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Is the duration of the spermatogenic cycle in Djungarian hamsters (Phodopus sungorus) under the influence of day lengths or clock genes?
No full textIn mammals, the duration of the cycle of the seminiferous epithelium (DCSE) is characteristic for each species, but varies greatly between species, e.g. in rodents between 6.7 days and 17.0 days. Within a species, in contrast, the DCSE is remarkably stable with variations of 1 % - 3 %. This accuracy is very conspicuous since other biological processes are much more variable. It is furthermore difficult to change the DCSE experimentally, e.g. by hormones or chemicals. One reason for the precise timing could be the existence of a testicular peripheral clockwork, as identified previously in other tissues. To test this hypothesis, adult male Djungarian hamsters (n = 20 per group) were exposed to normal day length (24 h), one hour shortened (23 h), or one hour prolonged (25 h) day lengths. Exposure lasted for 43 days and the entrainment to the photoperiods was verified individually by passive infrared detectors (PID). The DCSE was estimated by immunocytochemical localization of 5-bromo-2- deoxyuridine (BrdU)-labeled cells and microscopical identification of the 12 stages of the seminiferous epithelium. The results for the normal day length (24 h: 7.98 ± 0.05 days) are congruent with previous findings in this species. No effects of shortened or prolonged day lengths on the DCSE could be identified (23 h: 7.94 ± 0.04 days; 25 h: 7.91 ± 0.03 days; p = 0.50), despite the low variability of 1.4 % and 2.0 %, respectively. A further experiment was performed to investigate the diurnal variations of expression of two core clock genes haBmal1 and haPer1 in testes and kidneys of Djungarian hamsters using quantitative RT-PCR. Hamsters (n = 4 per time point) were sacrificed every 3 h during 24 h. While in kidneys typical anti-cyclical expressions of haPer1 and haBmal1 were observed, a completely different expression pattern was found in the testes. Here, levels of haBmal1 were almost constant, while the expression of haPer1 showed a distinct diurnal variation. These findings strongly support the hypothesis that a peripheral clock is responsible for the low variability of the DCSE
Interference Modeling for Next Generation Wireless Networks
No full textIn a wireless communication environment characterized by dynamic channels, high influence of interference, bandwidth shortage and strong demand for quality of service (QoS) support, the challenge for achieving maximal spectral efficiency and high data rate is unprecedented. The data rate achievable now with most practical systems is in the range of tens of megabits per second. As discussed by Shannon, the channel capacity limit is not dependent on the transmitter/ receiver technologies but on the properties of the communication channel. The SIR in the presence of multipath fading, shadowing and path loss is a very important parameter for studying the capacity of a wireless system. This thesis presents a statistical analysis of the SIR for next generation wireless networks. First a new analytical formula for the PDF of the signal to interference ratio for a single interferer is presented. Monte Carlo simulation is used to validate the analytical formula. However in a realistic environment there are often more than one active interferers in a given cell. Two distinct approaches are used to study the effect of multiple interferers on the statistics of the SIR. The sum of random vector approach is used to find the PDF of the SIR for the multiple interference scenario. Laguerre polynomial approximations are used to simplify the problem of finding the PDF of the SIR. A new algorithm is proposed to find the optimum free parameter for the Laguerre approximation. However even with the optimum free parameter, the computational burden required to approximate the PDF of the SIR for multiple interferers with a Laguerre polynomial was impractical. Therefore an alternative characteristics function approach was proposed in this thesis. In this approach the path loss, shadowing and multipath fading are assumed to be dependent random variables. The statistical analysis of the SIR is used to study the TDD inter-cell interference in a self-organizing user deployed femtocell systems
Accurate and efficient electromagnetic modeling of antenna-body interactions: application to speech sensing and BAN
No full textAccurate and efficient simulation of body-antenna interactions is identified as a vital requirement for the design and optimization of wireless systems that operate near the human body.
To this end, efficient simulation methods with high accuracy are developed for two important and diverse applications. First, speech sensing is considered, whose aim is to sense and track the process of human speech, requiring information about the position and movement of lips, tongue, glottis, etc., potentially improving synthetic speech production, speech pathology and therapy, and speech recognition. For this purpose, a simplified FDTD model of the head-vocal tract is used which is efficient enough to be simulated on a desktop PC.
To improve efficiency of the speech-sensing application, a mode-matching waveguide model is developed. Comparing simulation times, the proposed method is orders of magnitude more efficient than direct simulation with the FDTD solver.
