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In vivo Imaging of Bile Accumulation and Biliary Infarction after Common Bile Duct Ligation in Rats
(2011)
Obstructive cholestasis is caused by mechanical constriction or occlusion leading to reduced bile flow. Serious complications such as jaundice and even death may follow. Little is known about the initial phase of cholestasis and its consequences for the hepatic microarchitecture. This in vivo study aimed to characterize the nature and kinetics of developing obstructive cholestasis and focused on areas with biliary stasis and infarction by visualizing the autofluorescence of bile acids using intravital microscopy of the liver over a period of 30 h after bile duct ligation in rats. The innovation resided in performing fluorescence microscopy without applying fluorescent dyes. In animals subjected to obstructive cholestasis, the most significant changes observed in vivo were the concomitant appearance of (1) areas with bile accumulation increasing in size (6 h: 0.163 ± 0.043, 18 h: 0.180 ± 0.086, 30 h: 0.483 ± 0.176 mm<sup>2</sup>/field) and (2) areas with biliary infarction (6 h: 0.011 ± 0.006, 18 h: 0.010 ± 0.004, 30 h: 0.010 ± 0.050 mm<sup>2</sup>/field) as well as (3) a relation between the formation of hepatic lesions and enzyme activity in serum. The sequential in vivo analysis presented herein is a new method for the in vivo visualization of the very early changes in the hepatic parenchyma caused by obstructive cholestasis.
Purpose: To determine the surface characteristics of porcine corneal lenticules after Femtosecond Lenticule Extraction. Methods: The Carl Zeiss Meditec AG VisuMax® femtosecond laser system was used to create refractive corneal lenticules on 10 freshly isolated porcine eyes. The surface regularity on the corneal lenticules recovered was evaluated by assessing scanning electron microscopy images using an established scoring system. Results: All specimens yielded comparable score results of 5–7 points (SD = 0.59) per lenticule (score range minimum 4 to maximum 11 points). Surface irregularities were caused by tissue bridges, cavitation bubbles or scratches. Conclusion: The Femtosecond Lenticule Extraction procedure is capable of creating corneal lenticules of predictable surface quality. However, future studies should focus on the optimization of laser parameters as well as surgical technique to improve the regularity of the corneal stromal bed.
For surgery in congenital hyperinsulinism (CHI), a distinct surgical strategy and technique is required for focal, diffuse and atypical CHI. In focal CHI, a confined, localized and parenchyma-sparing resection which is guided by the PET-CT is always indicated in order to cure the patient. In diffuse CHI, however, the results of surgical therapy are unpredictable and cure is an exception. Therefore, a strong tendency exists nowadays that medical therapy should be preferred in diffuse CHI. In atypical CHI the situation is more complex: if the focal lesion or the segmental mosaic are not too extensive, cure by resection should be possible. But care must be taken in atypical cases not to resect too much of the gland in order not to induce diabetes.
Background: Therapyrelated mucositis is associated with considerable morbidity. This complication following allogeneic stem cell therapy (alloSCT) is less severe after reduced intense conditioning (RIC); however, even here it may be serious. Methods: 52 patients (male: n = 35 (67%), female: n = 17 (33%)) at a median age of 62 years (35–73 years) underwent alloSCT after RIC. Conditioning was either total body irradiation (TBI)<sub>2Gy</sub>/±fludarabine (n = 33, 63.5%) or chemotherapy based. Graftversushost disease (GvHD) prophylaxis was carried out with cyclosporine A ± mycophenolate mofetil (MMF). 45 patients (87%) received shortcourse methotrexate (MTX). Mucositis was graded according to the Bearman and the World Health Organisation (WHO) scale. A variety of parameters were correlated with mucositis. Results: The Bearman and WHO scales showed excellent correlation. Mucositis was significantly more severe after chemotherapybased conditioning compared to conditioning with TBI<sub>2Gy</sub>/±fludarabine (p < 0.002) as well as in cases with an increase in creatinine levels above the upper normal value (UNV) on day +1 after SCT (p < 0.05). Furthermore, the severity correlated with time to engraftment of leucocytes (correlation coefficient (cc) = 0.26, p < 0.02) and thrombocytes (cc = 0.38, p < 0.001). Conclusions: The conditioning regimen and increased creatinine levels at day +1 were identified as factors predicting the severity of mucositis after RICSCT. Creatinine levels on day +1 after SCT may help identify patients at risk for severe mucositis in the further course of transplantation.
