performing best and OMOPSO and SMPSO performing worst. Proofing is a key processing stage that contributes to the quality of the final product by developing flavor and fluffiness texture in bread. However, the duration of proofing is uncertain due to the complex interaction of multiple parameters: yeast condition, temperature in the proofing chamber, and chemical composition of flour. Due to the uncertainty of proofing time, a production plan optimized with the shortest makespan can be significantly inefficient. The computational results show that the schedules with the shortest and nearly shortest makespan have a significant (up to 18 %) increase in makespan due to proofing time deviation from expected duration. In this thesis, a method for developing resilient production planning that takes into account uncertain proofing time is proposed, so that even if the deviation in proofing time is extreme, the fluctuation in makespan is minimal. The experimental results with a production dataset revealed a proactive production plan, with only 5 minutes longer than the shortest makespan, but only 21 min fluctuating in makespan due to varying the proofing time from -10 % to +10 % of actual proofing time. This study proposed a common framework for small and medium-sized bakeries to improve their production efficiency in three steps: collecting production data, simulating production planning with the hybrid no-wait flow shop model, and running the optimization algorithm. The study suggests to use MPSO for solving single objective optimization problem and NSGA-II for multi-objective optimization problem. Based on real bakery production data, the results revealed that existing plans were significantly inefficient and could be optimized in a reasonable computational time using a robust optimization algorithm. Implementing such a framework in small and medium-sized bakery manufacturing operations could help to achieve an efficient and resilient production system.

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