Next, the FDTD model is used to design and optimize an antenna that enhances coupling of propagating waves to mouth and throat. To test the accuracy of the modeling procedures and explore the feasibility of speech sensing, a prototype speech sensing system is built and deployed. A speech recognition experiment is also performed as a proof-of-concept to motivate the idea of speech sensing.
As a second target application, modeling for body area networking is presented. This application focuses on the shadowing aspect of the body which is most challenging impediment to the communications. An efficient two-dimensional lossy dielectric cylinder model for the body is adopted and extended to arbitrary polarization and arbitrary cross section using a surface-based method of moments solution. Additionally, measurements with short dipoles are performed in a compact anechoic chamber and compared with simulations to illustrates utility and accuracy of the models
Synthesis, Structure and Catalytic Activity of Titanium, Zirconium and Hafnium-Containing Polyoxometalates
No full textPolyoxometalates (POMs) represent by now a well-known class of discrete, molecular metal-oxides, which are attractive due to a large structural and compositional variety combined with a multitude of properties. Vacant (lacunary) polytungstate precursors allow for incorporation of a vast number of electrophiles including transition metals. The resulting products often have properties which render them of interest for potential applications in different areas such as catalysis, medicine and materials science. The exploration of the interaction between lacunary polyoxometalates (POMs) and group 4 (Ti, Zr and Hf) transition metal ions has been mainly driven by the fact that potential products may serve as oxidation catalysts or even as soluble molecular analogues of known Ti and Zr-containing heterogeneous catalysts. This document is a summary of three-year research conducted in this specific area, that is investigation of titanium containing POMs, the chemistry involved, synthesis, solid state and solution characterization and catalytic performance
Functional characterization and molecular evolution of E.coli DNA methyltransferase (EcoDam)
No full textDNA from most prokaryotes and eukaryotes contains methylated bases, i.e. 4- methylcytosine (N4mC), 5-methylcytosine (5mC) and 6-methyladenine (N6mA). These modifications are introduced after DNA replication by DNA methyltransferases (MTases), which catalyze methyl group transfer from the donor S-adenosyl-L-methionine (AdoMet), producing S-adenosyl-L-homocysteine (AdoHcy) and methylated DNA. DNA-adenine methylation at specific GATC sites plays a pivotal role in bacterial gene expression, DNA replication, mismatch repair, and bacterial virulence among gramnegative bacteria.
DNA MTases are attractive model system to study how proteins recognize specific sequences of DNA and how their specificity changes during molecular evolution. DNA methyltransferases (MTases) allow powerful combinations of in vivo and in vitro mutagenesis and DNA-based screening for enzymatic properties, which makes them one of the most powerful model system for directed in vitro evolution of proteins. In the present PhD work, through combination of various approaches of in vitro evolution, we have successfully changed the DNA recognition specificity of E. coli DNA methyltransferase (EcoDam) enzyme, that recognizes GATC palindromic sequence and methylates adenine at N6 position, and have generated novel variants of EcoDam with new recognition specificity.
Understanding the pathways of natural evolution is a major scientific challenge. The EcoDam/T4Dam pair represents a very interesting model case to study molecular evolution. The EcoDam and T4Dam DNA-(adenine N6)-methyltransferases both methylate the adenine residue in GATC sites. These enzymes are highly related in amino acid sequence, but they deviate in their contact to the first base pair of the target sequence. EcoDam contacts Gua1 with K9 (which corresponds to T4Dam A6), while T4Dam contacts Gua1 with R130 (which corresponds to EcoDam Y138). In a rational protein design study of EcoDam, we have “transplanted” the T4Dam DNA recognition into EcoDam and show that the EcoDam K9A/Y138R double mutant is highly active and specific. We also studied the intermediates of this transition and report that the evolutionary transition from EcoDam to T4Dam might be driven by a selection pressure for increased catalytic activity.
Besides their prominent biological roles, Dam MTases are an ideal model system for a structure-based drug design studies. We have studied the inhibition mechanism of inhibitor-58 on EcoDam and characterized its biochemical properties.