Aim: The efficacy of antimicrobial compounds included in wound dressings has been determined using the quantitative suspension test according to EN 13727 before. However, as suspension tests are not an accurate reflection of the conditions under which wound antiseptics are used, it was investigated if a disc carrier test would yield results simulating practical conditions on wound surfaces. A silver-leaching foam wound dressing was used for evaluation of the disc carrier test method. Method: The disc carriers consisted of circular stainless-steel discs measuring 2 cm in diameter and 1.5 mm in thickness, complying with the requirements of EN 10088-2. Carriers were contaminated with Staphylococcus aureus, methicillin-resistant S. aureus or Pseudomonas aeruginosa, respectively, together with an artificial wound secretion and left to dry at room temperature for 30 min. The wound dressings being tested were placed on the discs for the length of the exposure time, and after neutralization by thioglycolate in phosphate-buffered saline the number of surviving test organisms was then counted. The logarithmic reduction factor was calculated from the difference between the initial inoculum and the number of recovered test organisms. Results: The disc carrier test allowed determination of an antimicrobial efficacy in a realistic setting. It also imposed more stringent requirements on efficacy over time than the quantitative suspension test. The silver foam wound dressing showed a time-dependent antimicrobial efficacy. After 24-hour application time, the reduction factors against S. aureus, P. aeruginosa and the methicillin-resistant S. aureus were 1.9 ± 0.15, 2.1 ± 0.14 and 3.1 ± 0.18, respectively. Conclusion: The disc carrier test was a useful method for testing the antimicrobial efficacy of a foam silver dressing. The antimicrobial dressing exhibited an antimicrobial effect after 3 h and achieved a reduction >2 log against the tested bacterial strains in the presence of a simulated wound secretion after 24 h.
The effect of water-filtered infrared-A radiation (wIRA) on normal skin flora was investigated by generating experimental wounds on the forearms of volunteers utilizing the suction blister technique. Over 7 days, recolonization was monitored parallel to wound healing. Four groups of treatment were compared: no therapy (A), dexpanthenol cream once daily (B), 20 min wIRA irradiation at 30 cm distance (C), and wIRA irradiation for 30 min once daily together with dexpanthenol cream once daily (D). All treatments strongly inhibited the recolonization of the wounds. Whereas dexpanthenol completely suppressed recolonization over the test period, recolonization after wIRA without (C) and in combination with dexpanthenol (D) was suppressed, but started on day 5 with considerably higher amounts after the combination treatment (D). Whereas the consequence without treatment (A) was an increasing amount of physiological skin flora including coagulase-negative staphylococci, all treatments (B–D) led to a reduction in physiological skin flora, including coagulase-negative staphylococci. In healthy volunteers, wIRA alone and in combination with dexpanthenol strongly inhibited bacterial recolonization with physiological skin flora after artificial wound setting using a suction-blister wound model. This could support the beneficial effects of wIRA in the promotion of wound healing.
The exact qualitative and quantitative analysis of wound healing processes is a decisive prerequisite for optimizing wound care and for therapy control. Transepidermal water loss (TEWL) measurements are considered to be the standard procedure for assessing the progress of epidermal wound healing. The damage to the stratum corneum correlates with an increased loss of water through the skin barrier. This method is highly susceptible to failure by environmental factors, in particular by temperature and moisture. This study was aimed at comparing TEWL measurements and in vivo laser scanning microscopy (LSM) for the characterization of the epidermal wound healing process. LSM is a high-resolution in vivo method permitting to analyze the kinetics and dynamics of wound healing at a cellular level. While the TEWL values for the individual volunteers showed a wide scattering, LSM permitted the wound healing process to be clearly characterized at the cellular level. However, a comparison between the two methods was very difficult, because the results provided by LSM were images and not numerical. Therefore, a scoring system was set up which evaluates the stages of wound healing. Thus, the healing process could be numerically described. This method is independent of any environmental factors. Providing morphologically qualitative and numerically quantitative analyses of the wound healing process and being far less vulnerable to failure, LSM is advantageous over TEWL.