GATC sites are the natural substrate for EcoDam to methylate adenine at N6 position. The methylation status of GATC sites (methylated, unmethylated, and hemimethylated) can affect specific binding of DNA-interacting proteins. The presence of this tetranucleotide in the promoter or the regulatory sequences can affect gene expression by regulating binding of RNA polymerase or transcriptional regulators. We have studied the global transcriptional changes in the dam negative E. coli strain SCS110 in the presence and absence of EcoDam and report that EcoDam can serve as regulator of gene transcription. Bacterial cells encounter varied environmental changes and make appropriate adjustments to ensure their survival. We have studied the polyphosphates accumulation generated during stress response in E. coli and report that EcoDam binds to polyphosphates in cells and meditates potential connections between metabolic signaling and epigenetic modifications
Model-Based Process Control of Fruit Ripening
No full textThe ripening of 6.0 million tonnes of imported dessert bananas each year in the European Union is an extensive but not well analysed process in the food industry. Data and information about the biochemistry and the technical realisation of the banana ripening process is missing. The control of the highly complex processes depends on the personal knowledge and experience of the ripening master. For a better understanding of the industrial process, an experimental banana ripening plant was developed, equipped with sensitive measuring technology and connected to a process control system. The produced data of the 4-day to 7-day ripening processes, carried out based on industrial standards and objectives, provides additional and new information about the food technological process. Based on the generated data and knowledge, a mathematical model of the banana ripening process was developed. Characteristic biochemical reactions, like the degradation of starch to soluble sugars and their further oxidation, the change of colour pigments and the ethene production, were described with the help of kinetics specified in related food technological and biotechnological processes. The plant effects and process characteristics were realised with the help of mass and energy balances. The simulation results confirm with the measured values with accuracy below 10%. With the help of the model significant banana ripening process variables, like the starch concentration in the pulp, the peel colour, the mass of bananas, the concentration of carbon dioxide, oxygen, water and ethene in the process air as well as the banana and process air temperature, are simulated and can be used for the process evaluation. Furthermore, the model can be used for the prediction of future process courses and thus help to ensure targeted ripening quality. The model was used to enhance the process control of industrial ripening procedures. For this purpose, the Open-Loop-Feedback-Optimal controller was applied for an adaptive and optimised banana ripening process control. Only two significant parameters, the starch oxidation speed factor and the colour change factor, were fitted to accurate describe the running process. A simplified model was used to calculate an optimised control function with the target of an optimal storage temperature the desired banana ripening degree. The adaption to varying process characteristics and changing ripening times was successfully applied in one ripening experiment. The model-based adaptive control can be used for high quality but practical banana ripening process control
Simulation of Transport through OmpF and OmpC Channels
No full textThe outer membrane porins F and C (OmpF and OmpC) are major pores in the cell membrane of the Gram-negative bacterium Escherichia coli. They are considered the main pathways for ions and molecules through the membrane. Using the crystal structures, it is possible to study OmpF and OmpC in computer simulations. In this thesis, the ion conductance through these nano pores is simulated in all-atom molecular dynamics. Although the amino acid sequences of both pores are similar, their conductance is different. The temperature dependence of the conductance is calculated for different salt concentrations. Good agreement is seen in the comparison between simulations and experiments. The advantage of molecular dynamics simulations is that they allow a deeper view on the molecular interaction leading to the macroscopic observation. Ion pathways can be followed, and the interaction of ions with certain residues can be observed. Both pores, OmpF and OmpC, have a charged constricted area in the middle of the pore. The behavior of the pore can be changed by mutating key residues in this constriction zone. The effect of mutations on the transport of ions is investigated and compared to the results obtained from wild type OmpF. Also here, experimental measurements show good agreement with the simulations.
Furthermore, porins are the main pathways of antibiotics into the cell. The translocation of antibiotics through membrane is not yet understood in all details. During translocation, a blocking of pores through antibiotics is observed. Here, blocking of porins by the beta lactam antibiotic ampicillin is simulated, as well as, translocation of ampicillin through OmpF
Applying OLAP Pre-Aggregation Techniques to Speed Up Aggregate Query Processing in Array Databases
No full textLarge multidimensional arrays of data are common in a variety of scientific applications. In the past, arrays have typically been stored in files, and then manipulated by customized programs operating on those files. Nowadays, with science moving toward computational databases, the trend is toward a new class of database, the array database. In the broadest sense, the array database supports various types of multidimensional array data, including remote-sensor data, satellite imagery, and data resulting from scientific simulations. As with traditional databases for business applications, analytics in array databases often involves the extraction of general characteristics from large repositories. This requires efficient methods for computing queries that involve data summarization, such as aggregate queries. A typical solution is to pre-compute the whole or parts of each query, and then save the results of those queries that are frequently submitted against the database and those that can be used to compute the results of similar future queries. This process is known as pre-aggregation. Unfortunately, pre-aggregation support for array databases is currently limited to one specific operation, scaling (zooming), and to two-dimensional datasets (images). In this aspect, database technology for business applications is much more mature. Technologies such as On-Line Analytical Processing (OLAP) provide the means to analyze business data from one or multiple sources, and thus facilitate the decision making process. In OLAP, the information is viewed as data cubes. These cubes are typically stored in relational tables, or in multidimensional arrays, or in a hybrid model. In order to enable fast interactive multidimensional data analysis, database systems frequently pre-compute and store the results of aggregate queries. While there are some valuable research results in the realm of OLAP pre-aggregation techniques with varying degrees of power and refinement, not enough work has been done and reported for array databases. The purpose of this thesis is to investigate the application of OLAP pre-aggregation techniques with the objective of speeding up aggregate operations in array databases. In particular, we consider enhancing aggregate computation in Geographic Information Systems (GIS) and remote-sensing imaging applications. To this end, we describe a set of fundamental operations in GIS based on a sound algebraic framework. This allows us to identify those operations that require data summarization and that therefore may benefit from pre-aggregation. We introduce a conceptual framework and cost model for rewriting basic aggregate queries in terms of pre-aggregated data, and conduct experiments to assess the performance of our algorithms. Results show that query response times can be substantially reduced by strategically selecting the pre-aggregate with the least cost in terms of execution time. We also investigate the problem of selecting a set of queries for pre-aggregation, but failed to find an analytical solution for all possible types of aggregate queries. Nevertheless, we present a framework and algorithms for the selection of scaling operations for pre-aggregation considering 2D, 3D, and 4D datasets. The results of our experiments with 2D datasets outperform the results of image pyramids, the current technique used to speed up scaling operations on 2D datasets. Furthermore, our experiments on 3D and 4D datasets show that query response types can also be substantially reduced by intelligently selecting a set of scaling operations for pre-aggregation. The work presented in this thesis is the first of its kind for array databases in scientific applications
Integrated Effciency Engineering in Solar Cell Mass Production
No full textIn order to promote solar cells to be a competitive source of electrical energy in the future, a structured optimization methodology is necessary in mass production. On the one hand it accelerates development for established cell concepts in order to reach higher conversion efficiency and thus lower cost per Watt. On the other hand also new technologies depend on a structured approach for efficiency engineering to enable substantial evaluation and fast implementation. The real potential of any cell technology is only shown by efficiency engineering in mass production.
In this study, the established optimization approaches of Quality Management and Six Sigma have been adapted for the solar cell industry. This led to a proposed procedure for efficiency engineering, formulated as nine steps of process optimization. This methodology was implemented in the mass production of the commercial solar cell manufacturer Q-Cells SE in Thalheim (Germany), and was successfully validated with results in stabilization, cell conversion efficiency and process knowledge. By implementation of the structured approach, the speed of improvement could be significantly increased in the concerned production line
Carbon and nitrogen fluxes in the marine coccolithophore Emiliania huxleyi grown under different nitrate concentrations
No full textCoccolithophores are important primary producers and the most prolific calcifiers in the ocean. Since carbon (C) and nitrogen (N) assimilation are tightly connected, N availability has a crucial impact on photosynthesis and calcification, and therefore affects the biogeochemical function of coccolithophores in the sea. In general, N availability limits primary production in many areas in the ocean. Furthermore, N availability is expected to decrease in the near future, due to increased thermal stratification in the surface ocean and reduced nutrient input from deeper waters. Keeping this in mind, we examined the effects of NO3- availability on C and N assimilation in the marine coccolithophore Emiliania huxleyi under saturating light and present day pCO2. Although growth rates and C to N ratios were similar in low and high NO3--grown cells, cellular organic C and N, and also inorganic C decreased under low NO3-. Growth at low NO3- caused a higher proportion of fixed C to be allocated to lipids relative to carbohydrates and proteins. Low NO3- availability led to downregulation of nitrate reductase (NR), nitrite reductase (NiR) and phosphoenolpyruvate carboxykinase (PEPCK) maximal activities (Vmax), up-regulation of glutamine synthetase (GS) and glutamate synthase (GOGAT) Vmax, and down-regulation of net photosynthesis and HCO3- uptake. The apparent Chl α specific efficiency of light harvesting (α) and CO2 uptake remained similar, irrespective of the NO3- concentration in the culture medium. The affinity of NR for NO3-, NiR for NO2- and GS for Glu, as well as the affinities of inorganic C uptake were higher under low NO3-. This study suggests that maintenance of a constant C to N ratio under low and high NO3- requires a concerted regulation of the intracellular CO2 and NO3- concentrations to equilibrate the fluxes through the C and N assimilation pathway