Wound healing disorders frequently occur due to biofilm formation on wound surfaces requiring conscientious wound hygiene. Often, the application of conventional liquid antiseptics is not sufficient and sustainable as (1) the borders and the surrounding of chronic wounds frequently consist of sclerotic skin, impeding an effectual penetration of these products, and (2) the hair follicles representing the reservoir for bacterial recolonization of skin surfaces are not affected. Recently, it has been reported that tissue-tolerable plasma (TTP), which is used at a temperature range between 35 and 45°C, likewise has disinfecting properties. In the present study, the effectivity of TTP and a standard liquid antiseptic was compared in vitro on porcine skin. The results revealed that TTP was able to reduce the bacterial load by 94%, although the application of the liquid antiseptic remained superior as it reduced the bacteria by almost 99%. For in vivo application, however, TTP offers several advantages. On the one hand, TTP enables the treatment of sclerotic skin as well, and on the other hand, a sustainable disinfection can be realized as, obviously, also the follicular reservoir is affected by TTP.
Postoperative Immune Suppression in Visceral Surgery: Characterisation of an Intestinal Mouse Model
(2011)
Background: Postoperatively acquired immune dysfunction is associated with a higher mortality rate in case of septic complications. As details of this severe clinical problem are still unknown, animal models are essential to characterise the mechanisms involved. Methods: Mice were laparotomised and the small intestine was pressed smoothly in antegrade direction. For extension of trauma, the intestine was manipulated three times consecutively. Following this, the ex vivo cytokine release of splenocytes was determined. The degree of surgical trauma was analysed by detection of HMGB1 and IL-6 in serum and by neutrophil staining in the muscularis mucosae. Results: We adapted the previously described animal model of intestinal manipulation to provide a model of surgically induced immune dysfunction. Following intestinal manipulation, the mice showed elevated serum levels of HMGB1 and IL-6 and increased infiltration of granulocytes into the muscularis mucosae. Ex vivo cytokine release by splenocytes was suppressed in the postoperative period. The degree of suppression correlated with the extent of surgical trauma. Conclusions: In this study, we describe a surgically induced immune dysfunction animal model, in which a significant surgical trauma is followed by an immune dysfunction. This model may be ideal for the characterisation of the postoperative immune dysfunction syndrome.
Currently, there are no generally accepted definitions for wounds at risk of infection. In clinical practice, too many chronic wounds are regarded as being at risk of infection, and therefore many topical antimicrobials – in terms of frequency and duration of use – are applied to wounds. Based on expert discussion and current knowledge, a clinical assessment score was developed. The objective of this wounds at risk (W.A.R.) score is to allow decision-making on the indication for the use of antiseptics on the basis of polihexanide. The proposed clinical classification of W.A.R. shall facilitate the decision for wound antisepsis and allow an appropriate general treatment regimen with the focus on the prevention of wound infection. The W.A.R. score is based on a clinically oriented risk assessment using concrete patient circumstances. The indication for the use of antiseptics results from the addition of differently weighted risk causes, for which points are assigned. Antimicrobial treatment is justified in the case of 3 or more points.
In the search for bioactive compounds, 32 fungal strains were isolated from Indonesian marine habitats. Ethyl acetate extracts of their culture broth were tested for cytotoxic activity against a urinary bladder carcinoma cell line and for antifungal and antibacterial activities against fish and human pathogenic bacteria as well as against plant and human pathogenic fungi. Bioassay-guided fractionation led to the isolation of bioactive compounds. Altogether 14 compounds were isolated and further elucidated. The compounds were obtained from the ethyl acetate and dichloromethane extracts of six fungal strains. They included 9 polyketides, 2 terpenes, 1 alkaloid and 2 till now undefined structures.
District hospitals are the only solution to guarantee basic health care including life-saving surgeries and hospitalisations in rural SSA areas. Neither regional nor national hospitals, financially and geographically out of reach for the majority of the population, nor rural health care centres, mostly staffed with a nurse only, can cover these tasks adequately. However, only little research exists on care giving processes, cost and efficiency of district hospitals in SSA. The general problem in health economics is that limited resources should be used in order to maximise health effects. This dissertation evaluates the actual treatment pathways and their average provider’s cost per patient for four different diagnoses at Nouna district hospital in Burkina Faso. A total of 95 patient records was analysed in detail and discussed with the health personnel in charge. Cost information for the year 2005 was taken from the well-established provider cost information system. Cost were broken down to the different sequences of the treatment pathway and summed up at the end. Average provider’s cost for paediatric Malaria were U$ 6.71 for outpatients, US$ 60.59 for inpatients with anaemia and US$ 75.11 for inpatients with neurological affection. Average provider’s cost for treating hypertension were US$ 67.94 per year. Average cost for hernia cure were US$ 146.85 under local anaesthesia, US$ 153.08 under spinal anaesthesia and US$ 169.78 under general anaesthesia. Average provider’s cost for Caesarean sections were US$ 140.15 under spinal anaesthesia and US$ 180.41 under general anaesthesia. This means that cost per patient are comparable to or even lower than provider’s cost found for other SSA setting in the literature. Cost would decrease between 20% (a hypertensive outpatient) and 46% for Malaria with neurological affection as complication, if utilisation rates rose from actually 20 to 80%. Patients paid between 35 and 94% of total provider’s cost in form of user fees. If fees would not change and the utilisation rate increased to 80%, cost-recovery for the considered diseases would then be between 63 and 117%. Although this would not allow the hospital to break even in its current configuration, the cost-recovery rate would be considerably higher, especially when taking into account that a full cost analysis was done including all investment cost. The introduction of clinical pathways based on the actual treatment pathways is suggested to improve process structure and documentation and to standardise the treatment according to national and international guidelines.
Protein quality control systems are essential for the viability and growth of all living organisms. They protect the cell from irreversible protein aggregation. Because the frequency of protein misfolding, which ultimately results in protein aggregation, varies with the environmental conditions, the amount and activity of protein quality systems have to be accurately adapted to the rate of protein misfolding. The main goal of this thesis was to gain detailed molecular insights into the transcriptional and post-translational regulation of these protein quality control networks in the ecologically, medically and industrially important phylum of low GC, Gram-positive bacteria. In these bacteria the core protein quality control systems are under the transcriptional control of the global repressor CtsR. In a first study it was demonstrated that the arginine kinase McsB is not responsible for the regulation of CtsR activity during heat stress, as was concluded by others on the basis of previous in vitro data. Rather, it was demonstrated that CtsR acts as an intrinsic thermosensor that adapts its activity to the surrounding temperature. CtsR displays a decreased DNA binding at higher temperatures, which leads to induction of transcription of the protein quality control systems under these conditions. This CtsR feature is conserved in all low GC, Gram-positive bacteria. However, the CtsR proteins of various low GC, Gram-positive species do not have the same temperature optima. CtsR responds to heat in a species-specific manner according to their corresponding growth temperature. Detailed analysis revealed that a highly conserved tetra-glycine loop within the winged helix-turn-helix domain of CtsR is responsible for thermosensing. Dual control of CtsR activity during different stresses was demonstrated for the first time in this work. In addition to heat-dependent de-repression, CtsR is inactivated by thiol-specific stress conditions. This latter de-repression depends on a molecular redox-switch that is independent of CtsR auto-regulation. In Bacillus subtilis and its closest relatives the McsA/McsB stress-sensing complex is responsible for CtsR de-repression during redox stress conditions. McsA is able to sense the redox state of the cell via its highly conserved cysteine residues. When these cysteines are reduced, McsA is able to bind and inhibit McsB. But when these cysteine residues are oxidized, McsB is released from McsA. Thereby, McsB is activated and removes CtsR from the DNA. However, the McsA/McsB complex is not present in all low GC, Gram-positive bacteria. In the species lacking this complex, ClpE is able to act as a redox-sensor probably via its highly conserved N-terminal zinc finger domain. When these cysteine residues are oxidized, ClpE is activated which results in CtsR de-repression. In addition to the transcriptional regulation of CtsR low GC, Gram-positive protein quality control systems are regulated post-transcriptionally. The expression of the McsA/McsB adaptor pair is regulated by CtsR. However, McsB activity is also tightly regulated by three different regulatory proteins (McsA/ClpC/YwlE). McsB is needed to target specific substrates to ClpC, either for refolding or degradation by the ClpCP protease. It was demonstrated that only the auto- phosphorylated form of McsB is able to bind to its substrates. This McsB function is inhibited in non-stressed cells by a direct interaction with ClpC. Consequently, McsB is activated by a release from ClpC during protein stress. In addition, McsB activation depends on the presence of its activator McsA. Accordingly, McsB cannot be activated as an adaptor protein during thiol-specific stress because McsA is no longer able to bind to McsB under these conditions. However, also active McsB is subject to post-translational control. Activated McsB is either de-phosphorylated by McaP or degraded by ClpCP ensuring an appropriate shut-down of the McsB adaptor. Both McaP and ClpC inhibit McsB activity with different intensities. ClpC possesses a stronger impact on McsB activity than McaP but both proteins are needed for an adequate silencing of McsB activity. In addition, it was shown for the first time that B. subtilis McsB is a global adaptor that influences the stability of multiple proteins. The B. subtilis ClpC protein is unlike most members of the Hsp100 family because it not only requires several adaptor proteins for substrate recognition but also for its general ATP- dependent activity. Biochemical analysis revealed how ClpC is activated by distinct adaptor proteins. McsB modulates ClpC activity by regulatory phosphorylation of arginine residues. Moreover, McaP (formerly YwlE) was identified as an arginine phosphatase that modulates the McsB mediated ClpC activity. MecA, another known adaptor protein for ClpC, activates ClpC independently of these arginine phosphorylations, which demonstrates the existence of multiple pathways for ClpC activation.
The pUS3, a serine/threonine protein kinase that is conserved in Alphaherpesvirinae may play an important in phosphorylation and regulation of the activities of viral and cellular proteins. It has also been proposed that pUS3 affects virulence. Whereas many studies of the pUS3 functions of HSV-1 and PrV, a closely related homolog of BHV-1 have supported these assumptions, the role of BHV-1pUS3 is not yet fully understood so far. The aims of this study therefore were to investigate the functions of BHV-1pUS3 for virus replication in cultured cells, effect on apoptosis and identification of protein interactions with cellular proteins and addressed the function of the aminoterminal region by generating a short isoform of BHV-1pUS3 which corresponds in size to the natural short isoforms of PrVpUS3 and HSV-1pUS3. Results of the study are briefly summarized here: -BHV-1pUS3 is, although not essential, beneficial for infectious replication of BHV-1 in-vitro. It also supports direct cell-to-cell spread of BHV-1/Aus12 and prevents the formation of electron dense aggregates with embedded capsids in nuclei of BHV-1 infected cells, a phenotype that may affect nuclear egress of BHV-1 nucleocapsids. -The protein, independent from other BHV-1 encoded functions, located mainly to the nuclei of cells. -In contrast to functions of pUS3 in PrV and HSV-1, the protein of BHV-1 has no anti-apoptotic activity. -Biologically active BHV-1pUS3 physically interacts with the cellular SET protein and overexpression of SET, independent from the expression of the protein, inhibits productive BHV-1 replication in a dose dependent manner. -The aminoterminal 101 amino acids of the protein are dispensable for all in-vitro functions tested whereas kinase activity is required.
The key objective of this dissertation is to study the expected impact of the introduction of the Social Health Insurance (SHI) on the public hospital management and to develop recommendations that will improve this management. In addition to the key objective, this study aims to analyze the health sector financing in Syria, to outline problems affecting on management of public hospitals in Syria. Furthermore, it aims to study the various countries' experience with SHI and analyze key components of the Syrian SHI.
Main drivers for biodiversity loss in terrestrial ecosystems are changes in land use, climate change, enhanced nitrogen deposition and biotic exchange (invasive species). These drivers also affect dry, nutrient-poor open anthropo-zoogenic inland and coastal heathlands which often harbor a high biodiversity. To counteract biodiversity loss in coastal ecosystems, a basic step is the assessment of the various threats. Therefore it is important to select suitable model organisms for analyses of biodiversity dynamics. In this thesis the three arthropod groups Orthoptera (Ensifera and Caelifera), carabid beetles (Coleoptera: Carabidae) and spiders (Araneae) were studied, as they are very useful indicators. Besides sampling of the three arthropod groups vegetation and microclimate parameters were recorded. The studies were done between 2008 and 2010 in the coastal heathland on the Baltic island of Hiddensee, Germany. The main aim of the thesis was to analyze the impact of three drivers of heathland biodiversity loss (succession, grass encroachment, moss invasion) on the selected indicator arthropod groups. Based on this multi-level and -species approach, implications for the conservation of coastal heathlands are given. The results show that successional processes and grass encroachment have strong impact on species richness and abundance, species composition and functional groups, as well as life-history traits and functional diversity of the arthropod groups. Main findings were: Orthoptera species richness was highest in the intermediate stages (heath encroached by grasses and heath with shrubs) because of higher habitat heterogeneity and higher food supply (grasses). Opposed to that, species richness of ground-dwelling carabid beetles and spiders did not differ among the five successional stages, which contradicts the ‘habitat heterogeneity hypothesis’. In contrast to species richness, functional diversity differed among successional stages. The concept of functional diversity – which integrates species life-history trait data – therefore might be particularly suitable for biodiversity research, while the explanatory power of species richness alone might not be sufficient. The species compositions of all three taxa changed remarkably along the coastal heathland gradient indicating a high species turnover. In particular, open, dynamic habitats (‘grey dunes’ and ‘dwarf-shrub heath’) could be separated. Here, several specialized, xerothermic and threatened species occurred due to the extreme habitat conditions, but are displaced during grass and shrub encroachment. On a smaller spatial scale, the invasion of Campylopus introflexus alters habitat conditions in grey dunes and therefore affects carabid beetle and spider species and the dominant Orthoptera species Myrmeleotettix maculatus. Species richness of carabid beetles and spiders, and the abundance of adult M. maculatus grasshoppers were reduced. Species compositions of carabids and spiders changed remarkably with a loss of several species. These negative impacts could be explained by the vegetation structure of the moss which is unsuitable for web-building spiders or large carabid beetles, and by reduced germination of higher plants and therefore reduced food supply for M. maculatus and phytophagous carabid species. Within the open coastal heathland, the mosaic of grey dunes and adjacent dwarf-shrubs is important since many species perform a habitat change during their development and, besides the scarcely vegetated, thermally benefited grey dunes, need denser vegetation of adjacent dwarf-shrubs for shelter, as song posts, or for foraging. As grey dunes harbor a high abundance and species richness of threatened and specialized, mainly xerothermic and geobiont species and are important as oviposition and nymphal habitat, they are regarded as a keystone habitat within the coastal heathland. Besides these ecological studies, two studies focused on the method of pitfall trapping. It could have been shown, that pitfall trapping might be a useful sampling method for Orthoptera in open habitats. The other study demonstrated that sampling interval has a strong influence on the capture efficiency of several arthropod groups (‘digging-in effect’). Conservation practices should aim at maintaining a heterogeneous heathland mosaic with open grey dunes and Calluna stands, in addition to scattered grassy and shrub-encroached heath for the survival of species-rich heathland arthropod assemblages with a high proportion of specialized and threatened species.
Background: Computational tools for the investigation of transcriptional regulation, in particular of transcription factor binding sites (TFBS), in evolutionary context are developed. Existing sequence based tools prediction such binding sites do not consider their actual functionality, although it is known that besides the base sequence many other aspects are relevant for binding and for the effects of that binding. In particular in Eukaryotes a perfectly matching sequence motif is neither necessary nor sufficient for a functional transcription factor binding site. Published work in the field of transcriptional regulation frequently focus on the prediction of putative transcription factor binding sites based on sequence similarity to known binding sites. Furthermore, among the related software, only a small number implements visualization of the evolution of transcription factor binding sites or the integration of other regulation related data. The interface of many tools is made for computer scientists, although the actual interpretation of their outcome needs profound biological background knowledge. Results and Discussion: The tool presented in this thesis, "ReXSpecies" is a web application. Therefore, it is ready to use for the end user without installation providing a graphical user interface. Besides extensive automation of analyses of transcriptional regulation (the only necessary input are the genomic coordinates of a regulatory region), new techniques to visualize the evolution of transcription factor binding sites were developed. Furthermore, an interface to genome browsers was implemented to enable scientists to comprehensively analyze their regulatory regions with respect to other regulation relevant data. ReXSpecies contains a novel algorithm that searches for evolutionary conserved patterns of transcription factor binding sites, which could imply functionality. Such patterns were verified using some known transcription factor binding sites of genes involved in pluripotency. In the appendix, efficiency and correctness of the used algorithm are discussed. Furthermore, a novel algorithm to color phylogenetic trees intuitively is presented. In the thesis, new possibilities to render evolutionary conserved sets of transcription factor binding sites are developed. The thesis also discusses the evolutionary conservation of regulation and its context dependency. An important source of errors in the analysis of regulatory regions using comparative genetics is probably to find and to align homologous regulatory regions. Some alternatives to using sequence similarity alone are discussed. Outlook: Other possibilities to find (functional) homologous regulatory regions (besides whole-genome-alignments currently used) are BLAST searches, local alignments, homology databases and alignment-free approaches. Using one ore more of these alternatives could reduce the number of artifacts by reduction of the number of regions that are erroneously declared homologous. To achieve more robust predictions of transcription, the author suggests to use other regulation related data besides sequence data only. Therefore, the use and extension of existing tools, in particular of systems biology, is proposed.
Computational chemical physics can give important input to astrophysical modelling and other fields of physics, where molecular properties are of importance. Understanding of spectroscopic and reactive behaviour is crucial for many systems of astrophysical interests like stars, interstellar medium and comets. Especially stellar atmospheres are of interest, because the complex physics of stars are not yet completely understood. Stars are in an unstable balance of gravitation and radiation pressure and the atmospheric dynamics have been subject of extensive modelling. Complete and accurate spectroscopic information of the atoms and molecules in these atmospheres is necessary for this attempt. In addition, the only information we have about astrophysical systems is light which is emitted or absorbed by particles in these media. This is not only true for astrophysics. In plasma physics sometimes the usage of invasive diagnostics, like Langmuir probes, is not wanted because they disturb the system. In these cases some information of the system can be regained by passively measuring infrared spectra of the plasma or by active induction of electronic transition like the laser-induced fluorescence method. Another remote sensing application is the measurement of the atmospheric composition on earth. Here, larger particles in the atmosphere as well as greenhouse gases are of current interest. Unfortunately, the experimental spectroscopic data, which is needed for the understanding and interpretation of the measured spectra, is often incomplete. This gap can be, to some extend, filled by computational chemical physics. The aim of this work was to investigate the capabilities and limitations of ab initio based potential energy surfaces for spectroscopic and reactive studies and to apply these methods to problems of rovibrational and rovibronic spectroscopy and reaction dynamics. The choice of ab initio methods and the potential fitting methods is critical for the computational chemical physics, as all further quantities directly depend on their quality. In this work modified versions of the Braams polynomial potential energy surface were used. A high level coupled cluster ab initio method was used to build potentials for a series of small hydrocarbons. Hydrocarbons can be found almost everywhere on earth and in the universe. They exist in laboratory plasmas, stellar and planetary atmospheres and interstellar gases. In all these cases, light emitted or absorbed by the molecules is an important diagnostics of the system. The potential constructed in this work partly included a cluster expansion, which adds reactant configuration spaces to the fits. This could not be done for CH_3 and higher hydrocarbons, because of the limitations of the Coupled Cluster ab initio method, which is well suited for the potential wells, but not for the dissociation regions. The examples of methyl and methane show how the potentials can be used for rovibrational spectroscopy. Results of radiation transport simulations illustrate the importance of as complete-as-possible line lists for radiation transport calculations.\\ The rovibronic spectroscopy of diatomic molecules is another important aspect for the stellar atmospheric modelling. Metal hydrides and oxides add opacity to the atmosphere in the visible light and ultraviolet frequency regions, as well as do the hydrocarbons in the infrared one. In addition the spectra of metal hydrides/oxides can be used to gather information about metal and their isotope abundances. They are used as markers for the conditions in the atmospheres of stars. In this work a new code was developed, that efficiently calculates bound-bound transitions between electronic states and bound-continuum cross sections for diatomic molecules. It also offers an adequate treatment of quasi-bound rovibrational states. One important representative of the diatoms is magnesium hydride, MgH. Before this work, line lists and photodissociation cross section were available involving the three lowest doublet states of MgH. In this work new potential energy curves were calculated and adapted to updated experimental data. This causes changes in the relative energies between the electronic states and therefore shifts in the line lists. These are important, because accurate line positions are needed for the identification of spectral lines. In addition two further electronic states were included in the calculations. This expands the spectral range of MgH into the near ultraviolet region. Radiation transport models showed significant absorption by MgH from the newly added electronic states. A second usage of the diatomic potential energy curves are photodissociation cross sections. As interstellar environments are chemically active, such data is necessary for a complete picture of the ongoing processes. The photodissociation cross sections of MgH reveal a stronger dependence of the underlying potential than the bound-bound lines. In the case of MgH the cross sections are rather weak, besides occasional resonance lines which can be several orders of magnitude stronger. As mentioned, not only spectroscopic, but also reactive behaviour of molecules is important in astrophysics. A current problem connected with this is the abundance of CH^+ in interstellar clouds. Its measured abundances do not fit the predictions from theoretical models. In addition Gerlich and co-workers recently measured low temperature H + CH^+ -> C^+ + H_2 reaction rates, which diverge from the theoretical picture and which could not be explained. In this work a reactive potential energy surface was built for the CH_2^+ system, which was then used to perform extensive calculations with quasi-classical trajectory and quantum scattering methods. It was found out, that the potentials used in previous works are not accurate enough to allow low temperature calculations. Results from these potentials must be taken with care. Furthermore, the results from the new potential energy surface indicate significantly reduced reaction rates compared to previous numerical studies. This is in agreement with the new results of Gerlich and co-workers. Nevertheless, the large error bars in the low temperature range for experimental as well as numerical results strongly suggest refined methods to be developed for both, before a final conclusion can be made. This work demonstrated the possibility of modern computational chemical physics to supply consistent data for spectroscopy and reaction dynamics. These are necessary and important inputs for fields like astrophysics, plasma physics and chemistry.
In this thesis wave propagation in the whistler wave frequency range ωci≤ω≤ωce in the linear magnetized plasma experiment VINETA is investigated. The plasma is generated by a helicon antenna and has a diameter of about 10 cm. Whistler waves are launched by a loop antenna with a diameter of 4.5 cm and the fluctuating magnetic field is mapped by Ḃ-probes. Experiments are carried out for plasma parameters γ≤1/ √ 2 under which the only transversal polarized wave according to plane wave dispersion theory is the whistler wave. Due to the small collision frequencies ν≪1 cyclotron damping of whistler waves in this parameter regime is dominant and depends only on the electron plasma-β. The influence of the inhomogeneous plasma profile and excitation by a loop antenna is investigated by measurements of the fluctuating magnetic field perpendicular to the ambient magnetic field in azimuthal and radial axial planes. A mode characterized by the number of wave lengths m in the azimuthal direction is found. The mode structure is modified by the specific shape of the plasma density profile. Profiles with a homogeneous density inside the plasma radius are found to posses a comparably simple mode structure. An agreement in the mode structure of full-wave simulations in three dimensions, including a Gaussian density profile and excitation of the wave by a loop antenna, with the experimental results is found. Conclusions on the spatial structure of the excited mode are drawn using the simulations which predict excitation of an m=2 mode. The wave is found to be ducted within the plasma radius over a wide parameter range. A Helmholtz decomposition of the simulations electric field exhibits the fluctuating space charge as the dominant source for the electric field, while the contribution due to induction is negligible. The magnetic field is given partially by the electron and displacement current. Both contributions to the magnetic field are of the same order of magnitude. The frequency dependency of the excited modes spatial damping increment is investigated using measurements of the magnetic fluctuations along the symmetry axis of the plasma. In order to illustrate the parameter dependency, the electron plasma-β is varied over two orders in magnitude in the range β = 4·10-4 - 2.4·10-2. The experimental result for the spatial damping increment of the mode yields a strong damping for wave frequencies ω/ωce > 0.5 at maximum plasma-β, which shifts to higher frequencies with decreasing β. The parameter dependency of the damping for a fixed frequency is studied in an axial ambient magnetic field gradient. In both cases an excellent agreement between the experimental result and predictions for cyclotron damping from plane wave dispersion theory is found.